1
|
Ghimenti F, Berthier L, Szamel G, van Wijland F. Irreversible Boltzmann samplers in dense liquids: Weak-coupling approximation and mode-coupling theory. Phys Rev E 2024; 110:034604. [PMID: 39425341 DOI: 10.1103/physreve.110.034604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Accepted: 07/29/2024] [Indexed: 10/21/2024]
Abstract
Exerting a nonequilibrium drive on an otherwise equilibrium Langevin process brings the dynamics out of equilibrium but can also speed up the approach to the Boltzmann steady state. Transverse forces are a minimal framework to achieve dynamical acceleration of the Boltzmann sampling. We consider a simple liquid in three space dimensions subjected to additional transverse pairwise forces, and quantify the extent to which transverse forces accelerate the dynamics. We first explore the dynamics of a tracer in a weak coupling regime describing high temperatures. The resulting acceleration is correlated with a monotonous increase of the magnitude of odd transport coefficients (mobility and diffusivity) with the amplitude of the transverse drive. We then develop a nonequilibrium version of the mode-coupling theory able to capture the effect of transverse forces, and more generally of forces created by additional degrees of freedom. Based on an analysis of transport coefficients, both odd and longitudinal, both for the collective modes and for a tracer particle, we find a systematic acceleration of the dynamics. Quantitatively, the gain, which is guaranteed throughout the ergodic phase, turns out to be a decreasing function of temperature beyond a temperature crossover, in particular as the glass transition is approached. Our theoretical results are in good agreement with available numerical results.
Collapse
|
2
|
Park JM, Park H, Lee JS. Stochastic differential equation for a system coupled to a thermostatic bath via an arbitrary interaction Hamiltonian. Phys Rev E 2024; 110:014143. [PMID: 39160900 DOI: 10.1103/physreve.110.014143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 06/20/2024] [Indexed: 08/21/2024]
Abstract
The conventional Langevin equation offers a mathematically convenient framework for investigating open stochastic systems interacting with their environment or a bath. However, it is not suitable for a wide variety of systems whose dynamics rely on the nature of the environmental interaction, as the equation does not incorporate any specific information regarding that interaction. Here, we present a stochastic differential equation (SDE) for an open system coupled to a thermostatic bath via an arbitrary interaction Hamiltonian. This SDE encodes the interaction information to a fictitious potential (mean force) and a position-dependent damping coefficient. Surprisingly, we find that the conventional Langevin equation can be recovered in the presence of arbitrary strong interactions given two conditions: translational invariance of the potential and mutual independence of baths. Our results provide a comprehensive framework for studying open stochastic systems with an arbitrary interaction Hamiltonian and yield deeper insight into why various experiments fit the conventional Langevin description regardless of the strength or type of interaction.
Collapse
|
3
|
Khali SS, Peruani F, Chaudhuri D. When an active bath behaves as an equilibrium one. Phys Rev E 2024; 109:024120. [PMID: 38491633 DOI: 10.1103/physreve.109.024120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 01/22/2024] [Indexed: 03/18/2024]
Abstract
Active scalar baths consisting of active Brownian particles are characterized by a non-Gaussian velocity distribution, a kinetic temperature, and a diffusion coefficient that scale with the square of the active velocity v_{0}. While these results hold in overdamped active systems, inertial effects lead to normal velocity distributions, with kinetic temperature and diffusion coefficient increasing as ∼v_{0}^{α} with 1<α<2. Remarkably, the late-time diffusivity and mobility decrease with mass. Moreover, we show that the equilibrium Einstein relation is asymptotically recovered with inertia. In summary, the inertial mass restores an equilibriumlike behavior.
Collapse
Affiliation(s)
| | - Fernando Peruani
- LPTM, CY Cergy Paris Université, 2 Avenue A. Chauvin, 95302 Cergy-Pontoise Cedex, France
| | - Debasish Chaudhuri
- Institute of Physics, Sachivalaya Marg, Bhubaneswar 751005, India
- Max-Planck Institute for the Physics of Complex Systems, Nöthnitzer Strasse 38, 01187 Dresden, Germany
| |
Collapse
|
4
|
Benois A, Jardat M, Dahirel V, Démery V, Agudo-Canalejo J, Golestanian R, Illien P. Enhanced diffusion of tracer particles in nonreciprocal mixtures. Phys Rev E 2023; 108:054606. [PMID: 38115513 DOI: 10.1103/physreve.108.054606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 10/19/2023] [Indexed: 12/21/2023]
Abstract
We study the diffusivity of a tagged particle in a binary mixture of Brownian particles with nonreciprocal interactions. Numerical simulations reveal that, for a broad class of interaction potentials, nonreciprocity can significantly increase the long-time diffusion coefficient of tracer particles and that this diffusion enhancement is associated with a breakdown of the Einstein relation. These observations are quantified and confirmed via two different and complementary analytical approaches: (i) a linearized stochastic density field theory, which is particularly accurate in the limit of soft interactions, and (ii) a reduced two-body description, which is exact at leading order in the density of particles. The latter reveals that diffusion enhancement can be attributed to the formation of transiently propelled dimers of particles, whose cohesion and speed are controlled by the nonreciprocal interactions.
Collapse
Affiliation(s)
- Anthony Benois
- Sorbonne Université, CNRS, Physico-Chimie des Électrolytes et Nanosystèmes Interfaciaux (PHENIX), 75005 Paris, France
| | - Marie Jardat
- Sorbonne Université, CNRS, Physico-Chimie des Électrolytes et Nanosystèmes Interfaciaux (PHENIX), 75005 Paris, France
| | - Vincent Dahirel
- Sorbonne Université, CNRS, Physico-Chimie des Électrolytes et Nanosystèmes Interfaciaux (PHENIX), 75005 Paris, France
| | - Vincent Démery
- Gulliver, UMR CNRS 7083, ESPCI Paris PSL, 75005 Paris, France
- Université Lyon, ENS de Lyon, Université Claude Bernard, CNRS, Laboratoire de Physique, F-69342 Lyon, France
| | - Jaime Agudo-Canalejo
- Department of Living Matter Physics, Max Planck Institute for Dynamics and Self-Organization, D-37077 Göttingen, Germany
| | - Ramin Golestanian
- Department of Living Matter Physics, Max Planck Institute for Dynamics and Self-Organization, D-37077 Göttingen, Germany
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, OX1 3PU Oxford, United Kingdom
| | - Pierre Illien
- Sorbonne Université, CNRS, Physico-Chimie des Électrolytes et Nanosystèmes Interfaciaux (PHENIX), 75005 Paris, France
| |
Collapse
|
5
|
Bernard O, Jardat M, Rotenberg B, Illien P. On analytical theories for conductivity and self-diffusion in concentrated electrolytes. J Chem Phys 2023; 159:164105. [PMID: 37873957 DOI: 10.1063/5.0165533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 09/19/2023] [Indexed: 10/25/2023] Open
Abstract
Describing analytically the transport properties of electrolytes, such as their conductivity or the self-diffusion of the ions, has been a central challenge of chemical physics for almost a century. In recent years, this question has regained some interest in light of Stochastic Density Field Theory (SDFT) - an analytical framework that allows the approximate determination of density correlations in fluctuating systems. In spite of the success of this theory to describe dilute electrolytes, its extension to concentrated solutions raises a number of technical difficulties, and requires simplified descriptions of the short-range repulsion between the ions. In this article, we discuss recent approximations that were proposed to compute the conductivity of electrolytes, in particular truncations of Coulomb interactions at short distances. We extend them to another observable (the self-diffusion coefficient of the ions) and compare them to earlier analytical approaches, such as the mean spherical approximation and mode-coupling theory. We show how the treatment of hydrodynamic effects in SDFT can be improved, that the choice of the modified Coulomb interactions significantly affects the determination of the properties of the electrolytes, and that comparison with other theories provides a guide to extend SDFT approaches in this context.
Collapse
Affiliation(s)
- Olivier Bernard
- Sorbonne Université, CNRS, Laboratoire PHENIX (Physicochimie des Electrolytes et Nanosystèmes Interfaciaux), 4 Place Jussieu, 75005 Paris, France
| | - Marie Jardat
- Sorbonne Université, CNRS, Laboratoire PHENIX (Physicochimie des Electrolytes et Nanosystèmes Interfaciaux), 4 Place Jussieu, 75005 Paris, France
| | - Benjamin Rotenberg
- Sorbonne Université, CNRS, Laboratoire PHENIX (Physicochimie des Electrolytes et Nanosystèmes Interfaciaux), 4 Place Jussieu, 75005 Paris, France
| | - Pierre Illien
- Sorbonne Université, CNRS, Laboratoire PHENIX (Physicochimie des Electrolytes et Nanosystèmes Interfaciaux), 4 Place Jussieu, 75005 Paris, France
| |
Collapse
|
6
|
Démery V, Gambassi A. Non-Gaussian fluctuations of a probe coupled to a Gaussian field. Phys Rev E 2023; 108:044604. [PMID: 37978697 DOI: 10.1103/physreve.108.044604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 10/02/2023] [Indexed: 11/19/2023]
Abstract
The motion of a colloidal probe in a complex fluid, such as a micellar solution, is usually described by the generalized Langevin equation, which is linear. However, recent numerical simulations and experiments have shown that this linear model fails when the probe is confined and that the intrinsic dynamics of the probe is actually nonlinear. Noting that the kurtosis of the displacement of the probe may reveal the nonlinearity of its dynamics also in the absence confinement, we compute it for a probe coupled to a Gaussian field and possibly trapped by a harmonic potential. We show that the excess kurtosis increases from zero at short times, reaches a maximum, and then decays algebraically at long times, with an exponent which depends on the spatial dimensionality and on the features and correlations of the dynamics of the field. Our analytical predictions are confirmed by numerical simulations of the stochastic dynamics of the probe and the field where the latter is represented by a finite number of modes.
Collapse
Affiliation(s)
- Vincent Démery
- Gulliver, CNRS, ESPCI Paris PSL, 75005 Paris, France and Univ Lyon, ENS de Lyon, CNRS, Laboratoire de Physique, F-69342 Lyon, France
| | - Andrea Gambassi
- SISSA-International School for Advanced Studies and INFN, 34136 Trieste, Italy
| |
Collapse
|
7
|
Jardat M, Dahirel V, Illien P. Diffusion of a tracer in a dense mixture of soft particles connected to different thermostats. Phys Rev E 2022; 106:064608. [PMID: 36671123 DOI: 10.1103/physreve.106.064608] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022]
Abstract
We study the dynamics of a tracer in a dense mixture of particles connected to different thermostats. Starting from the overdamped Langevin equations that describe the evolution of the system, we derive the expression of the self-diffusion coefficient of a tagged particle in the suspension, in the limit of soft interactions between the particles. Our derivation, which relies on the linearization of the Dean-Kawasaki equations obeyed by the density fields and on a path-integral representation of the dynamics of the tracer, extends previous derivations that held for tracers in contact with a single bath. Our analytical result is confronted to results from Brownian dynamics simulations. The agreement with numerical simulations is very good even for high densities. We show how the diffusivity of tracers can be affected by the activity of a dense environment of soft particles that may represent polymer coils-a result that could be of relevance in the interpretation of measurements of diffusivity in biological media. Finally, our analytical result is general and can be applied to the diffusion of tracers coupled to different types of fluctuating environments, provided that their evolution equations are linear and that the coupling between the tracer and the bath is weak.
Collapse
Affiliation(s)
- Marie Jardat
- Sorbonne Université, CNRS, Laboratoire PHENIX (Physico-Chimie des Électrolytes et Nanosystèmes Interfaciaux, PHENIX), 4 Place Jussieu, 75005 Paris, France
| | - Vincent Dahirel
- Sorbonne Université, CNRS, Laboratoire PHENIX (Physico-Chimie des Électrolytes et Nanosystèmes Interfaciaux, PHENIX), 4 Place Jussieu, 75005 Paris, France
| | - Pierre Illien
- Sorbonne Université, CNRS, Laboratoire PHENIX (Physico-Chimie des Électrolytes et Nanosystèmes Interfaciaux, PHENIX), 4 Place Jussieu, 75005 Paris, France
| |
Collapse
|
8
|
Meerson B, Bénichou O, Oshanin G. Path integrals for fractional Brownian motion and fractional Gaussian noise. Phys Rev E 2022; 106:L062102. [PMID: 36671110 DOI: 10.1103/physreve.106.l062102] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 11/23/2022] [Indexed: 12/15/2022]
Abstract
Wiener's path integral plays a central role in the study of Brownian motion. Here we derive exact path-integral representations for the more general fractional Brownian motion (FBM) and for its time derivative process, fractional Gaussian noise (FGN). These paradigmatic non-Markovian stochastic processes, introduced by Kolmogorov, Mandelbrot, and van Ness, found numerous applications across the disciplines, ranging from anomalous diffusion in cellular environments to mathematical finance. Their exact path-integral representations were previously unknown. Our formalism exploits the Gaussianity of the FBM and FGN, relies on the theory of singular integral equations, and overcomes some technical difficulties by representing the action functional for the FBM in terms of the FGN for the subdiffusive FBM and in terms of the derivative of the FGN for the super-diffusive FBM. We also extend the formalism to include external forcing. The exact and explicit path-integral representations make inroads in the study of the FBM and FGN.
Collapse
Affiliation(s)
- Baruch Meerson
- Racah Institute of Physics, Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Olivier Bénichou
- Laboratoire de Physique Théorique de la Matière Condensée, UMR CNRS 7600, CNRS, Sorbonne Université, 4 Place Jussieu, 75252 Paris Cedex 05, France
| | - Gleb Oshanin
- Laboratoire de Physique Théorique de la Matière Condensée, UMR CNRS 7600, CNRS, Sorbonne Université, 4 Place Jussieu, 75252 Paris Cedex 05, France.,Dipartimento di Scienze Matematiche, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy
| |
Collapse
|
9
|
Venturelli D, Gambassi A. Inducing oscillations of trapped particles in a near-critical Gaussian field. Phys Rev E 2022; 106:044112. [PMID: 36397516 DOI: 10.1103/physreve.106.044112] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 09/09/2022] [Indexed: 06/16/2023]
Abstract
We study the nonequilibrium dynamics of two particles confined in two spatially separated harmonic potentials and linearly coupled to the same thermally fluctuating scalar field, a cartoon for optically trapped colloids in contact with a medium close to a continuous phase transition. When an external periodic driving is applied to one of these particles, a nonequilibrium periodic state is eventually reached in which their motion synchronizes thanks to the field-mediated effective interaction, a phenomenon already observed in experiments. We fully characterize the nonlinear response of the second particle as a function of the driving frequency, in particular far from the adiabatic regime in which the field can be assumed to relax instantaneously. We compare the perturbative, analytic solution to its adiabatic approximation, thus determining the limits of validity of the latter, and we qualitatively test our predictions against numerical simulations.
Collapse
Affiliation(s)
- Davide Venturelli
- SISSA-International School for Advanced Studies and INFN, via Bonomea 265, 34136 Trieste, Italy
| | - Andrea Gambassi
- SISSA-International School for Advanced Studies and INFN, via Bonomea 265, 34136 Trieste, Italy
| |
Collapse
|
10
|
Rassolov G, Tociu L, Fodor E, Vaikuntanathan S. From predicting to learning dissipation from pair correlations of active liquids. J Chem Phys 2022; 157:054901. [DOI: 10.1063/5.0097863] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Active systems, which are driven out of equilibrium by local non-conservative forces, can adopt unique behaviors and configurations. Towards designing such materials, an important challenge is to precisely connect the static structure of active systems to the dissipation of energy induced by the local driving. Here, we use tools from liquid-state theories and machine learning to take on these challenges. We first demonstrate analytically for an isotropic active matter system that dissipation and pair correlations are closely related when driving forces behave like an active temperature. We then extend a nonequilibrium mean-field framework for predicting these pair correlations which, unlike most existing approaches, is applicable even for strongly interacting particles and far from equilibrium, to predict dissipation in these systems. Based on this theory, we reveal analytically a robust relation between dissipation and structure which holds even as the system approaches a nonequilibrium phase transition. Finally, we construct a neural network which maps static configurations of particles to their dissipation rate without any prior knowledge of the underlying dynamics. Our results open novel perspectives on the interplay between dissipation and organization out-of-equilibrium.
Collapse
Affiliation(s)
| | - Laura Tociu
- The University of Chicago, United States of America
| | | | | |
Collapse
|
11
|
Venturelli D, Ferraro F, Gambassi A. Nonequilibrium relaxation of a trapped particle in a near-critical Gaussian field. Phys Rev E 2022; 105:054125. [PMID: 35706305 DOI: 10.1103/physreve.105.054125] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 04/22/2022] [Indexed: 06/15/2023]
Abstract
We study the nonequilibrium relaxational dynamics of a probe particle linearly coupled to a thermally fluctuating scalar field and subject to a harmonic potential, which provides a cartoon for an optically trapped colloid immersed in a fluid close to its bulk critical point. The average position of the particle initially displaced from the position of mechanical equilibrium is shown to feature long-time algebraic tails as the critical point of the field is approached, the universal exponents of which are determined in arbitrary spatial dimensions. As expected, this behavior cannot be captured by adiabatic approaches which assumes fast field relaxation. The predictions of the analytic, perturbative approach are qualitatively confirmed by numerical simulations.
Collapse
Affiliation(s)
- Davide Venturelli
- SISSA-International School for Advanced Studies and INFN, via Bonomea 265, 34136 Trieste, Italy
| | - Francesco Ferraro
- Alumnus, Physics Department, University of Trento, via Sommarive, 14 I-38123 Trento, Italy
| | - Andrea Gambassi
- SISSA-International School for Advanced Studies and INFN, via Bonomea 265, 34136 Trieste, Italy
| |
Collapse
|
12
|
Gross M, Gambassi A, Dietrich S. Fluctuations of the critical Casimir force. Phys Rev E 2021; 103:062118. [PMID: 34271666 DOI: 10.1103/physreve.103.062118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 05/20/2021] [Indexed: 11/07/2022]
Abstract
The critical Casimir force (CCF) arises from confining fluctuations in a critical fluid and thus it is a fluctuating quantity itself. While the mean CCF is universal, its (static) variance has previously been found to depend on the microscopic details of the system which effectively set a large-momentum cutoff in the underlying field theory, rendering it potentially large. This raises the question how the properties of the force variance are reflected in experimentally observable quantities, such as the thickness of a wetting film or the position of a suspended colloidal particle. Here, based on a rigorous definition of the instantaneous force, we analyze static and dynamic correlations of the CCF for a conserved fluid in film geometry for various boundary conditions within the Gaussian approximation. We find that the dynamic correlation function of the CCF is independent of the momentum cutoff and decays algebraically in time. Within the Gaussian approximation, the associated exponent depends only on the dynamic universality class but not on the boundary conditions. We furthermore consider a fluid film, the thickness of which can fluctuate under the influence of the time-dependent CCF. The latter gives rise to an effective non-Markovian noise in the equation of motion of the film boundary and induces a distinct contribution to the position variance. Within the approximations used here, at short times, this contribution grows algebraically in time whereas, at long times, it saturates and contributes to the steady-state variance of the film thickness.
Collapse
Affiliation(s)
- Markus Gross
- Max-Planck-Institut für Intelligente Systeme, Heisenbergstraße 3, 70569 Stuttgart, Germany.,IV. Institut für Theoretische Physik, Universität Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Andrea Gambassi
- SISSA-International School for Advanced Studies and INFN, via Bonomea 265, 34136 Trieste, Italy
| | - S Dietrich
- Max-Planck-Institut für Intelligente Systeme, Heisenbergstraße 3, 70569 Stuttgart, Germany.,IV. Institut für Theoretische Physik, Universität Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| |
Collapse
|
13
|
Cividini J, Mukamel D, Posch HA. Driven tracers in narrow channels. Phys Rev E 2017; 95:012110. [PMID: 28208398 DOI: 10.1103/physreve.95.012110] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Indexed: 06/06/2023]
Abstract
Steady-state properties of a driven tracer moving in a narrow two-dimensional (2D) channel of quiescent medium are studied. The tracer drives the system out of equilibrium, perturbs the density and pressure fields, and gives the bath particles a nonzero average velocity, creating a current in the channel. Three models in which the confining effect of the channel is probed are analyzed and compared in this study: the first is the simple symmetric exclusion process (SSEP), for which the stationary density profile and the pressure on the walls in the frame of the tracer are computed. We show that the tracer acts like a dipolar source in an average velocity field. The spatial structure of this 2D strip is then simplified to a one-dimensional (1D) SSEP, in which exchanges of position between the tracer and the bath particles are allowed. Using a combination of mean-field theory and exact solution in the limit where no exchange is allowed gives good predictions of the velocity of the tracer and the density field. Finally, we show that results obtained for the 1D SSEP with exchanges also apply to a gas of overdamped hard disks in a narrow channel. The correspondence between the parameters of the SSEP and of the gas of hard disks is systematic and follows from simple intuitive arguments. Our analytical results are checked numerically.
Collapse
Affiliation(s)
- J Cividini
- Department of Physics of Complex Systems, Weizmann Institute of Science Rehovot, Israel 76100
| | - D Mukamel
- Department of Physics of Complex Systems, Weizmann Institute of Science Rehovot, Israel 76100
| | - H A Posch
- Computational Physics Group, Faculty of Physics, Universität Wien, Boltzmanngasse 5, 1090 Vienna, Austria
| |
Collapse
|
14
|
Camley BA, Lerner MG, Pastor RW, Brown FLH. Strong influence of periodic boundary conditions on lateral diffusion in lipid bilayer membranes. J Chem Phys 2016; 143:243113. [PMID: 26723598 DOI: 10.1063/1.4932980] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The Saffman-Delbrück hydrodynamic model for lipid-bilayer membranes is modified to account for the periodic boundary conditions commonly imposed in molecular simulations. Predicted lateral diffusion coefficients for membrane-embedded solid bodies are sensitive to box shape and converge slowly to the limit of infinite box size, raising serious doubts for the prospects of using detailed simulations to accurately predict membrane-protein diffusivities and related transport properties. Estimates for the relative error associated with periodic boundary artifacts are 50% and higher for fully atomistic models in currently feasible simulation boxes. MARTINI simulations of LacY membrane protein diffusion and LacY dimer diffusion in DPPC membranes and lipid diffusion in pure DPPC bilayers support the underlying hydrodynamic model.
Collapse
Affiliation(s)
- Brian A Camley
- Center for Theoretical Biological Physics and Department of Physics, University of California, San Diego, California 92093, USA
| | - Michael G Lerner
- Department of Physics and Astronomy, Earlham College, Richmond, Indiana 47374, USA
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Frank L H Brown
- Department of Physics, University of California, Santa Barbara, California 93106, USA
| |
Collapse
|
15
|
Camley BA, Brown FLH. Fluctuating hydrodynamics of multicomponent membranes with embedded proteins. J Chem Phys 2015; 141:075103. [PMID: 25149817 DOI: 10.1063/1.4892802] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A simulation method for the dynamics of inhomogeneous lipid bilayer membranes is presented. The membrane is treated using stochastic Saffman-Delbrück hydrodynamics, coupled to a phase-field description of lipid composition and discrete membrane proteins. Multiple applications are considered to validate and parameterize the model. The dynamics of membrane composition fluctuations above the critical point and phase separation dynamics below the critical point are studied in some detail, including the effects of adding proteins to the mixture.
Collapse
Affiliation(s)
- Brian A Camley
- Department of Physics and Center for Theoretical Biological Physics, University of California, San Diego, La Jolla, California 92093, USA
| | - Frank L H Brown
- Department of Physics, University of California, Santa Barbara, Santa Barbara, California 93106, USA
| |
Collapse
|
16
|
Démery V. Diffusion of a particle quadratically coupled to a thermally fluctuating field. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 87:052105. [PMID: 23767485 DOI: 10.1103/physreve.87.052105] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Revised: 04/02/2013] [Indexed: 06/02/2023]
Abstract
We study the diffusion of a Brownian particle quadratically coupled to a thermally fluctuating field. In the weak-coupling limit, a path-integral formulation allows us to compute the effective diffusion coefficient in the cases of an active particle, which tends to suppress field fluctuations, and of a passive particle, which only undergoes field fluctuations. We show that the behavior is similar to what was previously found for a linear coupling: an active particle is always slowed down, whereas a passive particle is slowed down in a slow field and accelerated in a fast field. Numerical simulations show a good agreement with the analytical calculations. The examples of a membrane protein coupled to the curvature or composition of the membrane are discussed, with a focus on the room for anomalous diffusion.
Collapse
Affiliation(s)
- Vincent Démery
- Institut Jean Le Rond d'Alembert, CNRS and UPMC, Université Paris 6, UMR 7190, F-75005 Paris, France.
| |
Collapse
|