Learning Force Fields from Stochastic Trajectories

When monitoring the dynamics of stochastic systems, such as interacting particles agitated by thermal noise, disentangling deterministic forces from Brownian motion is challenging. Indeed, we show that there is an information-theoretic bound, the capacity of the system when viewed as a communication channel, that limits the rate at which information about the force field can be extracted from a Brownian trajectory. This capacity provides an upper bound to the system's entropy production rate, and quantifies the rate at which the trajectory becomes distinguishable from pure Brownian motion. We propose a practical and principled method, Stochastic Force Inference, that uses this information to approximate force fields and spatially variable diffusion coefficients. It is data efficient, including in high dimensions, robust to experimental noise, and provides a self-consistent estimate of the inference error. In addition to forces, this technique readily permits the evaluation of out-of-equilibrium currents and the corresponding entropy production with a limited amount of data.

[1]  J. Neu,et al.  Fluctuation loops in noise-driven linear dynamical systems. , 2017, Physical Review E.

[2]  Jean-Baptiste Masson,et al.  A Bayesian inference scheme to extract diffusivity and potential fields from confined single-molecule trajectories. , 2012, Biophysical journal.

[3]  Federico S. Gnesotto,et al.  Broken detailed balance and non-equilibrium dynamics in living systems: a review , 2017, Reports on progress in physics. Physical Society.

[4]  M. Opper,et al.  Variational estimation of the drift for stochastic differential equations from the empirical density , 2016, 1603.01159.

[5]  M. Kunitski,et al.  Double-slit photoelectron interference in strong-field ionization of the neon dimer , 2018, Nature Communications.

[6]  M. Büttiker,et al.  Transport as a consequence of state-dependent diffusion , 1987 .

[7]  Veikko F. Geyer,et al.  Broken detailed balance at mesoscopic scales in active biological systems , 2016, Science.

[8]  K. Gawȩdzki,et al.  Eulerian and Lagrangian Pictures of Non-equilibrium Diffusions , 2009, 0905.4667.

[9]  K. Hasselmann Stochastic climate models Part I. Theory , 1976 .

[10]  S. Ciliberto,et al.  Experiments in Stochastic Thermodynamics: Short History and Perspectives , 2017 .

[11]  S. Brunton,et al.  Discovering governing equations from data by sparse identification of nonlinear dynamical systems , 2015, Proceedings of the National Academy of Sciences.

[12]  K. Gawȩdzki,et al.  Fluctuation Relations for Diffusion Processes , 2007, 0707.2725.

[13]  C. Broedersz,et al.  Broken Detailed Balance of Filament Dynamics in Active Networks. , 2016, Physical review letters.

[14]  Manifest and Subtle Cyclic Behavior in Nonequilibrium Steady States , 2016, 1610.02976.

[15]  Bo Sun,et al.  Influence of nonconservative optical forces on the dynamics of optically trapped colloidal spheres: the fountain of probability. , 2008, Physical review letters.

[16]  H. Risken Fokker-Planck Equation , 1996 .

[17]  H. Touchette Introduction to dynamical large deviations of Markov processes , 2017, Physica A: Statistical Mechanics and its Applications.

[18]  Eric Vanden-Eijnden,et al.  Diffusion Estimation from Multiscale Data by Operator Eigenpairs , 2011, Multiscale Model. Simul..

[19]  Rolf Landauer,et al.  Motion out of noisy states , 1988 .

[20]  John Bechhoefer,et al.  Real-time calibration of a feedback trap. , 2014, The Review of scientific instruments.

[21]  M. Hoffmann,et al.  Nonparametric estimation of scalar diffusions based on low frequency data , 2002, math/0503680.

[22]  Joachim Peinke,et al.  Reconstruction of complex dynamical systems affected by strong measurement noise. , 2006, Physical review letters.

[23]  Marc Hoffmann,et al.  Adaptive estimation in diffusion processes , 1999 .

[24]  M. Baiesi,et al.  Inflow rate, a time-symmetric observable obeying fluctuation relations. , 2015, Physical review. E, Statistical, nonlinear, and soft matter physics.

[25]  David J. Pine,et al.  Living Crystals of Light-Activated Colloidal Surfers , 2013, Science.

[26]  G. Roberts,et al.  Nonparametric estimation of diffusions: a differential equations approach , 2012 .

[27]  Paul C. Blainey,et al.  Optimal estimation of diffusion coefficients from single-particle trajectories. , 2013 .

[28]  Y. Kutoyants Statistical Inference for Ergodic Diffusion Processes , 2004 .

[29]  Cécile Penland,et al.  Prediction of Nino 3 sea surface temperatures using linear inverse modeling , 1993 .

[30]  Maxime Dahan,et al.  InferenceMAP: mapping of single-molecule dynamics with Bayesian inference , 2015, Nature Methods.

[31]  J. Marston,et al.  Statistics of the stochastically forced Lorenz attractor by the Fokker-Planck equation and cumulant expansions. , 2016, Physical review. E.

[32]  Jaya P. N. Bishwal,et al.  Parameter estimation in stochastic differential equations , 2007 .

[33]  Martin J. Lohse,et al.  Single-molecule imaging reveals receptor–G protein interactions at cell surface hot spots , 2017, Nature.

[34]  Juan Pablo Gonzalez,et al.  Experimental metrics for detection of detailed balance violation. , 2018, Physical review. E.

[35]  Massimo Vergassola,et al.  Bacterial strategies for chemotaxis response , 2010, Proceedings of the National Academy of Sciences.

[36]  Giorgio Volpe,et al.  High-performance reconstruction of microscopic force fields from Brownian trajectories , 2018, Nature Communications.

[37]  Eric R Dufresne,et al.  Many-body electrostatic forces between colloidal particles at vanishing ionic strength. , 2009, Physical review letters.

[38]  Muhammad Sahimi,et al.  Approaching complexity by stochastic methods: From biological systems to turbulence , 2011 .

[39]  T C Lubensky,et al.  State-dependent diffusion: Thermodynamic consistency and its path integral formulation. , 2007, Physical review. E, Statistical, nonlinear, and soft matter physics.

[40]  R. Zia,et al.  Exact results for a simple epidemic model on a directed network: explorations of a system in a nonequilibrium steady state. , 2014, Physical review. E, Statistical, nonlinear, and soft matter physics.

[41]  Raphael Sarfati,et al.  Maximum likelihood estimations of force and mobility from single short Brownian trajectories. , 2017, Soft matter.

[42]  U. Seifert,et al.  Noninvasive measurement of dissipation in colloidal systems. , 2012, Physical review. E, Statistical, nonlinear, and soft matter physics.

[43]  Jean-Baptiste Caussin,et al.  Emergence of macroscopic directed motion in populations of motile colloids , 2013, Nature.

[44]  Liang Li,et al.  ‘Dicty dynamics’: Dictyostelium motility as persistent random motion , 2011, Physical biology.

[45]  Patrick W. Oakes,et al.  Entropy production rate is maximized in non-contractile actomyosin , 2018, Nature Communications.

[46]  R. Brown XXVII. A brief account of microscopical observations made in the months of June, July and August 1827, on the particles contained in the pollen of plants; and on the general existence of active molecules in organic and inorganic bodies , 1828 .

[47]  C. Broedersz,et al.  Nonequilibrium Scaling Behavior in Driven Soft Biological Assemblies. , 2018, Physical review letters.

[48]  Udo Seifert,et al.  Thermodynamic uncertainty relation for biomolecular processes. , 2015, Physical review letters.

[49]  C. Maes,et al.  Steady state statistics of driven diffusions , 2007, 0708.0489.

[50]  U. Seifert Stochastic thermodynamics, fluctuation theorems and molecular machines , 2012, Reports on progress in physics. Physical Society.

[51]  Joachim O. Rädler,et al.  Stochastic nonlinear dynamics of confined cell migration in two-state systems , 2019, Nature Physics.

[52]  Yves Rozenholc,et al.  Penalized nonparametric mean square estimation of the coefficients of diffusion processes , 2007, 0708.4165.

[53]  S. Manley,et al.  Heterogeneity of AMPA receptor trafficking and molecular interactions revealed by superresolution analysis of live cell imaging , 2012, Proceedings of the National Academy of Sciences.

[54]  R. Tjian,et al.  Dynamics of CRISPR-Cas9 genome interrogation in living cells , 2015, Science.

[55]  M. Wheeler,et al.  An All-Season Real-Time Multivariate MJO Index: Development of an Index for Monitoring and Prediction , 2004 .

[56]  Greg J. Stephens,et al.  Dimensionality and Dynamics in the Behavior of C. elegans , 2007, PLoS Comput. Biol..

[57]  R. Netz,et al.  Butane dihedral angle dynamics in water is dominated by internal friction , 2018, Proceedings of the National Academy of Sciences.