@article{Allen1979,
  author = {S. M. Allen and J. W. Cahn},
  title = {A microscopic theory for antiphase boundary motion and its application to antiphase domain coarsening},
  journal = {Acta metall.},
  year = {1979},
  volume = {27},
  pages = {1085},
  doi = {10.1016/0001-6160(79)90196-2},
}

@article{Anton2005,
  author = {L. Anton and R. A. Blythe and A. J. Bray},
  title = {Spatial fluctuations of a surviving particle in the trapping reaction},
  journal = {J. Phys. A},
  year = {2005},
  volume = {38},
  pages = {133},
  doi = {10.1088/0305-4470/38/1/009},
}

@article{Blythe2002,
  author = {R. A. Blythe and A. J. Bray},
  title = {Perturbation theory for the one-dimensional trapping reaction},
  journal = {J. Phys. A},
  year = {2002},
  volume = {35},
  pages = {10503},
  doi = {10.1088/0305-4470/35/49/301},
}

@article{Blythe2003,
  author = {R. A. Blythe and A. J. Bray},
  title = {Survival probability of a diffusing particle in the presence of Poisson-distributed mobile traps},
  journal = {Phys. Rev. E},
  year = {2003},
  volume = {67},
  pages = {041101},
  doi = {10.1103/PhysRevE.67.041101},
}

@article{Bramson1980,
  author = {M. Bramson and D. Griffeath},
  title = {Asymptotics for Interacting Particle Systems on $Z^d$},
  journal = {Z. Wahrscheinlichkeitstheorie Geb.},
  year = {1980},
  volume = {53},
  pages = {183},
  doi = {10.1007/BF01013315},
}

@article{Bramson1988,
  author = {Maury Bramson and Joel L. Lebowitz},
  title = {Asymptotic Behavior of Densities in Diffusion-Dominated Annihilation Reactions},
  journal = {Phys. Rev. Lett.},
  year = {1988},
  volume = {61},
  pages = {2397},
  doi = {10.1103/PhysRevLett.61.2397},
}

@article{Bray2000,
  author = {A. J. Bray and S. J. O'Donoghue},
  title = {Unusual dynamical scaling in the spatial distribution of persistent sites in one-dimensional Potts models},
  journal = {Phys. Rev. E},
  year = {2000},
  volume = {62},
  pages = {3366},
  doi = {10.1103/PhysRevE.62.3366},
}

@article{Bray2002,
  author = {Alan J. Bray and Richard A. Blythe},
  title = {Exact Asymptotics for One-Dimensional Diffusion with Mobile Traps},
  journal = {Phys. Rev. Lett.},
  year = {2002},
  volume = {89},
  pages = {150601},
  doi = {10.1103/PhysRevLett.89.150601},
}

@article{Bray2003,
  author = {Alan J. Bray and Satya N. Majumdar and Richard A. Blythe},
  title = {Formal solution of a class of reaction-diffusion models: Reduction to a single-particle problem},
  journal = {Phys. Rev. E},
  year = {2003},
  volume = {67},
  pages = {060102},
  doi = {10.1103/PhysRevE.67.060102},
}

@article{Bray1989,
  author = {A. J. Bray},
  title = {Exact renormalization-group results for domain-growth scaling in spinodal decomposition},
  journal = {Phys. Rev. Lett.},
  year = {1989},
  volume = {62},
  pages = {2841},
  doi = {10.1103/PhysRevLett.62.2841},
}

@article{Bray1990,
  author = {A. J. Bray},
  title = {Renormalization-group approach to domain-growth scaling},
  journal = {Phys. Rev. B},
  year = {1990},
  volume = {41},
  pages = {6724},
  doi = {10.1103/PhysRevB.41.6724},
}

@article{Bray1993,
  author = {A. J. Bray and K. Humayun},
  title = {Universal amplitudes of power-law tails in the asymptotic structure factor of systems with topological defects},
  journal = {Phys. Rev. E},
  year = {1993},
  volume = {47},
  pages = {R9},
  doi = {10.1103/PhysRevE.47.R9},
}

@article{Bray1994,
  author = {A. J. Bray},
  title = {Theory of phase ordering kinetics},
  journal = {Adv. Phys.},
  year = {1994},
  volume = {43},
  pages = {357},
  doi = {10.1080/00018739400101505},
}

@article{Bray1994b,
  author = {A. J. Bray and A. D. Rutenberg},
  title = {Growth laws for phase ordering},
  journal = {Phys. Rev. E},
  year = {1994},
  volume = {49},
  pages = {R27},
  doi = {10.1103/PhysRevE.49.R27},
}

@article{Bray1995,
  author = {A. J. Bray and C. L. Emmott},
  title = {Lifshitz-Slyozov scaling for late-stage coarsening with an order-parameter-dependent mobility},
  journal = {Phys. Rev. B},
  year = {1995},
  volume = {52},
  pages = {R685},
  doi = {10.1103/PhysRevB.52.R685},
}

@article{Brown2002,
  author = {Gregory Brown and Per Arne Rikvold},
  title = {Numerical confirmation of late-time $t^{1/2}$ growth in three-dimensional phase ordering},
  journal = {Phys. Rev. E},
  year = {2002},
  volume = {65},
  pages = {036137},
  doi = {10.1103/PhysRevE.65.036137},
}

@article{Brown1997,
  author = {Gregory Brown and Per Arne Rikvold and Mark Sutton and Martin Grant},
  title = {Speckle from phase-ordering systems},
  journal = {Phys. Rev. E},
  year = {1997},
  volume = {56},
  pages = {6601},
  doi = {10.1103/PhysRevE.56.6601},
}

@article{Brown1998,
  author = {Gregory Brown and Per Arne Rikvold and Martin Grant},
  title = {Universality and scaling for the structure factor in dynamic order-disorder transitions},
  journal = {Phys. Rev. E},
  year = {1998},
  volume = {58},
  pages = {5501},
  doi = {10.1103/PhysRevE.58.5501},
}

@article{Burlatsky1995,
  author = {S. F. Burlatsky and M. Moreau},
  title = {Apparent rate constant for diffusion-controlled three-molecule reactions},
  journal = {Phys. Rev. E},
  year = {1995},
  volume = {51},
  pages = {2363},
  doi = {10.1103/PhysRevE.51.2363},
}

@article{Cahn1958,
  author = {J. W. Cahn and J. E. Hilliard},
  title = {Free Energy of a Nonuniform System. I. Interfacial Free Energy},
  journal = {J. Chem. Phys.},
  year = {1958},
  volume = {28},
  pages = {258},
  doi = {10.1063/1.1744102},
}

@article{Cardy1995,
  author = {John Cardy},
  title = {Proportion of unaffected sites in a reaction-diffusion process},
  journal = {J. Phys. A},
  year = {1995},
  volume = {28},
  pages = {L19},
  doi = {10.1088/0305-4470/28/1/004},
}

@article{Chakrabarti1988,
  author = {Amitabha Chakrabarti and J. D. Gunton},
  title = {Cell-dynamics approach to late-stage domain growth in phase-separating systems},
  journal = {Phys. Rev. B},
  year = {1988},
  volume = {37},
  pages = {3798},
  doi = {10.1103/PhysRevB.37.3798},
}

@article{Connaughton2004,
  author = {Colm Connaughton and R. Rajesh and Oleg Zaboronski},
  title = {Stationary Kolmogorov solutions of the Smoluchowski aggregation equation with a source term},
  journal = {Phys. Rev. E},
  year = {2004},
  volume = {69},
  pages = {061114},
  doi = {10.1103/PhysRevE.69.061114},
}

@article{Connaughton2005,
  author = {Colm Connaughton and R. Rajesh and Oleg Zaboronski},
  title = {Breakdown of Kolmogorov Scaling in Models of Cluster Aggregation},
  journal = {Phys. Rev. Lett.},
  year = {2005},
  volume = {94},
  pages = {194503},
  doi = {10.1103/PhysRevLett.94.194503},
}

@article{Conti2002,
  author = {Massimo Conti and Baruch Meerson and Avner Peleg and Pavel V. Sasorov},
  title = {Phase ordering with a global conservation law: Ostwald ripening and coalescence},
  journal = {Phys. Rev. E},
  year = {2002},
  volume = {65},
  pages = {046117},
  doi = {10.1103/PhysRevE.65.046117},
}

@article{Cueille1999,
  author = {S. Cueille and C. Sire},
  title = {Block persistence},
  year = {1999},
  journal = {Eur. Phys. J. B},
  volume = {7},
  pages = {111},
  doi = {10.1007/s100510050594},
}

@article{Derrida1995,
  author = {Bernard Derrida and Vincent Hakim and Vincent Pasquier},
  title = {Exact First-Passage Exponents of 1D Domain Growth: Relation to a Reaction-Diffusion Model},
  journal = {Phys. Rev. Lett.},
  year = {1995},
  volume = {75},
  pages = {751},
  doi = {10.1103/PhysRevLett.75.751},
}

@article{Doi1976,
  author = {M. Doi},
  title = {Second quantization representation for classical many-particle system},
  journal = {J. Phys. A},
  year = {1976},
  volume = {9},
  pages = {1465},
  doi = {10.1088/0305-4470/9/9/008},
}

@article{Doi1976b,
  author = {M. Doi},
  title = {Stochastic theory of diffusion-controlled reaction},
  journal = {J. Phys. A},
  year = {1976},
  volume = {9},
  pages = {1479},
  doi = {10.1088/0305-4470/9/9/009},
}

@article{Emmott1999,
  author = {C. L. Emmott and A. J. Bray},
  title = {Phase-ordering dynamics with an order-parameter-dependent mobility: The large-n limit},
  journal = {Phys. Rev. E},
  year = {1999},
  volume = {59},
  pages = {213},
  doi = {10.1103/PhysRevE.59.213},
}

@article{Fisher1988,
  author = {Daniel S. Fisher and David A. Huse},
  title = {Nonequilibrium dynamics of spin glasses},
  journal = {Phys. Rev. B},
  year = {1988},
  volume = {38},
  pages = {373},
  doi = {10.1103/PhysRevB.38.373},
}

@article{Fratzl1991,
  author = {P. Fratzl and J. L. Lebowitz and O. Penrose and J. Amar},
  title = {Scaling functions, self-similarity, and the morphology of phase-separating systems},
  journal = {Phys. Rev. B},
  year = {1991},
  volume = {44},
  pages = {4794},
  doi = {10.1103/PhysRevB.44.4794},
}

@article{Gaulin1987,
  author = {B. D. Gaulin and S. Spooner and Y. Morii},
  title = {Kinetics of phase separation in Mn$_{0.67}$Cu$_{0.33}$},
  journal = {Phys. Rev. Lett.},
  year = {1987},
  volume = {59},
  pages = {668},
  doi = {10.1103/PhysRevLett.59.668},
}

@article{Hinrichsen2000,
  author = {H. Hinrichsen},
  title = {Non-equilibrium critical phenomena and phase transitions into absorbing states},
  journal = {Adv. Phys.},
  year = {2000},
  volume = {49},
  pages = {815},
  doi = {10.1080/00018730050198152},
}

@article{Howard1996,
  author = {Martin Howard},
  title = {Fluctuation kinetics in a multispecies reaction-diffusion system},
  journal = {J. Phys. A},
  year = {1996},
  volume = {29},
  pages = {3437},
  doi = {10.1088/0305-4470/29/13/016},
}

@article{Huse1986,
  author = {David A. Huse},
  title = {Corrections to late-stage scaling behavior in spinodal decomposition: Lifshitz-Slyozov scaling and Monte Carlo simulations},
  journal = {Phys. Rev. B},
  year = {1986},
  volume = {34},
  pages = {7845},
  doi = {10.1103/PhysRevB.34.7845},
}

@article{Kang1985,
  author = {K. Kang and S. Redner},
  title = {Fluctuation-dominated kinetics in diffusion-controlled reactions},
  journal = {Phys. Rev. A},
  year = {1985},
  volume = {32},
  pages = {435},
  doi = {10.1103/PhysRevA.32.435},
}

@article{Kawasaki1978,
  author = {Kyozi Kawasaki and Mehmet C. Yalabik and J. D. Gunton},
  title = {Growth of fluctuations in quenched time-dependent Ginzburg-Landau model systems},
  journal = {Phys. Rev. A},
  year = {1978},
  volume = {17},
  pages = {455},
  doi = {10.1103/PhysRevA.17.455},
}

@article{Krapivsky1994,
  author = {P. L. Krapivsky},
  title = {Diffusion-limited-aggregation processes with three-particle elementary reactions},
  journal = {Phys. Rev. E},
  year = {1994},
  volume = {49},
  pages = {3233},
  doi = {10.1103/PhysRevE.49.3233},
}

@article{Krishnamurthy2003,
  author = {Supriya Krishnamurthy and R. Rajesh and Oleg Zaboronski},
  title = {Persistence properties of a system of coagulating and annihilating random walkers},
  journal = {Phys. Rev. E},
  year = {2003},
  volume = {68},
  pages = {046103},
  doi = {10.1103/PhysRevE.68.046103},
}

@article{Krishnamurthy2002,
  author = {Supriya Krishnamurthy and R. Rajesh and Oleg Zaboronski},
  title = {Kang-Redner small-mass anomaly in cluster-cluster aggregation},
  journal = {Phys. Rev. E},
  year = {2002},
  volume = {66},
  pages = {066118},
  doi = {10.1103/PhysRevE.66.066118},
}

@article{Lee1993,
  author = {Benjamin P. Lee and John Cardy},
  title = {Phase Ordering in One-Dimensional Systems with Long-Range Interactions},
  journal = {Phys. Rev. E},
  year = {1993},
  volume = {48},
  pages = {2452},
  doi = {10.1103/PhysRevE.48.2452},
}

@article{Lee1994,
  author = {Benjamin P. Lee},
  title = {Renormalization Group Calculation for the Reaction $kA\to 0$},
  journal = {J. Phys. A},
  year = {1994},
  volume = {27},
  pages = {2633},
  doi = {10.1088/0305-4470/27/8/004},
}

@article{Lee1994b,
  author = {Benjamin P. Lee and John Cardy},
  title = {Scaling of Reaction Zones in the $A+B\to 0$ Diffusion-Limited Reaction},
  journal = {Phys. Rev. E},
  year = {1994},
  volume = {50},
  pages = {R3287},
  doi = {10.1103/PhysRevE.50.R3287},
}

@article{Lee1995,
  author = {Benjamin P. Lee and John Cardy},
  title = {Renormalization Group Study of the $A+B\to 0$ Diffusion-Limited Reaction},
  journal = {J. Stat. Phys.},
  year = {1995},
  volume = {80},
  pages = {971},
  doi = {10.1007/BF02179861},
}

@article{Lee1997,
  author = {Benjamin P. Lee and Andrew D. Rutenberg},
  title = {Persistence, Poisoning, and Autocorrelations in Dilute Coarsening},
  journal = {Phys. Rev. Lett.},
  year = {1997},
  volume = {79},
  pages = {4842},
  doi = {10.1103/PhysRevLett.79.4842},
}

@article{Lifshitz1961,
  author = {I. M. Lifshitz and V. V. Slyozov},
  title = {The kinetics of precipitation from supersaturated solid solutions},
  journal = {J. Phys. Chem. Solids},
  year = {1961},
  volume = {19},
  pages = {35},
  doi = {10.1016/0022-3697(61)90054-3},
}

@article{Lushnikov1987,
  author = {A. A. Lushnikov},
  title = {Binary reaction $1+1\to 0$ in one dimension},
  journal = {Phys. Lett. A},
  year = {1987},
  volume = {120},
  pages = {135},
  doi = {10.1016/0375-9601(87)90714-6},
}

@article{Majumdar1995,
  author = {Satya N. Majumdar and David A. Huse},
  title = {Growth of long-range correlations after a quench in phase-ordering systems},
  journal = {Phys. Rev. E},
  year = {1995},
  volume = {52},
  pages = {270},
  doi = {10.1103/PhysRevE.52.270},
}

@article{Marko1995,
  author = {J. F. Marko and G. T. Barkema},
  title = {Phase ordering in the Ising model with conserved spin},
  journal = {Phys. Rev. E},
  year = {1995},
  volume = {52},
  pages = {2522},
  doi = {10.1103/PhysRevE.52.2522},
}

@article{McFadden1993,
  author = {G. B. McFadden and A. A. Wheeler and R. J. Braun and S. R. Coriell and R. F. Sekerka},
  title = {Phase-field models for anisotropic interfaces},
  journal = {Phys. Rev. E},
  year = {1993},
  volume = {48},
  pages = {2016},
  doi = {10.1103/PhysRevE.48.2016},
}

@article{Mehra2002,
  author = {Vishal Mehra and Peter Grassberger},
  title = {Trapping reaction with mobile traps},
  journal = {Phys. Rev. E},
  year = {2002},
  volume = {65},
  pages = {050101},
  doi = {10.1103/PhysRevE.65.050101},
}

@article{ODonoghue2001,
  author = {S. J. O'Donoghue and A. J. Bray},
  title = {Persistence in the one-dimensional $A+B\to\emptyset$ reaction-diffusion model},
  journal = {Phys. Rev. E},
  year = {2001},
  volume = {64},
  pages = {041105},
  doi = {10.1103/PhysRevE.64.041105},
}

@article{ODonoghue2002a,
  author = {S. J. O'Donoghue and A. J. Bray},
  title = {Uninfected random walkers in one dimension},
  journal = {Phys. Rev. E},
  year = {2002},
  volume = {65},
  pages = {051113},
  doi = {10.1103/PhysRevE.65.051113},
}

@article{ODonoghue2002b,
  author = {S. J. O'Donoghue and A. J. Bray},
  title = {Fraction of uninfected walkers in the one-dimensional Potts model},
  journal = {Phys. Rev. E},
  year = {2002},
  volume = {65},
  pages = {051114},
  doi = {10.1103/PhysRevE.65.051114},
}

@article{Odor2004,
  author = {G. {\'O}dor},
  title = {Universality classes in nonequilibrium lattice systems},
  journal = {Rev. Mod. Phys.},
  year = {2004},
  volume = {76},
  pages = {663},
  doi = {10.1103/RevModPhys.76.663},
}

@article{Ohta1982,
  author = {Takao Ohta and David Jasnow and Kyozi Kawasaki},
  title = {Universal Scaling in the Motion of Random Interfaces},
  journal = {Phys. Rev. Lett.},
  year = {1982},
  volume = {49},
  pages = {1223},
  doi = {10.1103/PhysRevLett.49.1223},
}

@article{Oono1987,
  author = {Y. Oono and S. Puri},
  title = {Computationally Efficient Modeling of Ordering of Quenched Phases},
  journal = {Phys. Rev. Lett.},
  year = {1987},
  volume = {58},
  pages = {836},
  doi = {10.1103/PhysRevLett.58.836},
}

@article{Oono1988,
  author = {Y. Oono and S. Puri},
  title = {Study of phase-separation dynamics by use of cell dynamical systems. I. Modeling},
  journal = {Phys. Rev. A},
  year = {1988},
  volume = {38},
  pages = {434},
  doi = {10.1103/PhysRevA.38.434},
}

@article{Oshanin1995,
  author = {G. Oshanin and A. Stemmer and S. Luding and A. Blumen},
  title = {Smoluchowski approach for three-body reactions in one dimension},
  journal = {Phys. Rev. E},
  year = {1995},
  volume = {52},
  pages = {5800},
  doi = {10.1103/PhysRevE.52.5800},
}

@article{Peliti1985,
  author = {L. Peliti},
  title = {Path integral approach to birth-death processes on a lattice},
  journal = {J. Phys.},
  year = {1985},
  volume = {46},
  pages = {1469},
  doi = {10.1051/jphys:019850046090146900},
}

@article{Peliti1986,
  author = {L. Peliti},
  title = {Renormalisation of fluctuation effects in the A+A to A reaction},
  journal = {J. Phys. A},
  year = {1986},
  volume = {19},
  pages = {L365},
  doi = {10.1088/0305-4470/19/6/012},
}

@article{Puri1988,
  author = {S. Puri and Y. Oono},
  title = {Study of phase-separation dynamics by use of cell dynamical systems. II. Two-dimensional demonstrations},
  journal = {Phys. Rev. A},
  year = {1988},
  volume = {38},
  pages = {1542},
  doi = {10.1103/PhysRevA.38.1542},
}

@article{Puri1997,
  author = {Sanjay Puri and Alan J. Bray and Joel L. Lebowitz},
  title = {Phase-separation kinetics in a model with order-parameter-dependent mobility},
  journal = {Phys. Rev. E},
  year = {1997},
  volume = {56},
  pages = {758},
  doi = {10.1103/PhysRevE.56.758},
}

@article{Queiroz2001,
  author = {S. L. A. {de Queiroz} and R. B. Stinchcombe},
  title = {Correlation functions, free energies, and magnetizations in the two-dimensional random-field Ising model},
  journal = {Phys. Rev. E},
  year = {2001},
  volume = {64},
  pages = {036117},
  doi = {10.1103/PhysRevE.64.036117},
}

@article{Rajesh2004,
  author = {R. Rajesh and O. Zaboronski},
  title = {Survival probability of a diffusing test particle in a system of coagulating and annihilating random walkers},
  journal = {Phys. Rev. E},
  year = {2004},
  volume = {70},
  pages = {036111},
  doi = {10.1103/PhysRevE.70.036111},
}

@article{Rogers1988,
  author = {T. M. Rogers and K. R. Elder and Rashmi C. Desai},
  title = {Numerical study of the late stages of spinodal decomposition},
  journal = {Phys. Rev. B},
  year = {1988},
  volume = {37},
  pages = {9638},
  doi = {10.1103/PhysRevB.37.9638},
}

@article{Rutenberg1995,
  author = {A. D. Rutenberg and A. J. Bray},
  title = {Energy-scaling approach to phase-ordering growth laws},
  journal = {Phys. Rev. E},
  year = {1995},
  volume = {51},
  pages = {5499},
  doi = {10.1103/PhysRevE.51.5499},
}

@article{Rutenberg1996,
  author = {Andrew D. Rutenberg},
  title = {Stress-free Spatial Anisotropy in Phase-Ordering},
  journal = {Phys. Rev. E},
  year = {1996},
  volume = {54},
  pages = {R2181},
  doi = {10.1103/PhysRevE.54.R2181},
}

@article{Rutenberg1996b,
  author = {Andrew D. Rutenberg},
  title = {Non-equilibrium Phase-Ordering with a Global Conservation Law},
  journal = {Phys. Rev. E},
  year = {1996},
  volume = {54},
  pages = {972},
  doi = {10.1103/PhysRevE.54.972},
}

@article{Rutenberg1999,
  author = {Andrew D. Rutenberg and Benjamin P. Vollmayr-Lee},
  title = {Anisotropic Coarsening: Grain Shapes and Nonuniversal Persistence},
  journal = {Phys. Rev. Lett.},
  year = {1999},
  volume = {83},
  pages = {3772},
  doi = {10.1103/PhysRevLett.83.3772},
}

@article{Siegert1990,
  author = {Martin Siegert},
  title = {Growth dynamics with an anisotropic surface tension},
  journal = {Phys. Rev. A},
  year = {1990},
  volume = {42},
  pages = {6268},
  doi = {10.1103/PhysRevA.42.6268},
}

@article{Tam2000,
  author = {W. Y. Tam and A. D. Rutenberg and B. P. Vollmayr-Lee and K. Y. Szeto},
  title = {Cluster Persistence: a Discriminating Probe of Soap Froth Dynamics},
  journal = {Europhys. Lett.},
  year = {2000},
  volume = {51},
  pages = {223},
  doi = {10.1209/epl/i2000-00535-4},
}

@article{Taeuber2005,
  author = {Uwe C. T{\"a}uber and Martin Howard and Benjamin P. Vollmayr-Lee},
  title = {Applications of Field-Theoretic Renormalization Group Methods to Reaction-Diffusion Problems},
  journal = {J. Phys. A},
  year = {2005},
  volume = {38},
  pages = {R79},
  doi = {10.1088/0305-4470/38/17/R01},
}

@article{Toral1988,
  author = {Ra{\'u}l Toral and Amitabha Chakrabarti and James D. Gunton},
  title = {Numerical Study of the Cahn-Hilliard Equation in Three Dimensions},
  journal = {Phys. Rev. Lett.},
  year = {1988},
  volume = {60},
  pages = {2311},
  doi = {10.1103/PhysRevLett.60.2311},
}

@article{Torney1983,
  author = {David C. Torney and Harden M. McConnell},
  title = {Diffusion-limited reactions in one dimension},
  journal = {J. Phys. Chem.},
  year = {1983},
  volume = {87},
  pages = {1941},
  doi = {10.1021/j100234a023},
}

@article{Tsypin1994,
  author = {M. M. Tsypin},
  title = {Universal Effective Potential for Scalar Field Theory in Three Dimensions by Monte Carlo Computation},
  journal = {Phys. Rev. Lett.},
  year = {1994},
  volume = {73},
  pages = {2015},
  doi = {10.1103/PhysRevLett.73.2015},
}

@article{Vernon2003,
  author = {Daniel C. Vernon},
  title = {Long range hops and the pair annihilation reaction $A + A \to 0$: Renormalization group and simulation},
  journal = {Phys. Rev. E},
  year = {2003},
  volume = {68},
  pages = {041103},
  doi = {10.1103/PhysRevE.68.041103},
}

@article{VollmayrLee2003,
  author = {Benjamin P. Vollmayr-Lee and Andrew D. Rutenberg},
  title = {Fast and Accurate Coarsening Simulation with an Unconditionally Stable Time Step},
  journal = {Phys. Rev. E},
  year = {2003},
  volume = {68},
  pages = {066703},
  doi = {10.1103/PhysRevE.68.066703},
}

@article{Yao1993,
  author = {Jian Hua Yao and K. R. Elder and Hong Guo and Martin Grant},
  title = {Theory and simulation of Ostwald ripening},
  journal = {Phys. Rev. B},
  year = {1993},
  volume = {47},
  pages = {14110},
  doi = {10.1103/PhysRevB.47.14110},
}

@article{Yeung1988,
  author = {C. Yeung},
  title = {Scaling and the Small-Wave-Vector Limit of the Form Factor in Phase-Ordering Dynamics},
  journal = {Phys. Rev. Lett.},
  year = {1988},
  volume = {61},
  pages = {1135},
  doi = {10.1103/PhysRevLett.61.1135},
}

@article{Yeung1996,
  author = {Chuck Yeung and Madan Rao and Rashmi C. Desai},
  title = {Bounds on the decay of the autocorrelation in phase ordering dynamics},
  journal = {Phys. Rev. E},
  year = {1996},
  volume = {53},
  pages = {3073},
  doi = {10.1103/PhysRevE.53.3073},
}

@article{Zaboronski2001,
  author = {O. Zaboronski},
  title = {Stochastic aggregation of diffusive particles revisited},
  journal = {Phys. Lett. A},
  year = {2001},
  volume = {281},
  pages = {119},
  doi = {10.1016/S0375-9601(01)00110-4},
}

@article{benAvraham1993,
  author = {Daniel ben-Avraham},
  title = {Diffusion-limited three-body reactions in one dimension},
  journal = {Phys. Rev. Lett.},
  year = {1993},
  volume = {71},
  pages = {3733},
  doi = {10.1103/PhysRevLett.71.3733},
}

@article{Zumofen1994,
  author = {G. Zumofen and J. Klafter},
  title = {Reaction dynamics controlled by enhanced diffusion},
  journal = {Phys. Rev. E},
  year = {1994},
  volume = {50},
  pages = {5119},
  doi = {10.1103/PhysRevE.50.5119},
}

@article{Zumofen1996,
  author = {G. Zumofen and J. Klafter and M. F. Shlesinger},
  title = {Breakdown of Ovchinnikov-Zeldovich Segregation in the $A+B\to 0$ Reaction under L{\'e}vy Mixing},
  journal = {Phys. Rev. Lett.},
  year = {1996},
  volume = {77},
  pages = {2830},
  doi = {10.1103/PhysRevLett.77.2830},
}

@article{Monthus1996,
  author = {C{\'e}cile Monthus},
  title = {Exponents appearing in heterogeneous reaction-diffusion models in one dimension},
  journal = {Phys. Rev. E},
  year = {1996},
  volume = {54},
  pages = {4844},
  doi = {10.1103/PhysRevE.54.4844},
}

@article{Fisher1988b,
  author = {Michael E. Fisher and Martin P. Gelfand},
  title = {The reunions of three dissimilar vicious walkers},
  journal = {J. Stat. Phys.},
  year = {1988},
  volume = {53},
  pages = {175},
  doi = {10.1007/BF01011551},
}

@article{Krapivsky1994b,
  author = {P. L. Krapivsky and E. Ben-Naim and S. Redner},
  title = {Kinetics of heterogeneous single-species annihilation},
  journal = {Phys. Rev. E},
  year = {1994},
  volume = {50},
  pages = {2474},
  doi = {10.1103/PhysRevE.50.2474},
}

@article{Majumdar1998,
  author = {Satya N. Majumdar and Stephen J. Cornell},
  title = {Survival probability of a mobile particle in a fluctuating field},
  journal = {Phys. Rev. E},
  year = {1998},
  volume = {57},
  pages = {3757},
  doi = {10.1103/PhysRevE.57.3757},
}

@article{Catanzaro2005,
  author = {Michele Catanzaro and Mari{\'a}n Bogu{\~n}{\'a} and Romualdo Pastor-Satorras},
  title = {Diffusion-annihilation processes in complex networks},
  journal = {Phys. Rev. E},
  year = {2005},
  volume = {71},
  pages = {056104},
  doi = {10.1103/PhysRevE.71.056104},
}

@article{Gallos2005,
  author = {Lazaros K. Gallos and Panos Argyrakis},
  title = {Reaction-diffusion processes on correlated and uncorrelated scale-free networks},
  journal = {Phys. Rev. E},
  year = {2005},
  volume = {72},
  pages = {017101},
  doi = {10.1103/PhysRevE.72.017101},
}

@article{Gallos2004,
  author = {Lazaros K. Gallos and Panos Argyrakis},
  title = {Absence of Kinetic Effects in Reaction-Diffusion Processes in Scale-Free Networks},
  journal = {Phys. Rev. Lett.},
  year = {2004},
  volume = {92},
  pages = {138301},
  doi = {10.1103/PhysRevLett.92.138301},
}

@article{Drouffe2001,
  author = {J.-M. Drouffe and C. Godr{\`e}che},
  title = {Temporal Correlations and Persistence in the Kinetic Ising Model: the Role of Temperature},
  journal = {Eur. Phys. J. B},
  year = {2001},
  volume = {20},
  pages = {281},
  doi = {10.1007/s100510170277},
}

@article{Manoj2003,
  author = {G. Manoj},
  title = {Persistence in $q$-state Potts model: A mean-field approach},
  journal = {Phys. Rev. E},
  year = {2003},
  volume = {67},
  pages = {026115},
  doi = {10.1103/PhysRevE.67.026115},
}

@article{Saharay2003,
  author = {Moumita Saharay and Parongama Sen},
  title = {Persistence in an antiferromagnetic Ising system with conserved magnetisation},
  journal = {Physica A},
  year = {2003},
  volume = {318},
  pages = {243},
  doi = {10.1016/S0378-4371(02)01423-1},
}

@article{Derrida1997,
  author = {B. Derrida},
  title = {How to extract information from simulations of coarsening at finite temperature},
  journal = {Phys. Rev. E},
  year = {1997},
  volume = {55},
  pages = {3705},
  doi = {10.1103/PhysRevE.55.3705},
}

@article{Jain1999,
  author = {S. Jain},
  title = {Zero-temperature dynamics of the weakly disordered Ising model},
  journal = {Phys. Rev. E},
  year = {1999},
  volume = {59},
  pages = {R2493},
  doi = {10.1103/PhysRevE.59.R2493},
}

@article{Jain2000,
  author = {S. Jain and H. Flynn},
  title = {Scaling and persistence in the two-dimensional Ising model},
  journal = {J. Phys. A},
  year = {2000},
  volume = {33},
  pages = {8383},
  doi = {10.1088/0305-4470/33/47/305},
}

@article{Luebeck2002,
  author = {S. L{\"u}beck and A. Misra},
  title = {Persistence distributions in a conserved lattice gas with absorbing states},
  journal = {Eur. Phys. J. B},
  year = {2002},
  volume = {26},
  pages = {75},
  doi = {10.1140/epjb/e20020068},
}

@article{Manoj2000,
  author = {G. Manoj and P. Ray},
  title = {Persistence in higher dimensions: A finite size scaling study},
  journal = {Phys. Rev. E},
  year = {2000},
  volume = {62},
  pages = {007755},
  doi = {10.1103/PhysRevE.62.007755},
}

@article{Yao1992,
  author = {Jian Hua Yao and K. R. Elder and Hong Guo and Martin Grant},
  title = {Ostwald ripening in two and three dimensions},
  journal = {Phys. Rev. B},
  year = {1992},
  volume = {45},
  pages = {8173},
  doi = {10.1103/PhysRevB.45.8173},
}

@article{Hilgenfeldt2001,
  author = {Sascha Hilgenfeldt and Stephan A. Koehler and Howard A. Stone},
  title = {Dynamics of Coarsening Foams: Accelerated and Self-Limiting Drainage},
  journal = {Phys. Rev. Lett.},
  year = {2001},
  volume = {86},
  pages = {4704},
  doi = {10.1103/PhysRevLett.86.4704},
}

@article{Hilgenfeldt2001b,
  author = {Sascha Hilgenfeldt and Andrew M. Kraynik and Stephan A. Koehler and Howard A. Stone},
  title = {An Accurate von Neumann's Law for Three-Dimensional Foams},
  journal = {Phys. Rev. Lett.},
  year = {2001},
  volume = {86},
  pages = {2685},
  doi = {10.1103/PhysRevLett.86.2685},
}

@article{Zhu1999,
  author = {Jingzhi Zhu and Long-Qing Chen and Jie Shen and Veena Tikare},
  title = {Coarsening kinetics from a variable-mobility Cahn-Hilliard equation: Application of a semi-implicit Fourier spectral method},
  journal = {Phys. Rev. E},
  year = {1999},
  volume = {60},
  pages = {3564},
  doi = {10.1103/PhysRevE.60.3564},
}

@article{Cheng2007,
  author = {Mowei Cheng and James A. Warren},
  title = {Controlling the accuracy of unconditionally stable algorithms in the Cahn-Hilliard equation},
  journal = {Phys. Rev. E},
  year = {2007},
  volume = {75},
  pages = {017702},
  doi = {10.1103/PhysRevE.75.017702},
}

@article{Cheng2005,
  author = {Mowei Cheng and Andrew D. Rutenberg},
  title = {Maximally fast coarsening algorithms},
  journal = {Phys. Rev. E},
  year = {2005},
  volume = {72},
  pages = {055701},
  doi = {10.1103/PhysRevE.72.055701},
}

@article{Teixeira1997,
  author = {P. I. C. Teixeira and B. M. Mulder},
  title = {Comment on ``Study of phase-separation dynamics by use of cell dynamical systems. I. Modeling''},
  journal = {Phys. Rev. E},
  year = {1997},
  volume = {55},
  pages = {3789},
  doi = {10.1103/PhysRevE.55.3789},
}

@article{Oono1997,
  author = {Y. Oono},
  title = {Reply to ``Comment on `Study of phase-separation dynamics by use of cell dynamical systems. I. Modeling'''},
  journal = {Phys. Rev. E},
  year = {1997},
  volume = {55},
  pages = {3792},
  doi = {10.1103/PhysRevE.55.3792},
}

@article{Alkemper1999,
  title = {Dynamics of Late-Stage Phase Separation: A Test of Theory},
  author = {J. Alkemper and V. A. Snyder and N. Akaiwa and P. W. Voorhees},
  year = {1999},
  journal = {Phys. Rev. Lett.},
  volume = {82},
  pages = {2725},
  doi = {10.1103/PhysRevLett.82.2725},
}

@article{Berthier2001,
  title = {Phase separation in a homogeneous shear flow: Morphology, growth laws, and dynamic scaling},
  author = {Ludovic Berthier},
  year = {2001},
  journal = {Phys. Rev. E},
  volume = {63},
  pages = {051503},
  doi = {10.1103/PhysRevE.63.051503},
}

@article{Berthier2001b,
  title = {Phase Separation in a Chaotic Flow},
  author = {Ludovic Berthier and Jean-Louis Barrat and Jorge Kurchan},
  year = {2001},
  journal = {Phys. Rev. Lett.},
  volume = {86},
  pages = {2014},
  doi = {10.1103/PhysRevLett.86.2014},
}

@article{Berti2005,
  title = {Turbulence and Coarsening in Active and Passive Binary Mixtures},
  author = {S. Berti and G. Boffetta and M. Cencini and A. Vulpiani},
  year = {2005},
  journal = {Phys. Rev. Lett.},
  volume = {95},
  pages = {224501},
  doi = {10.1103/PhysRevLett.95.224501},
}

@article{Lacasta1995,
  title = {Phase Separation Dynamics under Stirring},
  author = {A. M. Lacasta and J. M. Sancho and F. Sagu{\'e}s},
  year = {1995},
  journal = {Phys. Rev. Lett.},
  volume = {75},
  pages = {1791},
  doi = {10.1103/PhysRevLett.75.1791},
}

@article{ONaraigh2007,
  title = {Bubbles and filaments: Stirring a Cahn-Hilliard fluid},
  author = {{\'O} N{\'a}raigh, Lennon and Jean-Luc Thiffeault},
  year = {2007},
  journal = {Phys. Rev. E},
  volume = {75},
  pages = {016216},
  doi = {10.1103/PhysRevE.75.016216},
}

@article{Wijland2001,
  title = {Field theory for reaction-diffusion processes with hard-core particles},
  author = {van Wijland, Fr{\'e}d{\'e}ric},
  year = {2001},
  journal = {Phys. Rev. E},
  volume = {63},
  pages = {022101},
  doi = {10.1103/PhysRevE.63.022101},
}

@article{Arenzon2007,
  title = {Exact Results for Curvature-Driven Coarsening in Two Dimensions},
  author = {Jeferson J. Arenzon and Alan J. Bray and Leticia F. Cugliandolo and Alberto Sicilia},
  year = {2007},
  journal = {Phys. Rev. Lett.},
  volume = {98},
  pages = {145701},
  doi = {10.1103/PhysRevLett.98.145701},
}

@article{Sicilia2007,
  title = {Domain growth morphology in curvature-driven two-dimensional coarsening},
  author = {Alberto Sicilia and Jeferson J. Arenzon and Alan J. Bray and Leticia F. Cugliandolo},
  year = {2007},
  journal = {Phys. Rev. E},
  volume = {76},
  pages = {061116},
  doi = {10.1103/PhysRevE.76.061116},
}

@article{Sicilia2008,
  title = {Geometric properties of two-dimensional coarsening with weak disorder},
  author = {A. Sicilia and J. J. Arenzon and A. J. Bray and L. F. Cugliandolo},
  year = {2008},
  journal = {Europhys. Lett.},
  volume = {82},
  pages = {10001},
  doi = {10.1209/0295-5075/82/10001},
}

@article{Barros2009,
  title = {Freezing into stripe states in two-dimensional ferromagnets and crossing probabilities in critical percolation},
  author = {Kipton Barros and P. L. Krapivsky and S. Redner},
  year = {2009},
  journal = {Phys. Rev. E},
  volume = {80},
  pages = {040101},
  doi = {10.1103/PhysRevE.80.040101},
}

@article{Ahluwalia1999,
  title = {Phase separation in a simple model with dynamical asymmetry},
  author = {Rajeev Ahluwalia},
  year = {1999},
  journal = {Phys. Rev. E},
  volume = {59},
  pages = {263},
  doi = {10.1103/PhysRevE.59.263},
}

@article{Bertozzi2011,
  title = {A biharmonic-modified forward time stepping method for fourth order nonlinear diffusion equations},
  author = {Andrea L. Bertozzi and Ning Ju and Hsiang-Wei Lu},
  year = {2011},
  journal = {Discret. Contin. Dyn. S.},
  volume = {29},
  pages = {1367},
  doi = {10.3934/dcds.2011.29.1367},
}

@article{Chen2012,
  author = {Chen, Wenbin and Conde, Sidafa and Wang, Cheng and Wang, Xiaoming and Wise, Steven},
  affiliation = {School of Mathematical Sciences, Fudan University, Shanghai, 2 00433 China},
  title = {A Linear Energy Stable Scheme for a Thin Film Model Without Slope Selection},
  journal = {J. Sci. Comput.},
  publisher = {Springer Netherlands},
  keyword = {Mathematics and Statistics},
  pages = {546},
  volume = {52},
  issue = {3},
  year = {2012},
  doi = {10.1007/s10915-011-9559-2},
}

@article{Moldovan2000,
  title = {Interfacial coarsening dynamics in epitaxial growth with slope selection},
  author = {Moldovan, Dorel and Golubovic, Leonardo},
  year = {2000},
  journal = {Phys. Rev. E},
  volume = {61},
  pages = {6190},
  doi = {10.1103/PhysRevE.61.6190},
}

@article{Shen2012,
  title = {Second-order Convex Splitting Schemes for Gradient Flows with Ehrlich-Schwoebel Type Energy: Application to Thin Film Epitaxy},
  author = {Jie Shen and Cheng Wang and Xiaoming Wang and Steven M. Wise},
  year = {2012},
  journal = {SIAM J. Numer. Anal.},
  volume = {50},
  pages = {105},
  doi = {10.1137/110822839},
}

@article{Siegert1994,
  title = {Slope Selection and Coarsening in Molecular Beam Epitaxy},
  author = {Siegert, Martin and Plischke, Michael},
  year = {1994},
  journal = {Phys. Rev. Lett.},
  volume = {73},
  pages = {1517},
  doi = {10.1103/PhysRevLett.73.1517},
}

@article{Wang2010,
  title = {Unconditionally stable schemes for equations of thin film epitaxy},
  author = {Cheng Wang and Xiaoming Wang and Steven M. Wise},
  year = {2010},
  journal = {Discret. Contin. Dyn. S.},
  volume = {28},
  pages = {405},
  doi = {10.3934/dcds.2010.28.405},
}

@article{Watson2006,
  title = {Scaling Theory and Morphometrics for a Coarsening Multiscale Surface, via a Principle of Maximal Dissipation},
  author = {Watson, Stephen J. and Norris, Scott A.},
  year = {2006},
  journal = {Phys. Rev. Lett.},
  volume = {96},
  pages = {176103},
  doi = {10.1103/PhysRevLett.96.176103},
}

@article{Xu2006,
  title = {Stability Analysis of Large Time‐Stepping Methods for Epitaxial Growth Models},
  author = {Chuanju Xu and Tao Tang},
  year = {2006},
  journal = {SIAM J. Numer. Anal.},
  volume = {44},
  pages = {1759},
  doi = {10.1137/050628143},
}

@article{Chen2002,
  title = {Phase-Field Models for Microstructure Evolution},
  author = {Long-Qing Chen},
  year = {2002},
  journal = {Annu. Rev. Mater. Res.},
  volume = {32},
  pages = {113},
  doi = {10.1146/annurev.matsci.32.112001.132041},
}

@article{Sappelt1997,
  title = {Computer simulation study of phase separation in a binary mixture with a glass-forming component},
  journal = {Physica A: Statistical Mechanics and its Applications},
  volume = {240},
  number = {3–4},
  pages = {453 - 479},
  year = {1997},
  doi = {10.1016/S0378-4371(97)00048-4},
  author = {Dirk Sappelt and Josef J\"ackle},
}

@article{Cardy2003,
  author = {Cardy, John and Ziff, Robert},
  affiliation = {Theoretical Physics Department of Physics 1 Keble Road Oxford OX1 3NP United Kingdom},
  title = {Exact Results for the Universal Area Distribution of Clusters in Per colation, Ising, and Potts Models},
  journal = {J. Stat. Phys.},
  publisher = {Springer Netherlands},
  keyword = {Physics and Astronomy},
  pages = {1},
  volume = {110},
  issue = {1},
  year = {2003},
  doi = {10.1023/A:1021069209656},
}

@article{Loureiro2010,
  title = {Curvature-driven coarsening in the two-dimensional Potts model},
  author = {Loureiro, Marcos P. O. and Arenzon, Jeferson J. and Cugliandolo, Leticia F. and Sicilia, Alberto},
  year = {2010},
  journal = {Phys. Rev. E},
  volume = {81},
  pages = {021129},
  doi = {10.1103/PhysRevE.81.021129},
}

@article{Brunini2011,
  title = {Percolation of diffusionally evolved two-phase systems},
  author = {Brunini, Victor E. and Schuh, Christopher A. and Carter, W. Craig},
  year = {2011},
  journal = {Phys. Rev. E},
  volume = {83},
  pages = {021119},
  doi = {10.1103/PhysRevE.83.021119},
}

@article{Zhou2006,
  title = {Modified models of polymer phase separation},
  author = {Zhou, Douglas and Zhang, Pingwen and E, Weinan},
  year = {2006},
  journal = {Phys. Rev. E},
  volume = {73},
  pages = {061801},
  doi = {10.1103/PhysRevE.73.061801},
}

@article{Talkner2007,
  title = {Fluctuation theorems: Work is not an observable},
  author = {Talkner, Peter and Lutz, Eric and H\"anggi, Peter},
  journal = {Phys. Rev. E},
  volume = {75},
  issue = {5},
  pages = {050102},
  numpages = {2},
  year = {2007},
  month = {May},
  doi = {10.1103/PhysRevE.75.050102},
  publisher = {American Physical Society},
}

@article{Majumder2010,
  title = {Domain coarsening in two dimensions: Conserved dynamics and finite-size scaling},
  author = {Majumder, Suman and Das, Subir K.},
  year = {2010},
  journal = {Phys. Rev. E},
  volume = {81},
  pages = {050102},
  doi = {10.1103/PhysRevE.81.050102},
}

@article{Majumder2011,
  title = {Diffusive domain coarsening: Early time dynamics and finite-size effects},
  author = {Majumder, Suman and Das, Subir K.},
  year = {2011},
  journal = {Phys. Rev. E},
  volume = {84},
  pages = {021110},
  doi = {10.1103/PhysRevE.84.021110},
}

@article{Das2012,
  author = {Subir K. Das and Sutapa Roy and Suman Majumder and Shaista Ahmad},
  title = {Finite-size effects in dynamics: Critical vs. coarsening phenomena},
  journal = {Europhys. Lett.},
  volume = {97},
  number = {6},
  pages = {66006},
  year = {2012},
  abstract = {Finite-size effects in systems with diverging characteristic length scale have b een addressed via state-of-the-art Monte Carlo and molecular-dynamics simulations of various models exhibiting solid-solid, liquid-liquid and vapor-liquid transitions. Our simulations, combined with the appropriate application of the finite-size scaling theory, confirm variou s non-trivial singularities in equilibrium dynamic critical phenomena and non-equilibrium do main coarsening phenomena, as predicted by analytical theories. We convincingly demonstrate that the finite-size effects in the domain growth problems, with conserved order parameter d ynamics, is weak and universal, irrespective of the transport mechanism. This result is stri kingly different from the corresponding effects in critical dynamics. In critical phenomena, the difference in finite-size effects between statics and dynamics is also discussed.},
  doi = {10.1209/0295-5075/97/66006},
}

@article{Mao2001,
  author = {Mao, Y. and McLeish, T.C.B. and Teixeira, P.I.C. and Read, D.J.},
  affiliation = {IRC in Polymer Science and Technology, Department of Physics, University of Leeds, Leeds, LS2 9JT, UK GB},
  title = {Asymmetric landscapes of early spinodal decomposition},
  journal = {Eur. Phys. J. E Soft Matter},
  publisher = {Springer Berlin / Heidelberg},
  keyword = {Physics and Astronomy},
  pages = {69},
  volume = {6},
  issue = {1},
  year = {2001},
  doi = {10.1007/s101890170029},
}

@article{Loureiro2010b,
  author = {M. P. O. Loureiro and J. J. Arenzon and L. F. Cugliandolo and A. Sicilia},
  title = {Coarsening in the Potts model: out-of-equilibrium geometric properties},
  journal = {J. Phys.: Conf. Ser.},
  volume = {246},
  number = {1},
  pages = {012022},
  year = {2010},
  abstract = {Geometric properties of polymixtures after a sudden quench in temperature are studied through the q -states Potts model on a square lattice, and their evolution with Monte Carlo simulations with non-conserved order parameter. We analyse the distribution of hull enclosed areas for different initial conditions and compare with exact and numerical findings for the q = 2 (Ising) case.},
  doi = {10.1088/1742-6596/246/1/012022},
}

@article{Arenzon2008,
  author = {Arenzon, J. and Bray, A. and Cugliandolo, L. and Sicilia, A.},
  affiliation = {Universidade Federal do Rio Grande do Sul Instituto de Física CP 15051, 91501-970 Porto Alegre RS Brazil},
  title = {Exact results for two-dimensional coarsening},
  journal = {Eur. Phys. J. B},
  publisher = {Springer Berlin / Heidelberg},
  keyword = {Physics and Astronomy},
  pages = {403},
  volume = {64},
  issue = {3},
  year = {2008},
  doi = {10.1140/epjb/e2008-00020-6},
}

@article{Sicilia2009,
  title = {Geometry of phase separation},
  author = {Sicilia, Alberto and Sarrazin, Yoann and Arenzon, Jeferson J. and Bray, Alan J. and Cugliandolo, Leticia F.},
  year = {2009},
  journal = {Phys. Rev. E},
  volume = {80},
  pages = {031121},
  doi = {10.1103/PhysRevE.80.031121},
}

@article{Wagner1961,
  author = {Wagner, Carl},
  title = {Theorie der Alterung von Niederschl\"agen durch Uml\"osen (Ostwald-Reifung)},
  journal = {Z. Elektrochem.},
  volume = {65},
  number = {7-8},
  publisher = {Wiley-VCH Verlag GmbH & Co. KGaA},
  doi = {10.1002/bbpc.19610650704},
  pages = {581},
  year = {1961},
}

@article{Chakrabarti1993,
  title = {Lamellar phase in a model for block copolymers},
  author = {Chakrabarti, Amitabha and Gunton, James D.},
  year = {1993},
  journal = {Phys. Rev. E},
  volume = {47},
  pages = {R792},
  doi = {10.1103/PhysRevE.47.R792},
}

@article{Sicilia2008b,
  title = {Experimental Test of Curvature-Driven Dynamics in the Phase Ordering of a Two Dimensional Liquid Crystal},
  author = {Sicilia, Alberto and Arenzon, Jeferson J. and Dierking, Ingo and Bray, Alan J. and Cugliandolo, Leticia F. and Mart{\'i}nez-Perdiguero, Josu and Alonso, Ibon and Pintre, Inmaculada C.},
  year = {2008},
  journal = {Phys. Rev. Lett.},
  volume = {101},
  pages = {197801},
  doi = {10.1103/PhysRevLett.101.197801},
}

@article{Calabrese2009,
  author = {Pasquale Calabrese and John Cardy and Benjamin Doyon},
  title = {Entanglement entropy in extended quantum systems},
  journal = {J. Phys. A},
  volume = {42},
  number = {50},
  pages = {500301},
  doi = {10.1088/1751-8121/42/50/500301},
  year = {2009},
}

@article{Kalda2001,
  title = {Description of random Gaussian surfaces by a four-vertex model},
  author = {Kalda, Jaan},
  year = {2001},
  journal = {Phys. Rev. E},
  volume = {64},
  pages = {020101},
  doi = {10.1103/PhysRevE.64.020101},
}

@article{Weinrib1982,
  title = {Percolation threshold of a two-dimensional continuum system},
  author = {Weinrib, Abel},
  year = {1982},
  journal = {Phys. Rev. B},
  volume = {26},
  pages = {1352},
  doi = {10.1103/PhysRevB.26.1352},
}

@article{Zallen1971,
  title = {Percolation on a Continuum and the Localization-Delocalization Transition in Amorphous Semiconductors},
  author = {Zallen, Richard and Scher, Harvey},
  year = {1971},
  journal = {Phys. Rev. B},
  volume = {4},
  pages = {4471},
  doi = {10.1103/PhysRevB.4.4471},
}

@article{Ahmad2010,
  title = {Kinetics of phase separation in fluids: A molecular dynamics study},
  author = {Ahmad, Shaista and Das, Subir K. and Puri, Sanjay},
  year = {2010},
  journal = {Phys. Rev. E},
  volume = {82},
  pages = {040107},
  doi = {10.1103/PhysRevE.82.040107},
}

@article{Kondev1995,
  title = {Geometrical Exponents of Contour Loops on Random Gaussian Surfaces},
  author = {Kondev, Jan\'e and Henley, Christopher L.},
  year = {1995},
  journal = {Phys. Rev. Lett.},
  volume = {74},
  pages = {4580},
  doi = {10.1103/PhysRevLett.74.4580},
}

@article{Jaynes1957,
  title = {Information Theory and Statistical Mechanics},
  author = {Jaynes, E. T.},
  journal = {Phys. Rev.},
  volume = {106},
  issue = {4},
  pages = {620--630},
  year = {1957},
  month = {May},
  doi = {10.1103/PhysRev.106.620},
  publisher = {American Physical Society},
}

@article{Cugliandolo2010,
  title = {Topics in coarsening phenomena},
  journal = {Physica A},
  volume = {389},
  number = {20},
  pages = {4360},
  year = {2010},
  doi = {10.1016/j.physa.2009.12.036},
  author = {Leticia F. Cugliandolo},
}

@article{Thomas2006,
  title = {Coarsening of three-dimensional grains in crystals, or bubbles in dry foams, tends towards a universal, statistically scale-invariant regime},
  author = {Thomas, Gilberto L. and de Almeida, R. M. C. and Graner, F.},
  year = {2006},
  journal = {Phys. Rev. E},
  volume = {74},
  pages = {021407},
  doi = {10.1103/PhysRevE.74.021407},
}

@article{Lambert2010,
  title = {Coarsening Foams Robustly Reach a Self-Similar Growth Regime},
  author = {Lambert, J\'er\^ome and Mokso, Rajmund and Cantat, Isabelle and Cloetens, Peter and Glazier, James A. and Graner, Fran{\c c}ois and Delannay, Renaud},
  year = {2010},
  journal = {Phys. Rev. Lett.},
  volume = {104},
  pages = {248304},
  doi = {10.1103/PhysRevLett.104.248304},
}

@article{Stavans1993,
  author = {J Stavans},
  title = {The evolution of cellular structures},
  journal = {Rep. Prog. Phys.},
  volume = {56},
  number = {6},
  pages = {733},
  year = {1993},
  doi = {10.1088/0034-4885/56/6/002},
}

@article{Binder1974,
  title = {Theory for the Slowing Down of the Relaxation and Spinodal Decomposition of Binary Mixtures},
  author = {Binder, K. and Stauffer, D.},
  year = {1974},
  journal = {Phys. Rev. Lett.},
  volume = {33},
  pages = {1006},
  doi = {10.1103/PhysRevLett.33.1006},
}

@article{Babcock1990,
  title = {Avalanches and self-organization in cellular magnetic-domain patterns},
  author = {Babcock, K. L. and Westervelt, R. M.},
  year = {1990},
  journal = {Phys. Rev. Lett.},
  volume = {64},
  pages = {2168},
  doi = {10.1103/PhysRevLett.64.2168},
}

@article{Chuang1991,
  title = {Late-time coarsening dynamics in a nematic liquid crystal},
  author = {Chuang, Isaac and Turok, Neil and Yurke, Bernard},
  year = {1991},
  journal = {Phys. Rev. Lett.},
  volume = {66},
  pages = {2472},
  doi = {10.1103/PhysRevLett.66.2472},
}

@article{Cheng2008,
  title = {An efficient algorithm for solving the phase field crystal model},
  journal = {J. Comp. Phys.},
  volume = {227},
  number = {12},
  pages = {6241},
  year = {2008},
  doi = {10.1016/j.jcp.2008.03.012},
  author = {Mowei Cheng and James A. Warren},
}

@article{Swift1977,
  title = {Hydrodynamic fluctuations at the convective instability},
  author = {Swift, J. and Hohenberg, P. C.},
  year = {1977},
  journal = {Phys. Rev. A},
  volume = {15},
  pages = {319},
  doi = {10.1103/PhysRevA.15.319},
}

@article{Li2003,
  author = {Li,Bo and Liu,Jian-Guo},
  title = {Thin film epitaxy with or without slope selection},
  journal = {European J. Appl. Math.},
  volume = {14},
  issue = {06},
  month = {11},
  year = {2003},
  pages = {713},
  numpages = {31},
  doi = {10.1017/S095679250300528X},
}

@article{Chen2012b,
  year = {2012},
  journal = {Numer. Math.},
  volume = {122},
  issue = {4},
  doi = {10.1007/s00211-012-0473-9},
  title = {A mixed finite element method for thin film epitaxy},
  author = {Chen, Wenbin and Wang, Yanqiu},
  pages = {771},
}

@article{Golubovic1997,
  title = {Interfacial Coarsening in Epitaxial Growth Models without Slope Selection},
  author = {Golubovic, Leonardo},
  year = {1997},
  journal = {Phys. Rev. Lett.},
  volume = {78},
  pages = {90},
  doi = {10.1103/PhysRevLett.78.90},
}

@article{Qiao2012,
  author = {Qiao, Zhonghua and Sun, Zhi-zhong and Zhang, Zhengru},
  title = {The stability and convergence of two linearized finite difference schemes for the nonlinear epitaxial growth model},
  journal = {Numer. Methods for Partial Differential Eq.},
  volume = {28},
  number = {6},
  publisher = {Wiley Subscription Services, Inc., A Wiley Company},
  doi = {10.1002/num.20707},
  pages = {1893},
  year = {2012},
}

@article{Johnson1994,
  title = {Stable and unstable growth in molecular beam epitaxy},
  author = {Johnson, M. D. and Orme, C. and Hunt, A. W. and Graff, D. and Sudijono, J. and Sander, L. M. and Orr, B. G.},
  year = {1994},
  journal = {Phys. Rev. Lett.},
  volume = {72},
  pages = {116},
  doi = {10.1103/PhysRevLett.72.116},
}

@article{Eyre1998,
  title = {An Unconditionally Stable One-Step Scheme for Gradient Systems},
  author = {David J. Eyre},
  journal = {Unpublished},
  volume = {X},
  pages = {1},
  year = {1998},
  url = {www.math.utah.edu/~eyre/research/methods/stable.ps},
}

@article{Eyre1998b,
  author = {Eyre, David J.},
  title = {Unconditionally Gradient Stable Time Marching the Cahn-Hilliard Equation},
  journal = {MRS Proceedings},
  volume = {529},
  pages = {39},
  year = {1998},
  doi = {10.1557/PROC-529-39},
}

@article{Ortiz1999,
  title = {A continuum model of kinetic roughening and coarsening in thin films},
  journal = {J. Mech. Phys. Solids},
  volume = {47},
  number = {4},
  pages = {697 - 730},
  year = {1999},
  doi = {10.1016/S0022-5096(98)00102-1},
  author = {M. Ortiz and E.A. Repetto and H. Si},
}

@article{Rost1997,
  title = {Coarsening of surface structures in unstable epitaxial growth},
  author = {Rost, Martin and Krug, Joachim},
  year = {1997},
  journal = {Phys. Rev. E},
  volume = {55},
  pages = {3952},
  doi = {10.1103/PhysRevE.55.3952},
}

@article{Rost2005,
  year = {2005},
  isbn = {978-3-7643-7208-8},
  booktitle = {Multiscale Modeling in Epitaxial Growth},
  volume = {149},
  series = {ISNM International Series of Numerical Mathematics},
  editor = {Voigt, Axel},
  doi = {10.1007/3-7643-7343-1_12},
  title = {Continuum Models for Surface Growth},
  publisher = {Birkhäuser Basel},
  author = {Rost, Martin},
  pages = {195},
}

@article{Krug1997,
  author = {Krug, Joachim},
  title = {Origins of scale invariance in growth processes},
  journal = {Adv. Phys.},
  volume = {46},
  number = {2},
  pages = {139},
  year = {1997},
  doi = {10.1080/00018739700101498},
}

@article{Siegert1997,
  title = {Ordering dynamics of surfaces in molecular beam epitaxy},
  journal = {Physica A},
  volume = {239},
  number = {1–3},
  pages = {420},
  year = {1997},
  doi = {10.1016/S0378-4371(97)00032-0},
  author = {Martin Siegert},
}

@article{Siegert1998,
  title = {Coarsening Dynamics of Crystalline Thin Films},
  author = {Siegert, Martin},
  year = {1998},
  journal = {Phys. Rev. Lett.},
  volume = {81},
  pages = {5481},
  doi = {10.1103/PhysRevLett.81.5481},
}

@article{Ehrlich1966,
  author = {Gert Ehrlich and F. G. Hudda},
  collaboration = {},
  title = {Atomic View of Surface Self-Diffusion: Tungsten on Tungsten},
  publisher = {AIP},
  year = {1966},
  journal = {J. Chem. Phys.},
  volume = {44},
  number = {3},
  pages = {1039},
  doi = {10.1063/1.1726787},
}

@article{Schwoebel1966,
  author = {Richard L. Schwoebel and Edward J. Shipsey},
  title = {Step Motion on Crystal Surfaces},
  publisher = {AIP},
  year = {1966},
  journal = {J. Appl. Phys.},
  volume = {37},
  number = {10},
  pages = {3682},
  doi = {10.1063/1.1707904},
}

@article{Krug1993,
  title = {Surface diffusion currents and the universality classes of growth},
  author = {Krug, Joachim and Plischke, Michael and Siegert, Martin},
  year = {1993},
  journal = {Phys. Rev. Lett.},
  volume = {70},
  pages = {3271},
  doi = {10.1103/PhysRevLett.70.3271},
}

@article{Mullins1959,
  author = {William W. Mullins},
  title = {Flattening of a Nearly Plane Solid Surface due to Capillarity},
  publisher = {AIP},
  year = {1959},
  journal = {J. Appl. Phys.},
  volume = {30},
  number = {1},
  pages = {77},
  doi = {10.1063/1.1734979},
}

@article{Schweitzer1998,
  title = {Complex Motion of Brownian Particles with Energy Depots},
  author = {Schweitzer, Frank and Ebeling, Werner and Tilch, Benno},
  year = {1998},
  journal = {Phys. Rev. Lett.},
  volume = {80},
  pages = {5044},
  doi = {10.1103/PhysRevLett.80.5044},
}

@article{Seifert2005,
  title = {Entropy Production along a Stochastic Trajectory and an Integral Fluctuation Theorem},
  author = {Seifert, Udo},
  year = {2005},
  journal = {Phys. Rev. Lett.},
  volume = {95},
  pages = {040602},
  doi = {10.1103/PhysRevLett.95.040602},
}

@article{Kurchan1998,
  author = {Jorge Kurchan},
  title = {Fluctuation theorem for stochastic dynamics},
  journal = {J. Phys. A},
  volume = {31},
  number = {16},
  pages = {3719},
  year = {1998},
  doi = {10.1088/0305-4470/31/16/003},
}

@article{Haenggi1980,
  year = {1980},
  journal = {Z. Phys. B},
  volume = {36},
  doi = {10.1007/BF01325291},
  title = {Langevin description of markovian integro-differential master equations},
  publisher = {Springer-Verlag},
  author = {H{\"a}nggi, P.},
  pages = {271},
}

@article{Villain1991,
  author = {J. Villain},
  title = {Continuum models of crystal growth from atomic beams with and without desorption},
  doi = {10.1051/jp1:1991114},
  journal = {J. Phys. I France},
  year = {1991},
  volume = {1},
  number = {1},
  pages = {19},
}

@article{Tsui1996,
  title = {Morphology Transition and Layer-by-Layer Growth of Rh(111)},
  author = {Tsui, F. and Wellman, J. and Uher, C. and Clarke, Roy},
  year = {1996},
  journal = {Phys. Rev. Lett.},
  volume = {76},
  pages = {3164},
  doi = {10.1103/PhysRevLett.76.3164},
}

@article{Kohn2003,
  author = {Kohn, Robert V. and Yan, Xiaodong},
  title = {Upper bound on the coarsening rate for an epitaxial growth model},
  journal = {Comm. Pure App. Math.},
  volume = {56},
  number = {11},
  doi = {10.1002/cpa.10103},
  pages = {1549},
  year = {2003},
}

@article{VanDenBroeck1983,
  year = {1983},
  journal = {J. Stat. Phys.},
  volume = {31},
  issue = {3},
  doi = {10.1007/BF01019494},
  title = {On the relation between white shot noise, Gaussian white noise, and the dichotomic Markov process},
  author = {Van Den Broeck, C.},
  pages = {467},
  language = {English},
}

@article{Matthews1951,
  title = {The Renormalization of Meson Theories},
  author = {Matthews, P. T. and Salam, Abdus},
  journal = {Rev. Mod. Phys.},
  volume = {23},
  issue = {4},
  pages = {311--314},
  year = {1951},
  month = {Oct},
  doi = {10.1103/RevModPhys.23.311},
  publisher = {American Physical Society},
}

@article{Elder2004,
  title = {Modeling elastic and plastic deformations in nonequilibrium processing using phase field crystals},
  author = {Elder, K. R. and Grant, Martin},
  year = {2004},
  journal = {Phys. Rev. E},
  volume = {70},
  pages = {051605},
  doi = {10.1103/PhysRevE.70.051605},
}

@article{Elder2002,
  title = {Modeling Elasticity in Crystal Growth},
  author = {Elder, K. R. and Katakowski, Mark and Haataja, Mikko and Grant, Martin},
  year = {2002},
  journal = {Phys. Rev. Lett.},
  volume = {88},
  pages = {245701},
  doi = {10.1103/PhysRevLett.88.245701},
}

@article{Brazovskii1975,
  title = {Phase transition of an isotropic system to a nonuniform state},
  author = {S. A. Brazovskii},
  year = {1975},
  journal = {Sov. Phys. JETP},
  volume = {41},
  pages = {85},
}

@article{Hohenberg1977,
  title = {Theory of dynamic critical phenomena},
  author = {Hohenberg, P. C. and Halperin, B. I.},
  journal = {Rev. Mod. Phys.},
  volume = {49},
  issue = {3},
  pages = {435},
  year = {1977},
  month = {Jul},
  doi = {10.1103/RevModPhys.49.435},
}

@article{Ohta1986,
  author = {Ohta, Takao and Kawasaki, Kyozi},
  title = {Equilibrium morphology of block copolymer melts},
  journal = {Macromolecules},
  volume = {19},
  number = {10},
  pages = {2621},
  year = {1986},
  doi = {10.1021/ma00164a028},
}

@article{Haller2001,
  title = {Distinguished material surfaces and coherent structures in three-dimens ional fluid flows},
  journal = {Physica D},
  volume = {149},
  number = {4},
  pages = {248},
  year = {2001},
  doi = {10.1016/S0167-2789(00)00199-8},
  author = {G. Haller},
}

@article{Biagi2012,
  title = {Coarsening Scenarios in Unstable Crystal Growth},
  author = {Biagi, Sofia and Misbah, Chaouqi and Politi, Paolo},
  year = {2012},
  journal = {Phys. Rev. Lett.},
  volume = {109},
  pages = {096101},
  doi = {10.1103/PhysRevLett.109.096101},
}

@article{Levandovsky2004,
  title = {Epitaxial growth and erosion on (001) crystal surfaces: Far-from-equilibrium transitions, intermediary states, and vertical asymmetry},
  author = {Levandovsky, Artem and Golubovic, Leonardo},
  year = {2004},
  journal = {Phys. Rev. B},
  volume = {69},
  pages = {241402},
  doi = {10.1103/PhysRevB.69.241402},
}

@article{Misbah2010,
  title = {Crystal surfaces in and out of equilibrium: A modern view},
  author = {Misbah, Chaouqi and Pierre-Louis, Olivier and Saito, Yukio},
  journal = {Rev. Mod. Phys.},
  volume = {82},
  issue = {1},
  pages = {981},
  year = {2010},
  month = {Mar},
  doi = {10.1103/RevModPhys.82.981},
}

@article{Zuo1997,
  title = {Evolution of Mound Morphology in Reversible Homoepitaxy on Cu(100)},
  author = {Zuo, J.-K. and Wendelken, J. F.},
  year = {1997},
  journal = {Phys. Rev. Lett.},
  volume = {78},
  pages = {2791},
  doi = {10.1103/PhysRevLett.78.2791},
}

@article{ONaraigh2007b,
  title = {Dynamical effects and phase separation in cooled binary fluid films},
  author = {N\'araigh, Lennon \'O and Thiffeault, Jean-Luc},
  year = {2007},
  journal = {Phys. Rev. E},
  volume = {76},
  pages = {035303},
  doi = {10.1103/PhysRevE.76.035303},
}

@article{ONaraigh2008,
  title = {Bounds on the mixing enhancement for a stirred binary fluid},
  journal = {Physica D},
  volume = {237},
  number = {21},
  pages = {2673},
  year = {2008},
  doi = {10.1016/j.physd.2008.04.012},
  author = {Lennon \'O N\'araigh and Jean-Luc Thiffeault},
}

@article{ONaraigh2010,
  author = {\'O N\'araigh, Lennon and Jean-Luc Thiffeault},
  title = {Nonlinear dynamics of phase separation in thin films},
  journal = {Nonlinearity},
  volume = {23},
  pages = {1559},
  year = {2010},
  doi = {10.1088/0951-7715/23/7/003},
}

@article{Chen1998,
  title = {Applications of semi-implicit Fourier-spectral method to phase field equations},
  journal = {Comput. Phys. Commun.},
  volume = {108},
  pages = {147},
  year = {1998},
  doi = {10.1016/S0010-4655(97)00115-X},
  author = {L.Q. Chen and Jie Shen},
}

@article{Qin2010,
  author = {Qin, R. S. and Bhadeshia, H. K.},
  title = {Phase field method},
  journal = {Mater. Sci. Tech.},
  volume = {26},
  number = {7},
  year = {2010},
  pages = {803},
  doi = {10.1179/174328409X453190},
}

@article{Karma2001,
  title = {Phase-Field Model of Mode III Dynamic Fracture},
  author = {Karma, Alain and Kessler, David A. and Levine, Herbert},
  year = {2001},
  journal = {Phys. Rev. Lett.},
  volume = {87},
  pages = {045501},
  doi = {10.1103/PhysRevLett.87.045501},
}

@article{Langer1980,
  title = {Instabilities and pattern formation in crystal growth},
  author = {Langer, J. S.},
  journal = {Rev. Mod. Phys.},
  volume = {52},
  issue = {1},
  pages = {1},
  year = {1980},
  month = {Jan},
  doi = {10.1103/RevModPhys.52.1},
}

@article{Chen1994,
  title = {Computer simulation of the domain dynamics of a quenched system with a large number of nonconserved order parameters: The grain-growth kinetics},
  author = {Chen, Long-Qing and Yang, Wei},
  year = {1994},
  journal = {Phys. Rev. B},
  volume = {50},
  pages = {15752},
  doi = {10.1103/PhysRevB.50.15752},
}

@article{Gomez2011,
  title = {Provably unconditionally stable, second-order time-accurate, mixed variational methods for phase-field models},
  journal = {J. Comp. Phys.},
  volume = {230},
  number = {13},
  pages = {5310},
  year = {2011},
  doi = {10.1016/j.jcp.2011.03.033},
  author = {Hector Gomez and Thomas J.R. Hughes},
}

@article{Boettinger2002,
  title = {Phase-field simulation of solidification},
  author = {Boettinger, W. J. and Warren, J. A. and Beckermann, C. and Karma, A.},
  year = {2002},
  journal = {Annu. Rev. Mater. Res.},
  volume = {32},
  pages = {163},
  doi = {10.1146/annurev.matsci.32.101901.155803},
}

@article{Du1991,
  author = {Du, Q. and Nicolaides, R.},
  title = {Numerical Analysis of a Continuum Model of Phase Transition},
  journal = {SIAM J. Num. Anal.},
  volume = {28},
  number = {5},
  pages = {1310},
  year = {1991},
  doi = {10.1137/0728069},
}

@article{Moelans2008,
  title = {An introduction to phase-field modeling of microstructure evolution},
  journal = {Calphad},
  volume = {32},
  number = {2},
  pages = {268},
  year = {2008},
  doi = {10.1016/j.calphad.2007.11.003},
  author = {Nele Moelans and Bart Blanpain and Patrick Wollants},
}

@article{Steinbach2009,
  author = {Ingo Steinbach},
  title = {Phase-field models in materials science},
  journal = {Model. Simul. Mater. Sc.},
  volume = {17},
  number = {7},
  pages = {073001},
  doi = {10.1088/0965-0393/17/7/073001},
  year = {2009},
}

@article{Karma1998,
  title = {Quantitative phase-field modeling of dendritic growth in two and three dimensions},
  author = {Karma, Alain and Rappel, Wouter-Jan},
  year = {1998},
  journal = {Phys. Rev. E},
  volume = {57},
  pages = {4323},
  doi = {10.1103/PhysRevE.57.4323},
}

@article{Karma1996,
  title = {Phase-field method for computationally efficient modeling of solidification with arbitrary interface kinetics},
  author = {Karma, Alain and Rappel, Wouter-Jan},
  year = {1996},
  journal = {Phys. Rev. E},
  volume = {53},
  pages = {R3017},
  doi = {10.1103/PhysRevE.53.R3017},
}

@article{Wheeler1992,
  title = {Phase-field model for isothermal phase transitions in binary alloys},
  author = {Wheeler, A. A. and Boettinger, W. J. and McFadden, G. B.},
  year = {1992},
  journal = {Phys. Rev. A},
  volume = {45},
  pages = {7424},
  doi = {10.1103/PhysRevA.45.7424},
}

@article{Zhu2001,
  title = {Microstructure dependence of diffusional transport},
  journal = {Comp. Mater. Sci.},
  volume = {20},
  number = {1},
  pages = {37},
  year = {2001},
  doi = {10.1016/S0927-0256(00)00123-3},
  author = {Jingzhi Zhu and Long-Qing Chen and Jie Shen and Veena Tikare},
}

@article{Collins1985,
  title = {Diffuse interface model of diffusion-limited crystal growth},
  author = {Collins, Joseph B. and Levine, Herbert},
  year = {1985},
  journal = {Phys. Rev. B},
  volume = {31},
  pages = {6119},
  doi = {10.1103/PhysRevB.31.6119},
}

@article{Caginalp1986,
  year = {1986},
  journal = {Arch. Rat. Mech. Anal.},
  volume = {92},
  number = {3},
  doi = {10.1007/BF00254827},
  title = {An analysis of a phase field model of a free boundary},
  publisher = {Springer-Verlag},
  author = {Caginalp, Gunduz},
  pages = {205},
}

@article{McFadden2000,
  title = {Thin interface asymptotics for an energy/entropy approach to phase-field models with unequal conductivities},
  journal = {Physica D},
  volume = {144},
  number = {1–2},
  pages = {154},
  year = {2000},
  doi = {10.1016/S0167-2789(00)00064-6},
  author = {G.B. McFadden and A.A. Wheeler and D.M. Anderson},
}

@article{Wang1993,
  title = {Thermodynamically-consistent phase-field models for solidification},
  journal = {Physica D},
  volume = {69},
  number = {1–2},
  pages = {189},
  year = {1993},
  doi = {10.1016/0167-2789(93)90189-8},
  author = {S.-L. Wang and R.F. Sekerka and A.A. Wheeler and B.T. Murray and S.R. Coriell and R.J. Braun and G.B. McFadden},
}

@article{Penrose1990,
  title = {Thermodynamically consistent models of phase-field type for the kinetics of phase transitions},
  journal = {Physica D},
  volume = {43},
  number = {1},
  pages = {44},
  year = {1990},
  doi = {10.1016/0167-2789(90)90015-H},
  author = {Oliver Penrose and Paul C. Fife},
}

@article{BenNaim2005,
  title = {Power-law velocity distributions in granular gases},
  author = {Ben-Naim, E. and Machta, B. and Machta, J.},
  year = {2005},
  journal = {Phys. Rev. E},
  volume = {72},
  pages = {021302},
  doi = {10.1103/PhysRevE.72.021302},
}

@article{BenNaim2005b,
  title = {Stationary States and Energy Cascades in Inelastic Gases},
  author = {Ben-Naim, E. and Machta, J.},
  year = {2005},
  journal = {Phys. Rev. Lett.},
  volume = {94},
  pages = {138001},
  doi = {10.1103/PhysRevLett.94.138001},
}

@article{Stefanovic2006,
  title = {Phase-Field Crystals with Elastic Interactions},
  author = {Stefanovic, Peter and Haataja, Mikko and Provatas, Nikolas},
  year = {2006},
  journal = {Phys. Rev. Lett.},
  volume = {96},
  pages = {225504},
  doi = {10.1103/PhysRevLett.96.225504},
}

@article{Dean1996,
  author = {David S Dean},
  title = {Langevin equation for the density of a system of interacting Langevin processes},
  journal = {J. Phys. A},
  volume = {29},
  number = {24},
  pages = {L613},
  year = {1996},
  abstract = {We present a simple derivation of the stochastic equation obeyed by the density function for a system of Langevin processes interacting via a pairwise potential. The resulting equation is considerably different from the phenomenological equations usually used to describe the dynamics of non-conserved (model A) and conserved (model B) particle systems. The major feature is that the spatial white noise for this system appears not additively but multiplicatively. This simply expresses the fact that the density cannot fluctuate in regions devoid of particles. The steady state for the density function may, however, still be recovered formally as a functional integral over the coursed grained free energy of the system as in models A and B.},
  doi = {10.1088/0305-4470/29/24/001},
}

@article{Jarzynski1997b,
  title = {Equilibrium free-energy differences from nonequilibrium measurements: A master-equation approach},
  author = {Jarzynski, C.},
  journal = {Phys. Rev. E},
  volume = {56},
  issue = {5},
  pages = {5018},
  numpages = {0},
  year = {1997},
  month = {Nov},
  publisher = {American Physical Society},
  doi = {10.1103/PhysRevE.56.5018},
}

@article{Jarzynski1997,
  title = {Nonequilibrium Equality for Free Energy Differences},
  author = {Jarzynski, C.},
  journal = {Phys. Rev. Lett.},
  volume = {78},
  issue = {14},
  pages = {2690},
  numpages = {0},
  year = {1997},
  month = {Apr},
  publisher = {American Physical Society},
  doi = {10.1103/PhysRevLett.78.2690},
}

@article{Crooks1998,
  year = {1998},
  issn = {0022-4715},
  journal = {J. Stat. Phys.},
  volume = {90},
  number = {5-6},
  doi = {10.1023/A:1023208217925},
  title = {Nonequilibrium Measurements of Free Energy Differences for Microscopically Reversible Markovian Systems},
  publisher = {Kluwer Academic Publishers-Plenum Publishers},
  keywords = {Nonequilibrium statistical mechanics; free energy; work; thermodynamic integration; thermodynamic perturbation},
  author = {Crooks, Gavin E.},
  pages = {1481},
  language = {English},
}

@article{Crooks1999,
  title = {Entropy production fluctuation theorem and the nonequilibrium work relation for free energy differences},
  author = {Crooks, Gavin E.},
  journal = {Phys. Rev. E},
  volume = {60},
  issue = {3},
  pages = {2721--2726},
  numpages = {0},
  year = {1999},
  month = {Sep},
  publisher = {American Physical Society},
  doi = {10.1103/PhysRevE.60.2721},
}

@article{Crooks2000,
  title = {Path-ensemble averages in systems driven far from equilibrium},
  author = {Crooks, Gavin E.},
  journal = {Phys. Rev. E},
  volume = {61},
  issue = {3},
  pages = {2361},
  numpages = {0},
  year = {2000},
  month = {Mar},
  publisher = {American Physical Society},
  doi = {10.1103/PhysRevE.61.2361},
}

@article{Jarzynski2008,
  year = {2008},
  issn = {1434-6028},
  journal = {The European Physical Journal B},
  volume = {64},
  number = {3-4},
  doi = {10.1140/epjb/e2008-00254-2},
  title = {Nonequilibrium work relations: foundations and applications},
  publisher = {Springer-Verlag},
  keywords = {05.70.Ln Nonequilibrium and irreversible thermodynamics; 05.40.-a Fluctuation phenomena, random processes, noise, and Brownian motion; 82.37.Rs Single molecule manipulation of proteins and other biological molecules},
  author = {Jarzynski, C.},
  pages = {331},
  language = {English},
}

@article{Mallick2011,
  author = {Kirone Mallick and Moshe Moshe and Henri Orland},
  title = {A field-theoretic approach to non-equilibrium work identities},
  journal = {J. Phys. A},
  volume = {44},
  number = {9},
  doi = {10.1088/1751-8113/44/9/095002},
  pages = {095002},
  year = {2011},
}

@article{Kurchan2007,
  author = {Jorge Kurchan},
  title = {Non-equilibrium work relations},
  journal = {J. Stat. Mech.},
  volume = {2007},
  number = {07},
  doi = {10.1088/1742-5468/2007/07/P07005},
  pages = {P07005},
  year = {2007},
}

@article{Jarzynski2011,
  title = {Equalities and Inequalities: Irreversibility and the Second Law of Thermodynamics at the Nanoscale},
  author = {Christopher Jarzynski},
  year = {2011},
  journal = {Ann. Rev. of Cond. Matt. Phys.},
  volume = {2},
  pages = {329},
  doi = {10.1146/annurev-conmatphys-062910-140506},
}

@article{Lebowitz1999,
  year = {1999},
  issn = {0022-4715},
  journal = {Journal of Statistical Physics},
  volume = {95},
  number = {1-2},
  doi = {10.1023/A:1004589714161},
  title = {A Gallavotti–Cohen-Type Symmetry in the Large Deviation Functional for Stochastic Dynamics},
  publisher = {Kluwer Academic Publishers-Plenum Publishers},
  keywords = {fluctuation theorem; current fluctuations; asymmetric exclusion process},
  author = {Lebowitz, Joel L. and Spohn, Herbert},
  pages = {333},
  language = {English},
}

@article{Seifert2008,
  year = {2008},
  issn = {1434-6028},
  journal = {Eur. Phys. J. B},
  volume = {64},
  number = {3-4},
  doi = {10.1140/epjb/e2008-00001-9},
  title = {Stochastic thermodynamics: principles and perspectives},
  publisher = {Springer-Verlag},
  keywords = {05.40.-a Fluctuation phenomena, random processes, noise, and Brownian motion; 05.70.-a Thermodynamics},
  author = {Seifert, U.},
  pages = {423},
  language = {English},
}

@article{Ganguly2013,
  title = {Stochastic thermodynamics of active Brownian particles},
  author = {Ganguly, Chandrima and Chaudhuri, Debasish},
  journal = {Phys. Rev. E},
  volume = {88},
  issue = {3},
  pages = {032102},
  numpages = {7},
  year = {2013},
  month = {Sep},
  publisher = {American Physical Society},
  doi = {10.1103/PhysRevE.88.032102},
}

@article{Seifert2012,
  author = {Udo Seifert},
  title = {Stochastic thermodynamics, fluctuation theorems and molecular machines},
  journal = {Rep. Prog. Phys.},
  volume = {75},
  number = {12},
  doi = {10.1088/0034-4885/75/12/126001},
  pages = {126001},
  year = {2012},
}

@article{Hummer2001,
  author = {Hummer, Gerhard and Szabo, Attila},
  title = {Free energy reconstruction from nonequilibrium single-molecule pulling experiments},
  volume = {98},
  number = {7},
  pages = {3658},
  year = {2001},
  doi = {10.1073/pnas.071034098},
  journal = {Proc. Ntl. Acad. Sci.},
}

@article{Katriel2000,
  title = {Bell numbers and coherent states},
  journal = {Phys. Lett. A},
  volume = {273},
  pages = {159},
  year = {2000},
  doi = {10.1016/S0375-9601(00)00488-6},
  author = {J. Katriel},
}

@article{Katriel1974,
  title = {Combinatorial Aspects of Boson Algebra},
  author = {J. Katriel},
  year = {1974},
  journal = {Nuov. Cim.},
  volume = {10},
  pages = {565},
  doi = {10.1007/BF02784783},
}

@article{Chernyak2005,
  title = {Dynamical generalization of nonequilibrium work relation},
  author = {Chernyak, V. and Chertkov, M. and Jarzynski, C.},
  journal = {Phys. Rev. E},
  volume = {71},
  pages = {025102},
  year = {2005},
  doi = {10.1103/PhysRevE.71.025102},
}

@article{Narayan2004,
  author = {Onuttom Narayan and Abhishek Dhar},
  title = {Reexamination of experimental tests of the fluctuation theorem},
  journal = {J. Phys. A},
  volume = {37},
  pages = {63},
  year = {2004},
  doi = {10.1088/0305-4470/37/1/004},
}

@article{Parisi1979,
  title = {Random Magnetic Fields, Supersymmetry, and Negative Dimensions},
  author = {Parisi, G. and Sourlas, N.},
  journal = {Phys. Rev. Lett.},
  volume = {43},
  issue = {11},
  pages = {744--745},
  numpages = {0},
  year = {1979},
  month = {Sep},
  publisher = {American Physical Society},
  doi = {10.1103/PhysRevLett.43.744},
}

@article{Feigelman1983,
  title = {On the hidden supersymmetry of Fokker-Planck equations with potential forces},
  journal = {Phys. Lett. A},
  volume = {95},
  number = {9},
  pages = {469},
  year = {1983},
  doi = {10.1016/0375-9601(83)90497-8},
  author = {M.V. Feigel'man and A.M. Tsvelick},
}

@article{Hatano2001,
  title = {Steady-State Thermodynamics of Langevin Systems},
  author = {Hatano, Takahiro and Sasa, Shin-ichi},
  journal = {Phys. Rev. Lett.},
  volume = {86},
  issue = {16},
  pages = {3463},
  numpages = {0},
  year = {2001},
  month = {Apr},
  publisher = {American Physical Society},
  doi = {10.1103/PhysRevLett.86.3463},
}

@article{Sasa2006,
  year = {2006},
  issn = {0022-4715},
  journal = {J. Stat. Phys.},
  volume = {125},
  number = {1},
  doi = {10.1007/s10955-005-9021-7},
  title = {Steady State Thermodynamics},
  publisher = {Kluwer Academic Publishers-Plenum Publishers},
  keywords = {nonequilibrium steady state; thermodynamics; fluctuation},
  author = {Sasa, Shin-ichi and Tasaki, Hal},
  pages = {125},
  language = {English},
}

@article{Zia2007,
  author = {R K P Zia and B Schmittmann},
  title = {Probability currents as principal characteristics in the statistical mechanics of non-equilibrium steady states},
  journal = {J. Stat. Mech.: Theory and Experiment},
  volume = {2007},
  number = {07},
  pages = {P07012},
  year = {2007},
  doi = {10.1088/1742-5468/2007/07/P07012},
}

@article{Zia2006,
  author = {R K P Zia and B Schmittmann},
  title = {A possible classification of nonequilibrium steady states},
  journal = {J. Phys. A},
  volume = {39},
  number = {24},
  pages = {L407},
  doi = {10.1088/0305-4470/39/24/L04},
  year = {2006},
}

@article{Glauber1963,
  author = {Glauber, Roy J.},
  title = {Time‐Dependent Statistics of the Ising Model},
  journal = {J. Math. Phys.},
  year = {1963},
  volume = {4},
  number = {2},
  pages = {294},
  doi = {10.1063/1.1703954},
}

@article{Howard1997,
  author = {Martin J Howard and Uwe C T{\"a}uber},
  title = {`Real' versus `imaginary' noise in diffusion-limited reactions},
  journal = {J. Phys. A},
  volume = {30},
  number = {22},
  pages = {7721},
  year = {1997},
  doi = {10.1088/0305-4470/30/22/011},
}

@article{Masser2001,
  title = {Correlation functions for diffusion-limited annihilation, $A+A\rightarrow 0$},
  author = {Masser, Thomas O. and ben-Avraham, Daniel},
  journal = {Phys. Rev. E},
  volume = {64},
  pages = {062101},
  year = {2001},
  doi = {10.1103/PhysRevE.64.062101},
}

@article{Trimper1990,
  author = {S. Trimper},
  title = {Supersymmetry breaking for dynamical systems},
  journal = {J. Phys. A},
  volume = {23},
  pages = {L169},
  year = {1990},
  doi = {10.1088/0305-4470/23/4/008},
}

@article{Zimmer1993,
  author = {Zimmer, Michael F.},
  title = {Fluctuations in nonequilibrium systems and broken supersymmetry},
  journal = {J. Stat. Phys.},
  year = {1993},
  volume = {73},
  pages = {751},
  doi = {10.1007/BF01054348},
}

@article{Polettini2014,
  author = {Polettini, Matteo and Esposito, Massimiliano},
  title = {Irreversible thermodynamics of open chemical networks. I. Emergent cycles and broken conservation laws},
  journal = {J. Chem. Phys.},
  year = {2014},
  volume = {141},
  pages = {024117},
  doi = {10.1063/1.4886396},
}

@article{Schmiedl2007,
  author = {Schmiedl, Tim and Seifert, Udo},
  title = {Stochastic thermodynamics of chemical reaction networks},
  journal = {J. Chem. Phys.},
  year = {2007},
  volume = {126},
  pages = {044101},
  doi = {10.1063/1.2428297},
}

@article{Horowitz2015,
  author = {Horowitz, Jordan M.},
  title = {Diffusion approximations to the chemical master equation only have a consistent stochastic thermodynamics at chemical equilibrium},
  journal = {J. Chem. Phys.},
  year = {2015},
  volume = {143},
  pages = {044111},
  doi = {10.1063/1.4927395},
}

@article{Schnakenberg1976,
  title = {Network theory of microscopic and macroscopic behavior of master equation systems},
  author = {Schnakenberg, J.},
  journal = {Rev. Mod. Phys.},
  volume = {48},
  pages = {571},
  year = {1976},
  doi = {10.1103/RevModPhys.48.571},
}

@article{Bray2013,
  author = {Alan J. Bray and Satya N. Majumdar and Grégory Schehr},
  title = {Persistence and first-passage properties in nonequilibrium systems},
  journal = {Adv. Phys.},
  volume = {62},
  pages = {225},
  year = {2013},
  doi = {10.1080/00018732.2013.803819},
}

@article{Cornell1996,
  title = {Domain growth in a one-dimensional driven diffusive system},
  author = {Cornell, Stephen J. and Bray, Alan J.},
  journal = {Phys. Rev. E},
  volume = {54},
  pages = {1153},
  year = {1996},
  doi = {10.1103/PhysRevE.54.1153},
}

@article{Huse1984,
  title = {Commensurate melting, domain walls, and dislocations},
  author = {Huse, David A. and Fisher, Michael E.},
  journal = {Phys. Rev. B},
  volume = {29},
  pages = {239},
  year = {1984},
  doi = {10.1103/PhysRevB.29.239},
}

@article{BenNaim2010,
  author = {E Ben-Naim and P L Krapivsky},
  title = {Kinetics of first passage in a cone},
  journal = {J. Phys. A},
  volume = {43},
  pages = {495007},
  year = {2010},
  doi = {10.1088/1751-8113/43/49/495007},
}

@article{Ovchinnikov1978,
  title = {Role of density fluctuations in bimolecular reaction kinetics},
  journal = {Chem. Phys.},
  volume = {28},
  pages = {215},
  year = {1978},
  doi = {10.1016/0301-0104(78)85052-6},
  author = {A.A. Ovchinnikov and Ya.B. Zeldovich},
}

@article{Toussaint1983,
  author = {Doug Toussaint and Frank Wilczek},
  title = {Particle–antiparticle annihilation in diffusive motion},
  journal = {J. Chem. Phys.},
  volume = {78},
  pages = {2642},
  year = {1983},
  doi = {10.1063/1.445022},
}

@article{Cardy2003b,
  author = {John Cardy and Makoto Katori},
  title = {Families of vicious walkers},
  journal = {J. Phys. A},
  volume = {36},
  pages = {609},
  year = {2003},
  doi = {10.1088/0305-4470/36/3/302},
}

@article{benAvraham2003,
  author = {D ben-Avraham and B M Johnson and C A Monaco and P L Krapivsky and S Redner},
  title = {Ordering of random walks: the leader and the laggard},
  journal = {J. Phys. A},
  volume = {36},
  doi = {10.1088/0305-4470/36/7/301},
  pages = {1789},
  year = {2003},
}

@article{Cardy1996,
  title = {Theory of Branching and Annihilating Random Walks},
  author = {Cardy, John and T\"auber, Uwe C.},
  journal = {Phys. Rev. Lett.},
  volume = {77},
  pages = {4780},
  year = {1996},
  doi = {10.1103/PhysRevLett.77.4780},
}

@article{Cardy1998,
  author = {Cardy, John L. and T{\"a}uber, Uwe C.},
  title = {Field Theory of Branching and Annihilating Random Walks},
  journal = {J.Stat. Phys.},
  year = {1998},
  volume = {90},
  number = {1},
  doi = {10.1023/A:1023233431588},
  pages = {1},
}

@article{Krapivsky1996,
  author = {P L Krapivsky and S Redner},
  title = {Kinetics of a diffusive capture process: lamb besieged by a pride of lions},
  journal = {J. Phys. A},
  volume = {29},
  pages = {5347},
  doi = {10.1088/0305-4470/29/17/011},
  year = {1996},
}

@article{Redner1999,
  author = {S. Redner and P. L. Krapivsky},
  title = {Capture of the lamb: Diffusing predators seeking a diffusing prey},
  journal = {Am. J. Phys.},
  volume = {67},
  pages = {1277},
  year = {1999},
  doi = {10.1119/1.19115},
}

@article{Alfasi2015,
  title = {Diffusion in the presence of scale-free absorbing boundaries},
  author = {Alfasi, Nir and Kantor, Yacov},
  journal = {Phys. Rev. E},
  volume = {91},
  pages = {042126},
  year = {2015},
  doi = {10.1103/PhysRevE.91.042126},
}

@article{Hammer2014,
  title = {Ideal polymers near scale-free surfaces},
  author = {Hammer, Yosi and Kantor, Yacov},
  journal = {Phys. Rev. E},
  volume = {89},
  pages = {022601},
  year = {2014},
  doi = {10.1103/PhysRevE.89.022601},
}

@article{Grassberger1980,
  author = {Grassberger, P. and Scheunert, M.},
  title = {Fock-Space Methods for Identical Classical Objects},
  journal = {Fortschr. Phys.},
  volume = {28},
  doi = {10.1002/prop.19800281004},
  pages = {547},
  year = {1980},
}

@article{Chandrasekhar1943,
  title = {Stochastic Problems in Physics and Astronomy},
  author = {Chandrasekhar, S.},
  journal = {Rev. Mod. Phys.},
  volume = {15},
  pages = {1},
  year = {1943},
  doi = {10.1103/RevModPhys.15.1},
}

@article{Smoluchowski1917,
  title = {Attempt for a mathematical theory of kinetic coagulation of colloid solutions},
  author = {Smoluchowski, M. V.},
  journal = {Z. Phys. Chem.},
  volume = {92},
  pages = {129},
  year = {1917},
}

@article{Munasinghe2006,
  title = {Multiscaling of correlation functions in single species reaction-diffusion systems},
  author = {Munasinghe, Ranjiva M. and Rajesh, R. and Zaboronski, Oleg V.},
  journal = {Phys. Rev. E},
  volume = {73},
  pages = {051103},
  year = {2006},
  doi = {10.1103/PhysRevE.73.051103},
}

@article{Helenbrook2018,
  title = {Ordering statistics of four random walkers on a line},
  author = {Helenbrook, Brian and ben-Avraham, Daniel},
  journal = {Phys. Rev. E},
  volume = {97},
  pages = {052105},
  year = {2018},
  doi = {10.1103/PhysRevE.97.052105},
}

@article{Spouge1988,
  title = {Exact solutions for a diffusion-reaction process in one dimension},
  author = {Spouge, John L.},
  journal = {Phys. Rev. Lett.},
  volume = {60},
  pages = {871},
  year = {1988},
  doi = {10.1103/PhysRevLett.60.871},
}

@article{VollmayrLee2018,
  author = {Benjamin Vollmayr-Lee and Jack Hanson and R Scott McIsaac and Joshua D Hellerick},
  title = {Anomalous dimension in a two-species reaction–diffusion system},
  journal = {J. Phys. A: Math. Theor.},
  volume = {51},
  pages = {034002},
  year = {2018},
  doi = {10.1088/1751-8121/aa98cf},
}

@article{Taeuber2012,
  doi = {10.1088/1751-8113/45/40/405002},
  year = {2012},
  volume = {45},
  pages = {405002},
  author = {Uwe C T{\"a}uber},
  title = {Population oscillations in spatial stochastic Lotka-Volterra models: a field-theoretic perturbational analysis},
  journal = {J. Phys. A},
}

@article{Pietzonka2018,
  title = {Universal Trade-Off between Power, Efficiency, and Constancy in Steady-State Heat Engines},
  author = {Pietzonka, Patrick and Seifert, Udo},
  journal = {Phys. Rev. Lett.},
  volume = {120},
  issue = {19},
  pages = {190602},
  numpages = {6},
  year = {2018},
  month = {May},
  publisher = {American Physical Society},
  doi = {10.1103/PhysRevLett.120.190602},
}

@article{Horowitz2019,
  title = {Bacterial range expansions on a growing front: Roughness, fixation, and directed percolation},
  author = {Horowitz, Jordan M. and Kardar, Mehran},
  journal = {Phys. Rev. E},
  volume = {99},
  issue = {4},
  pages = {042134},
  numpages = {19},
  year = {2019},
  month = {Apr},
  publisher = {American Physical Society},
  doi = {10.1103/PhysRevE.99.042134},
}

@article{Seifert2019,
  author = {Seifert, Udo},
  doi = {10.1146/annurev-conmatphys-031218-013554},
  eprint = {https://doi.org/10.1146/annurev-conmatphys-031218-013554},
  journal = {Annu. Rev. Condens. Matt. Phys.},
  number = {1},
  pages = {171–192},
  title = {From Stochastic Thermodynamics to Thermodynamic Inference},
  volume = {10},
  year = {2019},
}

@article{Seifert2018,
  title = {Stochastic thermodynamics: From principles to the cost of precision},
  journal = {Physica A},
  volume = {504},
  pages = {176},
  year = {2018},
  note = {Lecture Notes of the 14th International Summer School on Fundamental Problems in Statistical Physics},
  issn = {0378-4371},
  doi = {10.1016/j.physa.2017.10.024},
  author = {Udo Seifert},
}

@article{Gingrich2016,
  title = {Dissipation Bounds All Steady-State Current Fluctuations},
  author = {Gingrich, Todd R. and Horowitz, Jordan M. and Perunov, Nikolay and England, Jeremy L.},
  journal = {Phys. Rev. Lett.},
  volume = {116},
  issue = {12},
  pages = {120601},
  numpages = {5},
  year = {2016},
  month = {Mar},
  publisher = {American Physical Society},
  doi = {10.1103/PhysRevLett.116.120601},
}

@article{Horowitz2017,
  title = {Proof of the finite-time thermodynamic uncertainty relation for steady-state currents},
  author = {Horowitz, Jordan M. and Gingrich, Todd R.},
  journal = {Phys. Rev. E},
  volume = {96},
  issue = {2},
  pages = {020103},
  numpages = {3},
  year = {2017},
  month = {Aug},
  publisher = {American Physical Society},
  doi = {10.1103/PhysRevE.96.020103},
}

@article{Friedman2006,
  title = {Linking Stochastic Dynamics to Population Distribution: An Analytical Framework of Gene Expression},
  author = {Friedman, Nir and Cai, Long and Xie, X. Sunney},
  journal = {Phys. Rev. Lett.},
  volume = {97},
  issue = {16},
  pages = {168302},
  numpages = {4},
  year = {2006},
  month = {Oct},
  publisher = {American Physical Society},
  doi = {10.1103/PhysRevLett.97.168302},
}

@article{Park2018,
  author = {Park, Seong Jun and Song, Sanggeun and Yang, Gil-Suk and Kim, Philip M. and Yoon, Sangwoon and Kim, Ji-Hyun and Sung, Jaeyoung},
  title = {The Chemical Fluctuation Theorem governing gene expression},
  journal = {Nature Communications},
  year = {2018},
  volume = {9},
  number = {1},
  pages = {297},
  issn = {2041-1723},
  doi = {10.1038/s41467-017-02737-0},
}

@article{Balaban2004,
  author = {Balaban, Nathalie Q. and Merrin, Jack and Chait, Remy and Kowalik, Lukasz and Leibler, Stanislas},
  title = {Bacterial Persistence as a Phenotypic Switch},
  volume = {305},
  number = {5690},
  pages = {1622},
  year = {2004},
  doi = {10.1126/science.1099390},
  publisher = {American Association for the Advancement of Science},
  issn = {0036-8075},
  eprint = {https://science.sciencemag.org/content/305/5690/1622.full.pdf},
  journal = {Science},
}

@article{Brauner2016,
  author = {Brauner, Asher and Fridman, Ofer and Gefen, Orit and Balaban, Nathalie Q.},
  title = {Distinguishing between resistance, tolerance and persistence to antibiotic treatment},
  journal = {Nature Reviews Microbiology},
  year = {2016},
  month = {Apr},
  day = {15},
  publisher = {Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved. SN -},
  volume = {14},
  pages = {320 EP -},
  note = {Perspective},
  doi = {10.1038/nrmicro.2016.34},
}

@article{Zhao2016,
  title = {A decoupled energy stable scheme for a hydrodynamic phase-field model of mixtures of nematic liquid crystals and viscous fluids},
  journal = {J. Comp. Phys.},
  volume = {305},
  pages = {539},
  year = {2016},
  issn = {0021-9991},
  doi = {10.1016/j.jcp.2015.09.044},
  author = {Jia Zhao and Xiaofeng Yang and Jie Shen and Qi Wang},
}

@article{Klumpp2009,
  title = {Growth Rate-Dependent Global Effects on Gene Expression in Bacteria},
  journal = {Cell},
  volume = {139},
  number = {7},
  pages = {1366},
  year = {2009},
  issn = {0092-8674},
  doi = {10.1016/j.cell.2009.12.001},
  author = {Stefan Klumpp and Zhongge Zhang and Terence Hwa},
  keywords = {CELLBIO},
}

@article{Roy2018,
  title = {Simulating Genetic Circuits in Bacterial Populations with Growth Heterogeneity},
  journal = {Biophysical Journal},
  volume = {114},
  number = {2},
  pages = {484},
  year = {2018},
  issn = {0006-3495},
  doi = {10.1016/j.bpj.2017.11.3745},
  author = {Anjan Roy and Stefan Klumpp},
}

@article{Klumpp2014,
  title = {Bacterial growth: global effects on gene expression, growth feedback and proteome partition},
  journal = {Current Opinion in Biotechnology},
  volume = {28},
  pages = {96},
  year = {2014},
  note = {Nanobiotechnology • Systems biology},
  issn = {0958-1669},
  doi = {10.1016/j.copbio.2014.01.001},
  author = {Stefan Klumpp and Terence Hwa},
}

@article{ElMeouche2016,
  author = {El Meouche, Imane and Siu, Yik and Dunlop, Mary J.},
  title = {Stochastic expression of a multiple antibiotic resistance activator confers transient resistance in single cells},
  journal = {Scientific Reports},
  year = {2016},
  month = {Jan},
  day = {13},
  volume = {6},
  pages = {19538},
  doi = {10.1038/srep19538},
}

@article{Elowitz2002,
  author = {Elowitz, Michael B. and Levine, Arnold J. and Siggia, Eric D. and Swain, Peter S.},
  title = {Stochastic Gene Expression in a Single Cell},
  volume = {297},
  number = {5584},
  pages = {1183},
  year = {2002},
  doi = {10.1126/science.1070919},
  journal = {Science},
}

@article{GarciaBernardo2016,
  title = {Phenotypic Diversity Using Bimodal and Unimodal Expression of Stress Response Proteins},
  journal = {Biophysical Journal},
  volume = {110},
  number = {10},
  pages = {2278},
  year = {2016},
  doi = {10.1016/j.bpj.2016.04.012},
  author = {Javier Garcia-Bernardo and Mary J. Dunlop},
}

@article{Rossi2019,
  author = {Rossi, Nicholas A. and El Meouche, Imane and Dunlop, Mary J.},
  title = {Forecasting cell fate during antibiotic exposure using stochastic gene expression},
  journal = {Communications Biology},
  year = {2019},
  volume = {2},
  number = {1},
  pages = {259},
  issn = {2399-3642},
  doi = {10.1038/s42003-019-0509-0},
}

@article{ElMeouche2018,
  author = {El Meouche, Imane and Dunlop, Mary J.},
  title = {Heterogeneity in efflux pump expression predisposes antibiotic-resistant cells to mutation},
  volume = {362},
  number = {6415},
  pages = {686},
  year = {2018},
  doi = {10.1126/science.aar7981},
  journal = {Science},
}

@article{Thomas2019,
  author = {Thomas, Philipp},
  title = {Intrinsic and extrinsic noise of gene expression in lineage trees},
  journal = {Scientific Reports},
  year = {2019},
  volume = {9},
  number = {1},
  pages = {474},
  doi = {10.1038/s41598-018-35927-x},
}

@article{Vlamakis2013,
  author = {Vlamakis, Hera and Chai, Yunrong and Beauregard, Pascale and Losick, Richard and Kolter, Roberto},
  title = {Sticking together: building a biofilm the Bacillus subtilis way},
  journal = {Nature Reviews Microbiology},
  year = {2013},
  volume = {11},
  number = {3},
  pages = {157},
  doi = {10.1038/nrmicro2960},
}

@article{Alon2009,
  title = {How To Choose a Good Scientific Problem},
  journal = {Molecular Cell},
  volume = {35},
  number = {6},
  pages = {726},
  year = {2009},
  issn = {1097-2765},
  doi = {10.1016/j.molcel.2009.09.013},
  author = {Uri Alon},
}

@article{Scott2010,
  author = {Scott, Matthew and Gunderson, Carl W. and Mateescu, Eduard M. and Zhang, Zhongge and Hwa, Terence},
  title = {Interdependence of Cell Growth and Gene Expression: Origins and Consequences},
  volume = {330},
  number = {6007},
  pages = {1099},
  year = {2010},
  doi = {10.1126/science.1192588},
  journal = {Science},
}

@article{Schultz2009,
  author = {Schultz, Daniel and Wolynes, Peter G. and Jacob, Eshel Ben and Onuchic, Jos{\'e} N.},
  title = {Deciding fate in adverse times: Sporulation and competence in Bacillus subtilis},
  volume = {106},
  number = {50},
  pages = {21027},
  year = {2009},
  doi = {10.1073/pnas.0912185106},
  journal = {Proceedings of the National Academy of Sciences},
}

@article{Cao2010,
  author = {Cao, Youfang and Lu, Hsiao-Mei and Liang, Jie},
  title = {Probability landscape of heritable and robust epigenetic state of lysogeny in phage lambda},
  volume = {107},
  number = {43},
  pages = {18445},
  year = {2010},
  doi = {10.1073/pnas.1001455107},
  journal = {Proceedings of the National Academy of Sciences},
}

@article{Balaban2019,
  author = {Balaban, Nathalie Q. and Helaine, Sophie and Lewis, Kim and Ackermann, Martin and Aldridge, Bree and Andersson, Dan I. and Brynildsen, Mark P. and Bumann, Dirk and Camilli, Andrew and Collins, James J. and Dehio, Christoph and Fortune, Sarah and Ghigo, Jean-Marc and Hardt, Wolf-Dietrich and Harms, Alexander and Heinemann, Matthias and Hung, Deborah T. and Jenal, Urs and Levin, Bruce R. and Michiels, Jan and Storz, Gisela and Tan, Man-Wah and Tenson, Tanel and Van Melderen, Laurence and Zinkernagel, Annelies},
  title = {Definitions and guidelines for research on antibiotic persistence},
  journal = {Nature Reviews Microbiology},
  year = {2019},
  volume = {17},
  number = {7},
  pages = {441},
  doi = {10.1038/s41579-019-0196-3},
}

@article{Lewis2010,
  author = {Lewis, Kim},
  title = {Persister Cells},
  journal = {Annual Review of Microbiology},
  volume = {64},
  number = {1},
  pages = {357},
  year = {2010},
  doi = {10.1146/annurev.micro.112408.134306},
}

@article{LevinReisman2017,
  author = {Levin-Reisman, Irit and Ronin, Irine and Gefen, Orit and Braniss, Ilan and Shoresh, Noam and Balaban, Nathalie Q.},
  title = {Antibiotic tolerance facilitates the evolution of resistance},
  volume = {355},
  number = {6327},
  pages = {826},
  year = {2017},
  doi = {10.1126/science.aaj2191},
  journal = {Science},
}

@article{Locke2011,
  author = {Locke, James C. W. and Young, Jonathan W. and Fontes, Michelle and Jim{\'e}nez, Mar{\'\i}a Jes{\'u}s Hern{\'a}ndez and Elowitz, Michael B.},
  title = {Stochastic Pulse Regulation in Bacterial Stress Response},
  volume = {334},
  number = {6054},
  pages = {366},
  year = {2011},
  doi = {10.1126/science.1208144},
  journal = {Science},
}

@article{Schneiders2004,
  author = {Schneiders, Thamarai and Barbosa, Teresa M. and McMurry, Laura M. and Levy, Stuart B.},
  title = {The Escherichia coli Transcriptional Regulator MarA Directly Represses Transcription of purA and hdeA},
  volume = {279},
  number = {10},
  pages = {9037-9042},
  year = {2004},
  doi = {10.1074/jbc.M313602200},
  journal = {Journal of Biological Chemistry},
}

@article{Mitosch2017,
  author = {Mitosch, Karin and Rieckh, Georg and Bollenbach, Tobias},
  title = {Noisy Response to Antibiotic Stress Predicts Subsequent Single-Cell Survival in an Acidic Environment},
  journal = {Cell Systems},
  year = {2017},
  month = {Apr},
  day = {26},
  publisher = {Elsevier},
  volume = {4},
  number = {4},
  pages = {393-403.e5},
  doi = {10.1016/j.cels.2017.03.001},
}

@article{Lee2018,
  author = {Lee, Anna J. and Wang, Shangying and Meredith, Hannah R. and Zhuang, Bihan and Dai, Zhuojun and You, Lingchong},
  title = {Robust, linear correlations between growth rates and β-lactam-mediated lysis rates},
  volume = {115},
  number = {16},
  pages = {4069--4074},
  year = {2018},
  doi = {10.1073/pnas.1719504115},
  journal = {Proceedings of the National Academy of Sciences},
}

@article{VanDenBroeck2015,
  title = {Ensemble and trajectory thermodynamics: A brief introduction},
  journal = {Physica A},
  volume = {418},
  pages = {6},
  year = {2015},
  doi = {10.1016/j.physa.2014.04.035},
  author = {C. Van den Broeck and M. Esposito},
}

@article{Chetrite2008,
  author = {Chetrite, Rapha{\"e}l and Gawȩdzki, Krzysztof},
  title = {Fluctuation Relations for Diffusion Processes},
  journal = {Communications in Mathematical Physics},
  year = {2008},
  month = {Sep},
  day = {01},
  volume = {282},
  number = {2},
  pages = {469--518},
  doi = {10.1007/s00220-008-0502-9},
}

@article{Chetrite2008b,
  doi = {10.1088/1742-5468/2008/08/p08005},
  year = {2008},
  volume = {2008},
  number = {08},
  pages = {P08005},
  author = {Raphaël Chetrite and Gregory Falkovich and Krzysztof Gawedzki},
  title = {Fluctuation relations in simple examples of non-equilibrium steady states},
  journal = {J. Stat. Mech.: Theory and Experiment},
}

@article{Chetrite2009,
  author = {Chetrite, Rapha{\"e}l and Gaw{\k{e}}dzki, Krzysztof},
  title = {Eulerian and Lagrangian Pictures of Non-equilibrium Diffusions},
  journal = {Journal of Statistical Physics},
  year = {2009},
  month = {Aug},
  day = {19},
  volume = {137},
  number = {5},
  pages = {890},
  doi = {10.1007/s10955-009-9803-4},
}

@article{Verley2011,
  doi = {10.1088/1742-5468/2011/10/p10025},
  year = {2011},
  volume = {2011},
  number = {10},
  pages = {P10025},
  author = {Gatien Verley and Raphaël Ch{\'{e}}trite and David Lacoste},
  title = {Modified fluctuation-dissipation theorem for general non-stationary states and application to the Glauber-Ising chain},
  journal = {J. Stat. Mech.: Theory and Experiment},
}

@article{Seifert2010,
  title = {Generalized Einstein or Green-Kubo Relations for Active Biomolecular Transport},
  author = {Seifert, Udo},
  journal = {Phys. Rev. Lett.},
  volume = {104},
  issue = {13},
  pages = {138101},
  numpages = {4},
  year = {2010},
  month = {Mar},
  publisher = {American Physical Society},
  doi = {10.1103/PhysRevLett.104.138101},
}

@article{Kim2008,
  doi = {10.1088/1742-5468/2008/02/p02004},
  year = {2008},
  month = {feb},
  publisher = {{IOP} Publishing},
  volume = {2008},
  number = {02},
  pages = {P02004},
  author = {Bongsoo Kim and Kyozi Kawasaki},
  title = {A fluctuation-dissipation relationship-preserving field theory for interacting Brownian particles: one-loop theory and mode coupling theory},
  journal = {J. Stat. Mech.: Theory and Experiment},
}

@article{Timme2014,
  author = {Timme, Nicholas and Alford, Wesley and Flecker, Benjamin and Beggs, John M.},
  title = {Synergy, redundancy, and multivariate information measures: an experimentalist's perspective},
  journal = {Journal of Computational Neuroscience},
  year = {2014},
  month = {Apr},
  day = {01},
  volume = {36},
  number = {2},
  pages = {119--140},
  doi = {10.1007/s10827-013-0458-4},
}

@article{Bintu2005,
  title = {Transcriptional regulation by the numbers: models},
  journal = {Current Opinion in Genetics & Development},
  volume = {15},
  number = {2},
  pages = {116 - 124},
  year = {2005},
  note = {Chromosomes and expression mechanisms},
  issn = {0959-437X},
  doi = {10.1016/j.gde.2005.02.007},
  author = {Lacramioara Bintu and Nicolas E Buchler and Hernan G Garcia and Ulrich Gerland and Terence Hwa and Jané Kondev and Rob Phillips},
}

@article{Zampieri2017,
  title = {Nontargeted Metabolomics Reveals the Multilevel Response to Antibiotic Perturbations},
  journal = {Cell Reports},
  volume = {19},
  number = {6},
  pages = {1214 - 1228},
  year = {2017},
  issn = {2211-1247},
  doi = {10.1016/j.celrep.2017.04.002},
  author = {Mattia Zampieri and Michael Zimmermann and Manfred Claassen and Uwe Sauer},
}

@article{Yang2017,
  title = {Antibiotic efficacy—context matters},
  journal = {Current Opinion in Microbiology},
  volume = {39},
  pages = {73 - 80},
  year = {2017},
  note = {Antimicrobials * Bacterial Systems Biology},
  issn = {1369-5274},
  doi = {10.1016/j.mib.2017.09.002},
  author = {Jason H Yang and Sarah C Bening and James J Collins},
}

@article{Gardner2000,
  author = {Gardner, Timothy S. and Cantor, Charles R. and Collins, James J.},
  title = {Construction of a genetic toggle switch in Escherichia coli},
  journal = {Nature},
  year = {2000},
  volume = {403},
  number = {6767},
  pages = {339-342},
  issn = {1476-4687},
  doi = {10.1038/35002131},
}

@article{Schellenberger1981,
  title = {Selforganization of a glycoltylic reconstituted enzyme system: Alternate stable stationary states, hysteretic transitions and stabilization of the energy charge},
  journal = {Advances in Enzyme Regulation},
  volume = {19},
  pages = {257 - 284},
  year = {1981},
  issn = {0065-2571},
  doi = {10.1016/0065-2571(81)90019-4},
  author = {Wolfgang Schellenberger and Klaus Eschrich and Eberhard Hofmann},
}

@article{Lopatkin2019,
  author = {Lopatkin, Allison J. and Stokes, Jonathan M. and Zheng, Erica J. and Yang, Jason H. and Takahashi, Melissa K. and You, Lingchong and Collins, James J.},
  title = {Bacterial metabolic state more accurately predicts antibiotic lethality than growth rate},
  journal = {Nature Microbiology},
  year = {2019},
  issn = {2058-5276},
  doi = {10.1038/s41564-019-0536-0},
  volume = {4},
  pages = {2109--2117},
}

@article{Touchette2009,
  title = {The large deviation approach to statistical mechanics},
  journal = {Physics Reports},
  volume = {478},
  number = {1},
  pages = {1 - 69},
  year = {2009},
  issn = {0370-1573},
  doi = {10.1016/j.physrep.2009.05.002},
  author = {Hugo Touchette},
}

@article{Bertini2015,
  title = {Flows, currents, and cycles for Markov chains: Large deviation asymptotics},
  journal = {Stochastic Processes and their Applications},
  volume = {125},
  number = {7},
  pages = {2786 - 2819},
  year = {2015},
  issn = {0304-4149},
  doi = {10.1016/j.spa.2015.02.001},
  author = {Lorenzo Bertini and Alessandra Faggionato and Davide Gabrielli},
}

@article{Maes2008,
  doi = {10.1209/0295-5075/82/30003},
  year = {2008},
  month = {apr},
  publisher = {{IOP} Publishing},
  volume = {82},
  number = {3},
  pages = {30003},
  author = {C. Maes and K. Neto{\v{c}}n{\'{y}}},
  title = {Canonical structure of dynamical fluctuations in mesoscopic nonequilibrium steady states},
  journal = {Europhys. Lett.},
}

@article{Andreanov2006,
  doi = {10.1088/1742-5468/2006/07/p07008},
  year = {2006},
  month = {jul},
  publisher = {{IOP} Publishing},
  volume = {2006},
  number = {07},
  pages = {P07008},
  author = {A Andreanov and G Biroli and A Lef{\`{e}}vre},
  title = {Dynamical field theory for glass-forming liquids, self-consistent resummations and time-reversal symmetry},
  journal = {J. Stat. Mech.},
}

@article{Kawasaki1994,
  title = {Stochastic model of slow dynamics in supercooled liquids and dense colloidal suspensions},
  journal = {Physica A},
  volume = {208},
  number = {1},
  pages = {35 - 64},
  year = {1994},
  issn = {0378-4371},
  doi = {10.1016/0378-4371(94)90533-9},
  author = {Kyozi Kawasaki},
}

@article{Corberi2007,
  doi = {10.1088/1742-5468/2007/07/p07002},
  year = {2007},
  month = {jul},
  publisher = {{IOP} Publishing},
  volume = {2007},
  number = {07},
  pages = {P07002--P07002},
  author = {Federico Corberi and Eugenio Lippiello and Marco Zannetti},
  title = {Fluctuation dissipation relations far from equilibrium},
  journal = {J. Stat. Mech.},
}

@article{Kubo1966,
  doi = {10.1088/0034-4885/29/1/306},
  year = {1966},
  month = {jan},
  publisher = {{IOP} Publishing},
  volume = {29},
  number = {1},
  pages = {255--284},
  author = {R Kubo},
  title = {The fluctuation-dissipation theorem},
  journal = {Reports on Progress in Physics},
}

@article{Kim2014,
  title = {Equilibrium dynamics of the Dean-Kawasaki equation: Mode-coupling theory and its extension},
  author = {Kim, Bongsoo and Kawasaki, Kyozi and Jacquin, Hugo and van Wijland, Fr\'ed\'eric},
  journal = {Phys. Rev. E},
  volume = {89},
  issue = {1},
  pages = {012150},
  numpages = {12},
  year = {2014},
  month = {Jan},
  publisher = {American Physical Society},
  doi = {10.1103/PhysRevE.89.012150},
}

@article{Andreanov2006b,
  title = {Field theories and exact stochastic equations for interacting particle systems},
  author = {Andreanov, Alexei and Biroli, Giulio and Bouchaud, Jean-Philippe and Lef\`evre, Alexandre},
  journal = {Phys. Rev. E},
  volume = {74},
  issue = {3},
  pages = {030101},
  numpages = {4},
  year = {2006},
  month = {Sep},
  publisher = {American Physical Society},
  doi = {10.1103/PhysRevE.74.030101},
}

@article{Lefevre2007,
  doi = {10.1088/1742-5468/2007/07/p07024},
  year = {2007},
  month = {jul},
  publisher = {{IOP} Publishing},
  volume = {2007},
  number = {07},
  pages = {P07024},
  author = {Alexandre Lef{\`{e}}vre and Giulio Biroli},
  title = {Dynamics of interacting particle systems: stochastic process and field theory},
  journal = {J. Stat. Mech.},
}

@article{Weber2017,
  doi = {10.1088/1361-6633/aa5ae2},
  year = {2017},
  month = {mar},
  publisher = {{IOP} Publishing},
  volume = {80},
  number = {4},
  pages = {046601},
  author = {Markus F Weber and Erwin Frey},
  title = {Master equations and the theory of stochastic path integrals},
  journal = {Rep. Prog. Phys.},
}

@article{Benitez2016,
  title = {Langevin Equations for Reaction-Diffusion Processes},
  author = {Benitez, Federico and Duclut, Charlie and Chat\'e, Hugues and Delamotte, Bertrand and Dornic, Ivan and Mu\~noz, Miguel A.},
  journal = {Phys. Rev. Lett.},
  volume = {117},
  issue = {10},
  pages = {100601},
  numpages = {6},
  year = {2016},
  month = {Sep},
  publisher = {American Physical Society},
  doi = {10.1103/PhysRevLett.117.100601},
}

@article{Dornic2005,
  title = {Integration of Langevin Equations with Multiplicative Noise and the Viability of Field Theories for Absorbing Phase Transitions},
  author = {Dornic, Ivan and Chat\'e, Hugues and Mu\~noz, Miguel A.},
  journal = {Phys. Rev. Lett.},
  volume = {94},
  issue = {10},
  pages = {100601},
  numpages = {4},
  year = {2005},
  month = {Mar},
  publisher = {American Physical Society},
  doi = {10.1103/PhysRevLett.94.100601},
}

@article{Wiese2016,
  title = {Coherent-state path integral versus coarse-grained effective stochastic equation of motion: From reaction diffusion to stochastic sandpiles},
  author = {Wiese, Kay J\"org},
  journal = {Phys. Rev. E},
  volume = {93},
  issue = {4},
  pages = {042117},
  numpages = {27},
  year = {2016},
  month = {Apr},
  publisher = {American Physical Society},
  doi = {10.1103/PhysRevE.93.042117},
}

@article{Velenich2008,
  doi = {10.1088/1751-8113/41/23/235002},
  year = {2008},
  month = {may},
  publisher = {{IOP} Publishing},
  volume = {41},
  number = {23},
  pages = {235002},
  author = {Andrea Velenich and Claudio Chamon and Leticia F Cugliandolo and Dirk Kreimer},
  title = {On the Brownian gas: a field theory with a Poissonian ground state},
  journal = {J. Phys. A},
}

@article{Harris2007,
  doi = {10.1088/1742-5468/2007/07/p07020},
  year = {2007},
  month = {jul},
  publisher = {{IOP} Publishing},
  volume = {2007},
  number = {07},
  pages = {P07020--P07020},
  author = {R J Harris and G M Schütz},
  title = {Fluctuation theorems for stochastic dynamics},
  journal = {J. Stat. Mech.},
}

@article{Assaf2017,
  doi = {10.1088/1751-8121/aa669a},
  year = {2017},
  month = {jun},
  publisher = {{IOP} Publishing},
  volume = {50},
  number = {26},
  pages = {263001},
  author = {Michael Assaf and Baruch Meerson},
  title = {{WKB} theory of large deviations in stochastic populations},
  journal = {J. Phys. A},
}

@article{HerreraDelgado2018,
  author = {Herrera-Delgado, Edgar AND Perez-Carrasco, Ruben AND Briscoe, James AND Sollich, Peter},
  doi = {10.1371/journal.pcbi.1006003},
  journal = {PLOS Computational Biology},
  month = {02},
  number = {2},
  pages = {1–25},
  publisher = {Public Library of Science},
  title = {Memory functions reveal structural properties of gene regulatory networks},
  volume = {14},
  year = {2018},
}

@article{Yeung2018,
  title = {Direct test of the Gaussian auxiliary field ansatz in nonconserved order parameter phase ordering dynamics},
  author = {Yeung, Chuck},
  journal = {Phys. Rev. E},
  volume = {97},
  issue = {6},
  pages = {062107},
  numpages = {6},
  year = {2018},
  month = {Jun},
  publisher = {American Physical Society},
  doi = {10.1103/PhysRevE.97.062107},
}

@article{Rao2018,
  author = {Rao, Riccardo and Esposito, Massimiliano},
  doi = {10.1063/1.5042253},
  eprint = {https://doi.org/10.1063/1.5042253},
  journal = {J. Chem. Phys.},
  number = {24},
  pages = {245101},
  title = {Conservation laws and work fluctuation relations in chemical reaction networks},
  volume = {149},
  year = {2018},
}

@article{Gillespie1992,
  title = {A rigorous derivation of the chemical master equation},
  journal = {Physica A},
  volume = {188},
  number = {1},
  pages = {404 - 425},
  year = {1992},
  issn = {0378-4371},
  doi = {10.1016/0378-4371(92)90283-V},
  author = {Daniel T. Gillespie},
}

@article{McQuarrie1967,
  title = {Stochastic approach to chemical kinetics},
  volume = {4},
  doi = {10.2307/3212214},
  number = {3},
  journal = {Journal of Applied Probability},
  publisher = {Cambridge University Press},
  author = {McQuarrie, Donald A.},
  year = {1967},
  pages = {413–478},
}

@article{Gillespie2007,
  author = {Gillespie, Daniel T.},
  title = {Stochastic Simulation of Chemical Kinetics},
  journal = {Annual Review of Physical Chemistry},
  volume = {58},
  number = {1},
  pages = {35-55},
  year = {2007},
  doi = {10.1146/annurev.physchem.58.032806.104637},
}

@article{Katriel2002,
  doi = {10.1088/1464-4266/4/3/375},
  year = {2002},
  month = {apr},
  publisher = {{IOP} Publishing},
  volume = {4},
  number = {3},
  pages = {S200--S203},
  author = {Jacob Katriel},
  title = {Coherent states and combinatorics},
  journal = {Journal of Optics B},
}

@article{Blasiak2003,
  title = {The general boson normal ordering problem},
  journal = {Physics Letters A},
  volume = {309},
  number = {3},
  pages = {198 - 205},
  year = {2003},
  issn = {0375-9601},
  doi = {10.1016/S0375-9601(03)00194-4},
  author = {P Blasiak and K.A Penson and A.I Solomon},
}

@article{Blasiak2007,
  author = {Blasiak,P. and Horzela,A. and Penson,K. A. and Solomon,A. I. and Duchamp,G. H. E.},
  title = {Combinatorics and Boson normal ordering: A gentle introduction},
  journal = {American Journal of Physics},
  volume = {75},
  number = {7},
  pages = {639-646},
  year = {2007},
  doi = {10.1119/1.2723799},
}

@book{Taeuber2014,
  author = {Uwe C. T{\"a}uber},
  title = {Critical Dynamics: A Field Theory Approach to Equilibrium and Non-Equilibrium Scaling Behavior},
  publisher = {Cambridge University Press},
  address = {Cambridge, UK},
  year = {2014},
}

@article{Alikakos1999,
  author = {Alikakos, Nicholas D. and Fusco, Giorgio},
  title = {The Equations of Ostwald Ripening for Dilute Systems},
  journal = {J. Stat. Phys.},
  year = {1999},
  month = {Jun},
  day = {01},
  volume = {95},
  number = {5},
  pages = {851--866},
  issn = {1572-9613},
  doi = {10.1023/A:1004594131850},
}

@book{Cardy2008,
  author = {John Cardy},
  title = {Non-equilibrium Statistical Mechanics and Turbulence},
  publisher = {Cambridge University Press},
  address = {Cambridge, UK},
  year = {2008},
  editor = {Sergey Nazarenko and Oleg Zaboronski},
  pages = {108--161},
  volume = {},
  edition = {},
  doi = {},
}

@article{Kuzovkov1988,
  doi = {10.1088/0034-4885/51/12/001},
  year = {1988},
  month = {dec},
  publisher = {{IOP} Publishing},
  volume = {51},
  number = {12},
  pages = {1479--1523},
  author = {V Kuzovkov and E Kotomin},
  title = {Kinetics of bimolecular reactions in condensed media: critical phenomena and microscopic self-organisation},
  journal = {Rep. Prog. Phys.},
}

@article{Mazharimousavi2017,
  author = {Mazharimousavi, S. Habib and Forghani, S. Danial and Abtahi, S. Niloufar},
  title = {Generalized Monge gauge},
  journal = {International Journal of Geometric Methods in Modern Physics},
  volume = {14},
  number = {04},
  pages = {1750062},
  year = {2017},
  doi = {10.1142/S0219887817500621},
}

@article{Soriano2009,
  title = {Universality of Persistence Exponents in Two-Dimensional Ostwald Ripening},
  author = {Soriano, Jordi and Braslavsky, Ido and Xu, Di and Krichevsky, Oleg and Stavans, Joel},
  journal = {Phys. Rev. Lett.},
  volume = {103},
  issue = {22},
  pages = {226101},
  numpages = {4},
  year = {2009},
  month = {Nov},
  publisher = {American Physical Society},
  doi = {10.1103/PhysRevLett.103.226101},
}

@article{Pierrehumbert2000,
  author = {Pierrehumbert,Raymond T.},
  title = {Lattice models of advection-diffusion},
  journal = {Chaos},
  volume = {10},
  number = {1},
  pages = {61-74},
  year = {2000},
  doi = {10.1063/1.166476},
}

@article{Cugliandolo2016,
  doi = {10.1088/1742-5468/2016/11/114001},
  year = {2016},
  month = {nov},
  publisher = {{IOP} Publishing},
  volume = {2016},
  number = {11},
  pages = {114001},
  author = {Leticia F Cugliandolo},
  title = {Critical percolation in bidimensional coarsening},
  journal = {J. Stat. Mech.},
}

@article{Pietzonka2016,
  doi = {10.1088/1742-5468/2016/12/124004},
  year = {2016},
  month = {dec},
  publisher = {{IOP} Publishing},
  volume = {2016},
  number = {12},
  pages = {124004},
  author = {Patrick Pietzonka and Andre C Barato and Udo Seifert},
  title = {Universal bound on the efficiency of molecular motors},
  journal = {J. Stat. Mech.},
}

@article{Ramaswamy2017,
  doi = {10.1088/1742-5468/aa6bc5},
  year = {2017},
  month = {may},
  publisher = {{IOP} Publishing},
  volume = {2017},
  number = {5},
  pages = {054002},
  author = {Sriram Ramaswamy},
  title = {Active matter},
  journal = {J. Stat. Mech.},
}

@article{Deloubriere2002,
  title = {Imaginary noise and parity conservation in the reaction $A+A\leftrightharpoons 0$},
  journal = {Physica A},
  volume = {308},
  number = {1},
  pages = {135 - 147},
  year = {2002},
  issn = {0378-4371},
  doi = {10.1016/S0378-4371(02)00548-4},
  author = {O. Deloubri{\`e}re and L. Frachebourg and H.J. Hilhorst and K. Kitahara},
}

@book{Altland2010,
  author = {Alexander Altland and Ben Simons},
  title = {Condensed Matter Field Theory},
  publisher = {Cambridge University Press},
  address = {Cambridge, UK},
  year = {2010},
  edition = {2},
  editor = {},
  pages = {},
  volume = {},
  doi = {},
}

@article{Martin1973,
  title = {Statistical Dynamics of Classical Systems},
  author = {Martin, P. C. and Siggia, E. D. and Rose, H. A.},
  journal = {Phys. Rev. A},
  volume = {8},
  issue = {1},
  pages = {423--437},
  numpages = {0},
  year = {1973},
  month = {Jul},
  publisher = {American Physical Society},
  doi = {10.1103/PhysRevA.8.423},
}

@article{Janssen1976,
  author = {Janssen, Hans-Karl},
  title = {On a Lagrangean for classical field dynamics and renormalization group calculations of dynamical critical properties},
  journal = {Z. Phys. B},
  year = {1976},
  month = {Dec},
  day = {01},
  volume = {23},
  number = {4},
  pages = {377--380},
  issn = {1431-584X},
  doi = {10.1007/BF01316547},
}

@article{deDominicis1976,
  author = {C. de Dominicis},
  title = {Techniques de Renormalisation de la Th{\'e}orie des Champs et Dynamique des Ph{\'e}nom{\`e}nes Critiques},
  journal = {J. Phys. Colloques},
  volume = {37},
  pages = {C1-247--C1-253},
  year = {1976},
  doi = {10.1051/jphyscol:1976138},
}

@book{Janssen1979,
  author = {H. K. Janssen},
  title = {Lecture Notes in Physics: Dynamical Critical Phenomena and Related Topics},
  editor = {C. P. Enz},
  volume = {104},
  publisher = {Springer},
  address = {Berlin},
  year = {1979},
  pages = {25--47},
}

@article{Wang2019,
  title = {Salicylate Increases Fitness Cost Associated with MarA-Mediated Antibiotic Resistance},
  author = {Tiebin Wang and Colin Kunze and Mary J. Dunlop},
  journal = {Biophysical Journal},
  volume = {117},
  pages = {563--571},
  year = {2019},
  doi = {10.1016/j.bpj.2019.07.005},
}

@article{Rossi2018,
  author = {Rossi, Nicholas A. AND Mora, Thierry AND Walczak, Aleksandra M. AND Dunlop, Mary J.},
  journal = {PLOS Computational Biology},
  publisher = {Public Library of Science},
  title = {Active degradation of MarA controls coordination of its downstream targets},
  year = {2018},
  month = {12},
  volume = {14},
  pages = {1-16},
  number = {12},
  doi = {10.1371/journal.pcbi.1006634},
}

@article{Wang2017,
  author = {Wang, Tiebin and El Meouche, Imane and Dunlop, Mary J.},
  title = {Bacterial persistence induced by salicylate via reactive oxygen species},
  journal = {Scientific Reports},
  year = {2017},
  volume = {7},
  number = {1},
  pages = {43839},
  issn = {2045-2322},
  doi = {10.1038/srep43839},
}

@article{Gillespie1996,
  title = {Exact numerical simulation of the Ornstein-Uhlenbeck process and its integral},
  author = {Gillespie, Daniel T.},
  journal = {Phys. Rev. E},
  volume = {54},
  issue = {2},
  pages = {2084--2091},
  numpages = {0},
  year = {1996},
  month = {Aug},
  publisher = {American Physical Society},
  doi = {10.1103/PhysRevE.54.2084},
}

@article{Gillespie1976,
  title = {A general method for numerically simulating the stochastic time evolution of coupled chemical reactions},
  journal = {J. Comp. Phys.},
  volume = {22},
  number = {4},
  pages = {403 - 434},
  year = {1976},
  issn = {0021-9991},
  doi = {10.1016/0021-9991(76)90041-3},
  author = {Daniel T Gillespie},
}

@article{Gillespie1977,
  author = {Gillespie, Daniel T.},
  title = {Exact stochastic simulation of coupled chemical reactions},
  journal = {J. Phys. Chem.},
  volume = {81},
  number = {25},
  pages = {2340-2361},
  year = {1977},
  doi = {10.1021/j100540a008},
}

@article{Rossi2017,
  author = {Rossi, Nicholas A. AND Dunlop, Mary J.},
  journal = {PLOS Computational Biology},
  publisher = {Public Library of Science},
  title = {Customized Regulation of Diverse Stress Response Genes by the Multiple Antibiotic Resistance Activator MarA},
  year = {2017},
  month = {01},
  volume = {13},
  pages = {1--15},
  number = {1},
  doi = {10.1371/journal.pcbi.1005310},
}

@article{Vinue2013,
  author = {Vinu{\'e}, Laura and McMurry, Laura M. and Levy, Stuart B.},
  title = {{The 216-bp marB gene of the marRAB operon in Escherichia coli encodes a periplasmic protein which reduces the transcription rate of marA}},
  journal = {FEMS Microbiology Letters},
  volume = {345},
  number = {1},
  pages = {49-55},
  year = {2013},
  month = {08},
  issn = {0378-1097},
  doi = {10.1111/1574-6968.12182},
  eprint = {http://oup.prod.sis.lan/femsle/article-pdf/345/1/49/19128140/345-1-49.pdf},
}

@article{GarciaBernardo2013,
  author = {Garcia-Bernardo, Javier AND Dunlop, Mary J.},
  journal = {PLOS Computational Biology},
  publisher = {Public Library of Science},
  title = {Tunable Stochastic Pulsing in the Escherichia coli Multiple Antibiotic Resistance Network from Interlinked Positive and Negative Feedback Loops},
  year = {2013},
  month = {09},
  volume = {9},
  pages = {1-11},
  number = {9},
  doi = {10.1371/journal.pcbi.1003229},
}

@article{Prajapat2015,
  author = {Prajapat, Mahendra Kumar and Jain, Kirti and Saini, Supreet},
  title = {Control of MarRAB Operon in Escherichia coli via Autoactivation and Autorepression},
  journal = {Biophysical Journal},
  year = {2015},
  month = {Oct},
  day = {06},
  publisher = {The Biophysical Society},
  volume = {109},
  number = {7},
  pages = {1497-1508},
  issn = {1542-0086},
  doi = {10.1016/j.bpj.2015.08.017},
}

@article{Bottani2017,
  author = {Bottani, Samuel and Veitia, Reiner A.},
  title = {Hill function-based models of transcriptional switches: impact of specific, nonspecific, functional and nonfunctional binding},
  journal = {Biological Reviews},
  volume = {92},
  number = {2},
  pages = {953-963},
  keywords = {transcription, transcriptional response, cooperativity, synergy, Hmill function},
  doi = {10.1111/brv.12262},
  eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1111/brv.12262},
  year = {2017},
}

@book{Schulman1996,
  title = {Techniques and Applications of Path Integration},
  author = {Schulman, L.S.},
  isbn = {9780471166108},
  lccn = {gb96078932},
  year = {1996},
  publisher = {Wiley},
  address = {New York},
}

@article{Rodrigo2017,
  author = {Rodrigo, Guillermo and Bajic, Djordje and Elola, Ignacio and Poyatos, Juan F.},
  title = {Deconstructing a multiple antibiotic resistance regulation through the quantification of its input function},
  journal = {npj Systems Biology and Applications},
  year = {2017},
  volume = {3},
  number = {1},
  pages = {30},
  issn = {2056-7189},
  doi = {10.1038/s41540-017-0031-2},
}

@article{Rodrigo2016,
  author = {Rodrigo, Guillermo and Bajic, Djordje and Elola, Ignacio and Poyatos, Juan F.},
  title = {Antagonistic autoregulation speeds up a homogeneous response in Escherichia coli},
  journal = {Scientific Reports},
  year = {2016},
  volume = {6},
  number = {1},
  pages = {36196},
  issn = {2045-2322},
  doi = {10.1038/srep36196},
}

@article{Jain2016,
  author = {Jain, Kirti and Saini, Supreet},
  title = {MarRA{,} SoxSR{,} and Rob encode a signal dependent regulatory network in Escherichia coli},
  journal = {Mol. BioSyst.},
  year = {2016},
  volume = {12},
  issue = {6},
  pages = {1901-1912},
  publisher = {The Royal Society of Chemistry},
  doi = {10.1039/C6MB00263C},
}

@article{Rosenfeld2002,
  title = {Negative Autoregulation Speeds the Response Times of Transcription Networks},
  journal = {Journal of Molecular Biology},
  volume = {323},
  number = {5},
  pages = {785 - 793},
  year = {2002},
  issn = {0022-2836},
  doi = {https://doi.org/10.1016/S0022-2836(02)00994-4},
  author = {Nitzan Rosenfeld and Michael B Elowitz and Uri Alon},
}

@article{Bintu2005b,
  title = {Transcriptional regulation by the numbers: applications},
  journal = {Current Opinion in Genetics & Development},
  volume = {15},
  number = {2},
  pages = {125 - 135},
  year = {2005},
  note = {Chromosomes and expression mechanisms},
  issn = {0959-437X},
  doi = {10.1016/j.gde.2005.02.006},
  author = {Lacramioara Bintu and Nicolas E Buchler and Hernan G Garcia and Ulrich Gerland and Terence Hwa and Jané Kondev and Thomas Kuhlman and Rob Phillips},
}

@article{Garcia2011,
  author = {Garcia, Hernan G. and Phillips, Rob},
  title = {Quantitative dissection of the simple repression input--output function},
  volume = {108},
  number = {29},
  pages = {12173--12178},
  year = {2011},
  doi = {10.1073/pnas.1015616108},
  publisher = {National Academy of Sciences},
  issn = {0027-8424},
  eprint = {https://www.pnas.org/content/108/29/12173.full.pdf},
  journal = {Proc. Natl. Acad. Sci.},
}

@article{Phillips2019,
  author = {Phillips, Rob and Belliveau, Nathan M. and Chure, Griffin and Garcia, Hernan G. and Razo-Mejia, Manuel and Scholes, Clarissa},
  title = {Figure 1 Theory Meets Figure 2 Experiments in the Study of Gene Expression},
  journal = {Annual Review of Biophysics},
  volume = {48},
  number = {1},
  pages = {121-163},
  year = {2019},
  doi = {10.1146/annurev-biophys-052118-115525},
}

@article{Alekshun1997,
  author = {Alekshun, M N and Levy, S B},
  title = {Regulation of chromosomally mediated multiple antibiotic resistance: the mar regulon.},
  volume = {41},
  number = {10},
  pages = {2067--2075},
  year = {1997},
  doi = {10.1128/AAC.41.10.2067},
  publisher = {American Society for Microbiology Journals},
  issn = {0066-4804},
  eprint = {https://aac.asm.org/content/41/10/2067.full.pdf},
  journal = {Antimicrobial Agents and Chemotherapy},
}

@article{Martin2008,
  title = {Activation of the Escherichia coli marA/soxS/rob Regulon in Response to Transcriptional Activator Concentration},
  journal = {Journal of Molecular Biology},
  volume = {380},
  number = {2},
  pages = {278 - 284},
  year = {2008},
  issn = {0022-2836},
  doi = {10.1016/j.jmb.2008.05.015},
  author = {Robert G. Martin and Emily S. Bartlett and Judah L. Rosner and Michael E. Wall},
}

@article{Duval2013,
  author = {Duval, Val{\'e}rie and McMurry, Laura M and Foster, Kimberly and Head, James F and Levy, Stuart B},
  title = {Mutational analysis of the multiple-antibiotic resistance regulator MarR reveals a ligand binding pocket at the interface between the dimerization and DNA binding domains},
  journal = {J. Bactriol.},
  volume = {195},
  pages = {3341--3351},
  year = {2013},
  doi = {10.1128/JB.02224-12},
}

@article{Martin1995,
  author = {Martin, R G and Rosner, J L},
  title = {Binding of purified multiple antibiotic-resistance repressor protein (MarR) to mar operator sequences},
  volume = {92},
  number = {12},
  pages = {5456--5460},
  year = {1995},
  doi = {10.1073/pnas.92.12.5456},
  issn = {0027-8424},
  eprint = {https://www.pnas.org/content/92/12/5456.full.pdf},
  journal = {Proc. Natl. Acad. Sci.},
}

@article{Monod1965,
  title = {On the nature of allosteric transitions: A plausible model},
  journal = {Journal of Molecular Biology},
  volume = {12},
  number = {1},
  pages = {88 - 118},
  year = {1965},
  issn = {0022-2836},
  doi = {https://doi.org/10.1016/S0022-2836(65)80285-6},
  author = {Jacque Monod and Jeffries Wyman and Jean-Pierre Changeux},
}

@article{Martin1996,
  author = {Martin, R G and Jair, K W and Wolf, R E and Rosner, J L},
  title = {Autoactivation of the marRAB multiple antibiotic resistance operon by the MarA transcriptional activator in Escherichia coli.},
  volume = {178},
  number = {8},
  pages = {2216--2223},
  year = {1996},
  doi = {10.1128/jb.178.8.2216-2223.1996},
  journal = {J. Bacteriol.},
}

@article{Bramson1991,
  author = {Bramson, Maury and Lebowitz, Joel L.},
  title = {Asymptotic behavior of densities for two-particle annihilating random walks},
  journal = {J. Stat. Phys.},
  year = {1991},
  month = {Jan},
  day = {01},
  volume = {62},
  number = {1},
  pages = {297--372},
  issn = {1572-9613},
  doi = {10.1007/BF01020872},
}

@article{Martin2004,
  author = {Martin, Robert G. and Rosner, Judah L.},
  title = {Transcriptional and translational regulation of the marRAB multiple antibiotic resistance operon in Escherichia coli},
  journal = {Molecular Microbiology},
  volume = {53},
  number = {1},
  pages = {183-191},
  doi = {10.1111/j.1365-2958.2004.04080.x},
  year = {2004},
}

@article{Chowdhury2013,
  title = {Stochastic mechano-chemical kinetics of molecular motors: A multidisciplinary enterprise from a physicist’s perspective},
  journal = {Physics Reports},
  volume = {529},
  number = {1},
  pages = {1 - 197},
  year = {2013},
  note = {Stochastic mechano-chemical kinetics of molecular motors: A multidisciplinary enterprise from a physicist’s perspective},
  issn = {0370-1573},
  doi = {10.1016/j.physrep.2013.03.005},
  author = {Debashish Chowdhury},
}

@article{Peebles1969,
  author = {Peebles,P. J. E.},
  title = {Cosmology for Everyphysicist},
  journal = {American Journal of Physics},
  volume = {37},
  number = {4},
  pages = {410-422},
  year = {1969},
  doi = {10.1119/1.1975596},
}

@article{Neidhardt1999,
  author = {Neidhardt, Frederick C.},
  title = {Bacterial Growth: Constant Obsession with $dN/dt$},
  volume = {181},
  number = {24},
  pages = {7405--7408},
  year = {1999},
  journal = {Journal of Bacteriology},
}

@article{Dong2010,
  author = {P. V. Dong and L. T. Hue and H. T. Hung and H. N. Long and N. H. Thao},
  title = {Symmetry factors of Feynman diagrams for scalar fields},
  journal = {Theor. Math. Phys.},
  pages = {1500},
  year = {2010},
  doi = {10.1007/s11232-010-0124-1},
  volume = {165},
}

@article{Birnsteinova2020,
  author = {Birnsteinov\'a, Sarlota and Hnatic, Michal and Luivjansk\'y, Tom\'as},
  title = {Two-Species Reaction-Diffusion System: the Effect of Long-Range Spreading},
  doi = {10.1051/epjconf/202022602005},
  journal = {EPJ Web Conf.},
  year = {2020},
  volume = {226},
  pages = {02005},
}

@article{Greulich2015,
  author = {Greulich, Philip and Scott, Matthew and Evans, Martin R and Allen, Rosalind J},
  title = {Growth-dependent bacterial susceptibility to ribosome-targeting antibiotics},
  journal = {Molec. Sys. Biol.},
  volume = {11},
  number = {3},
  pages = {796},
  doi = {10.15252/msb.20145949},
  year = {2015},
}

@article{VollmayrLee2006,
  title = {Single-species three-particle reactions in one dimension},
  author = {Vollmayr-Lee, Benjamin P. and Gildner, Melinda M.},
  journal = {Phys. Rev. E},
  volume = {73},
  issue = {4},
  pages = {041103},
  numpages = {7},
  year = {2006},
  month = {Apr},
  publisher = {American Physical Society},
  doi = {10.1103/PhysRevE.73.041103},
}

@book{Rice1985,
  title = {Diffusion-limited Reactions},
  author = {S. A. Rice},
  publisher = {Elsevier},
  address = {Amsterdam},
  year = {1985},
}

@book{Abramowitz1972,
  title = {Handbook of Mathematical Functions},
  author = {Abramowitz, M. and Stegun, I. A.},
  publisher = {Dover},
  address = {New York},
  year = {1972},
}

@book{Privman1997,
  title = {Nonequilibrium Statistical Mechanics in One Dimension},
  author = {V. Privman},
  publisher = {Cambridge University Press},
  address = {Cambridge},
  year = {1997},
}

@incollection{Krug1991,
  booktitle = {Solids Far From Equilibrium},
  title = {Kinetic Roughening of Growing Surfaces},
  editor = {C. Godr\`eche},
  author = {J. Krug and H. Spohn},
  publisher = {Cambridge University Press},
  address = {Cambridge},
  year = {1991},
}

@article{Gao2017,
  author = {Gao, Yun-Rong and Li, De-Feng and Fleming, Joy and Zhou, Ya-Feng and Liu, Ying and Deng, Jiao-Yu and Zhou, Lin and Zhou, Jie and Zhu, Guo-Feng and Zhang, Xian-En and Wang, Da-Cheng and Bi, Li-Jun},
  title = {Structural analysis of the regulatory mechanism of MarR protein Rv2887 in M. tuberculosis},
  journal = {Scientific Reports},
  year = {2017},
  volume = {7},
  number = {1},
  pages = {6471},
  issn = {2045-2322},
  doi = {10.1038/s41598-017-01705-4},
}

@article{Grove2013,
  title = {MarR family transcription factors},
  journal = {Current Biology},
  volume = {23},
  number = {4},
  pages = {R142 - R143},
  year = {2013},
  issn = {0960-9822},
  doi = {10.1016/j.cub.2013.01.013},
  author = {Anne Grove},
}

@article{Lin2018,
  author = {Lin, Jie and Amir, Ariel},
  title = {Homeostasis of protein and mRNA concentrations in growing cells},
  journal = {Nature Communications},
  year = {2018},
  volume = {9},
  number = {1},
  pages = {4496},
  issn = {2041-1723},
  doi = {10.1038/s41467-018-06714-z},
}

@article{Martin2000,
  author = {Martin, R. G. and Gillette, W. K. and Rosner, J. L.},
  title = {Promoter discrimination by the related transcriptional activators MarA and SoxS: differential regulation by differential binding},
  journal = {Molecular Microbiology},
  volume = {35},
  number = {3},
  pages = {623-634},
  doi = {10.1046/j.1365-2958.2000.01732.x},
  year = {2000},
}

@article{Griffith2004,
  author = {Griffith, Kevin L. and Shah, Ishita M. and E. Wolf Jr, Richard},
  title = {Proteolytic degradation of Escherichia coli transcription activators SoxS and MarA as the mechanism for reversing the induction of the superoxide (SoxRS) and multiple antibiotic resistance (Mar) regulons},
  journal = {Molecular Microbiology},
  volume = {51},
  number = {6},
  pages = {1801-1816},
  doi = {10.1046/j.1365-2958.2003.03952.x},
  year = {2004},
}

@article{Bhaskarla2016,
  author = {Bhaskarla, Chetana and Das, Mrinmoy and Verma, Taru and Kumar, Anujith and Mahadevan, S. and Nandi, Dipankar},
  title = {Roles of Lon protease and its substrate MarA during sodium salicylate-mediated growth reduction and antibiotic resistance in Escherichia coli},
  journal = {Microbiology},
  year = {2016},
  volume = {162},
  number = {5},
  pages = {764-776},
  doi = {https://doi.org/10.1099/mic.0.000271},
}

@article{Chubiz2012,
  author = {Chubiz, Lon M. and Glekas, George D. and Rao, Christopher V.},
  title = {Transcriptional Cross Talk within the mar-sox-rob Regulon in Escherichia coli Is Limited to the rob and marRAB Operons},
  volume = {194},
  number = {18},
  pages = {4867--4875},
  year = {2012},
  doi = {10.1128/JB.00680-12},
  journal = {Journal of Bacteriology},
}

@article{Seoane1995,
  author = {Seoane, A. S. and Levy, S. B.},
  title = {Characterization of MarR, the repressor of the multiple antibiotic resistance (mar) operon in Escherichia coli},
  journal = {Journal of Bacteriology},
  year = {1995},
  month = {Jun},
  volume = {177},
  number = {12},
  pages = {3414-3419},
  doi = {10.1128/jb.177.12.3414-3419.1995},
}

@article{Deris2013,
  author = {Deris, J. Barrett and Kim, Minsu and Zhang, Zhongge and Okano, Hiroyuki and Hermsen, Rutger and Groisman, Alexander and Hwa, Terence},
  title = {The Innate Growth Bistability and Fitness Landscapes of Antibiotic-Resistant Bacteria},
  volume = {342},
  number = {6162},
  year = {2013},
  doi = {10.1126/science.1237435},
  journal = {Science},
  pages = {1237435},
}

@article{Ji2013,
  author = {Ji, Ni and Middelkoop, Teije C. and Mentink, Remco A. and Betist, Marco C. and Tonegawa, Satto and Mooijman, Dylan and Korswagen, Hendrik C. and van Oudenaarden, Alexander},
  title = {Feedback Control of Gene Expression Variability in the <em>Caenorhabditis elegans</em> Wnt Pathway},
  journal = {Cell},
  year = {2013},
  month = {Nov},
  day = {07},
  publisher = {Elsevier},
  volume = {155},
  number = {4},
  pages = {869-880},
  issn = {0092-8674},
  doi = {10.1016/j.cell.2013.09.060},
}

@article{Kang1984,
  title = {Fluctuation effects in Smoluchowski reaction kinetics},
  author = {Kang, K. and Redner, S.},
  journal = {Phys. Rev. A},
  volume = {30},
  issue = {5},
  pages = {2833--2836},
  numpages = {0},
  year = {1984},
  month = {Nov},
  publisher = {American Physical Society},
  doi = {10.1103/PhysRevA.30.2833},
}

@article{Mattis1998,
  title = {The uses of quantum field theory in diffusion-limited reactions},
  author = {Mattis, Daniel C. and Glasser, M. Lawrence},
  journal = {Rev. Mod. Phys.},
  volume = {70},
  issue = {3},
  pages = {979--1001},
  numpages = {0},
  year = {1998},
  month = {Jul},
  publisher = {American Physical Society},
  doi = {10.1103/RevModPhys.70.979},
}

@article{VollmayrLee2020,
  doi = {10.1088/1751-8121/ab7780},
  year = {2020},
  volume = {53},
  number = {17},
  pages = {179501},
  author = {Benjamin Vollmayr-Lee and Jack Hanson and R Scott McIsaac and Joshua D Hellerick},
  title = {Corrigendum: Anomalous dimension in a two-species reaction-diffusion system (2018 J. Phys. A: Math. Theor. 51 034002)},
  journal = {J. Phys. A: Math. and Theor.},
}

@article{Ghosh2011,
  author = {Ghosh,Kingshuk},
  title = {Stochastic dynamics of complexation reaction in the limit of small numbers},
  journal = {J. Chem. Phys.},
  volume = {134},
  number = {19},
  pages = {195101},
  year = {2011},
  doi = {10.1063/1.3590918},
}

@article{Hellerick2020,
  title = {Numerical simulation of the trapping reaction with mobile and reacting traps},
  author = {Hellerick, Joshua D. and Rhoades, Robert C. and Vollmayr-Lee, Benjamin P.},
  journal = {Phys. Rev. E},
  volume = {101},
  issue = {4},
  pages = {042112},
  numpages = {10},
  year = {2020},
  doi = {10.1103/PhysRevE.101.042112},
}

@article{Scott2014,
  author = {Scott, Matthew and Klumpp, Stefan and Mateescu, Eduard M and Hwa, Terence},
  title = {Emergence of robust growth laws from optimal regulation of ribosome synthesis},
  journal = {Molecular Systems Biology},
  volume = {10},
  number = {8},
  pages = {747},
  keywords = {growth control, metabolic control, phenomenological model, resource allocation, synthetic biology},
  doi = {10.15252/msb.20145379},
  year = {2014},
}

@article{Erickson2017,
  author = {Erickson, David W. and Schink, Severin J. and Patsalo, Vadim and Williamson, James R. and Gerland, Ulrich and Hwa, Terence},
  title = {A global resource allocation strategy governs growth transition kinetics of Escherichia coli},
  journal = {Nature},
  year = {2017},
  month = {Nov},
  day = {01},
  volume = {551},
  number = {7678},
  pages = {119-123},
  issn = {1476-4687},
  doi = {10.1038/nature24299},
}

@article{Hertz2016,
  doi = {10.1088/1751-8121/50/3/033001},
  year = {2016},
  volume = {50},
  number = {3},
  pages = {033001},
  author = {John A Hertz and Yasser Roudi and Peter Sollich},
  title = {Path integral methods for the dynamics of stochastic and disordered systems},
  journal = {J. Phys. A},
}

@article{Kostinski2020,
  title = {Ribosome composition maximizes cellular growth rates in E. coli},
  author = {Sarah Kostinski and Shlomi Reuveni},
  journal = {Phys. Rev. Lett.},
  year = {2020},
  volume = {XX},
  pages = {YYY},
  doi = {123.abc},
}

@article{Kuehn2017,
  author = {K{\"u}hn, Marco J. and Schmidt, Felix K. and Eckhardt, Bruno and Thormann, Kai M.},
  title = {Bacteria exploit a polymorphic instability of the flagellar filament to escape from traps},
  volume = {114},
  number = {24},
  pages = {6340--6345},
  year = {2017},
  doi = {10.1073/pnas.1701644114},
  journal = {Proceedings of the National Academy of Sciences},
}

@article{Owen2020,
  title = {Universal Thermodynamic Bounds on Nonequilibrium Response with Biochemical Applications},
  author = {Owen, Jeremy A. and Gingrich, Todd R. and Horowitz, Jordan M.},
  journal = {Phys. Rev. X},
  volume = {10},
  pages = {011066},
  year = {2020},
  doi = {10.1103/PhysRevX.10.011066},
}

@article{Barato2015,
  title = {Thermodynamic Uncertainty Relation for Biomolecular Processes},
  author = {Barato, Andre C. and Seifert, Udo},
  journal = {Phys. Rev. Lett.},
  volume = {114},
  issue = {15},
  pages = {158101},
  year = {2015},
  doi = {10.1103/PhysRevLett.114.158101},
}

@article{Bothe2021,
  title = {Doi-Peliti field theory of free active Ornstein-Uhlenbeck particles},
  author = {Bothe, Marius and Pruessner, Gunnar},
  journal = {Phys. Rev. E},
  volume = {103},
  issue = {6},
  pages = {062105},
  numpages = {7},
  year = {2021},
  month = {Jun},
  publisher = {American Physical Society},
  doi = {10.1103/PhysRevE.103.062105},
  url = {https://link.aps.org/doi/10.1103/PhysRevE.103.062105},
}

@article{Maggi2021,
  author = {Maggi, Claudio and Paoluzzi, Matteo and Crisanti, Andrea and Zaccarelli, Emanuela and Gnan, Nicoletta},
  title = {Universality class of the motility-induced critical point in large scale off-lattice simulations of active particles},
  journal = {Soft Matter},
  year = {2021},
  volume = {17},
  pages = {3807},
  doi = {10.1039/D0SM02162H},
}

@article{Fodor2016,
  title = {How Far from Equilibrium Is Active Matter?},
  author = {Fodor, \'Etienne and Nardini, Cesare and Cates, Michael E. and Tailleur, Julien and Visco, Paolo and van Wijland, Fr\'ed\'eric},
  journal = {Phys. Rev. Lett.},
  volume = {117},
  issue = {3},
  pages = {038103},
  numpages = {6},
  year = {2016},
  month = {Jul},
  publisher = {American Physical Society},
  doi = {10.1103/PhysRevLett.117.038103},
}

@article{Nardini2017,
  title = {Entropy Production in Field Theories without Time-Reversal Symmetry: Quantifying the Non-Equilibrium Character of Active Matter},
  author = {Nardini, Cesare and Fodor, \'Etienne and Tjhung, Elsen and van Wijland, Fr\'ed\'eric and Tailleur, Julien and Cates, Michael E.},
  journal = {Phys. Rev. X},
  volume = {7},
  issue = {2},
  pages = {021007},
  numpages = {20},
  year = {2017},
  month = {Apr},
  publisher = {American Physical Society},
  doi = {10.1103/PhysRevX.7.021007},
  url = {https://link.aps.org/doi/10.1103/PhysRevX.7.021007},
}

@article{Stenhammar2013,
  title = {Continuum Theory of Phase Separation Kinetics for Active Brownian Particles},
  author = {Stenhammar, Joakim and Tiribocchi, Adriano and Allen, Rosalind J. and Marenduzzo, Davide and Cates, Michael E.},
  journal = {Phys. Rev. Lett.},
  volume = {111},
  issue = {14},
  pages = {145702},
  numpages = {5},
  year = {2013},
  month = {Oct},
  publisher = {American Physical Society},
  doi = {10.1103/PhysRevLett.111.145702},
  url = {https://link.aps.org/doi/10.1103/PhysRevLett.111.145702},
}

@article{Li2021,
  doi = {10.1088/1742-5468/abd311},
  url = {https://doi.org/10.1088/1742-5468/abd311},
  year = {2021},
  month = {jan},
  publisher = {{IOP} Publishing},
  volume = {2021},
  number = {1},
  pages = {013211},
  author = {Yuting I Li and Michael E Cates},
  title = {Steady state entropy production rate for scalar Langevin field theories},
  journal = {J. Stat. Mech.: Theory and Experiment},
}

@article{GarciaMillan2021,
  doi = {10.1088/1742-5468/ac014d},
  url = {https://doi.org/10.1088/1742-5468/ac014d},
  year = {2021},
  month = {jun},
  publisher = {{IOP} Publishing},
  volume = {2021},
  number = {6},
  pages = {063203},
  author = {Rosalba Garcia-Millan and Gunnar Pruessner},
  title = {Run-and-tumble motion in a harmonic potential: field theory and entropy production},
  journal = {J. Stat. Mech.: Theory and Experiment},
}

@article{Copenhagen2021,
  author = {Copenhagen, Katherine and Alert, Ricard and Wingreen, Ned S. and Shaevitz, Joshua W.},
  title = {Topological defects promote layer formation in Myxococcus xanthus colonies},
  journal = {Nature Physics},
  year = {2021},
  month = {Feb},
  day = {01},
  volume = {17},
  number = {2},
  pages = {211},
  doi = {10.1038/s41567-020-01056-4},
}

@article{Ali2020,
  article_type = {journal},
  title = {Inherent regulatory asymmetry emanating from network architecture in a prevalent autoregulatory motif},
  author = {Ali, Md Zulfikar and Parisutham, Vinuselvi and Choubey, Sandeep and Brewster, Robert C},
  editor = {Krishna, Sandeep and Barkai, Naama},
  volume = {9},
  year = {2020},
  month = {aug},
  pub_date = {2020-08-18},
  pages = {e56517},
  citation = {eLife 2020;9:e56517},
  doi = {10.7554/eLife.56517},
  journal = {eLife},
  issn = {2050-084X},
  publisher = {eLife Sciences Publications, Ltd},
}

@article{Schultz2017,
  title = {Regulatory Dynamics Determine Cell Fate following Abrupt Antibiotic Exposure},
  journal = {Cell Systems},
  volume = {5},
  number = {5},
  pages = {509-517.e3},
  year = {2017},
  issn = {2405-4712},
  doi = {https://doi.org/10.1016/j.cels.2017.10.002},
  author = {Daniel Schultz and Adam C. Palmer and Roy Kishony},
}

@article{Alon2007,
  author = {Alon, Uri},
  title = {Network motifs: theory and experimental approaches},
  journal = {Nature Reviews Genetics},
  year = {2007},
  month = {Jun},
  day = {01},
  volume = {8},
  number = {6},
  pages = {450},
  issn = {1471-0064},
  doi = {10.1038/nrg2102},
}

@article{Langevin2017,
  author = {Langevin, Ariel and Dunlop, Mary},
  year = {2017},
  month = {10},
  pages = {JB.00525-17},
  title = {Stress introduction rate alters benefit of AcrAB-TolC efflux pumps},
  volume = {200},
  journal = {Journal of Bacteriology},
  doi = {10.1128/JB.00525-17},
}

@article{Wen2018,
  author = {Wen, Xi and Langevin, Ariel M. and Dunlop, Mary J.},
  title = {Antibiotic export by efflux pumps affects growth of neighboring bacteria},
  journal = {Scientific Reports},
  year = {2018},
  month = {Oct},
  day = {11},
  volume = {8},
  number = {1},
  pages = {15120},
  issn = {2045-2322},
  doi = {10.1038/s41598-018-33275-4},
  url = {https://doi.org/10.1038/s41598-018-33275-4},
}

@article{Langevin2020,
  author = {Ariel M. Langevin and Imane El Meouche and Mary J. Dunlop},
  title = {Mapping the Role of AcrAB-TolC Efflux Pumps in the Evolution of Antibiotic Resistance Reveals Near-MIC Treatments Facilitate Resistance Acquisition},
  journal = {mSphere},
  volume = {5},
  pages = {e01056},
  year = {2020},
  doi = {10.1128/mSphere.01056-20},
}

@article{Sasai2003,
  author = {Sasai, Masaki and Wolynes, Peter G.},
  title = {Stochastic gene expression as a many-body problem},
  volume = {100},
  number = {5},
  pages = {2374},
  year = {2003},
  doi = {10.1073/pnas.2627987100},
  publisher = {National Academy of Sciences},
  url = {https://www.pnas.org/content/100/5/2374},
  eprint = {https://www.pnas.org/content/100/5/2374.full.pdf},
  journal = {PNAS},
}

@article{Lathouwers2020,
  doi = {10.1021/acs.jpclett.0c01055},
  url = {https://doi.org/10.1021%2Facs.jpclett.0c01055},
  year = {2020},
  month = {jun},
  publisher = {American Chemical Society ({ACS})},
  volume = {11},
  number = {13},
  pages = {5273},
  author = {Emma Lathouwers and Joseph N. E. Lucero and David A. Sivak},
  title = {Nonequilibrium Energy Transduction in Stochastic Strongly Coupled Rotary Motors},
  journal = {J. Phys. Chem. Lett.},
}

@article{Wittkowski2014,
  doi = {10.1038/ncomms5351},
  url = {https://doi.org/10.1038%2Fncomms5351},
  year = {2014},
  month = {jul},
  publisher = {Springer Science and Business Media {LLC}},
  volume = {5},
  number = {1},
  author = {Raphael Wittkowski and Adriano Tiribocchi and Joakim Stenhammar and Rosalind J. Allen and Davide Marenduzzo and Michael E. Cates},
  title = {Scalar $\phi^4$ field theory for active-particle phase separation},
  journal = {Nature Communications},
  pages = {4351},
}

@article{Skinner2021,
  title = {Estimating Entropy Production from Waiting Time Distributions},
  author = {Skinner, Dominic J. and Dunkel, J\"orn},
  journal = {Phys. Rev. Lett.},
  volume = {127},
  issue = {19},
  pages = {198101},
  year = {2021},
  doi = {10.1103/PhysRevLett.127.198101},
}

@article{Zuckerman2021,
  author = {Zuckerman,Daniel M. and Russo,John D.},
  title = {A gentle introduction to the non-equilibrium physics of trajectories: Theory, algorithms, and biomolecular applications},
  journal = {American Journal of Physics},
  volume = {89},
  number = {11},
  pages = {1048},
  year = {2021},
  doi = {10.1119/10.0005603},
}

@article{Lee1996,
  doi = {10.1103/physrevlett.76.2906},
  url = {https://doi.org/10.1103%2Fphysrevlett.76.2906},
  year = {1996},
  month = {apr},
  publisher = {American Physical Society ({APS})},
  volume = {76},
  number = {16},
  pages = {2906--2909},
  author = {Benjamin P. Lee and Michael E. Fisher},
  title = {Density Fluctuations in an Electrolyte from Generalized Debye-Hückel Theory},
  journal = {Phys. Rev. Lett.},
}

@article{Fisher1996,
  doi = {10.1103/physrevlett.77.3561},
  url = {https://doi.org/10.1103%2Fphysrevlett.77.3561},
  year = {1996},
  month = {oct},
  publisher = {American Physical Society ({APS})},
  volume = {77},
  number = {17},
  pages = {3561--3564},
  author = {Michael E. Fisher and Benjamin P. Lee},
  title = {Ginzburg Criterion for Coulombic Criticality},
  journal = {Phys. Rev. Lett.},
}

@article{Lee1997b,
  doi = {10.1209/epl/i1997-00402-x},
  url = {https://doi.org/10.1209/epl/i1997-00402-x},
  year = {1997},
  month = {sep},
  publisher = {{IOP} Publishing},
  volume = {39},
  number = {6},
  pages = {611--616},
  author = {B. P Lee and M. E Fisher},
  title = {Charge oscillations in Debye-Hückel theory},
  journal = {Europhys. Lett.},
}

@article{Konkoli1999,
  doi = {10.1103/physreve.59.r3787},
  url = {https://doi.org/10.1103%2Fphysreve.59.r3787},
  year = {1999},
  month = {apr},
  publisher = {American Physical Society ({APS})},
  volume = {59},
  number = {4},
  pages = {R3787--R3790},
  author = {Zoran Konkoli and Henrik Johannesson and Benjamin P. Lee},
  title = {Fluctuation effects in steric reaction-diffusion systems},
  journal = {Phys. Rev. E},
}

@article{Lee1999,
  doi = {10.1103/physreve.60.5812},
  url = {https://doi.org/10.1103%2Fphysreve.60.5812},
  year = {1999},
  month = {nov},
  publisher = {American Physical Society ({APS})},
  volume = {60},
  number = {5},
  pages = {5812},
  author = {Benjamin P. Lee and Jack F. Douglas and Sharon C. Glotzer},
  title = {Filler-induced composition waves in phase-separating polymer blends},
  journal = {Phys. Rev. E},
}

@article{Seifert2016,
  doi = {10.1103/physrevlett.116.020601},
  year = {2016},
  month = {jan},
  publisher = {American Physical Society ({APS})},
  volume = {116},
  number = {2},
  author = {Udo Seifert},
  title = {First and Second Law of Thermodynamics at Strong Coupling},
  journal = {Physical Review Letters},
  pages = {020601},
}

@article{Jarzynski2017,
  title = {Stochastic and Macroscopic Thermodynamics of Strongly Coupled Systems},
  author = {Jarzynski, Christopher},
  journal = {Phys. Rev. X},
  volume = {7},
  issue = {1},
  pages = {011008},
  numpages = {20},
  year = {2017},
  month = {Jan},
  publisher = {American Physical Society},
  doi = {10.1103/PhysRevX.7.011008},
  url = {https://link.aps.org/doi/10.1103/PhysRevX.7.011008},
}

@article{Markovich2021,
  title = {Thermodynamics of Active Field Theories: Energetic Cost of Coupling to Reservoirs},
  author = {Markovich, Tomer and Fodor, \'Etienne and Tjhung, Elsen and Cates, Michael E.},
  journal = {Phys. Rev. X},
  volume = {11},
  issue = {2},
  pages = {021057},
  numpages = {23},
  year = {2021},
  month = {Jun},
  publisher = {American Physical Society},
  doi = {10.1103/PhysRevX.11.021057},
  url = {https://link.aps.org/doi/10.1103/PhysRevX.11.021057},
}

@article{Freitas2021,
  doi = {10.1088/1367-2630/ac1bf5},
  url = {https://doi.org/10.1088%2F1367-2630%2Fac1bf5},
  year = {2021},
  month = {sep},
  publisher = {{IOP} Publishing},
  volume = {23},
  number = {9},
  pages = {093003},
  author = {Nahuel Freitas and Gianmaria Falasco and Massimiliano Esposito},
  title = {Linear response in large deviations theory: a method to compute non-equilibrium distributions},
  journal = {New Journal of Physics},
}

@article{Skinner2021b,
  doi = {10.1073/pnas.2024300118},
  url = {https://doi.org/10.1073%2Fpnas.2024300118},
  year = {2021},
  month = {apr},
  publisher = {Proceedings of the National Academy of Sciences},
  volume = {118},
  number = {18},
  author = {Dominic J. Skinner and Jörn Dunkel},
  title = {Improved bounds on entropy production in living systems},
  journal = {Proceedings of the National Academy of Sciences},
  pages = {e2024300118},
}

@article{Meibohm2022,
  doi = {10.1103/physrevlett.128.110603},
  url = {https://doi.org/10.1103%2Fphysrevlett.128.110603},
  year = {2022},
  month = {mar},
  publisher = {American Physical Society ({APS})},
  volume = {128},
  number = {11},
  author = {Jan Meibohm and Massimiliano Esposito},
  title = {Finite-Time Dynamical Phase Transition in Nonequilibrium Relaxation},
  journal = {Physical Review Letters},
  pages = {110603},
}

@article{Rao2018b,
  doi = {10.1088/1367-2630/aaa15f},
  url = {https://doi.org/10.1088%2F1367-2630%2Faaa15f},
  year = {2018},
  month = {feb},
  publisher = {{IOP} Publishing},
  volume = {20},
  number = {2},
  pages = {023007},
  author = {Riccardo Rao and Massimiliano Esposito},
  title = {Conservation laws shape dissipation},
  journal = {New Journal of Physics},
}

@article{Esposito2007,
  doi = {10.1103/physreve.76.031132},
  url = {https://doi.org/10.1103%2Fphysreve.76.031132},
  year = {2007},
  month = {sep},
  publisher = {American Physical Society ({APS})},
  volume = {76},
  number = {3},
  author = {Massimiliano Esposito and Upendra Harbola and Shaul Mukamel},
  title = {Entropy fluctuation theorems in driven open systems: Application to electron counting statistics},
  journal = {Physical Review E},
  pages = {031132},
}

@article{Esposito2010,
  doi = {10.1103/physreve.82.011143},
  url = {https://doi.org/10.1103%2Fphysreve.82.011143},
  year = {2010},
  month = {jul},
  publisher = {American Physical Society ({APS})},
  volume = {82},
  number = {1},
  author = {Massimiliano Esposito and Christian Van den Broeck},
  title = {Three faces of the second law. I. Master equation formulation},
  journal = {Physical Review E},
  pages = {011143},
}

@article{Freitas2021b,
  doi = {10.1103/physrevx.11.031064},
  url = {https://doi.org/10.1103%2Fphysrevx.11.031064},
  year = {2021},
  month = {sep},
  publisher = {American Physical Society ({APS})},
  volume = {11},
  number = {3},
  author = {Nahuel Freitas and Jean-Charles Delvenne and Massimiliano Esposito},
  title = {Stochastic Thermodynamics of Nonlinear Electronic Circuits: A Realistic Framework for Computing Around $kT$},
  journal = {Physical Review X},
  pages = {031064},
}

@article{Price2000,
  title = {The effects of salicylate on bacteria},
  journal = {The International Journal of Biochemistry & Cell Biology},
  volume = {32},
  number = {10},
  pages = {1029-1043},
  year = {2000},
  issn = {1357-2725},
  doi = {10.1016/S1357-2725(00)00042-X},
  author = {Christopher T.D Price and Ian R Lee and John E Gustafson},
}

@article{Hermsen2015,
  doi = {10.15252/msb.20145537},
  year = {2015},
  month = {apr},
  publisher = {{EMBO}},
  volume = {11},
  number = {4},
  pages = {801},
  author = {Rutger Hermsen and Hiroyuki Okano and Conghui You and Nicole Werner and Terence Hwa},
  title = {A growth-rate composition formula for the growth of E.~coli on co-utilized carbon substrates},
  journal = {Molecular Systems Biology},
}

@article{Cohen1993,
  doi = {10.1128/jb.175.5.1484-1492.1993},
  year = {1993},
  month = {mar},
  publisher = {American Society for Microbiology},
  volume = {175},
  number = {5},
  pages = {1484--1492},
  author = {S P Cohen and H Hächler and S B Levy},
  title = {Genetic and functional analysis of the multiple antibiotic resistance (mar) locus in Escherichia coli},
  journal = {Journal of Bacteriology},
}

@article{Cohen1993b,
  doi = {10.1128/jb.175.24.7856-7862.1993},
  year = {1993},
  month = {dec},
  publisher = {American Society for Microbiology},
  volume = {175},
  number = {24},
  pages = {7856--7862},
  author = {S P Cohen and S B Levy and J Foulds and J L Rosner},
  title = {Salicylate induction of antibiotic resistance in Escherichia coli: activation of the mar operon and a mar-independent pathway},
  journal = {Journal of Bacteriology},
}

@article{Haechler1991,
  doi = {10.1128/jb.173.17.5532-5538.1991},
  year = {1991},
  month = {sep},
  publisher = {American Society for Microbiology},
  volume = {173},
  number = {17},
  pages = {5532--5538},
  author = {H Hächler and S P Cohen and S B Levy},
  title = {{marA}, a regulated locus which controls expression of chromosomal multiple antibiotic resistance in Escherichia coli},
  journal = {Journal of Bacteriology},
}

@article{Elowitz2000,
  doi = {10.1038/35002125},
  year = {2000},
  month = {jan},
  publisher = {Springer Science and Business Media {LLC}},
  volume = {403},
  number = {6767},
  pages = {335--338},
  author = {Michael B. Elowitz and Stanislas Leibler},
  title = {A synthetic oscillatory network of transcriptional regulators},
  journal = {Nature},
}

@article{PotvinTrottier2016,
  doi = {10.1038/nature19841},
  year = {2016},
  month = {oct},
  publisher = {Springer Science and Business Media {LLC}},
  volume = {538},
  number = {7626},
  pages = {514--517},
  author = {Laurent Potvin-Trottier and Nathan D. Lord and Glenn Vinnicombe and Johan Paulsson},
  title = {Synchronous long-term oscillations in a synthetic gene circuit},
  journal = {Nature},
}

@article{Onuki1992,
  title = {Scattering from interfaces and its finite curvature corrections},
  author = {Onuki, A},
  journal = {Phys. Rev. A},
  publisher = {American Physical Society (APS)},
  volume = {45},
  number = {6},
  pages = {R3384},
  month = {March},
  year = {1992},
  doi = {10.1103/PhysRevA.45.R3384},
}


@article{Tomita1984,
  doi = {10.1143/ptp.72.656},
  year = {1984},
  volume = {72},
  number = {3},
  pages = {656},
  author = {H. Tomita},
  title = {Sum Rules for Small Angle Scattering by Random Interface},
  journal = {Prog. Theor. Phys.}
}

@article{Tomita1986,
  doi = {10.1143/ptp.75.482},
  year = {1986},
  volume = {75},
  number = {3},
  pages = {482},
  author = {H. Tomita},
  title = {Statistical Properties of Random Interface System},
  journal = {Prog. Theor. Phys.}
}

@article{Shinozaki1991,
  doi = {10.1103/physrevlett.66.173},
  year = {1991},
  month = {jan},
  publisher = {American Physical Society ({APS})},
  volume = {66},
  number = {2},
  pages = {173},
  author = {Aritomo Shinozaki and Yoshitsugu Oono},
  title = {Asymptotic form factor for spinodal decomposition in three-space},
  journal = {Phys. Rev. Lett.}
}

@article{VanKampen1981,
  doi = {10.1007/bf01007642},
  year = {1981},
  month = {January},
  publisher = {Springer Science and Business Media {LLC}},
  volume = {24},
  number = {1},
  pages = {175},
  author = {N. G. van Kampen},
  title = {It{\^{o}} versus Stratonovich},
  journal = {J. Stat. Phys.}
}

@article{Nicholson2023,
  title = {Quantifying Rare Events in Stochastic Reaction-Diffusion Dynamics Using Tensor Networks},
  author = {Nicholson, Schuyler B. and Gingrich, Todd R.},
  journal = {Phys. Rev. X},
  volume = {13},
  issue = {4},
  pages = {041006},
  numpages = {25},
  year = {2023},
  month = {Oct},
  publisher = {American Physical Society},
  doi = {10.1103/PhysRevX.13.041006}
}

@article{Vellela2009,
  author = {Vellela, Melissa and Qian, Hong},
  title = {Stochastic dynamics and non-equilibrium thermodynamics of a bistable chemical system: the Schlögl model revisited},
  journal = {Journal of The Royal Society Interface},
  volume = {6},
  number = {39},
  pages = {925-940},
  year = {2009},
  doi = {10.1098/rsif.2008.0476}
}

@article{Fritz2020,
  title = {Stochastic thermodynamics of chemical reactions coupled to finite reservoirs: A case study for the Brusselator},
  volume = {152},
  issn = {1089-7690},
  doi = {10.1063/5.0006115},
  number = {23},
  journal = {The Journal of Chemical Physics},
  publisher = {AIP Publishing},
  author = {Fritz, Jonas H. and Nguyen, Basile and Seifert, Udo},
  year = {2020},
  month = {June}
}