Physics of Living Systems Paper Summaries

   Nonequilibrium Thermodynamics and Statistical Physics

 Thermodynamic Cost and Benefit of Memory by Still, S.

  How far from equilibrium is active matter? by Fodor, E. et. al.

  Non-equilibrium phase separation with reactions: A canonical model and its behaviour by Li, Y. & Cates, M.

  Generalized Thermodynamics of Phase Equilibria in Scalar Active Matter by Solon, A. et. al.

  Size-Regulated Symmetry Breaking in Reaction-Diffusion Models of Developmental Transitions by Scoones, J. et. al.

  Irreversibility in dynamical phases and transitions by Seara, D. et. al.

  Beyond Boltzmann-Gibbs statistics: Maximum entropy hyperensembles out of equilibrium by Crooks, G.

  Thermodynamic uncertainty relations constrain non-equilibrium fluctuations by Horowitz, J. M. & Gingrich, T. R.

  Dissipative adaptation in driven self-assembly by England, J. L.

  Length of Time's Arrow by Feng, E. & Crooks, G.

  Entropy production fluctuation theorem and the nonequilibrium work relation for free energy differences by Crooks, G.

  Dynamical Ensembles in Nonequilibrium Statistical Mechanics by Gallavotti, G. & Cohen, E. G. D.

  Measuring Thermodynamic Length by Crooks, G.

  Dissipation and lag in irreversible processes by Vaikuntanathan, S. & Jarzynski, C.

  Good Practices in Free Energy Calculations by Pohorille, A. et. al.

  Near-Equilibrium Measurements of Nonequilibrium Free Energy by Sivak, D. & Crooks, G.

  Thermodynamic Metrics and Optimal Paths by Sivak, D. & Crooks, G.

  Thermodynamics of Prediction, by Still, S, et. al.

  Statistical Physics of Self-Replication by England, J. L.

  Biology and Nonequilibrium: Remarks on England's Paper by Ruelle, D.

  Optimizing Non-Ergodic Feedback Engines by Horowitz, J. M. & Parrondo, J. M. R.

  Thermodynamics of Information by Horowitz, J. M. & Parrondo, J. M. R.

  Optimal control in nonequilibrium systems: Dynamic Riemannian geometry of Ising model by Rotskoff, G. & Crooks, G.

  Dissipation Bounds All Steady-State Current Fluctuations by Gingrich, T. et. al.

  Universal bound on the efficiency of molecular motors by Pietzonka, P. et. al.

  Inferring dissipation from current fluctuations by Gingrich, T. et. al.

  Minimum energetic cost to maintain a target nonequilibrium state by Horowitz, J. et. al.

  Spontaneous fine-tuning to environment in many-species chemical reaction networks by Horowitz, J. & England, J.

  On Measures of Entropy and Information by Crooks, G.

  Maximizing Influence in an Ising Network: A Mean-Field Optimal Solution by Lynn, C. & Lee, D.

  Marginal and Conditional Second Laws of Thermodynamics by Crooks, G. & Still, S.

  A geometric approach to optimal nonequilibrium control: Minimizing dissipation in nanomagnetic spin systems by Rotskoff, G. et. al.

  Limits of predictions in thermodynamic systems: a review by Marsland, R. & England, J.

  Arrow of Time in Active Fluctuations by Roldan, E. et. al.

  Quantifying dissipation using fluctuating currents by Li, J. et. al.

  Inferring broken detailed balance in the absence of observable currents by Martinez, I. et. al.

  Nonequilibrium abundances for the building blocks of life by Stopnitzky, E. & Still, S.

  Nonequilibrium physics in biology by Fang, X. et. al.

  Autonomous Engines Driven by Active Matter: Energetics and Design Principles by Pietzonka, P. et. al.

  Nonequilibrium phase transitions and pattern formation as consequences of second-order thermodynamic induction by Patitsas, S.

  Universal Thermodynamic Bounds on Nonequilibrium Response with Biochemical Applications by Owen, J. et. al.

  Design of conditions for self-replication by Sarkar, S. & England, J. L.

  Exponential volume dependence of entropy-current fluctuations at first-order phase transitions in chemical reaction networks by Nguyen, B. & Seifert, U.

  Stochastic thermodynamics of chemical reactions coupled to finite reservoirs: A case study for the Brusselator by Fritz, J. et. al.

 

   Nonlinear Dynamics

 Stability of Localized Wave Fronts in Bistable Systems by Rulands, S. et. al.

 

   Active Field Theories

 Active Field Theories by Cates, M.

  Entropy Production in Field Theories without Time-Reversal Symmetry: Quantifying the Non-Equilibrium Character of Active Matter by Nardini, C. et. al.

  Steady state entropy production rate for scalar Langevin field theories by Li, Y. & Cates, M.

  Thermodynamics of active field theories: Energetic cost of coupling to reservoirs by Markovich, T. et. al.

  Stealth entropy production in active field theories near Ising critical points by Caballero, F. & Cates, M.

  Field-Theoretic Thermodynamic Uncertainty Relations by Niggemann, O. & Seifert, U.

 

   Topology

  Topological turbulence on the membrane of a living cell by Tan, T. et. al.

  Topology in Biology by Blevins, A.S. & Bassett, D.

  Topological Active Matter by Shankar, S. et. al.

  Planar morphometrics using Teichmüller maps by Choi, G. & Mahadevan, L.

  Reorderability of node-filtered order complexes by Blevins, A.S. & Bassett, D.

 

   Hydrodynamics of Active Matter

  Meso-scale turbulence in living fluids by Wensink, H. et. al.

 

   Organisms

  Capturing the continuous complexity of behaviour in Caenorhabditis elegans by Ahamed, T. et. al.

 

   Cells

  Tissue fluidity promotes epithelial wound healing by Tetley, R. et. al.

  Sub-nanowatt resolution direct calorimetry for probing real-time metabolic activity of individual C. elegans worms by Hur, S. et. al.

  Contact area–dependent cell communication and the morphological invariance of ascidian embryogenesis by Guignard, L. et. al.

  High-resolution mapping of intracellular fluctuations using carbon nanotubes by Fakhri, N. et. al.

  Broken detailed balance at mesoscopic scales in active biological systems by Fakhri, N. et. al.

  Scaling laws governing stochastic growth and division of single bacterial cells by Iyer-Biswas, S. et. al.

  Universality of clone dynamics during tissue development by Rulands, S. et. al.

 

   Subcellular

  Size regulation of multiple organelles competing for a shared subunit pool by Banerjee, D. & Banerjee, S.

  Protein secondary structure: entropy, correlations and prediction by Crooks, G. & Brenner, S.

  Verification of the Crooks fluctuation theorem and recovery of RNA folding free energies by Collin, D. et. al.

  Stochastic gene expression conditioned on large deviations by Horowitz, J. & Kulkarni, R.

  Stable colloids in molten inorganic salts by Zhang, H. et. al.

  Theory of Nonequilibrium Free Energy Transduction by Molecular Machines by Brown, A. & Sivak, D.

  Unified prebiotically plausible synthesis of pyrimidine and purine RNA ribonucleotides by Becker, S. et. al.

  Design of biochemical pattern forming systems from minimal motifs by Glock, P. et. al.

  Phenotypic states become increasingly sensitive to perturbations near a bifurcation in a synthetic gene network by Axelrod, K. et. al.

  The yin and yang of nature by Gore, J. & Oudenaarden, A.

 

   Plants

  Photonic multilayer structure of Begonia chloroplasts enhances photosynthetic efficiency by Jacobs, M. et. al.

  Lattice models for protein organization throughout thylakoid membrane stacks by Rosnik, A. & Geissler, P.

 

   Neuroscience

  Nonequilibrium dynamics and entropy production in the human brain by Lynn, C. et. al.

  The physics of brain network structure, function and control by Lynn, C. & Bassett, D.

  Abstract representations of events arise from mental errors in learning and memory by Lynn, C. et. al.

  Human information processing in complex networks by Lynn, C. et. al.

  Relations between large-scale brain connectivity and effects of regional stimulation depend on collective dynamical state by Papadopoulos, L. et. al.

  How humans learn and represent networks by Lynn, C. & Bassett, D.

 

   Communities & Ecosystems

  Turning ecology and evolution against cancer by Korolev, K. et. al.

  Generic Indicators for Loss of Resilience Before a Tipping Point Leading to Population Collapse by Dai, L. et. al.

  Direct observation of increasing recovery length before collapse of a marine benthic ecosystem by Rindi, L. et. al.

  Ecological suicide in microbes by Ratzke, C. et. al.

  Random sequences rapidly evolve into de novo promoters by Yona, A. et. al.

  Microbial interactions lead to rapid micro-scale successions on model marine particles by Datta, M. et. al.

  Community structure follows simple assembly rules in microbial microcosms by Friedman, J. et. al.

  Strength of species interactions determines biodiversity and stability in microbial communities by Ratzke, C. et. al.

  Slower recovery in space before collapse of connected populations by Dai, L. et. al.

 

   Quantum Systems

  Predicting many properties of a quantum system from very few measurements by Huang, H. et. al.

  Quantum Chaotic Environments, the Butterfly Effect, and Decoherence by Karkuszewski, Z. et. al.

 

   Inorganic "Life"

  Light-induced self assembly of active rectification devices by Stenhammar, J. et. al.

  Does a growing static length scale control the glass transition? by Wyart, M. & Cates, M.

  Self-Excited Motions of Volatile Drops on Swellable Sheets by Chakrabarti, A. et. al.

 

   Artificial Intelligence

  Thermodynamic Computing by Still, S. et. al.

  Statistical Mechanics of Deep Learning by Bahri, Y. et. al.