Related papers: Exact dynamical coarse-graining without time-scale…
When simulating molecular systems using deterministic equations of motion (e.g., Newtonian dynamics), such equations are generally numerically integrated according to a well-developed set of algorithms that share commonly agreed-upon…
We present a differentiable formalism for learning free energies that is capable of capturing arbitrarily complex model dependencies on coarse-grained coordinates and finite-temperature response to variation of general system parameters.…
Fourier acceleration has been successfully applied to the simulation of lattice field theories for more than a decade. In this paper, we extend the method to the dynamics of discrete particles moving in continuum. Although our method is…
Nonlinear, multiplicative Langevin equations for a complete set of slow variables in equilibrium systems are generally derived on the basis of the separation of time scales. The form of the equations is universal and equivalent to that…
We consider the convergence of kinetic Langevin dynamics to its ergodic invariant measure, which is Gibbs distribution. Instead of the standard setup where the friction coefficient is a constant scalar, we investigate position-dependent…
A novel scheme to simulate the evolution of a restricted set of observables of a quantum system is proposed. The set comprises the spectrum-generating algebra of the Hamiltonian. The idea is to consider a certain open-system evolution,…
Dynamics simulations of constrained particles can greatly aid in understanding the temporal and spatial evolution of biological processes such as lateral transport along membranes and self-assembly of viruses. Most theoretical efforts in…
A variety of enhanced sampling methods predict multidimensional free energy landscapes associated with biological and other molecular processes as a function of a few selected collective variables (CVs). The accuracy of these methods is…
Stochastic modelling of complex systems plays an essential, yet often computationally intensive role across the quantitative sciences. Recent advances in quantum information processing have elucidated the potential for quantum simulators to…
Designing an appropriate set of collective variables is crucial to the success of several enhanced sampling methods. Here we focus on how to obtain such variables from information limited to the metastable states. We characterize these…
High-dimensional recordings of dynamical processes are often characterized by a much smaller set of effective variables, evolving on low-dimensional manifolds. Identifying these latent dynamics requires solving two intertwined problems:…
We analyze Lindblad-Gorini-Kossakowski-Sudarshan-type generators for selected periodically driven open quantum systems. All these generators can be obtained by temporal coarse-graining procedures, and we compare different coarse-graining…
The combination of high-dimensionality and disparity of time scales encountered in many problems in computational physics has motivated the development of coarse-grained (CG) models. In this paper, we advocate the paradigm of data-driven…
Developing effective descriptions of the microscopic dynamics of many physical phenomena can both dramatically enhance their computational exploration and lead to a more fundamental understanding of the underlying physics. Previously, an…
Understanding kinetics and thermodynamics profile of biomolecules is necessary to understand their functional roles which has a major impact in mechanism driven drug discovery. Molecular dynamics simulation has been routinely used to…
Understanding the emergence of macroscopic irreversible hydrodynamics from the reversible unitary dynamics of isolated quantum many-body systems remains a fundamental challenge. Conventional approaches often force spin density dynamics into…
Inspired by problems in biochemical kinetics, we study statistical properties of an overdamped Langevin process whose friction coefficient depends on the state of a similar, unobserved process. Integrating out the latter, we derive the long…
We review some recent coarse-graining and multi-scale methods, but also put forward some new ideas for addressing such issues. We find that, if one is guided by nonequilibrium statistical mechanics and thermodynamics, it is possible to…
Dynamic heterogeneity has often been modeled by assuming that a single-particle observable, fluctuating at a molecular scale, is influenced by its coupling to environmental variables fluctuating on a second, perhaps slower, time scale.…
Granular materials such as sand, powders, and food grains are ubiquitous in civil engineering, geoscience, agriculture, and medicine. While the influence of friction between the grains on the static structure of these systems is well…