Related papers: Relative Entropy Methods for the Approximation of …
We introduce a scheme for deriving an optimally-parametrised Langevin dynamics of few collective variables from data generated in molecular dynamics simulations. The drift and the position-dependent diffusion profiles governing the Langevin…
We derive and analyze numerical methods for underdamped (kinetic) Langevin dynamics in a domain with elastic reflection at the boundary. First-order approximations are based on an Euler-type scheme incorporating collision-handling at the…
Langevin integrators based on operator splitting are widely used in molecular dynamics. This work examines Langevin splitting schemes from the perspective of their internal trajectories and observation points, complementing existing…
We present a comparative study of Langevin dynamics and a Metropolis random walk model applied to thermal neutron-induced fission of $^{229}$Th, $^{235}$U, $^{239}$Pu, $^{245}$Cm, $^{249}$Cf, and $^{255}$Fm. Both methods are implemented…
The quantitative convergence to equilibrium for reaction-diffusion systems arising from complex balanced chemical reaction networks with mass action kinetics is studied by using the so-called entropy method. In the first part of the paper,…
A theory for chemical reaction dynamics in condensed phase systems based on the generalized Langevin formalism of Grote and Hynes is presented. A microscopic approach to calculate the dynamic friction is developed within the framework of a…
Microscopic formula to describe the entropy of biomolecular solutions are derived based on the Gibbs formula of entropy, and the generalized Langevin theory combined with the RISM/3D-RISM theory. Two formula are derived: one is concerned…
Following [21, 23], the present work investigates a new relative entropy-regularized algorithm for solving the optimal transport on a graph problem within the randomized shortest paths formalism. More precisely, a unit flow is injected into…
Reaction-diffusion equations are widely used as the governing evolution equations for modeling many physical, chemical, and biological processes. Here we derive reaction-diffusion equations to model transport with reactions on a…
Simplicity is a critical inductive bias for designing data-driven controllers, especially when robustness is important. Despite the impressive results of deep reinforcement learning in complex control tasks, it is prone to capturing…
A central object in the computational studies of rare events is the committor function. Though costly to compute, the committor function encodes complete mechanistic information of the processes involving rare events, including reaction…
We study the trajectories of a solution $X_t$ to an It\^o stochastic differential equation in $\Rm^d$, as the process passes between two disjoint open sets, $A$ and $B$. These segments of the trajectory are called transition paths or…
We consider the problem of approximating the Langevin dynamics of inertial particles being transported by a background flow. In particular, we study an acceleration corrected advection-diffusion approximation to the Langevin dynamics, a…
We investigate random walks on a lattice with imperfect traps. In one dimension, we perturbatively compute the survival probability by reducing the problem to a particle diffusing on a closed ring containing just one single trap. Numerical…
We propose a trajectory-based quasiclassical method for approximating dynamics in condensed phase systems. Building upon the previously developed Optimized Mean Trajectory (OMT) approximation that has been used to compute linear and…
We propose a method to exactly generate bridge run-and-tumble trajectories that are constrained to start at the origin with a given velocity and to return to the origin after a fixed time with another given velocity. The method extends the…
Relativistic effects in the thermodynamical properties of interacting particle systems are investigated within the framework of the relativistic direct interaction theory in various forms of dynamics. In the front form of relativistic…
Trajectories represent the mobility of moving objects and thus is of great value in data mining applications. However, trajectory data is enormous in volume, so it is expensive to store and process the raw data directly. Trajectories are…
Condensed ionic systems are described in the framework of a combined approach that takes into account both long-range and short-range interactions. Short-range interaction is expressed in terms of mean potentials and long-range interaction…
Transfer entropy has been used to quantify the directed flow of information between source and target variables in many complex systems. While transfer entropy was originally formulated in discrete time, in this paper we provide a framework…