skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

This content will become publicly available on December 19, 2020

Title: Nonequilibrium physics in biology

Authors:
; ; ; ORCiD logo
Publication Date:
Sponsoring Org.:
USDOE
OSTI Identifier:
1580187
Grant/Contract Number:  
SC0018420; SC0019185
Resource Type:
Publisher's Accepted Manuscript
Journal Name:
Reviews of Modern Physics
Additional Journal Information:
Journal Name: Reviews of Modern Physics Journal Volume: 91 Journal Issue: 4; Journal ID: ISSN 0034-6861
Publisher:
American Physical Society
Country of Publication:
United States
Language:
English

Citation Formats

Fang, Xiaona, Kruse, Karsten, Lu, Ting, and Wang, Jin. Nonequilibrium physics in biology. United States: N. p., 2019. Web. doi:10.1103/RevModPhys.91.045004.
Fang, Xiaona, Kruse, Karsten, Lu, Ting, & Wang, Jin. Nonequilibrium physics in biology. United States. doi:10.1103/RevModPhys.91.045004.
Fang, Xiaona, Kruse, Karsten, Lu, Ting, and Wang, Jin. Fri . "Nonequilibrium physics in biology". United States. doi:10.1103/RevModPhys.91.045004.
@article{osti_1580187,
title = {Nonequilibrium physics in biology},
author = {Fang, Xiaona and Kruse, Karsten and Lu, Ting and Wang, Jin},
abstractNote = {},
doi = {10.1103/RevModPhys.91.045004},
journal = {Reviews of Modern Physics},
number = 4,
volume = 91,
place = {United States},
year = {2019},
month = {12}
}

Journal Article:
Free Publicly Available Full Text
This content will become publicly available on December 19, 2020
Publisher's Version of Record

Save / Share:

Works referenced in this record:

Spontaneous symmetry breaking in active droplets provides a generic route to motility
journal, July 2012

  • Tjhung, E.; Marenduzzo, D.; Cates, M. E.
  • Proceedings of the National Academy of Sciences, Vol. 109, Issue 31
  • DOI: 10.1073/pnas.1200843109

Integrative Analysis of Cell Cycle Control in Budding Yeast
journal, August 2004

  • Chen, Katherine C.; Calzone, Laurence; Csikasz-Nagy, Attila
  • Molecular Biology of the Cell, Vol. 15, Issue 8
  • DOI: 10.1091/mbc.e03-11-0794

Modeling crawling cell movement on soft engineered substrates
journal, January 2014

  • Löber, Jakob; Ziebert, Falko; Aranson, Igor S.
  • Soft Matter, Vol. 10, Issue 9
  • DOI: 10.1039/C3SM51597D

Photosynthetic reaction center as a quantum heat engine
journal, January 2013

  • Dorfman, K. E.; Voronine, D. V.; Mukamel, S.
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 8
  • DOI: 10.1073/pnas.1212666110

Electronic resonance with anticorrelated pigment vibrations drives photosynthetic energy transfer outside the adiabatic framework
journal, December 2012

  • Tiwari, Vivek; Peters, William K.; Jonas, David M.
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 4
  • DOI: 10.1073/pnas.1211157110

Control of Development by Altered Localization of a Transcription Factor in B. subtilis
journal, November 1999


Classical and quantum pictures of reaction dynamics in condensed matter: resonances, dephasing, and all that
journal, November 1988

  • Onuchic, Jose Nelson; Wolynes, Peter G.
  • The Journal of Physical Chemistry, Vol. 92, Issue 23
  • DOI: 10.1021/j100334a007

Direct calculation of the tunneling current
journal, June 1971

  • Caroli, C.; Combescot, R.; Nozieres, P.
  • Journal of Physics C: Solid State Physics, Vol. 4, Issue 8
  • DOI: 10.1088/0022-3719/4/8/018

Simpson's Paradox in a Synthetic Microbial System
journal, January 2009


Crossover from ‘mesoscopic’ to ‘universal’ phase for electron transmission in quantum dots
journal, July 2005

  • Avinun-Kalish, M.; Heiblum, M.; Zarchin, O.
  • Nature, Vol. 436, Issue 7050
  • DOI: 10.1038/nature03899

On collisional energy transfer in recombination and dissociation reactions: A Wiener–Hopf problem and the effect of a near elastic peak
journal, December 2008

  • Zhu, Zhaoyan; Marcus, R. A.
  • The Journal of Chemical Physics, Vol. 129, Issue 21
  • DOI: 10.1063/1.3026605

Entanglement of Formation of an Arbitrary State of Two Qubits
journal, March 1998


Fluctuation-dissipation theorem in nonequilibrium steady states
journal, January 2010


Cell Motility Resulting from Spontaneous Polymerization Waves
journal, December 2011


Understanding stochastic simulations of the smallest genetic networks
journal, June 2007

  • Schultz, Daniel; Onuchic, José N.; Wolynes, Peter G.
  • The Journal of Chemical Physics, Vol. 126, Issue 24
  • DOI: 10.1063/1.2741544

A synthetic gene–metabolic oscillator
journal, May 2005

  • Fung, Eileen; Wong, Wilson W.; Suen, Jason K.
  • Nature, Vol. 435, Issue 7038
  • DOI: 10.1038/nature03508

Spontaneous Contractility-Mediated Cortical Flow Generates Cell Migration in Three-Dimensional Environments
journal, September 2011

  • Hawkins, Rhoda J.; Poincloux, Renaud; Bénichou, Olivier
  • Biophysical Journal, Vol. 101, Issue 5
  • DOI: 10.1016/j.bpj.2011.07.038

Germline P Granules Are Liquid Droplets That Localize by Controlled Dissolution/Condensation
journal, May 2009


Self-organization of microtubules and motors
journal, September 1997

  • Ndlec, F. J.; Surrey, T.; Maggs, A. C.
  • Nature, Vol. 389, Issue 6648
  • DOI: 10.1038/38532

A brief history of synthetic biology
journal, April 2014

  • Cameron, D. Ewen; Bashor, Caleb J.; Collins, James J.
  • Nature Reviews Microbiology, Vol. 12, Issue 5
  • DOI: 10.1038/nrmicro3239

α-Catenin Is a Molecular Switch that Binds E-Cadherin-β-Catenin and Regulates Actin-Filament Assembly
journal, December 2005


A synthetic Escherichia coli predator–prey ecosystem
journal, January 2008

  • Balagaddé, Frederick K.; Song, Hao; Ozaki, Jun
  • Molecular Systems Biology, Vol. 4, Issue 1
  • DOI: 10.1038/msb.2008.24

Periodic Lamellipodial Contractions Correlate with Rearward Actin Waves
journal, February 2004


Calculation of classical trajectories with a very large time step: Formalism and numerical examples
journal, November 1996

  • Olender, Roberto; Elber, Ron
  • The Journal of Chemical Physics, Vol. 105, Issue 20
  • DOI: 10.1063/1.472727

Stochastic Liouville, Langevin, Fokker–Planck, and Master Equation Approaches to Quantum Dissipative Systems
journal, August 2006


The physics of cancer: the role of physical interactions and mechanical forces in metastasis
journal, June 2011

  • Wirtz, Denis; Konstantopoulos, Konstantinos; Searson, Peter C.
  • Nature Reviews Cancer, Vol. 11, Issue 7
  • DOI: 10.1038/nrc3080

Epigenetics as a First Exit Problem
journal, January 2002


Origin of Long-Lived Coherences in Light-Harvesting Complexes
journal, June 2012

  • Christensson, Niklas; Kauffmann, Harald F.; Pullerits, Tõnu
  • The Journal of Physical Chemistry B, Vol. 116, Issue 25
  • DOI: 10.1021/jp304649c

Electronic excitation dynamics in multichromophoric systems described via a polaron-representation master equation
journal, October 2011

  • Kolli, Avinash; Nazir, Ahsan; Olaya-Castro, Alexandra
  • The Journal of Chemical Physics, Vol. 135, Issue 15
  • DOI: 10.1063/1.3652227

Spontaneous motion in hierarchically assembled active matter
journal, November 2012

  • Sanchez, Tim; Chen, Daniel T. N.; DeCamp, Stephen J.
  • Nature, Vol. 491, Issue 7424
  • DOI: 10.1038/nature11591

Reciprocal Relations in Irreversible Processes. I.
journal, February 1931


Confinement Stabilizes a Bacterial Suspension into a Spiral Vortex
journal, June 2013


Quantum master equation for electron transport through quantum dots and single molecules
journal, December 2006


Constructing the Energy Landscape for Genetic Switching System Driven by Intrinsic Noise
journal, February 2014


Impulses and Physiological States in Theoretical Models of Nerve Membrane
journal, July 1961


Synthetic microbial communities
journal, April 2014


Quorum Sensing in Bacteria
journal, October 2001


Cell motility driven by actin polymerization
journal, December 1996


Asters, Vortices, and Rotating Spirals in Active Gels of Polar Filaments
journal, February 2004


Quantum Spin Hall Effect
journal, March 2006


A quantitative description of membrane current and its application to conduction and excitation in nerve
journal, August 1952


Phosphorylation Energy Hypothesis: Open Chemical Systems and Their Biological Functions
journal, May 2007


Spontaneous flow transition in active polar gels
journal, May 2005


Separation of Liquid Phases in Giant Vesicles of Ternary Mixtures of Phospholipids and Cholesterol
journal, November 2003


Spiral actin-polymerization waves can generate amoeboidal cell crawling
journal, May 2014


Landscape and Global Stability of Nonadiabatic and Adiabatic Oscillations in a Gene Network
journal, March 2012


Electron Transport in Single Molecules: From Benzene to Graphene
journal, March 2009

  • Chen, F.; Tao, N. J.
  • Accounts of Chemical Research, Vol. 42, Issue 3
  • DOI: 10.1021/ar800199a

Self-Concentration and Large-Scale Coherence in Bacterial Dynamics
journal, August 2004


Simultaneous Measurements of Electronic Conduction and Raman Response in Molecular Junctions
journal, March 2008

  • Ward, Daniel R.; Halas, Naomi J.; Ciszek, Jacob W.
  • Nano Letters, Vol. 8, Issue 3
  • DOI: 10.1021/nl073346h

Active torque generation by the actomyosin cell cortex drives left–right symmetry breaking
journal, December 2014

  • Naganathan, Sundar Ram; Fürthauer, Sebastian; Nishikawa, Masatoshi
  • eLife, Vol. 3
  • DOI: 10.7554/eLife.04165

Hydrodynamics of soft active matter
journal, July 2013


Active contraction of microtubule networks
journal, December 2015

  • Foster, Peter J.; Fürthauer, Sebastian; Shelley, Michael J.
  • eLife, Vol. 4
  • DOI: 10.7554/eLife.10837

Active gel model of amoeboid cell motility
journal, February 2013


Engineering microbial consortia: a new frontier in synthetic biology
journal, September 2008


Tunability and Noise Dependence in Differentiation Dynamics
journal, March 2007


Negative autoregulation linearizes the dose-response and suppresses the heterogeneity of gene expression
journal, March 2009

  • Nevozhay, D.; Adams, R. M.; Murphy, K. F.
  • Proceedings of the National Academy of Sciences, Vol. 106, Issue 13
  • DOI: 10.1073/pnas.0809901106

Topology and dynamics of active nematic vesicles
journal, September 2014


Entropy production fluctuation theorem and the nonequilibrium work relation for free energy differences
journal, September 1999


Contraction-Driven Cell Motility
journal, September 2013


Potential landscape and flux framework of nonequilibrium networks: Robustness, dissipation, and coherence of biochemical oscillations
journal, August 2008

  • Wang, J.; Xu, L.; Wang, E.
  • Proceedings of the National Academy of Sciences, Vol. 105, Issue 34
  • DOI: 10.1073/pnas.0800579105

Principles of maximum entropy and maximum caliber in statistical physics
journal, July 2013


A general method for numerically simulating the stochastic time evolution of coupled chemical reactions
journal, December 1976


Viscous-Fingering-Like Instability of Cell Fragments
journal, June 2008


Network theory of microscopic and macroscopic behavior of master equation systems
journal, October 1976


Stochastic Gene Expression in a Single Cell
journal, August 2002


Prediction and measurement of an autoregulatory genetic module
journal, June 2003

  • Isaacs, F. J.; Hasty, J.; Cantor, C. R.
  • Proceedings of the National Academy of Sciences, Vol. 100, Issue 13
  • DOI: 10.1073/pnas.1332628100

Entropy Production along a Stochastic Trajectory and an Integral Fluctuation Theorem
journal, July 2005


Active gels: dynamics of patterning and self-organization
journal, December 2006


Polar patterns of driven filaments
journal, September 2010

  • Schaller, Volker; Weber, Christoph; Semmrich, Christine
  • Nature, Vol. 467, Issue 7311
  • DOI: 10.1038/nature09312

On the spontaneous collective motion of active matter
journal, August 2011

  • Wang, S.; Wolynes, P. G.
  • Proceedings of the National Academy of Sciences, Vol. 108, Issue 37
  • DOI: 10.1073/pnas.1112034108

Intra-tumour heterogeneity: a looking glass for cancer?
journal, April 2012

  • Marusyk, Andriy; Almendro, Vanessa; Polyak, Kornelia
  • Nature Reviews Cancer, Vol. 12, Issue 5
  • DOI: 10.1038/nrc3261

Fluctuations and Irreversible Processes
journal, September 1953


Polar location of the chemoreceptor complex in the Escherichia coli cell
journal, March 1993


Bidirectional cooperative motion of myosin-II motors on actin tracks with randomly alternating polarities
journal, January 2009

  • Gilboa, Barak; Gillo, David; Farago, Oded
  • Soft Matter, Vol. 5, Issue 11
  • DOI: 10.1039/b823400k

The fluctuation-dissipation theorem
journal, January 1966


A fast, robust and tunable synthetic gene oscillator
journal, October 2008

  • Stricker, Jesse; Cookson, Scott; Bennett, Matthew R.
  • Nature, Vol. 456, Issue 7221
  • DOI: 10.1038/nature07389

Transport in molecular states language: Generalized quantum master equation approach
journal, May 2009


Anomalous Quantum Hall Effect: An Incompressible Quantum Fluid with Fractionally Charged Excitations
journal, May 1983


Yeast kinesin-8 depolymerizes microtubules in a length-dependent manner
journal, August 2006

  • Varga, Vladimir; Helenius, Jonne; Tanaka, Kozo
  • Nature Cell Biology, Vol. 8, Issue 9
  • DOI: 10.1038/ncb1462

Intrinsic and extrinsic contributions to stochasticity in gene expression
journal, September 2002

  • Swain, P. S.; Elowitz, M. B.; Siggia, E. D.
  • Proceedings of the National Academy of Sciences, Vol. 99, Issue 20
  • DOI: 10.1073/pnas.162041399

Quantum coherence in photosynthesis for efficient solar-energy conversion
journal, July 2014

  • Romero, Elisabet; Augulis, Ramunas; Novoderezhkin, Vladimir I.
  • Nature Physics, Vol. 10, Issue 9
  • DOI: 10.1038/nphys3017

Experimental Test of the Fluctuation Theorem for a Driven Two-Level System with Time-Dependent Rates
journal, May 2005


Symmetry and the energy landscapes of biomolecules
journal, December 1996


Generic theory of active polar gels: a paradigm for cytoskeletal dynamics
journal, January 2005


A mutant of the motor protein kinesin that moves in both directions on microtubules
journal, August 2000

  • Endow, Sharyn A.; Higuchi, Hideo
  • Nature, Vol. 406, Issue 6798
  • DOI: 10.1038/35022617

Theory of Mitotic Spindle Oscillations
journal, March 2005


Density functional calculations of nanoscale conductance
journal, February 2008


Self-regulating gene: An exact solution
journal, November 2005


Two competing orientation patterns explain experimentally observed anomalies in growing actin networks
journal, March 2010

  • Weichsel, J.; Schwarz, U. S.
  • Proceedings of the National Academy of Sciences, Vol. 107, Issue 14
  • DOI: 10.1073/pnas.0913730107

Generalized Fluctuation-Dissipation Theorem for Steady-State Systems
journal, August 2009


Velocity Correlations in an Active Nematic
journal, September 2013


Synthetic microbial ecosystems: an exciting tool to understand and apply microbial communities: Synthetic microbial ecosystems
journal, December 2013

  • De Roy, Karen; Marzorati, Massimo; Van den Abbeele, Pieter
  • Environmental Microbiology, Vol. 16, Issue 6
  • DOI: 10.1111/1462-2920.12343

Non-classicality of the molecular vibrations assisting exciton energy transfer at room temperature
journal, January 2014

  • O’Reilly, Edward J.; Olaya-Castro, Alexandra
  • Nature Communications, Vol. 5, Issue 1
  • DOI: 10.1038/ncomms4012

Periodic Migration in a Physical Model of Cells on Micropatterns
journal, October 2013


Protein Self-Organization: Lessons from the Min System
journal, June 2011


Verification of the Crooks fluctuation theorem and recovery of RNA folding free energies
journal, September 2005


Modeling molecular motors
journal, October 1997


Computational Model for Cell Morphodynamics
journal, September 2010


Adiabatic and Non-Adiabatic Non-Equilibrium Stochastic Dynamics of Single Regulating Genes
journal, February 2011

  • Feng, Haidong; Han, Bo; Wang, Jin
  • The Journal of Physical Chemistry B, Vol. 115, Issue 5
  • DOI: 10.1021/jp109036y

Topology, structures, and energy landscapes of human chromosomes
journal, April 2015

  • Zhang, Bin; Wolynes, Peter G.
  • Proceedings of the National Academy of Sciences, Vol. 112, Issue 19
  • DOI: 10.1073/pnas.1506257112

Quantitative model for gene regulation by lambda phage repressor.
journal, February 1982

  • Ackers, G. K.; Johnson, A. D.; Shea, M. A.
  • Proceedings of the National Academy of Sciences, Vol. 79, Issue 4
  • DOI: 10.1073/pnas.79.4.1129

Intracellular Mechanochemical Waves in an Active Poroelastic Model
journal, March 2013


The Hallmarks of Cancer
journal, January 2000


Vibronic Enhancement of Exciton Sizes and Energy Transport in Photosynthetic Complexes
journal, February 2011

  • Womick, Jordan M.; Moran, Andrew M.
  • The Journal of Physical Chemistry B, Vol. 115, Issue 6
  • DOI: 10.1021/jp106713q

Induction of Pluripotent Stem Cells from Mouse Embryonic and Adult Fibroblast Cultures by Defined Factors
journal, August 2006


Single-molecule chemistry
journal, December 2002


Control of Relative Tunneling Rates in Single Molecule Bipolar Electron Transport
journal, December 2004


Local dispersal promotes biodiversity in a real-life game of rock–paper–scissors
journal, July 2002

  • Kerr, Benjamin; Riley, Margaret A.; Feldman, Marcus W.
  • Nature, Vol. 418, Issue 6894
  • DOI: 10.1038/nature00823

Effects of Adhesion Dynamics and Substrate Compliance on the Shape and Motility of Crawling Cells
journal, May 2013


Coherent Multidimensional Optical Spectroscopy of Excitons in Molecular Aggregates; Quasiparticle versus Supermolecule Perspectives
journal, June 2009

  • Abramavicius, Darius; Palmieri, Benoit; Voronine, Dmitri V.
  • Chemical Reviews, Vol. 109, Issue 6
  • DOI: 10.1021/cr800268n

Stochastic thermodynamics, fluctuation theorems and molecular machines
journal, November 2012


Evolutionary cycling in predator-prey interactions: population dynamics and the red queen
journal, September 1995

  • Dieckmann, Ulf; Marrow, Paul; Law, Richard
  • Journal of Theoretical Biology, Vol. 176, Issue 1
  • DOI: 10.1006/jtbi.1995.0179

Defect Annihilation and Proliferation in Active Nematics
journal, May 2013


Contractility and retrograde flow in lamellipodium motion
journal, June 2006


Theory of multichromophoric coherent resonance energy transfer: A polaronic quantum master equation approach
journal, July 2011

  • Jang, Seogjoo
  • The Journal of Chemical Physics, Vol. 135, Issue 3
  • DOI: 10.1063/1.3608914

Water Dynamics:  Fluctuation, Relaxation, and Chemical Reactions in Hydrogen Bond Network Rearrangement
journal, September 1999

  • Ohmine, Iwao; Saito, Shinji
  • Accounts of Chemical Research, Vol. 32, Issue 9
  • DOI: 10.1021/ar970161g

The Local Structure of Turbulence in Incompressible Viscous Fluid for Very Large Reynolds Numbers
journal, July 1991

  • Kolmogorov, A. N.
  • Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, Vol. 434, Issue 1890
  • DOI: 10.1098/rspa.1991.0075

The Role of Mechanical Forces in Plant Morphogenesis
journal, June 2011


Dissipation of Energy in the Locally Isotropic Turbulence
journal, July 1991

  • Kolmogorov, A. N.
  • Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, Vol. 434, Issue 1890
  • DOI: 10.1098/rspa.1991.0076

Coherence Dynamics in Photosynthesis: Protein Protection of Excitonic Coherence
journal, June 2007


Fluid flows created by swimming bacteria drive self-organization in confined suspensions
journal, June 2014

  • Lushi, Enkeleida; Wioland, Hugo; Goldstein, Raymond E.
  • Proceedings of the National Academy of Sciences, Vol. 111, Issue 27
  • DOI: 10.1073/pnas.1405698111

Persistent, directional motility of cells and cytoplasmic fragments in the absence of microtubules
journal, July 1984

  • Euteneuer, Ursula; Schliwa, Manfred
  • Nature, Vol. 310, Issue 5972
  • DOI: 10.1038/310058a0

Kinetic paths, time scale, and underlying landscapes: A path integral framework to study global natures of nonequilibrium systems and networks
journal, September 2010

  • Wang, Jin; Zhang, Kun; Wang, Erkwang
  • The Journal of Chemical Physics, Vol. 133, Issue 12
  • DOI: 10.1063/1.3478547

Synthetic cooperation in engineered yeast populations
journal, January 2007

  • Shou, W.; Ram, S.; Vilar, J. M. G.
  • Proceedings of the National Academy of Sciences, Vol. 104, Issue 6
  • DOI: 10.1073/pnas.0610575104

A synchronized quorum of genetic clocks
journal, January 2010

  • Danino, Tal; Mondragón-Palomino, Octavio; Tsimring, Lev
  • Nature, Vol. 463, Issue 7279
  • DOI: 10.1038/nature08753

XMAP215 activity sets spindle length by controlling the total mass of spindle microtubules
journal, August 2013

  • Reber, Simone B.; Baumgart, Johannes; Widlund, Per O.
  • Nature Cell Biology, Vol. 15, Issue 9
  • DOI: 10.1038/ncb2834

Experimental observation of the quantum Hall effect and Berry's phase in graphene
journal, November 2005

  • Zhang, Yuanbo; Tan, Yan-Wen; Stormer, Horst L.
  • Nature, Vol. 438, Issue 7065, p. 201-204
  • DOI: 10.1038/nature04235

Physics of adherent cells
journal, August 2013


Adiabaticity of electron transfer at an electrode
journal, February 1987

  • Morgan, John D.; Wolynes, Peter G.
  • The Journal of Physical Chemistry, Vol. 91, Issue 4
  • DOI: 10.1021/j100288a023

Selection and Covariance
journal, August 1970


More Is Different
journal, August 1972


Nanoclusters of GPI-Anchored Proteins Are Formed by Cortical Actin-Driven Activity
journal, December 2008


Probability landscape of heritable and robust epigenetic state of lysogeny in phage lambda
journal, October 2010

  • Cao, Y.; Lu, H. -M.; Liang, J.
  • Proceedings of the National Academy of Sciences, Vol. 107, Issue 43
  • DOI: 10.1073/pnas.1001455107

Thermodynamics with Continuous Information Flow
journal, July 2014


Dynamic structures in Escherichia coli: Spontaneous formation of MinE rings and MinD polar zones
journal, October 2003

  • Huang, K. C.; Meir, Y.; Wingreen, N. S.
  • Proceedings of the National Academy of Sciences, Vol. 100, Issue 22
  • DOI: 10.1073/pnas.2135445100

Coexisting Liquid Phases Underlie Nucleolar Subcompartments
journal, June 2016


Stochastic model for Soj relocation dynamics in Bacillus subtilis
journal, July 2005

  • Doubrovinski, K.; Howard, M.
  • Proceedings of the National Academy of Sciences, Vol. 102, Issue 28
  • DOI: 10.1073/pnas.0500529102

Equilibrium free-energy differences from nonequilibrium measurements: A master-equation approach
journal, November 1997


Pattern formation of microtubules and motors: Inelastic interaction of polar rods
journal, May 2005


Spontaneous Motility of Actin Lamellar Fragments
journal, February 2013


Instabilities and oscillations in isotropic active gels
journal, January 2011

  • Banerjee, Shiladitya; Marchetti, M. Cristina
  • Soft Matter, Vol. 7, Issue 2
  • DOI: 10.1039/C0SM00494D

An Adhesion-Dependent Switch between Mechanisms That Determine Motile Cell Shape
journal, May 2011


Pattern Formation in Active Fluids
journal, January 2011


Vibronic Resonances Facilitate Excited-State Coherence in Light-Harvesting Proteins at Room Temperature
journal, October 2015

  • Novelli, Fabio; Nazir, Ahsan; Richards, Gethin H.
  • The Journal of Physical Chemistry Letters, Vol. 6, Issue 22
  • DOI: 10.1021/acs.jpclett.5b02058

An excitable gene regulatory circuit induces transient cellular differentiation
journal, March 2006

  • Süel, Gürol M.; Garcia-Ojalvo, Jordi; Liberman, Louisa M.
  • Nature, Vol. 440, Issue 7083
  • DOI: 10.1038/nature04588

Physical Properties Determining Self-Organization of Motors and Microtubules
journal, May 2001


Spontaneous segregation of self-propelled particles with different motilities
journal, January 2012

  • McCandlish, Samuel R.; Baskaran, Aparna; Hagan, Michael F.
  • Soft Matter, Vol. 8, Issue 8
  • DOI: 10.1039/c2sm06960a

Emergent cellular self-organization and mechanosensation initiate follicle pattern in the avian skin
journal, July 2017

  • Shyer, Amy E.; Rodrigues, Alan R.; Schroeder, Grant G.
  • Science, Vol. 357, Issue 6353
  • DOI: 10.1126/science.aai7868

Fully developed turbulence and statistical mechanics
journal, January 1978


Direct, high-resolution measurement of furrow stiffening during division of adherent cells
journal, May 2001

  • Matzke, Rainer; Jacobson, Ken; Radmacher, Manfred
  • Nature Cell Biology, Vol. 3, Issue 6
  • DOI: 10.1038/35078583

Imaging coexisting fluid domains in biomembrane models coupling curvature and line tension
journal, October 2003

  • Baumgart, Tobias; Hess, Samuel T.; Webb, Watt W.
  • Nature, Vol. 425, Issue 6960
  • DOI: 10.1038/nature02013

Neural networks and physical systems with emergent collective computational abilities.
journal, April 1982

  • Hopfield, J. J.
  • Proceedings of the National Academy of Sciences, Vol. 79, Issue 8
  • DOI: 10.1073/pnas.79.8.2554

Chemical and Electrochemical Electron-Transfer Theory
journal, October 1964


The Taylor–Couette motor: spontaneous flows of active polar fluids between two coaxial cylinders
journal, February 2012


Asymmetry between pushing and pulling for crawling cells
journal, February 2013


Nanomechanical oscillations in a single-C60 transistor
journal, September 2000

  • Park, Hongkun; Park, Jiwoong; Lim, Andrew K. L.
  • Nature, Vol. 407, Issue 6800
  • DOI: 10.1038/35024031

Emergent genetic oscillations in a synthetic microbial consortium
journal, August 2015


A synthetic oscillatory network of transcriptional regulators
journal, January 2000

  • Elowitz, Michael B.; Leibler, Stanislas
  • Nature, Vol. 403, Issue 6767
  • DOI: 10.1038/35002125

Conductance of a Molecular Junction
journal, October 1997


Construction of a genetic toggle switch in Escherichia coli
journal, January 2000

  • Gardner, Timothy S.; Cantor, Charles R.; Collins, James J.
  • Nature, Vol. 403, Issue 6767
  • DOI: 10.1038/35002131

Ever-fluctuating single enzyme molecules: Michaelis-Menten equation revisited
journal, December 2005

  • English, Brian P.; Min, Wei; van Oijen, Antoine M.
  • Nature Chemical Biology, Vol. 2, Issue 2
  • DOI: 10.1038/nchembio759

Domain Shapes and Patterns: The Phenomenology of Modulated Phases
journal, January 1995


The role of non-equilibrium vibrational structures in electronic coherence and recoherence in pigment–protein complexes
journal, January 2013

  • Chin, A. W.; Prior, J.; Rosenbach, R.
  • Nature Physics, Vol. 9, Issue 2
  • DOI: 10.1038/nphys2515

Multiscale Polar Theory of Microtubule and Motor-Protein Assemblies
journal, January 2015


Cellular Decision Making and Biological Noise: From Microbes to Mammals
journal, March 2011


Nonequilibrium thermal entanglement
journal, March 2007


Cell surface mechanics and the control of cell shape, tissue patterns and morphogenesis
journal, August 2007

  • Lecuit, Thomas; Lenne, Pierre-François
  • Nature Reviews Molecular Cell Biology, Vol. 8, Issue 8
  • DOI: 10.1038/nrm2222

A Quantitative Analysis of Contractility in Active Cytoskeletal Protein Networks
journal, April 2008


The Kinesin-Related Protein MCAK Is a Microtubule Depolymerase that Forms an ATP-Hydrolyzing Complex at Microtubule Ends
journal, February 2003


Snowdrift game dynamics and facultative cheating in yeast
journal, April 2009

  • Gore, Jeff; Youk, Hyun; van Oudenaarden, Alexander
  • Nature, Vol. 459, Issue 7244
  • DOI: 10.1038/nature07921

Reaction-Controlled Morphology of Phase-Separating Mixtures
journal, March 1995


Irreversibility and Heat Generation in the Computing Process
journal, July 1961

  • Landauer, R.
  • IBM Journal of Research and Development, Vol. 5, Issue 3
  • DOI: 10.1147/rd.53.0183

Enhanced flow in carbon nanotubes
journal, November 2005

  • Majumder, Mainak; Chopra, Nitin; Andrews, Rodney
  • Nature, Vol. 438, Issue 7064
  • DOI: 10.1038/438044a

Vibrational Energy Flow and Chemical Reactions
journal, April 2004

  • Gruebele, M.; Wolynes, P. G.
  • Accounts of Chemical Research, Vol. 37, Issue 4, p. 261-267
  • DOI: 10.1021/ar030230t

Meso-scale turbulence in living fluids
journal, August 2012

  • Wensink, H. H.; Dunkel, J.; Heidenreich, S.
  • Proceedings of the National Academy of Sciences, Vol. 109, Issue 36
  • DOI: 10.1073/pnas.1202032109

Stochastic thermodynamics: principles and perspectives
journal, January 2008


Nonequilibrium Equality for Free Energy Differences
journal, April 1997


Dynamics of the dissipative two-state system
journal, January 1987

  • Leggett, A. J.; Chakravarty, S.; Dorsey, A. T.
  • Reviews of Modern Physics, Vol. 59, Issue 1
  • DOI: 10.1103/RevModPhys.59.1

Hallmarks of Cancer: The Next Generation
journal, March 2011


Enzyme Kinetics, Past and Present
journal, December 2013


Interactions Between the Immune System and Cancer: A Brief Review of Non-spatial Mathematical Models
journal, March 2010

  • Eftimie, Raluca; Bramson, Jonathan L.; Earn, David J. D.
  • Bulletin of Mathematical Biology, Vol. 73, Issue 1
  • DOI: 10.1007/s11538-010-9526-3

Quantum Theory, the Church-Turing Principle and the Universal Quantum Computer
journal, July 1985

  • Deutsch, D.
  • Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, Vol. 400, Issue 1818
  • DOI: 10.1098/rspa.1985.0070

Lessons from hydrodynamic turbulence
journal, April 2006

  • Falkovich, Gregory; Sreenivasan, Katepalli R.
  • Physics Today, Vol. 59, Issue 4
  • DOI: 10.1063/1.2207037

Model for self-polarization and motility of keratocyte fragments
journal, September 2011

  • Ziebert, Falko; Swaminathan, Sumanth; Aranson, Igor S.
  • Journal of The Royal Society Interface, Vol. 9, Issue 70
  • DOI: 10.1098/rsif.2011.0433

Growth Velocities of Branched Actin Networks
journal, May 2003


Dynamic instability of microtubule growth
journal, November 1984

  • Mitchison, Tim; Kirschner, Marc
  • Nature, Vol. 312, Issue 5991
  • DOI: 10.1038/312237a0

Origin of long-lived oscillations in 2D-spectra of a quantum vibronic model: Electronic versus vibrational coherence
journal, December 2013

  • Plenio, M. B.; Almeida, J.; Huelga, S. F.
  • The Journal of Chemical Physics, Vol. 139, Issue 23
  • DOI: 10.1063/1.4846275

Tug-of-war as a cooperative mechanism for bidirectional cargo transport by molecular motors
journal, March 2008

  • Muller, M. J. I.; Klumpp, S.; Lipowsky, R.
  • Proceedings of the National Academy of Sciences, Vol. 105, Issue 12
  • DOI: 10.1073/pnas.0706825105

Spatial Regulators for Bacterial Cell Division Self-Organize into Surface Waves in Vitro
journal, May 2008


Design principles of biochemical oscillators
journal, October 2008

  • Novák, Béla; Tyson, John J.
  • Nature Reviews Molecular Cell Biology, Vol. 9, Issue 12
  • DOI: 10.1038/nrm2530

Coupling actin flow, adhesion, and morphology in a computational cell motility model
journal, April 2012

  • Shao, D.; Levine, H.; Rappel, W. -J.
  • Proceedings of the National Academy of Sciences, Vol. 109, Issue 18
  • DOI: 10.1073/pnas.1203252109

The TetR Family of Transcriptional Repressors
journal, June 2005

  • Ramos, J. L.; Martinez-Bueno, M.; Molina-Henares, A. J.
  • Microbiology and Molecular Biology Reviews, Vol. 69, Issue 2
  • DOI: 10.1128/MMBR.69.2.326-356.2005

The middle way
journal, January 2000

  • Laughlin, R. B.; Pines, D.; Schmalian, J.
  • Proceedings of the National Academy of Sciences, Vol. 97, Issue 1
  • DOI: 10.1073/pnas.97.1.32

Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation
journal, June 2003

  • Elena, Santiago F.; Lenski, Richard E.
  • Nature Reviews Genetics, Vol. 4, Issue 6
  • DOI: 10.1038/nrg1088

Nonequilibrium statistical mechanics of mixtures of particles in contact with different thermostats
journal, September 2015