Coarse-Grained Modelling Out of Equilibrium
arXiv:2107.09972 · doi:10.1016/j.physrep.2022.04.006
Abstract
Active matter, responsive ("smart") materials and materials under time-dependent load are systems out of thermal equilibrium. To construct coarse-grained models for such systems, one needs to integrate out a distribution of microstates that evolves in time. This is a challenging task. As a preparation to the topic, we recall equilibrium coarse-graining methods, both theoretical and numerical, such as projection operator formalisms, united atom simulations, numerical reconstruction of memory and Markov State Modelling. Then we review recent developments in theoretical approaches to the non-equilibrium coarse-graining problem, in particular, time-dependent projection operator formalisms, dynamic density functional theory and power functional theory, as well as numerical schemes to contruct explicitly time-dependent memory kernels.
References in corpus (55)
- A nonequilibrium equality for free energy differences
- Stochastic thermodynamics, fluctuation theorems, and molecular machines
- Interatomic potentials from first-principles calculations: the force-matching method
- Identification of slow molecular order parameters for Markov model construction
- Dynamic Density Functional Theory of Fluids
- Perspective: Dissipative Particle Dynamics
- Structural, mechanical and thermodynamic properties of a coarse-grained DNA model
- Stochastic thermodynamics: Principles and perspectives
- Dynamical density functional theory and its application to spinodal decomposition
- Adaptive Resolution Molecular Dynamics Simulation: Changing the Degrees of Freedom on the Fly
- Lattice Boltzmann simulations of soft matter systems
- Variational cross-validation of slow dynamical modes in molecular kinetics
- Hamiltonian adaptive resolution simulation for molecular liquids
- Data-driven parameterization of the generalized Langevin equation
- Iterative Reconstruction of Memory Kernels
- Adaptive Resolution Simulation of Liquid Water
- From Electrons to Finite Elements: A Concurrent Multiscale Approach for Metals
- Power functional theory for Brownian dynamics
- Molecular hydrodynamics from memory kernels
- Brownian motion from molecular dynamics
- Hamiltonian and Brownian systems with long-range interactions
- The Generalized Langevin Equation: An efficient approach to non-equilibrium molecular dynamics of open systems
- Generalized Langevin equation and fluctuation-dissipation theorem for particle-bath systems in external oscillating fields
- Markov State Models from short non-Equilibrium Simulations - Analysis and Correction of Estimation Bias
- Numerical Integration of the Extended Variable Generalized Langevin Equation with a Positive Prony Representable Memory Kernel
- On the "generalized Generalized Langevin Equation"
- Hamiltonian and Brownian systems with long-range interactions: V. Stochastic kinetic equations and theory of fluctuations
- Adaptive Markov State Model estimation using short reseeding trajectories
- A Dynamic Subgrid Scale Model for Large Eddy Simulations Based on the Mori-Zwanzig Formalism
- Mori-Zwanzig projection operator formalism for systems with time-dependent Hamiltonians
- Application of the t-model of optimal prediction to the estimation of the rate of decay of solutions of the Euler equations in two and three dimensions
- Data-driven molecular modeling with the generalized Langevin equation
- Hamiltonian and Brownian systems with long-range interactions: III. The BBGKY hierarchy for spatially inhomogeneous systems
- The Derivation and Approximation of Coarse-grained Dynamics from Langevin Dynamics
- Velocity gradient power functional for Brownian dynamics
- Projection operators in statistical mechanics: a pedagogical approach
- Hamiltonian and Brownian systems with long-range interactions: IV. General kinetic equations from the quasilinear theory
- On the dynamics of reaction coordinates in classical, time-dependent, many-body processes
- Identification of kinetic order parameters for non-equilibrium dynamics
- Data-driven closures for stochastic dynamical systems
- Optimal data-driven estimation of generalized Markov state models for non-equilibrium dynamics
- Accretion of the relativistic Vlasov gas onto a moving Schwarzschild black hole: Exact solutions
- The Glass Transition in Driven Granular Fluids: A Mode-Coupling Approach
- Cycle representatives for the coarse-graining of systems driven into a non-equilibrium steady state
- Parametrizing linear generalized Langevin dynamics from explicit molecular dynamics simulations
- Reconsidering the structure of nucleation theories
- Model reduction techniques for the computation of extended Markov parameterizations for generalized Langevin equations
- Structure and position-dependent properties of inhomogeneous suspensions of responsive colloids
- Renormalized reduced models for singular PDEs
- Memory effects in the Fermi-Pasta-Ulam Model
- Channel Flow of a Tensorial Shear-Thinning Maxwell Model: Lattice Boltzmann Simulations
- Non-equilibrium Markov state modeling of periodically driven biomolecules
- Non-Equilibrium Markov State Modeling of the Globule-Stretch Transition
- Extrapolation to nonequilibrium from coarse grained response theory
- Comments on the validity of the non-stationary Generalized Langevin Equation as a coarse-grained evolution equation for microscopic stochastic dynamics
Cited by in corpus (35)
- Power functional theory for many-body dynamics
- A review of active matter reviews
- Perspective: How to overcome dynamical density functional theory
- Perspective: New directions in dynamical density functional theory
- Why neural functionals suit statistical mechanics
- Ab Initio Generalized Langevin Equation
- Generalized Langevin dynamics simulation with non-stationary memory kernels: How to make noise
- Mechanical feedback controls the emergence of dynamical memory in growing tissue monolayers
- Mori-Zwanzig formalism for general relativity: a new approach to the averaging problem
- Neural force functional for non-equilibrium many-body colloidal systems
- Understanding probability and irreversibility in the Mori-Zwanzig projection operator formalism
- Learning protein-ligand unbinding pathways via single-parameter community detection
- Modeling of biomolecular machines in non-equilibrium steady states
- Force renormalization for probes immersed in an active bath
- Memory effects in colloidal motion under confinement and driving
- Unraveling Internal Friction in a Coarse-Grained Protein Model
- Molecular origin of driving-dependent friction in fluids
- A Gauss-Newton method for iterative optimization of memory kernels for generalized Langevin thermostats in coarse-grained molecular dynamics simulations
- Generalized nonlinear Langevin equation from quantum nonlinear projection operator
- Machine learning stochastic differential equations for the evolution of order parameters of classical many-body systems in and out of equilibrium
- Viscosity of polymer melts using non-affine theory based on vibrational modes
- Langevin equations and a geometric integration scheme for the overdamped limit of rotational Brownian motion of axisymmetric particles
- Dynamics of micro and nanoscale systems in the weak-memory regime: A mathematical framework beyond the Markov approximation
- On the generalized Langevin equation and the Mori projection operator technique
- Nonlinear Langevin functionals for a driven probe
- Active Ornstein-Uhlenbeck Model for Bacterial Heat Engines
- Non-equilibrium attractor for non-linear stochastic dynamics
- Nonequilibrium free energy during polymer chain growth
- Nonequilibrium friction and free energy estimates for kinetic coarse-graining -- Driven particles in responsive media
- Coarse-graining nonequilibrium diffusions with Markov chains
- Position-dependent memory kernel in generalized Langevin equations: theory and numerical estimation
- Non-equilibrium (thermo)dynamics of colloids under mobile piston compression
- The concept of minimal dissipation and the identification of work in autonomous systems: A view from classical statistical physics
- Weak-Memory Dynamics in Discrete Time
- Modulating internal transition kinetics in responsive macromolecules by collective crowding