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Title: Nonequilibrium physics in biology

Authors:
; ; ; ORCiD logo
Publication Date:
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER); National Natural Science Foundation of China (NNSFC); Ministry of Science and Technology of the People's Republic of China (MOST); National Science Foundation (NSF); US Department of the Navy, Office of Naval Research (ONR); Deutsche Forschungsgemeinschaft (DFG), Bonn (Germany); National Institutes of Health (NIH)
OSTI Identifier:
1580187
Grant/Contract Number:  
SC0018420; SC0019185; NSFC-91430217; 2016YFA0203200; 2013YQ170585; N000141622525; NSF-76066; NSF-1808474; NIH-1R01GM124177-01A1
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 (APS)
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
Publisher's Version of Record
DOI: 10.1103/RevModPhys.91.045004

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Cited by: 2 works
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Works referenced in this record:

Robustness of circadian rhythms with respect to molecular noise
journal, January 2002

  • Gonze, D.; Halloy, J.; Goldbeter, A.
  • Proceedings of the National Academy of Sciences, Vol. 99, Issue 2
  • DOI: 10.1073/pnas.022628299

Stochastic formulation of ecological models and their applications
journal, June 2012


Dynamic control of positional information in the early Drosophila embryo
journal, July 2004

  • Jaeger, Johannes; Surkova, Svetlana; Blagov, Maxim
  • Nature, Vol. 430, Issue 6997
  • DOI: 10.1038/nature02678

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

Actin kinetics shapes cortical network structure and mechanics
journal, April 2016

  • Fritzsche, Marco; Erlenkämper, Christoph; Moeendarbary, Emad
  • Science Advances, Vol. 2, Issue 4
  • DOI: 10.1126/sciadv.1501337

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


Development of Genetic Circuitry Exhibiting Toggle Switch or Oscillatory Behavior in Escherichia coli
journal, May 2003


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

SYSTEMS BIOLOGY: Attractors and Democratic Dynamics
journal, February 2009


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


An actin molecular treadmill and myosins maintain stereocilia functional architecture and self-renewal
journal, March 2004

  • Rzadzinska, Agnieszka K.; Schneider, Mark E.; Davies, Caroline
  • The Journal of Cell Biology, Vol. 164, Issue 6
  • DOI: 10.1083/jcb.200310055

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


Temporal self-organization of the cyclin/Cdk network driving the mammalian cell cycle
journal, December 2009

  • Gerard, C.; Goldbeter, A.
  • Proceedings of the National Academy of Sciences, Vol. 106, Issue 51
  • DOI: 10.1073/pnas.0903827106

Switches in Bacteriophage Lambda Development
journal, December 2005


Cell Motility Resulting from Spontaneous Polymerization Waves
journal, December 2011


Ultrafast Dynamics of Nonequilibrium Electron Transfer in Photoinduced Redox Cycle: Solvent Mediation and Conformation Flexibility
journal, July 2012

  • Kao, Ya-Ting; Guo, Xunmin; Yang, Yi
  • The Journal of Physical Chemistry B, Vol. 116, Issue 30
  • DOI: 10.1021/jp304518f

A new mechanism of stem cell differentiation through slow binding/unbinding of regulators to genes
journal, August 2012

  • Feng, Haidong; Wang, Jin
  • Scientific Reports, Vol. 2, Issue 1
  • DOI: 10.1038/srep00550

A Motor-Driven Mechanism for Cell-Length Sensing
journal, June 2012


Uncovering the mechanisms of Caenorhabditis elegans ageing from global quantification of the underlying landscape
journal, November 2016


Modelling the fission yeast cell cycle
journal, January 2004

  • Sveiczer, A.
  • Briefings in Functional Genomics and Proteomics, Vol. 2, Issue 4
  • DOI: 10.1093/bfgp/2.4.298

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

Mutation Rate Evolution in Replicator Dynamics
journal, September 2012


Head to tail polymerization of actin
journal, November 1976


Actin Depolymerizing Factor (ADF/Cofilin) Enhances the Rate of Filament Turnover: Implication in Actin-based Motility
journal, March 1997

  • Carlier, Marie-France; Laurent, Valérie; Santolini, Jérôme
  • The Journal of Cell Biology, Vol. 136, Issue 6
  • DOI: 10.1083/jcb.136.6.1307

Furrow Constriction in Animal Cell Cytokinesis
journal, January 2014


Nonequilibrium entanglement and noise in coupled qubits
journal, January 2007


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

Phosphatidylserine is polarized and required for proper Cdc42 localization and for development of cell polarity
journal, October 2011

  • Fairn, Gregory D.; Hermansson, Martin; Somerharju, Pentti
  • Nature Cell Biology, Vol. 13, Issue 12
  • DOI: 10.1038/ncb2351

Steady quantum coherence in non-equilibrium environment
journal, September 2015


Stability and Instability in the Lysogenic State of Phage Lambda
journal, September 2010

  • Little, J. W.; Michalowski, C. B.
  • Journal of Bacteriology, Vol. 192, Issue 22
  • DOI: 10.1128/JB.00726-10

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


Disordered actomyosin networks are sufficient to produce cooperative and telescopic contractility
journal, August 2016

  • Linsmeier, Ian; Banerjee, Shiladitya; Oakes, Patrick W.
  • Nature Communications, Vol. 7, Issue 1
  • DOI: 10.1038/ncomms12615

A Multiple-Choice Task with Changes of Mind
journal, August 2012


Path integral solutions of stochastic equations for nonlinear irreversible processes: The uniqueness of the thermodynamic Lagrangian
journal, July 1981

  • Hunt, Katharine L. C.; Ross, John
  • The Journal of Chemical Physics, Vol. 75, Issue 2
  • DOI: 10.1063/1.442098

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

Molecular level stochastic model for competence cycles in Bacillus subtilis
journal, October 2007

  • Schultz, D.; Ben Jacob, E.; Onuchic, J. N.
  • Proceedings of the National Academy of Sciences, Vol. 104, Issue 45
  • DOI: 10.1073/pnas.0707965104

Dynamics of microtubule asters in microfabricated chambers: The role of catastrophes
journal, December 2002

  • Faivre-Moskalenko, C.; Dogterom, M.
  • Proceedings of the National Academy of Sciences, Vol. 99, Issue 26
  • DOI: 10.1073/pnas.252407099

Synchronous behavior of spontaneous oscillations of sarcomeres in skeletal myofibrils under isotonic conditions
journal, April 1996


Robust ecological pattern formation induced by demographic noise
journal, September 2009


Reconstitution of Pole-to-Pole Oscillations of Min Proteins in Microengineered Polydimethylsiloxane Compartments
journal, November 2012

  • Zieske, Katja; Schwille, Petra
  • Angewandte Chemie International Edition, Vol. 52, Issue 1
  • DOI: 10.1002/anie.201207078

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


Programming the group behaviors of bacterial communities with synthetic cellular communication
journal, November 2014


Antenna Mechanism of Length Control of Actin Cables
journal, June 2015


Determining the Stability of Genetic Switches: Explicitly Accounting for mRNA Noise
journal, June 2011


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

Polar actomyosin contractility destabilizes the position of the cytokinetic furrow
journal, August 2011

  • Sedzinski, Jakub; Biro, Maté; Oswald, Annelie
  • Nature, Vol. 476, Issue 7361
  • DOI: 10.1038/nature10286

The Evolutionary Interaction Among Species: Selection, Escalation, and Coevolution
journal, November 1994


Instability of Spatial Patterns and Its Ambiguous Impact on Species Diversity
journal, July 2008


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


Fluctuation-Dissipation Theorems and Entropy Production in Relaxational Systems
journal, September 1997


Neural circuit dynamics underlying accumulation of time-varying evidence during perceptual decision making
journal, January 2007


Stress Generation and Filament Turnover during Actin Ring Constriction
journal, August 2007


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

On the role of the filament length distribution in the mechanics of semiflexible networks
journal, May 2011


Dynamics of defects in an active nematic layer
journal, November 2013


Epigenetics as a First Exit Problem
journal, January 2002


Hydrodynamics of active permeating gels
journal, September 2011


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

Stochastic gene expression as a many-body problem
journal, February 2003

  • Sasai, M.; Wolynes, P. G.
  • Proceedings of the National Academy of Sciences, Vol. 100, Issue 5
  • DOI: 10.1073/pnas.2627987100

Fisher's ?fundamental theorem? made clear
journal, November 1972


Statistical physics of self-replication
journal, September 2013

  • England, Jeremy L.
  • The Journal of Chemical Physics, Vol. 139, Issue 12
  • DOI: 10.1063/1.4818538

Energy Landscape Reveals That the Budding Yeast Cell Cycle Is a Robust and Adaptive Multi-stage Process
journal, March 2015


Positional Cloning of the Mouse Circadian Clock Gene
journal, May 1997


Potential and flux landscapes quantify the stability and robustness of budding yeast cell cycle network
journal, April 2010

  • Wang, J.; Li, C.; Wang, E.
  • Proceedings of the National Academy of Sciences, Vol. 107, Issue 18
  • DOI: 10.1073/pnas.0910331107

Entanglement in the XX spin chain with an energy current
journal, April 2005


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

Optimal path to epigenetic switching
journal, January 2005

  • Roma, David Marin; O’Flanagan, Ruadhan A.; Ruckenstein, Andrei E.
  • Physical Review E, Vol. 71, Issue 1
  • DOI: 10.1103/PhysRevE.71.011902

Turbulence as a Problem in Non-equilibrium Statistical Mechanics
journal, December 2016


Response of Neurons in the Lateral Intraparietal Area during a Combined Visual Discrimination Reaction Time Task
journal, November 2002


Reconciling taxon senescence with the Red Queen’s hypothesis
journal, November 2017

  • Žliobaitė, Indrė; Fortelius, Mikael; Stenseth, Nils C.
  • Nature, Vol. 552, Issue 7683
  • DOI: 10.1038/nature24656

Boolean Network Model Predicts Cell Cycle Sequence of Fission Yeast
journal, February 2008


Micromechanical Architecture of the Endothelial Cell Cortex
journal, January 2005


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


Limiting Exit Location Distributions in the Stochastic Exit Problem
journal, June 1997


Rapid treadmilling of brain microtubules free of microtubule-associated proteins in vitro and its suppression by tau
journal, October 1999

  • Panda, D.; Miller, H. P.; Wilson, L.
  • Proceedings of the National Academy of Sciences, Vol. 96, Issue 22
  • DOI: 10.1073/pnas.96.22.12459

General Mechanism of Actomyosin Contractility
journal, September 2011


Assembly and positioning of microtubule asters in microfabricated chambers
journal, June 1997

  • Holy, T. E.; Dogterom, M.; Yurke, B.
  • Proceedings of the National Academy of Sciences, Vol. 94, Issue 12
  • DOI: 10.1073/pnas.94.12.6228

Bacterial solutions to multicellularity: a tale of biofilms, filaments and fruiting bodies
journal, January 2014

  • Claessen, Dennis; Rozen, Daniel E.; Kuipers, Oscar P.
  • Nature Reviews Microbiology, Vol. 12, Issue 2
  • DOI: 10.1038/nrmicro3178

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


Changes of Mind in an Attractor Network of Decision-Making
journal, June 2011


An Actin-Based Wave Generator Organizes Cell Motility
journal, August 2007


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


Self-organization and mechanical properties of active filament bundles
journal, May 2003


Dynamics of Actin Waves on Patterned Substrates: A Quantitative Analysis of Circular Dorsal Ruffles
journal, January 2015


Geometry sensing by self-organized protein patterns
journal, September 2012

  • Schweizer, J.; Loose, M.; Bonny, M.
  • Proceedings of the National Academy of Sciences, Vol. 109, Issue 38
  • DOI: 10.1073/pnas.1206953109

Cancer immunoediting: from immunosurveillance to tumor escape
journal, November 2002

  • Dunn, Gavin P.; Bruce, Allen T.; Ikeda, Hiroaki
  • Nature Immunology, Vol. 3, Issue 11
  • DOI: 10.1038/ni1102-991

Designing microbial consortia with defined social interactions
journal, June 2018

  • Kong, Wentao; Meldgin, David R.; Collins, James J.
  • Nature Chemical Biology, Vol. 14, Issue 8
  • DOI: 10.1038/s41589-018-0091-7

Potential and flux field landscape theory. I. Global stability and dynamics of spatially dependent non-equilibrium systems
journal, September 2013

  • Wu, Wei; Wang, Jin
  • The Journal of Chemical Physics, Vol. 139, Issue 12
  • DOI: 10.1063/1.4816376

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


Cytoplasts made from human blood polymorphonuclear leukocytes with or without heat: preservation of both motile function and respiratory burst oxidase activity.
journal, January 1987

  • Malawista, S. E.; Van Blaricom, G.
  • Proceedings of the National Academy of Sciences, Vol. 84, Issue 2
  • DOI: 10.1073/pnas.84.2.454

Emerging of Stochastic Dynamical Equalities and Steady State Thermodynamics from Darwinian Dynamics
journal, May 2008


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


Synthetic microbial communities
journal, April 2014


Stress generation by myosin minifilaments in actin bundles
journal, April 2013


Mapping out Min protein patterns in fully confined fluidic chambers
journal, November 2016


Quorum Sensing in Bacteria
journal, October 2001


Exclusion and Hierarchy of Time Scales Lead to Spatial Segregation of Molecular Motors in Cellular Protrusions
journal, January 2017


Volume of the set of separable states
journal, August 1998

  • Życzkowski, Karol; Horodecki, Paweł; Sanpera, Anna
  • Physical Review A, Vol. 58, Issue 2
  • DOI: 10.1103/PhysRevA.58.883

Anisotropies in cortical tension reveal the physical basis of polarizing cortical flows
journal, September 2010

  • Mayer, Mirjam; Depken, Martin; Bois, Justin S.
  • Nature, Vol. 467, Issue 7315
  • DOI: 10.1038/nature09376

Probing Gene Expression in Live Cells, One Protein Molecule at a Time
journal, March 2006


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


Least dissipation cost as a design principle for robustness and function of cellular networks
journal, March 2008


Actomyosin contraction, aggregation and traveling waves in a treadmilling actin array
journal, April 2016


Genetics of Longevity in Model Organisms: Debates and Paradigm Shifts
journal, February 2013


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


Spontaneous flow transition in active polar gels
journal, May 2005


Monitoring Actin Cortex Thickness in Live Cells
journal, August 2013


Cortical Dynein Controls Microtubule Dynamics to Generate Pulling Forces that Position Microtubule Asters
journal, February 2012


Using hidden Markov models to analyze gene expression time course data
journal, July 2003


Cycling in simple genetic systems
journal, January 1982


Origin of long-lived quantum coherence and excitation dynamics in pigment-protein complexes
journal, November 2016

  • Zhang, Zhedong; Wang, Jin
  • Scientific Reports, Vol. 6, Issue 1
  • DOI: 10.1038/srep37629

Cell fate potentials and switching kinetics uncovered in a classic bistable genetic switch
journal, July 2018


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


Myxobacteria: Moving, Killing, Feeding, and Surviving Together
journal, May 2016

  • Muñoz-Dorado, José; Marcos-Torres, Francisco J.; García-Bravo, Elena
  • Frontiers in Microbiology, Vol. 7
  • DOI: 10.3389/fmicb.2016.00781

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

Pattern Generation in Space and Aspect
journal, March 1985

  • Levin, Simon A.; Segel, Lee A.
  • SIAM Review, Vol. 27, Issue 1
  • DOI: 10.1137/1027002

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

Exploring the Underlying Mechanisms of the Xenopus laevis Embryonic Cell Cycle
journal, January 2018


Non-equilibrium transition state rate theory
journal, January 2014

  • Feng, Haidong; Zhang, Kun; Wang, Jin
  • Chem. Sci., Vol. 5, Issue 10
  • DOI: 10.1039/C4SC00831F

Landscape, Flux, Correlation, Resonance, Coherence, Stability, and Key Network Wirings of Stochastic Circadian Oscillation
journal, September 2011


Landscape and flux for quantifying global stability and dynamics of game theory
journal, August 2018


Induction of T-cell memory by a dendritic cell vaccine: a computational model
journal, March 2014


Anatomy and Dynamics of a Supramolecular Membrane Protein Cluster
journal, August 2007


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

Time Scales in Epigenetic Dynamics and Phenotypic Heterogeneity of Embryonic Stem Cells
journal, December 2013


A novel construction of complex-valued Gaussian processes with arbitrary spectral densities and its application to excitation energy transfer
journal, June 2013

  • Chen, Xin; Cao, Jianshu; Silbey, Robert J.
  • The Journal of Chemical Physics, Vol. 138, Issue 22
  • DOI: 10.1063/1.4808377

Motion perception: seeing and deciding.
journal, January 1996

  • Shadlen, M. N.; Newsome, W. T.
  • Proceedings of the National Academy of Sciences, Vol. 93, Issue 2
  • DOI: 10.1073/pnas.93.2.628

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

A Role for Neural Integrators in Perceptual Decision Making
journal, November 2003

  • Mazurek, Mark E.; Roitman, Jamie D.; Ditterich, Jochen
  • Cerebral Cortex, Vol. 13, Issue 11
  • DOI: 10.1093/cercor/bhg097

Active gel model of amoeboid cell motility
journal, February 2013


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


Mutual entropy production in bipartite systems
journal, April 2014


Michaelis−Menten Equation and Detailed Balance in Enzymatic Networks
journal, May 2011

  • Cao, Jianshu
  • The Journal of Physical Chemistry B, Vol. 115, Issue 18
  • DOI: 10.1021/jp110924w

Fitness flux and ubiquity of adaptive evolution
journal, February 2010

  • Mustonen, V.; Lassig, M.
  • Proceedings of the National Academy of Sciences, Vol. 107, Issue 9
  • DOI: 10.1073/pnas.0907953107

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

Construction of the landscape for multi-stable systems: Potential landscape, quasi-potential, A-type integral and beyond
journal, March 2016

  • Zhou, Peijie; Li, Tiejun
  • The Journal of Chemical Physics, Vol. 144, Issue 9
  • DOI: 10.1063/1.4943096

Nonequilibrium thermodynamics as a gauge theory
journal, January 2012


Single-molecule enzymology: stochastic Michaelis–Menten kinetics
journal, December 2002


Exact solution of a 1D asymmetric exclusion model using a matrix formulation
journal, April 1993

  • Derrida, B.; Evans, M. R.; Hakim, V.
  • Journal of Physics A: Mathematical and General, Vol. 26, Issue 7
  • DOI: 10.1088/0305-4470/26/7/011

Instabilities of Monolayered Epithelia: Shape and Structure of Villi and Crypts
journal, August 2011


Framework for analyzing ecological trait-based models in multidimensional niche spaces
journal, May 2015


Physics, Computation, and Why Biology Looks so Different
journal, July 1994


Changes of mind in decision-making
journal, August 2009

  • Resulaj, Arbora; Kiani, Roozbeh; Wolpert, Daniel M.
  • Nature, Vol. 461, Issue 7261
  • DOI: 10.1038/nature08275

Vesicle coats: structure, function, and general principles of assembly
journal, June 2013


A simple mechanism of raft formation in two-component fluid membranes
journal, August 2005


Absolute rate theories of epigenetic stability
journal, December 2005

  • Walczak, A. M.; Onuchic, J. N.; Wolynes, P. G.
  • Proceedings of the National Academy of Sciences, Vol. 102, Issue 52
  • DOI: 10.1073/pnas.0509547102

Role of Turnover in Active Stress Generation in a Filament Network
journal, May 2016


The Logic of Animal Conflict
journal, November 1973

  • Smith, J. Maynard; Price, G. R.
  • Nature, Vol. 246, Issue 5427
  • DOI: 10.1038/246015a0

Nonequilibrium-induced enhancement of dynamical quantum coherence and entanglement of spin arrays
journal, April 2017


Gene activities that mediate increased life span of C. elegans insulin-like signaling mutants
journal, November 2007

  • Samuelson, A. V.; Carr, C. E.; Ruvkun, G.
  • Genes & Development, Vol. 21, Issue 22
  • DOI: 10.1101/gad.1588907

Global stability in two species interactions
journal, September 1976


Topology and dynamics of active nematic vesicles
journal, September 2014


Unbounded growth patterns of reproducing, competing polymers—similarities to biological evolution
journal, October 2016


Myosin Motors Drive Long Range Alignment of Actin Filaments
journal, November 2009

  • Butt, Tariq; Mufti, Tabish; Humayun, Ahmad
  • Journal of Biological Chemistry, Vol. 285, Issue 7
  • DOI: 10.1074/jbc.M109.044792

Robust circadian clocks from coupled protein-modification and transcription-translation cycles
journal, December 2010

  • Zwicker, D.; Lubensky, D. K.; ten Wolde, P. R.
  • Proceedings of the National Academy of Sciences, Vol. 107, Issue 52
  • DOI: 10.1073/pnas.1007613107

Cancer as robust intrinsic state of endogenous molecular-cellular network shaped by evolution
journal, January 2008


Mathematical models of immune-induced cancer dormancy and the emergence of immune evasion
journal, August 2013


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


Contraction-Driven Cell Motility
journal, September 2013


The Potential and Flux Landscape Theory of Ecology
journal, January 2014


Leading-edge–gel coupling in lamellipodium motion
journal, November 2010


Locally and Globally Coupled Oscillators in Muscle
journal, September 2013


Pulsatory Patterns in Active Fluids
journal, May 2014


Kinetic equations from Hamiltonian dynamics: Markovian limits
journal, July 1980


A thermodynamically consistent model of the post-translational Kai circadian clock
journal, March 2017

  • Paijmans, Joris; Lubensky, David K.; ten Wolde, Pieter Rein
  • PLOS Computational Biology, Vol. 13, Issue 3
  • DOI: 10.1371/journal.pcbi.1005415

Isoform-specific insulin receptor signaling involves different plasma membrane domains
journal, December 2003

  • Uhles, Sabine; Moede, Tilo; Leibiger, Barbara
  • The Journal of Cell Biology, Vol. 163, Issue 6
  • DOI: 10.1083/jcb.200306093

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

A physical mechanism of cancer heterogeneity
journal, February 2016


Statistical genetics and evolution of quantitative traits
journal, November 2011


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


Dynamical Modeling of Three-Dimensional Genome Organization in Interphase Budding Yeast
journal, January 2012


Vascular remodelling of an arterio-venous blood vessel network during solid tumour growth
journal, August 2009


Potential landscape and flux field theory for turbulence and nonequilibrium fluid systems
journal, February 2018


Polarization of PAR Proteins by Advective Triggering of a Pattern-Forming System
journal, October 2011


Simple membrane-based model of the Min oscillator
journal, April 2015


Stochastic thermodynamics with information reservoirs
journal, October 2014


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


Ordered Phosphorylation Governs Oscillation of a Three-Protein Circadian Clock
journal, November 2007


Acting on actin: the electric motility assay
journal, June 1998

  • Riveline, Daniel; Ott, A.; Jülicher, Frank
  • European Biophysics Journal, Vol. 27, Issue 4
  • DOI: 10.1007/s002490050147

Syntaxins 3 and 4 Are Concentrated in Separate Clusters on the Plasma Membrane before the Establishment of Cell Polarity
journal, February 2006

  • Low, Seng Hui; Vasanji, Amit; Nanduri, Jayasri
  • Molecular Biology of the Cell, Vol. 17, Issue 2
  • DOI: 10.1091/mbc.e05-05-0462

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


Optimal Prediction by Cellular Signaling Networks
journal, December 2015


An allosteric model of circadian KaiC phosphorylation
journal, April 2007

  • van Zon, J. S.; Lubensky, D. K.; Altena, P. R. H.
  • Proceedings of the National Academy of Sciences, Vol. 104, Issue 18
  • DOI: 10.1073/pnas.0608665104

Spontaneous Oscillations of Elastic Contractile Materials with Turnover
journal, October 2014


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


Noise Contributions in an Inducible Genetic Switch: A Whole-Cell Simulation Study
journal, March 2011


Physics of Bacterial Morphogenesis
journal, November 2011

  • Sun, S. X.; Jiang, H.
  • Microbiology and Molecular Biology Reviews, Vol. 75, Issue 4
  • DOI: 10.1128/MMBR.00006-11

Membrane Binding of MinE Allows for a Comprehensive Description of Min-Protein Pattern Formation
journal, December 2013


Stochastic Gene Expression in a Single Cell
journal, August 2002


A Model for Membrane Patchiness: Lateral Diffusion in the Presence of Barriers and Vesicle Traffic
journal, December 1999


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

Scanning Tunneling Microscopy Observations of Benzene Molecules on the Rh(111)-(3 × 3) ( C 6 H 6 + 2CO) Surface
journal, June 1988


Generic aspects of axonemal beating
journal, February 2000


Laws in Darwinian evolutionary theory
journal, June 2005


The actin cortex as an active wetting layer
journal, May 2013


A Minimal Midzone Protein Module Controls Formation and Length of Antiparallel Microtubule Overlaps
journal, August 2010


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


Still and rotating myosin clusters determine cytokinetic ring constriction
journal, July 2016

  • Wollrab, Viktoria; Thiagarajan, Raghavan; Wald, Anne
  • Nature Communications, Vol. 7, Issue 1
  • DOI: 10.1038/ncomms11860

Differentiation of malignant to benign cells
journal, June 1971


Spontaneous waves in muscle fibres
journal, November 2007


Striations in chemical reactions
journal, September 1976

  • Huberman, B. A.
  • The Journal of Chemical Physics, Vol. 65, Issue 5
  • DOI: 10.1063/1.433272

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

Genetic studies of diseases: Cancer systems biology: exploring cancer-associated genes on cellular networks
journal, April 2007

  • Wang, E.; Lenferink, A.; O’Connor-McCourt, M.
  • Cellular and Molecular Life Sciences, Vol. 64, Issue 14
  • DOI: 10.1007/s00018-007-7054-6

Maintaining coherence in quantum computers
journal, February 1995


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


Rapid pole-to-pole oscillation of a protein required for directing division to the middle of Escherichia coli
journal, April 1999

  • Raskin, D. M.; de Boer, P. A. J.
  • Proceedings of the National Academy of Sciences, Vol. 96, Issue 9
  • DOI: 10.1073/pnas.96.9.4971

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

Synchronous oscillations in microtubule polymerization.
journal, August 1987

  • Carlier, M. F.; Melki, R.; Pantaloni, D.
  • Proceedings of the National Academy of Sciences, Vol. 84, Issue 15
  • DOI: 10.1073/pnas.84.15.5257

Membrane Waves Driven by Actin and Myosin
journal, April 2007


Homeostatic competition drives tumor growth and metastasis nucleation
journal, August 2009

  • Basan, Markus; Risler, Thomas; Joanny, Jean‐François
  • HFSP Journal, Vol. 3, Issue 4
  • DOI: 10.2976/1.3086732

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


Potential Landscape and Probabilistic Flux of a Predator Prey Network
journal, March 2011


Sewall Wright’s adaptive landscapes: 1932 vs. 1988
journal, August 2008


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


Logical Reversibility of Computation
journal, November 1973

  • Bennett, C. H.
  • IBM Journal of Research and Development, Vol. 17, Issue 6
  • DOI: 10.1147/rd.176.0525

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

Shape oscillations of non-adhering fibroblast cells
journal, November 2007


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

Cancer stem cells: a model in the making
journal, February 2009

  • Marotta, Lauren L. Campbell; Polyak, Kornelia
  • Current Opinion in Genetics & Development, Vol. 19, Issue 1
  • DOI: 10.1016/j.gde.2008.12.003

Filament turnover stabilizes contractile cytoskeletal structures
journal, September 2010


Nonlinear self-adapting wave patterns
journal, December 2016


Interstitial Fluid Flow and Drug Delivery in Vascularized Tumors: A Computational Model
journal, August 2013


Hydrostatic theory of liquid crystals
journal, January 1962

  • Ericksen, J. L.
  • Archive for Rational Mechanics and Analysis, Vol. 9, Issue 1
  • DOI: 10.1007/BF00253358

A Computational Model for Understanding Stem Cell, Trophectoderm and Endoderm Lineage Determination
journal, October 2008


Measurement of the Force-Velocity Relation for Growing Microtubules
journal, October 1997


Dynamic Instabilities in Assemblies of Molecular Motors with Finite Stiffness
journal, June 2010


Microtubule dynamics: Treadmilling comes around again
journal, June 1997


Landscape and flux theory of non-equilibrium open economy
journal, September 2017


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

Motion Reversal of Molecular Motor Assemblies due to Weak Noise
journal, February 2011


Quantifying the Waddington landscape and biological paths for development and differentiation
journal, May 2011

  • Wang, J.; Zhang, K.; Xu, L.
  • Proceedings of the National Academy of Sciences, Vol. 108, Issue 20
  • DOI: 10.1073/pnas.1017017108

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


A core Klf circuitry regulates self-renewal of embryonic stem cells
journal, February 2008

  • Jiang, Jianming; Chan, Yun-Shen; Loh, Yuin-Han
  • Nature Cell Biology, Vol. 10, Issue 3
  • DOI: 10.1038/ncb1698

Quasi-potential landscape in complex multi-stable systems
journal, July 2012

  • Zhou, Joseph Xu; Aliyu, M. D. S.; Aurell, Erik
  • Journal of The Royal Society Interface, Vol. 9, Issue 77
  • DOI: 10.1098/rsif.2012.0434

Centrosomes are autocatalytic droplets of pericentriolar material organized by centrioles
journal, June 2014

  • Zwicker, David; Decker, Markus; Jaensch, Steffen
  • Proceedings of the National Academy of Sciences, Vol. 111, Issue 26
  • DOI: 10.1073/pnas.1404855111

Quantum transport efficiency and Fourier's law
journal, December 2012


Potential in stochastic differential equations: novel construction
journal, January 2004


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

Min protein patterns emerge from rapid rebinding and membrane interaction of MinE
journal, April 2011

  • Loose, Martin; Fischer-Friedrich, Elisabeth; Herold, Christoph
  • Nature Structural & Molecular Biology, Vol. 18, Issue 5
  • DOI: 10.1038/nsmb.2037

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


Velocity Correlations in an Active Nematic
journal, September 2013


Homeostasis and Differentiation in Random Genetic Control Networks
journal, October 1969


Collective Langevin dynamics of flexible cytoskeletal fibers
journal, November 2007


The fluctuating enzyme: a single molecule approach
journal, August 1999


From fitness landscapes to seascapes: non-equilibrium dynamics of selection and adaptation
journal, March 2009


Global stability of two species systems
journal, January 1977


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

Random Matrix Theory and the Master Equation for Finite Systems
journal, December 1972

  • Gelbart, William M.; Rice, Stuart A.; Freed, Karl F.
  • The Journal of Chemical Physics, Vol. 57, Issue 11
  • DOI: 10.1063/1.1678139

The energy–speed–accuracy trade-off in sensory adaptation
journal, March 2012

  • Lan, Ganhui; Sartori, Pablo; Neumann, Silke
  • Nature Physics, Vol. 8, Issue 5
  • DOI: 10.1038/nphys2276

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

Hydrodynamic theory for multi-component active polar gels
journal, November 2007


A Recurrent Network Mechanism of Time Integration in Perceptual Decisions
journal, January 2006


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


Quantifying the Kinetic Paths of Flexible Biomolecular Recognition
journal, August 2006


Global Stability in Many-Species Systems
journal, January 1977

  • Goh, B. S.
  • The American Naturalist, Vol. 111, Issue 977
  • DOI: 10.1086/283144

Requirements for contractility in disordered cytoskeletal bundles
journal, March 2012


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


The red Queen Hypothesis and Plant/Pathogen Interactions
journal, September 1996


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


Modeling molecular motors
journal, October 1997


The Functional Response of Predators to Prey Density and its Role in Mimicry and Population Regulation
journal, January 1965

  • Holling, C. S.
  • Memoirs of the Entomological Society of Canada, Vol. 97, Issue S45
  • DOI: 10.4039/entm9745fv

Noise and Correlations in a Spatial Population Model with Cyclic Competition
journal, December 2007


Engineered genetic information processing circuits: Engineered genetic information processing circuits
journal, February 2013

  • Qi, Hao; Blanchard, Andrew; Lu, Ting
  • Wiley Interdisciplinary Reviews: Systems Biology and Medicine, Vol. 5, Issue 3
  • DOI: 10.1002/wsbm.1216

A limit cycle mathematical model of the REM sleep oscillator system
journal, December 1986

  • McCarley, R. W.; Massaquoi, S. G.
  • American Journal of Physiology-Regulatory, Integrative and Comparative Physiology, Vol. 251, Issue 6
  • DOI: 10.1152/ajpregu.1986.251.6.R1011

Computational Model for Cell Morphodynamics
journal, September 2010


Transformation from Spots to Waves in a Model of Actin Pattern Formation
journal, May 2009


The trifecta of aging in Caenorhabditis elegans
journal, October 2006


Phase transitions in an exactly soluble one-dimensional exclusion process
journal, July 1993

  • Sch�tz, G.; Domany, E.
  • Journal of Statistical Physics, Vol. 72, Issue 1-2
  • DOI: 10.1007/BF01048050

Statistical genetics and evolution
journal, April 1942


Optimal Signal Processing in Small Stochastic Biochemical Networks
journal, October 2007


The potential and flux landscape theory of evolution
journal, August 2012

  • Zhang, Feng; Xu, Li; Zhang, Kun
  • The Journal of Chemical Physics, Vol. 137, Issue 6
  • DOI: 10.1063/1.4734305

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

Centrosome Size Sets Mitotic Spindle Length in Caenorhabditis elegans Embryos
journal, February 2010

  • Greenan, Garrett; Brangwynne, Clifford P.; Jaensch, Steffen
  • Current Biology, Vol. 20, Issue 4
  • DOI: 10.1016/j.cub.2009.12.050

Funneled potential and flux landscapes dictate the stabilities of both the states and the flow: Fission yeast cell cycle
journal, September 2017


On global stability of a predator-prey system
journal, May 1978


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

Reversing the Life Cycle: Medusae Transforming into Polyps and Cell Transdifferentiation in Turritopsis nutricula (Cnidaria, Hydrozoa)
journal, June 1996

  • Piraino, S.; Boero, F.; Aeschbach, B.
  • The Biological Bulletin, Vol. 190, Issue 3
  • DOI: 10.2307/1543022

Ecological collapse and the emergence of travelling waves at the onset of shear turbulence
journal, November 2015

  • Shih, Hong-Yan; Hsieh, Tsung-Lin; Goldenfeld, Nigel
  • Nature Physics, Vol. 12, Issue 3
  • DOI: 10.1038/nphys3548

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


The Hallmarks of Cancer
journal, January 2000


Global stability of predator-prey interactions
journal, January 1979

  • Harrison, Gary W.
  • Journal of Mathematical Biology, Vol. 8, Issue 2
  • DOI: 10.1007/BF00279719

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


Three faces of the second law. II. Fokker-Planck formulation
journal, July 2010


Instabilities of Isotropic Solutions of Active Polar Filaments
journal, April 2003


Molecular Motor-Induced Instabilities and Cross Linkers Determine Biopolymer Organization
journal, December 2007


Single-molecule chemistry
journal, December 2002


On the evolution of bacterial multicellularity
journal, April 2015


Molecular Interactions of the Min Protein System Reproduce Spatiotemporal Patterning in Growing and Dividing Escherichia coli Cells
journal, May 2015


Modeling the Cell Cycle: Why Do Certain Circuits Oscillate?
journal, March 2011


Quantifying the potential and flux landscapes of multi-locus evolution
journal, June 2017


Navigating cancer network attractors for tumor-specific therapy
journal, September 2012

  • Creixell, Pau; Schoof, Erwin M.; Erler, Janine T.
  • Nature Biotechnology, Vol. 30, Issue 9
  • DOI: 10.1038/nbt.2345

No Transcription-Translation Feedback in Circadian Rhythm of KaiC Phosphorylation
journal, January 2005


Regulated Fluctuations in Nanog Expression Mediate Cell Fate Decisions in Embryonic Stem Cells
journal, July 2009


Delayed Feedback Model of Axonal Length Sensing
journal, May 2015


Convergence of multilocus systems under weak epistasis or weak selection
journal, February 1999

  • Nagylaki, Thomas; Hofbauer, Josef; Brunovský, Pavol
  • Journal of Mathematical Biology, Vol. 38, Issue 2
  • DOI: 10.1007/s002850050143

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

Stochastic thermodynamics of bipartite systems: transfer entropy inequalities and a Maxwell’s demon interpretation
journal, February 2014


Stem cell differentiation as a many-body problem
journal, June 2014

  • Zhang, B.; Wolynes, P. G.
  • Proceedings of the National Academy of Sciences, Vol. 111, Issue 28
  • DOI: 10.1073/pnas.1408561111

Buyer search and price dispersion:a laboratory study
journal, October 2003


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


Forces Driving Epithelial Spreading in Zebrafish Gastrulation
journal, October 2012


Contractile Units in Disordered Actomyosin Bundles Arise from F-Actin Buckling
journal, June 2012


A direct calculation of the tunnelling current. III. Effect of localized impurity states in the barrier
journal, November 1971


Red Queen hypothesis supported by parasitism in sexual and clonal fish
journal, April 1990

  • Lively, Curtis M.; Craddock, Clark; Vrijenhoek, Robert C.
  • Nature, Vol. 344, Issue 6269
  • DOI: 10.1038/344864a0

A sensing array of radically coupled genetic ‘biopixels’
journal, December 2011

  • Prindle, Arthur; Samayoa, Phillip; Razinkov, Ivan
  • Nature, Vol. 481, Issue 7379
  • DOI: 10.1038/nature10722

Dynamics of nonequilibrium thermal entanglement
journal, December 2008


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

Optimal rectification in the ultrastrong coupling regime
journal, June 2014


Theoretical Neuroscience Rising
journal, November 2008


Geometrical Origins of Contractility in Disordered Actomyosin Networks
journal, October 2014


Bidirectional cooperative motion of molecular motors
journal, May 2002

  • Badoual, M.; Julicher, F.; Prost, J.
  • Proceedings of the National Academy of Sciences, Vol. 99, Issue 10
  • DOI: 10.1073/pnas.102692399

Quantifying the underlying landscape and paths of cancer
journal, November 2014

  • Li, Chunhe; Wang, Jin
  • Journal of The Royal Society Interface, Vol. 11, Issue 100
  • DOI: 10.1098/rsif.2014.0774

The evolution of multilocus systems under weak selection.
journal, June 1993


Real-Time Measurements of Actin Filament Polymerization by Total Internal Reflection Fluorescence Microscopy
journal, February 2005


Lateral Membrane Waves Constitute a Universal Dynamic Pattern of Motile Cells
journal, July 2006

  • Döbereiner, Hans-Günther; Dubin-Thaler, Benjamin J.; Hofman, Jake M.
  • Physical Review Letters, Vol. 97, Issue 3
  • DOI: 10.1103/PhysRevLett.97.038102

When Does the Michaelis−Menten Equation Hold for Fluctuating Enzymes?
journal, October 2006

  • Min, Wei; Gopich, Irina V.; English, Brian P.
  • The Journal of Physical Chemistry B, Vol. 110, Issue 41
  • DOI: 10.1021/jp065187g

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

The Cdk1–APC/C cell cycle oscillator circuit functions as a time-delayed, ultrasensitive switch
journal, April 2013

  • Yang, Qiong; Ferrell, James E.
  • Nature Cell Biology, Vol. 15, Issue 5
  • DOI: 10.1038/ncb2737

Cortical Actomyosin Breakage Triggers Shape Oscillations in Cells and Cell Fragments
journal, July 2005


Defect Annihilation and Proliferation in Active Nematics
journal, May 2013


Contractility and retrograde flow in lamellipodium motion
journal, June 2006


Vibrational and coherence dynamics of molecules
journal, January 2015

  • Zhang, Zhedong; Wang, Jin
  • Physical Chemistry Chemical Physics, Vol. 17, Issue 37
  • DOI: 10.1039/C5CP03623B

Dynamic assembly of MinD on phospholipid vesicles regulated by ATP and MinE
journal, April 2002

  • Hu, Z.; Gogol, E. P.; Lutkenhaus, J.
  • Proceedings of the National Academy of Sciences, Vol. 99, Issue 10
  • DOI: 10.1073/pnas.102059099

The genetics of ageing
journal, March 2010


Modeling putative therapeutic implications of exosome exchange between tumor and immune cells
journal, September 2014

  • Lu, Mingyang; Huang, Bin; Hanash, Samir M.
  • Proceedings of the National Academy of Sciences, Vol. 111, Issue 40
  • DOI: 10.1073/pnas.1416745111

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


Cancer attractors: A systems view of tumors from a gene network dynamics and developmental perspective
journal, September 2009

  • Huang, Sui; Ernberg, Ingemar; Kauffman, Stuart
  • Seminars in Cell & Developmental Biology, Vol. 20, Issue 7
  • DOI: 10.1016/j.semcdb.2009.07.003

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

Bacterial cheating drives the population dynamics of cooperative antibiotic resistance plasmids
journal, January 2013

  • Yurtsev, Eugene A.; Chao, Hui Xiao; Datta, Manoshi S.
  • Molecular Systems Biology, Vol. 9, Issue 1
  • DOI: 10.1038/msb.2013.39

Crowding of Molecular Motors Determines Microtubule Depolymerization
journal, November 2011


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


The Price Equilibrium Existence Problem in Topological Vector Lattices
journal, September 1986


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

The yeast cell-cycle network is robustly designed
journal, March 2004

  • Li, F.; Long, T.; Lu, Y.
  • Proceedings of the National Academy of Sciences, Vol. 101, Issue 14
  • DOI: 10.1073/pnas.0305937101

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

Hypothesis for origin of planktonic patchiness
journal, February 1976

  • Levin, Simon A.; Segel, Lee A.
  • Nature, Vol. 259, Issue 5545
  • DOI: 10.1038/259659a0

Active elastic thin shell theory for cellular deformations
journal, June 2014

  • Berthoumieux, Hélène; Maître, Jean-Léon; Heisenberg, Carl-Philipp
  • New Journal of Physics, Vol. 16, Issue 6
  • DOI: 10.1088/1367-2630/16/6/065005

Dominant Kinetic Paths on Biomolecular Binding-Folding Energy Landscape
journal, April 2006


Direct visualization of Ras proteins in spatially distinct cell surface microdomains
journal, January 2003

  • Prior, Ian A.; Muncke, Cornelia; Parton, Robert G.
  • The Journal of Cell Biology, Vol. 160, Issue 2
  • DOI: 10.1083/jcb.200209091

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

Environmental control of microtubule-based bidirectional cargo transport
journal, July 2014


Physics of adherent cells
journal, August 2013


Potential and flux field landscape theory. II. Non-equilibrium thermodynamics of spatially inhomogeneous stochastic dynamical systems
journal, September 2014

  • Wu, Wei; Wang, Jin
  • The Journal of Chemical Physics, Vol. 141, Issue 10
  • DOI: 10.1063/1.4894389

Dendritic Actin Filament Nucleation Causes Traveling Waves and Patches
journal, June 2010


Simultaneous Price and Quantity Adjustment in a Single Market
journal, August 1969

  • Beckmann, Martin J.; Ryder, Harl E.
  • Econometrica, Vol. 37, Issue 3
  • DOI: 10.2307/1912794

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

Polymerization kinetics of ADP- and ADP-Pi-actin determined by fluorescence microscopy
journal, May 2007

  • Fujiwara, I.; Vavylonis, D.; Pollard, T. D.
  • Proceedings of the National Academy of Sciences, Vol. 104, Issue 21
  • DOI: 10.1073/pnas.0702510104

Selection and Covariance
journal, August 1970


Force and focal adhesion assembly: a close relationship studied using elastic micropatterned substrates
journal, April 2001

  • Balaban, Nathalie Q.; Schwarz, Ulrich S.; Riveline, Daniel
  • Nature Cell Biology, Vol. 3, Issue 5
  • DOI: 10.1038/35074532

More Is Different
journal, August 1972


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


Coevolution of nodes and links: Diversity-driven coexistence in cyclic competition of three species
journal, February 2019


Spatial interference scale as a determinant of microbial range expansion
journal, November 2018

  • Celik Ozgen, Venhar; Kong, Wentao; Blanchard, Andrew E.
  • Science Advances, Vol. 4, Issue 11
  • DOI: 10.1126/sciadv.aau0695

Boundary-induced phase transitions in driven diffusive systems
journal, September 1991


Energy and momentum balance equations: An approach to quantum transport in closed circuits
journal, July 2002


A Physical Mechanism and Global Quantification of Breast Cancer
journal, July 2016


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

New quantum oscillations in current driven small junctions
journal, April 1985


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

Phase Coexistence in Driven One-Dimensional Transport
journal, February 2003


Coexisting Liquid Phases Underlie Nucleolar Subcompartments
journal, June 2016


Plasma membrane nanoswitches generate high-fidelity Ras signal transduction
journal, July 2007

  • Tian, Tianhai; Harding, Angus; Inder, Kerry
  • Nature Cell Biology, Vol. 9, Issue 8
  • DOI: 10.1038/ncb1615

Chemosensory pathways, motility and development in Myxococcus xanthus
journal, November 2007

  • Zusman, David R.; Scott, Ansley E.; Yang, Zhaomin
  • Nature Reviews Microbiology, Vol. 5, Issue 11
  • DOI: 10.1038/nrmicro1770

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


Changes in Oscillatory Dynamics in the Cell Cycle of Early Xenopus laevis Embryos
journal, February 2014


On the complex dynamics of savanna landscapes
journal, January 2018

  • Touboul, Jonathan David; Staver, Ann Carla; Levin, Simon Asher
  • Proceedings of the National Academy of Sciences, Vol. 115, Issue 7
  • DOI: 10.1073/pnas.1712356115

Design Principles of Length Control of Cytoskeletal Structures
journal, July 2016


Probability currents as principal characteristics in the statistical mechanics of non-equilibrium steady states
journal, July 2007


Multicopy plasmids are clustered and localized in Escherichia coli
journal, March 2001

  • Pogliano, J.; Ho, T. Q.; Zhong, Z.
  • Proceedings of the National Academy of Sciences, Vol. 98, Issue 8
  • DOI: 10.1073/pnas.081075798

Multi-scale modelling of cancer cell intravasation: the role of cadherins in metastasis
journal, March 2009


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


Correction: Funneled Landscape Leads to Robustness of Cell Networks: Yeast Cell Cycle
journal, September 2013


Spontaneous Motility of Actin Lamellar Fragments
journal, February 2013


A frequency-dependent decoding mechanism for axonal length sensing
journal, July 2015


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


Period Robustness and Entrainability of the Kai System to Changing Nucleotide Concentrations
journal, July 2017

  • Paijmans, Joris; Lubensky, David K.; ten Wolde, Pieter Rein
  • Biophysical Journal, Vol. 113, Issue 1
  • DOI: 10.1016/j.bpj.2017.05.048

Information-theoretic versus thermodynamic entropy production in autonomous sensory networks
journal, April 2013


Kinesin-8 Motors Act Cooperatively to Mediate Length-Dependent Microtubule Depolymerization
journal, September 2009


Pattern Formation in Active Fluids
journal, January 2011


Pattern formation in active cytoskeletal networks
journal, March 2008


Membrane waves driven by forces from actin filaments
journal, November 2012


MicroRNA-based regulation of epithelial-hybrid-mesenchymal fate determination
journal, October 2013

  • Lu, M.; Jolly, M. K.; Levine, H.
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 45
  • DOI: 10.1073/pnas.1318192110

Memory landscapes of single-enzyme molecules
journal, July 2000

  • Edman, L.; Rigler, R.
  • Proceedings of the National Academy of Sciences, Vol. 97, Issue 15
  • DOI: 10.1073/pnas.130589397

Mobile Actin Clusters and Traveling Waves in Cells Recovering from Actin Depolymerization
journal, November 2004

  • Gerisch, Günther; Bretschneider, Till; Müller-Taubenberger, Annette
  • Biophysical Journal, Vol. 87, Issue 5
  • DOI: 10.1529/biophysj.104.047589

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 Active Pulse Transmission Line Simulating Nerve Axon
journal, October 1962


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

Isolated cell behavior drives the evolution of antibiotic resistance
journal, July 2015

  • Artemova, Tatiana; Gerardin, Ylaine; Dudley, Carmel
  • Molecular Systems Biology, Vol. 11, Issue 7
  • DOI: 10.15252/msb.20145888

Nanog safeguards pluripotency and mediates germline development
journal, December 2007

  • Chambers, Ian; Silva, Jose; Colby, Douglas
  • Nature, Vol. 450, Issue 7173
  • DOI: 10.1038/nature06403

Rapid leukocyte migration by integrin-independent flowing and squeezing
journal, May 2008

  • Lämmermann, Tim; Bader, Bernhard L.; Monkley, Susan J.
  • Nature, Vol. 453, Issue 7191
  • DOI: 10.1038/nature06887

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

Actively Contracting Bundles of Polar Filaments
journal, August 2000


Analysis of turnover dynamics of the submembranous actin cortex
journal, March 2013

  • Fritzsche, Marco; Lewalle, Alexandre; Duke, Tom
  • Molecular Biology of the Cell, Vol. 24, Issue 6
  • DOI: 10.1091/mbc.e12-06-0485

Quantum localization and protein-assisted vibrational energy flow in cofactors
journal, August 2010


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


Extension of covariance selection mathematics
journal, April 1972


Toward Decoding the Principles of Cancer Metastasis Circuits
journal, September 2014


Nonequilibrium landscape theory of neural networks
journal, October 2013

  • Yan, H.; Zhao, L.; Hu, L.
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 45
  • DOI: 10.1073/pnas.1310692110

Dynamic disorder in horseradish peroxidase observed with total internal reflection fluorescence correlation spectroscopy
journal, January 2007


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

Architecture and Connectivity Govern Actin Network Contractility
journal, March 2016


Domain Formation in the Plasma Membrane: Roles of Nonequilibrium Lipid Transport and Membrane Proteins
journal, April 2008


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


Active polar fluid flow in finite droplets
journal, February 2014

  • A. Whitfield, Carl; Marenduzzo, Davide; Voituriez, Raphaël
  • The European Physical Journal E, Vol. 37, Issue 2
  • DOI: 10.1140/epje/i2014-14008-3

DAF-16 Target Genes That Control C. elegans Life-Span and Metabolism
journal, April 2003


Quantifying Kinetic Paths of Protein Folding
journal, September 2005


The Debt-Deflation Theory of Great Depressions
journal, October 1933


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


The Potential Landscape of Genetic Circuits Imposes the Arrow of Time in Stem Cell Differentiation
journal, July 2010


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

Flagellar rotation and the mechanism of bacterial motility
journal, May 1974

  • Silverman, Michael; Simon, Melvin
  • Nature, Vol. 249, Issue 5452
  • DOI: 10.1038/249073a0

Stochastic Path Approach to Compute Atomically Detailed Trajectories:  Application to the Folding of C Peptide
journal, February 1999

  • Elber, Ron; Meller, Jaroslaw; Olender, Roberto
  • The Journal of Physical Chemistry B, Vol. 103, Issue 6
  • DOI: 10.1021/jp983774z

Pushing off the Walls: A Mechanism of Cell Motility in Confinement
journal, February 2009


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

Cooperative Molecular Motors
journal, September 1995


The energy pump and the origin of the non-equilibrium flux of the dynamical systems and the networks
journal, April 2012

  • Xu, Liufang; Shi, Hualin; Feng, Haidong
  • The Journal of Chemical Physics, Vol. 136, Issue 16
  • DOI: 10.1063/1.3703514

Cilia-Like Beating of Active Microtubule Bundles
journal, July 2011


Conductance of a Molecular Junction
journal, October 1997


Quantifying the Landscape for Development and Cancer from a Core Cancer Stem Cell Circuit
journal, May 2015


Blebs lead the way: how to migrate without lamellipodia
journal, July 2008

  • Charras, Guillaume; Paluch, Ewa
  • Nature Reviews Molecular Cell Biology, Vol. 9, Issue 9
  • DOI: 10.1038/nrm2453

Soft active aggregates: mechanics, dynamics and self-assembly of liquid-like intracellular protein bodies
journal, January 2011


Excitable Actin Dynamics in Lamellipodial Protrusion and Retraction
journal, April 2012

  • Ryan, Gillian L.; Petroccia, Heather M.; Watanabe, Naoki
  • Biophysical Journal, Vol. 102, Issue 7
  • DOI: 10.1016/j.bpj.2012.03.005

The interplay of tunneling, resonance, and dissipation in quantum barrier crossing: A numerical study
journal, June 1992

  • Tanimura, Yoshitaka; Wolynes, Peter G.
  • The Journal of Chemical Physics, Vol. 96, Issue 11
  • DOI: 10.1063/1.462301

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

Mechanics of actomyosin bonds in different nucleotide states are tuned to muscle contraction
journal, June 2006

  • Guo, B.; Guilford, W. H.
  • Proceedings of the National Academy of Sciences, Vol. 103, Issue 26
  • DOI: 10.1073/pnas.0601255103

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


Neural Basis of a Perceptual Decision in the Parietal Cortex (Area LIP) of the Rhesus Monkey
journal, October 2001


Multiple coupled landscapes and non-adiabatic dynamics with applications to self-activating genes
journal, January 2015

  • Chen, Cong; Zhang, Kun; Feng, Haidong
  • Physical Chemistry Chemical Physics, Vol. 17, Issue 43
  • DOI: 10.1039/C5CP04780C

Nonequilibrium Raftlike Membrane Domains under Continuous Recycling
journal, October 2005


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

Biomolecules: Where the Physics of Complexity and Simplicity Meet
journal, February 1994

  • Frauenfelder, Hans; Wolynes, Peter G.
  • Physics Today, Vol. 47, Issue 2
  • DOI: 10.1063/1.881414

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


A Dynamic Model for Determining the Middle of Escherichia coli
journal, February 2002


Effects of Collective Histone State Dynamics on Epigenetic Landscape and Kinetics of Cell Reprogramming
journal, November 2015

  • Ashwin, S. S.; Sasai, Masaki
  • Scientific Reports, Vol. 5, Issue 1
  • DOI: 10.1038/srep16746

Spatiotemporal Patterns of Noise-Driven Confined Actin Waves in Living Cells
journal, January 2017


Microtubule Length Regulation by Molecular Motors
journal, June 2012


Length Regulation of Active Biopolymers by Molecular Motors
journal, June 2012


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


Nonequilibrium thermal entanglement
journal, March 2007


Simulation of cell motility that reproduces the force-velocity relationship
journal, May 2010

  • Schreiber, C. H.; Stewart, M.; Duke, T.
  • Proceedings of the National Academy of Sciences, Vol. 107, Issue 20
  • DOI: 10.1073/pnas.1002538107

Quantum effects in biology: golden rule in enzymes, olfaction, photosynthesis and magnetodetection
journal, May 2017

  • Brookes, Jennifer C.
  • Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, Vol. 473, Issue 2201
  • DOI: 10.1098/rspa.2016.0822

Spatial Organization of the Cell Cytoplasm by Position-Dependent Phase Separation
journal, August 2013


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


The Biology of Cancer Stem Cells
journal, November 2007


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

Landscape and flux reveal a new global view and physical quantification of mammalian cell cycle
journal, September 2014

  • Li, Chunhe; Wang, Jin
  • Proceedings of the National Academy of Sciences, Vol. 111, Issue 39
  • DOI: 10.1073/pnas.1408628111

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

Theory and measurements of room temperature transport in graphene using SiO[sub 2] backgate and electrochemical gate
journal, January 2009

  • Shishir, R. S.; Chen, F.; Xia, J.
  • Journal of Vacuum Science & Technology B: Microelectronics and Nanometer Structures, Vol. 27, Issue 4
  • DOI: 10.1116/1.3156733

Coupled Reversible and Irreversible Bistable Switches Underlying TGFβ-induced Epithelial to Mesenchymal Transition
journal, August 2013


Boundaries steer the contraction of active gels
journal, October 2016

  • Schuppler, Matthias; Keber, Felix C.; Kröger, Martin
  • Nature Communications, Vol. 7, Issue 1
  • DOI: 10.1038/ncomms13120

Mapping between dissipative and Hamiltonian systems
journal, July 2010


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

Spontaneous buckling of contractile poroelastic actomyosin sheets
journal, June 2018


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

The Actin Cortex: A Bridge between Cell Shape and Function
journal, September 2016


Steady-State Thermodynamics of Langevin Systems
journal, April 2001


A C. elegans mutant that lives twice as long as wild type
journal, December 1993

  • Kenyon, Cynthia; Chang, Jean; Gensch, Erin
  • Nature, Vol. 366, Issue 6454
  • DOI: 10.1038/366461a0

Fluctuation-dissipation theorem for nonequilibrium quantum systems
journal, July 2016


Stochastic thermodynamics: principles and perspectives
journal, January 2008


Cluster phases of membrane proteins
journal, January 2008


Diffusible Crosslinkers Generate Directed Forces in Microtubule Networks
journal, March 2015


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

Spontaneous Oscillations of Collective Molecular Motors
journal, June 1997


Hallmarks of Cancer: The Next Generation
journal, March 2011


Enzyme Kinetics, Past and Present
journal, December 2013


Dynamic determination of the functional state in photolyase and the implication for cryptochrome
journal, July 2013

  • Liu, Z.; Zhang, M.; Guo, X.
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 32
  • DOI: 10.1073/pnas.1311077110

Social interaction in synthetic and natural microbial communities
journal, January 2011


A Combination of Actin Treadmilling and Cross-Linking Drives Contraction of Random Actomyosin Arrays
journal, November 2015

  • Oelz, Dietmar B.; Rubinstein, Boris Y.; Mogilner, Alex
  • Biophysical Journal, Vol. 109, Issue 9
  • DOI: 10.1016/j.bpj.2015.09.013

Direct measurement of force generation by actin filament polymerization using an optical trap
journal, February 2007

  • Footer, M. J.; Kerssemakers, J. W. J.; Theriot, J. A.
  • Proceedings of the National Academy of Sciences, Vol. 104, Issue 7
  • DOI: 10.1073/pnas.0607052104

Reconstitution of Contractile Actomyosin Bundles
journal, June 2011


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

Exciton–Phonon Interactions in Molecular Crystals
journal, February 1970

  • Grover, M. K.; Silbey, R.
  • The Journal of Chemical Physics, Vol. 52, Issue 4
  • DOI: 10.1063/1.1673263

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

Evolutionary dynamics, intrinsic noise, and cycles of cooperation
journal, June 2010


Cytoskeletal waves in the absence of molecular motors
journal, June 2008


Determining Physical Properties of the Cell Cortex
journal, March 2016


Robustness and Coherence of a Three-Protein Circadian Oscillator: Landscape and Flux Perspectives
journal, December 2009


Finance and Economic Breakdown: Modeling Minsky’s “Financial Instability Hypothesis”
journal, July 1995


Cellular noise and information transmission
journal, August 2014


Heterogeneity in Cancer: Cancer Stem Cells versus Clonal Evolution
journal, September 2009


Treadmilling and length distributions of active polar filaments
journal, October 2013

  • Erlenkämper, C.; Kruse, K.
  • The Journal of Chemical Physics, Vol. 139, Issue 16
  • DOI: 10.1063/1.4825248

Hydrodynamics of Cellular Cortical Flows and the Formation of Contractile Rings
journal, July 2009


Dominant Kinetic Paths of Complex Systems: Gene Networks
journal, May 2010

  • Feng, Haidong; Han, Bo; Wang, Jin
  • The Journal of Physical Chemistry Letters, Vol. 1, Issue 12
  • DOI: 10.1021/jz100484p

C2-domain mediated nano-cluster formation increases calcium signaling efficiency
journal, November 2016

  • Bonny, Mike; Hui, Xin; Schweizer, Julia
  • Scientific Reports, Vol. 6, Issue 1
  • DOI: 10.1038/srep36028

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

Rafts defined: a report on the Keystone symposium on lipid rafts and cell function
journal, April 2006


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

Understanding the Odd Science of Aging
journal, February 2005


Intrinsic noise, dissipation cost, and robustness of cellular networks: The underlying energy landscape of MAPK signal transduction
journal, April 2008

  • Lapidus, S.; Han, B.; Wang, J.
  • Proceedings of the National Academy of Sciences, Vol. 105, Issue 16
  • DOI: 10.1073/pnas.0708708105

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

Quantum Dissipative Systems
book, March 2012


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


Dominant Pathways in Protein Folding
journal, September 2006


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

Kin I Kinesins Are Microtubule-Destabilizing Enzymes
journal, January 1999


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

Effects of molecular noise on bistable protein distributions in rod-shaped bacteria
journal, December 2014


Traveling waves in actin dynamics and cell motility
journal, February 2013


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

Cortical flow aligns actin filaments to form a furrow
journal, October 2016

  • Reymann, Anne-Cecile; Staniscia, Fabio; Erzberger, Anna
  • eLife, Vol. 5
  • DOI: 10.7554/eLife.17807

Actin Polymerization Overshoots and ATP Hydrolysis as Assayed by Pyrene Fluorescence
journal, August 2008


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

Segregation of diffusible and directionally moving particles on a polar filament
journal, April 2014


Dendritic-cell vaccines on the move
journal, March 2015


Eddy current and coupled landscapes for nonadiabatic and nonequilibrium complex system dynamics
journal, August 2013

  • Zhang, K.; Sasai, M.; Wang, J.
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 37
  • DOI: 10.1073/pnas.1305604110

Opposite end assembly and disassembly of microtubules at steady state in vitro
journal, January 1978


Quantum effects in thermal conduction: Nonequilibrium quantum discord and entanglement
journal, July 2011


Phenotypic variability of growing cellular populations
journal, November 2007

  • Lu, T.; Shen, T.; Bennett, M. R.
  • Proceedings of the National Academy of Sciences, Vol. 104, Issue 48
  • DOI: 10.1073/pnas.0706115104

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


Generation of stationary and moving vortices in active polar fluids in the planar Taylor-Couette geometry
journal, November 2014