Data-driven molecular modeling with the generalized Langevin equation
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Grogan, Francesca↗
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Coarse-Graining Conformational Dynamics with Multidimensional Generalized Langevin Equation: How, When, and Why
A data-driven ab initio generalized Langevin equation (AIGLE) approach is developed to learn and simulate high-dimensional, heterogeneous, coarse-grained (CG) conformational dynamics. Constrained by the fluctuation–dissipation theorem, the approach can build CG models in dynamical consistency (DC) with all-atom molecular dynamics. Here, we also propose practical criteria for AIGLE to enforce long-term DC. Case studies of a toy polymer, with 20 CG sites, and the alanine dipeptide, with two dihedral angles, elucidate why one should adopt AIGLE or its Markovian limit for modeling CG conformational dynamics in practice.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Ab initio generalized Langevin equation
We introduce a machine learning–based approach called ab initio generalized Langevin equation (AIGLE) to model the dynamics of slow collective variables (CVs) in materials and molecules. In this scheme, the parameters are learned from atomistic simulations based on ab initio quantum mechanical models. Force field, memory kernel, and noise generator are constructed in the context of the Mori–Zwanzig formalism, under the constraint of the fluctuation–dissipation theorem. Combined with deep potential molecular dynamics and electronic density functional theory, this approach opens the way to multiscale modeling in a variety of situations. Here, we demonstrate this capability with a study of two mesoscale processes in crystalline lead titanate, namely the field-driven dynamics of a planar ferroelectric domain wall, and the dynamics of an extensive lattice of coarse-grained electric dipoles. In the first case, AIGLE extends the reach of ab initio simulations to a regime of noise-driven motions not accessible to molecular dynamics. In the second case, AIGLE deals with an extensive set of CVs by adopting a local approximation for the memory kernel and retaining only short-range noise correlations. The scheme is computationally more efficient than molecular dynamics by several orders of magnitude and mimics the microscopic dynamics at low frequencies where it reproduces accurately the dominant far-infrared absorption frequency.
97 MATHEMATICS AND COMPUTING↗
Simulation and generalized Langevin equation study of lipid subdiffusion in biomembrane phases
In biomembranes lipid mobility exhibits deviations from the classical diffusive behavior of Brownian particles, i.e. ‘anomalous’ diffusion. The question arises as to how this anomalous diffusive behavior varies in gel, ripple, and fluid biomembrane phases. Here, in this study, we perform all-atom molecular dynamics (MD) simulations of dimyristoylphosphatidylcholine (DMPC) bilayers in the three different phases and analyze the results using the framework of the Generalized Langevin Equation (GLE). This analysis emphasizes sub-diffusive behavior on the relatively short, picosecond-nanosecond timescales, capturing local molecular constraints and transient caging effects during the crossover of atomic dynamics from vibrational to incipient anharmonic motion. The ripple and gel phases are found to exhibit strong transient caging and prolonged memory effects resulting in distinct sub-diffusive behavior. The role of hydrogen bonding in lipid confinement is also examined, demonstrating its influence on phase-dependent molecular ordering and on short-time diffusional constraints. These findings demonstrate the GLE framework’s utility in characterizing molecular transport and lipid dynamics, with implications for longer timescale membrane dynamics.
Malik, Sheeba [Oak Ridge National Laboratory (ORNL↗
Description of quantum noise by a Langevin equation
General features of the quantum noise problem expressed as the equations of motion for a particle coupled to a set of oscillators are investigated analytically. Account is taken of the properties of the companion oscillators by formulating quantum statistical correlation Langevin equations (QSLE). The frequency of the oscillators is then retained as a natural cut-off for the quantum noise. The QSLE is further extended to encompass the particle trajectory and is bounded by initial and final states of the oscillator. The states are expressed as the probability of existence at the moment of particle collision that takes the oscillator into a final state. Two noise sources then exist: a statistical uncertainty of the initial state and the quantum dynamical uncertainty associated with a transition from the initial to final state. Feynman's path-integral formulation is used to characterize the functional of the particle trajectory, which slows the particle. It is shown that the energy loss may be attributed to friction, which satisfies energy conservation laws.
Metiu, H.↗
Data-Driven Learning for the Mori--Zwanzig Formalism: A Generalization of the Koopman Learning Framework
A theoretical framework which unifies the conventional Mori--Zwanzig formalism and the approximate Koopman learning of deterministic dynamical systems from noiseless observation is presented. In this framework, the Mori--Zwanzig formalism, developed in statistical mechanics to tackle the hard problem of construction of reduced-order dynamics for high-dimensional dynamical systems, can be considered as a natural generalization of the Koopman description of the dynamical system. We next show that, similar to the approximate Koopman learning methods, data-driven methods can be developed for the Mori--Zwanzig formalism with Mori's linear projection operator. We have developed two algorithms to extract the key operators, the Markov and the memory kernel, using time series of a reduced set of observables in a dynamical system. We have adopted the Lorenz `96 system as a test problem and solved for the above operators. These operators exhibit complex behaviors, which are unlikely to be captured by traditional modeling approaches in Mori--Zwanzig analysis. The nontrivial generalized fluctuation-dissipation relationship, which relates the memory kernel with the two-time correlation statistics of the orthogonal dynamics, was numerically verified as a validation of the solved operators. Here we present numerical evidence that the generalized Langevin equation, a key construct in the Mori--Zwanzig formalism, is more advantageous in predicting the evolution of the reduced set of observables than the conventional approximate Koopman operators.
97 MATHEMATICS AND COMPUTING↗
Lectures on statistical mechanics
Presented here is a transcription of the lecture notes from Professor Allan N. Kaufman’s graduate statistical mechanics course Physics 212A and 212B at the University of California Berkeley from the 1972–1973 academic year. 212A addressed equilibrium statistical mechanics with topics: fundamentals (micro-canonical and sub-canonical ensembles, adiabatic law and action conservation, fluctuations, pressure, and virial theorem), classical fluids and other systems (equation of state, deviations from ideality, virial coefficients and van der Waals potential, canonical ensemble and partition function, quasistatic evolution, grand-canonical ensemble and partition function, chemical potential, simple model of a phase transition, quantum virial expansion, numerical simulation of equations of state, and phase transition), chemical equilibrium (systems with multiple species and chemical reactions, law of mass action, Saha equation, chemical equilibrium including ionization and excited states), and long-range interactions (including Coulomb, dipole, and gravitational interactions, Debye–Hückel theory, and shielding). 212B addressed nonequilibrium statistical mechanics with topics: fundamentals (definitions: realizations, moments, characteristic function, and discrete variables), Brownian motion (Langevin equation, fluctuation–dissipation theorem, spatial diffusion, Boltzmann’s H-theorem), Liouville and Klimontovich equations, Landau equation (derivation, elaboration, and H-theorem, and irreversibility), Markov processes and Fokker–Planck equation (derivations of the Fokker–Planck equation and a master equation), linear response and transport theory (linear Boltzmann equation, linear response theory of Kubo and Mori, relation of entropy production to electrical conductivity, transport relations and coefficients, normal mode solutions of the transport equations, sketch of a generalized Langevin equation method for transport theory), and an introduction to nonequilibrium quantum statistical mechanics.
plasma dynamics↗
Microscopic Theory of Long-Time Center-of-Mass Self-Diffusion and Anomalous Transport in Ring Polymer Liquids
We construct a microscopic theory at the level of segment-scale correlated space–time intermolecular forces for the long-time center-of-mass (CM) diffusion constant and intermediate-time non-Fickian transport in dense solutions and melts of ring polymers. The approach combines ideas of polymer, colloid, and liquid-state statistical mechanics to quantify how the multifractal intra-ring conformational structure and inter-ring packing correlations determine dynamic caging constraints and time-dependent friction. Breakdown of Rouse theory is predicted to occur due to length scale-dependent temporal correlation of forces exerted on pairs of tagged ring segments from surrounding polymers. At large enough degrees of polymerization (N), a stronger scaling of the CM diffusion constant (D ∝ N –2 ) is predicted, with a crossover N D proportional to the product of the system-specific macromolecular volume fraction and dimensionless compressibility. In analogy with caging effects in glass-forming fluids, the theory does appear to begin to fail at sufficiently high N/N D for the center-of-mass diffusivity, likely due to another crossover to an even slower activated transport regime. However, use of N/N D with the theoretically predicted N D , in conjunction with dynamic blob scaling ideas for local Rouse friction, collapses semidilute and concentrated solution simulation data onto a master curve. Based on the same physical ideas employed to predict the diffusion constant, a generalized Langevin equation description is formulated for intermediate-time CM transport. It predicts two subdiffusive regimes that emerge due to the self-similar nature of internal ring structure. Analytic and numerical predictions for the apparent non-Fickian exponent as a function of time, N/N D and dimensionless compressibility, the evolution of the maximum degree of subdiffusive motion with N/N D , and the time scale for recovering Fickian diffusion are made, all of which are in good accordance with melt simulations. Furthermore, the present work sets the stage to address activated dynamics and glass formation on the macromolecular scale.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Transfer learning of memory kernels for transferable coarse-graining of polymer dynamics
The present work concerns the transferability of coarse-grained (CG) modeling in reproducing the dynamic properties of the reference atomistic systems across a range of parameters. In particular, we focus on implicit-solvent CG modeling of polymer solutions. The CG model is based on the generalized Langevin equation, where the memory kernel plays the critical role in determining the dynamics in all time scales. Thus, we propose methods for transfer learning of memory kernels. The key ingredient of our methods is Gaussian process regression. By integration with the model order reduction via proper orthogonal decomposition and the active learning technique, the transfer learning can be practically efficient and requires minimum training data. Through two example polymer solution systems, we demonstrate the accuracy and efficiency of the proposed transfer learning methods in the construction of transferable memory kernels. The transferability allows for out-of-sample predictions, even in the extrapolated domain of parameters. Built on the transferable memory kernels, the CG models can reproduce the dynamic properties of polymers in all time scales at different thermodynamic conditions (such as temperature and solvent viscosity) and for different systems with varying concentrations and lengths of polymers.
Ma, Zhan↗
A theory of phonon-induced friction on molecular adsorbates
In this manuscript, we provide a general theory for how surface phonons couple to molecular adsorbates. Our theory maps the extended dynamics of a surface’s atomic vibrational motions to a generalized Langevin equation, and by doing so captures these dynamics in a single quantity: the non-Markovian friction. The different frequency components of this friction are the phonon modes of the surface slab weighted by their coupling to the adsorbate degrees of freedom. Using this formalism, we demonstrate that physisorbed species couple primarily to acoustic phonons while chemisorbed species couple to dispersionless local vibrations. We subsequently derive equations for phonon-adjusted reaction rates using transition state theory and demonstrate that these corrections improve agreement with experimental results for CO desorption rates from Pt(111).
Science & Technology - Other Topics↗
QES-Plume v1.0: a Lagrangian dispersion model
Low-cost simulations providing accurate predictions of transport of airborne material in urban areas, vegetative canopies, and complex terrain are demanding because of the small-scale heterogeneity of the features influencing the mean flow and turbulence fields. Common models used to predict turbulent transport of passive scalars are based on the Lagrangian stochastic dispersion model. The Quick Environmental Simulation (QES) tool is a low-computational-cost framework developed to provide high-resolution wind and concentration fields in a variety of complex atmospheric-boundary-layer environments. Part of the framework, QES-Plume, is a Lagrangian dispersion code that uses a time-implicit integration scheme to solve the generalized Langevin equations which require mean flow and turbulence fields. Here, QES-Plume is driven by QES-Winds, a 3D fast-response model that computes mass-consistent wind fields around buildings, vegetation, and hills using empirical parameterizations, and QES-Turb, a local-mixing-length turbulence model. In this paper, the particle dispersion model is presented and validated against analytical solutions to examine QES-Plume’s performance under idealized conditions. In particular, QES-Plume is evaluated against a classical Gaussian plume model for an elevated continuous point-source release in uniform flow, the Lagrangian scaling of dispersion in isotropic turbulence, and a non-Gaussian plume model for an elevated continuous point-source release in a power-law boundary-layer flow. In these cases, QES-Plume yields a maximum relative error below 6 % when compared with analytical solutions. In addition, the model is tested against wind-tunnel data for a uniform array of cubical buildings. QES-Plume exhibits good agreement with the experiment with 99 % of matched zeros and 59 % of the predicted concentrations falling within a factor of 2 of the experimental concentrations. Furthermore, results also emphasize the importance of using high-quality turbulence models for particle dispersion in complex environments. Finally, QES-Plume demonstrates excellent computational performance.
58 GEOSCIENCES↗
On the Stochastic Quantization Method: Characteristics and Applications to Singular Systems
Introducing the generalized Langevin equation, we extend the stochastic quantization method so as to deal with singular dynamical systems beyond the ordinary territory of quantum mechanics. We also show how the uncertainty relation is built up to the quantum mechanical limit with respect to fictitious time, irrespective of its initial value, within the framework of the usual stochastic quantization method.
Kanenaga, Masahiko↗
Modeling of Cavity Residence Time via Modeled Lagrangian Particle Tracking
One of the critical components in a scramjet is the cavity flame holder. In evaluating the sizing of this component, the residence time of the fuel in the cavity is a common parameter used. However, to obtain the residence time via CFD is an expensive undertaking. One method is to perform an LES simulation of the cavity and use Lagrangian particle tracking to obtain both the mean and probability density function of the time that the particles remain in the cavity. While this method affords a significant amount of information, it is very costly in CPU run time. A simpler method involves performing a time accurate RANS simulation of the cavity, and when converged, overlay a traceable scalar in the cavity region, and then record the decay of this scalar’s flux at a downstream location. The time scale of the decay rate can then be estimated and a residence time inferred. This method is less computationally expensive than the LES approach, but still requires a time-accurate solution while only providing a mean cavity residence time evaluation. In this paper a method of determining the mean cavity residence time as well as the Probability Density Function (PDF) of the residence time is proposed and demonstrated. This method is based on Lagrangian particle tracking modeled by the Generalized Langevin Equation and is implemented as a post-processing step for a steady RANS solution. Computational cost is on the order of minutes and the results are in agreement with values obtained by the LES and scalar decay methods.
Langevin↗
Dissipation in a squeezed-state environment
The problem of a quantum particle coupled to a quantum mechanical heat bath has a broad and general description in terms of a generalized quantum Langevin equation. Here we show how a squeezed state environment may be incorporated in this general framework.
Oconnell, R. F.↗
Microscopic activated dynamics theory of the shear rheology and stress overshoot in ultradense glass-forming fluids and colloidal suspensions
We formulate a particle and force level, activated dynamics-based statistical mechanical theory for the continuous startup nonlinear shear rheology of ultradense glass-forming hard sphere fluids and colloidal suspensions in the context of the elastically collective nonlinear Langevin equation approach and a generalized Maxwell model constitutive equation. Activated structural relaxation is described as a coupled local-nonlocal event involving caging and longer range collective elasticity which controls the characteristic stress relaxation time. Theoretical predictions for the deformation-induced enhancement of mobility, the onset of relaxation acceleration at remarkably low values of stress, strain, or shear rate, apparent power law thinning of the steady-state structural relaxation time and viscosity, a nonvanishing activation barrier in the shear thinning regime, an apparent Herschel–Buckley form of the shear rate dependence of the steady-state shear stress, exponential growth of different measures of a yield or flow stress with packing fraction, and reduced fragility and dynamic heterogeneity under deformation were previously shown to be in good agreement with experiments. The central new question we address here is the defining feature of the transient response—the stress overshoot. In contrast to the steady-state flow regime, understanding the transient response requires an explicit treatment of the coupled nonequilibrium evolution of structure, elastic modulus, and stress relaxation time. We formulate a new quantitative model for this aspect in a physically motivated and computationally tractable manner. Theoretical predictions for the stress overshoot are shown to be in good agreement with experimental observations in the metastable ultradense regime of hard sphere colloidal suspensions as a function of shear rate and packing fraction, and accounting for deformation-assisted activated motion appears to be crucial for both the transient and steady-state responses.
Mechanics↗
Quantum Langevin theory for two coupled phase-conjugated electromagnetic waves
We provide a general macroscopic phenomenological formula of quantum Langevin equations for two coupled phase-conjugated electromagnetic fields with linear loss (gain) and complex nonlinear coupling coefficient. The macroscopic phenomenological formula is obtained from the coupling matrix to preserve the field commutation relations and correlations, which does not require knowing the microscopic details of light-matter interaction and internal atomic structures. To validate this phenomenological formula, we take spontaneous four-wave mixing in a double-Λ four-level atomic system as an example to numerically confirm that our macroscopic phenomenological result is consistent with that obtained from the microscopic Heisenberg-Langevin theory. We find that a complex-valued nonlinear coupling coefficient can lead to noises even without linear gain or loss. Lastly, we apply the quantum Langevin equations to study the effects of linear gain and loss, complex phase mismatching, as well as complex nonlinear coupling coefficient in entangled photon pair (biphoton) generation, particularly to their temporal quantum correlations.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Electron-induced massive dynamics of magnetic domain walls
We study the dynamics of domain walls (DWs) in a metallic, ferromagnetic nanowire, focusing on inertial effects on the DW due to interaction with a conduction electron bath. In this work, we develop a Keldysh collective coordinate technique to describe the effect of conduction electrons on rigid magnetic structures. The effective Lagrangian and Langevin equations of motion for a DW are derived microscopically, including the full response kernel which is nonlocal in time. The DW dynamics is described by two collective degrees of freedom: position and tilt angle. The coupled Langevin equations therefore involve two correlated noise sources, leading to a generalized fluctuation-dissipation theorem (FDT). The DW response kernel due to electrons contains two parts: one related to dissipation via FDT and another reactive part. We prove that the latter term leads to a mass for both degrees of freedom, even though the intrinsic bare mass is zero. The electron-induced mass is present even in a clean system without pinning or specifically engineered potentials. The resulting equations of motion contain rich dynamical solutions and point toward a way to control domain wall motion in metals via the electronic system properties. We discuss two observable consequences of the mass, hysteresis in the DW dynamics, and resonant response to ac current.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Droplet model for autocorrelation functions in an Ising ferromagnet
The autocorrelation function of Ising spins in an ordered phase is studied via a droplet model. Only noninteracting spherical droplets are considered. The Langevin equation which describes fluctuations in the radius of a single droplet is studied in detail. A general description of the transformation to a Fokker-Planck equations and the ways in which a spectral analysis of that equation can be used to compute the autocorrelation function is given. It is shown that the eigenvalues of the Fokker-Planck operator form (1) a continuous spectrum of relaxation rates starting from zero for d = 2, (2) a continuous spectrum with a finite gap for d = 3, and (3) a discrete spectrum for d greater than 4, where d is the spatial dimensionality. Detailed solutions for various cases are presented.
Tang, Chao↗