Related papers: Computing Surface Reaction Rates by Adaptive Multi…
The efficiency of atomic simulations of materials and molecules can rapidly deteriorate when large free energy barriers exist between local minima. We propose smooth basin classification, a universal method to define reaction coordinates…
We apply the Adaptive Multilevel Splitting method to the Ceq -> Cax transition of alanine dipeptide in vacuum. Some properties of the algorithm are numerically illustrated, such as the unbiasedness of the probability estimator and the…
The means to obtain the rate constants of a chemical reaction is a fundamental open problem in both science and the industry. Traditional techniques for finding rate constants require either chemical modifications of the reactants or…
Modern potential energy surfaces have shifted attention to molecular simulations of chemical reactions. While various methods can estimate rate constants for conformational transitions in molecular dynamics simulations, their applicability…
Adaptive multilevel splitting algorithms have been introduced rather recently for estimating tail distributions in a fast and efficient way. In particular, they can be used for computing the so-called reactive trajectories corresponding to…
The primary emphasis of this work on kinetics is to illustrate the a posteriori approach to applications, where focus on data leads to novel outcomes, rather than the a priori tendencies of applied analysis which imposes constructs on the…
Finding optimal reaction coordinates and predicting accurate kinetic rates for activated processes are two of the foremost challenges of molecular simulations. We introduce an algorithm that tackles the two problems at once: starting from a…
The Adaptive Resolution Scheme (AdResS) is a hybrid scheme that allows one to treat a molecular system with different levels of resolution depending on the location of the molecules. The construction of a Hamiltonian based on the this idea…
The minimum action method (MAM) is to calculate the most probable transition path in randomly perturbed stochastic dynamics, based on the idea of action minimization in the path space. The accuracy of the numerical path between different…
Real-time video inference on edge devices like mobile phones and drones is challenging due to the high computation cost of Deep Neural Networks. We present Adaptive Model Streaming (AMS), a new approach to improving performance of efficient…
Multiphase flows are an important class of fluid flow and their study facilitates the development of diverse applications in industrial, natural, and biomedical systems. We consider a model that uses a continuum description of both phases…
We present a dual-resolution molecular dynamics (MD) simulation of liquid water employing a recently introduced Adaptive Resolution Scheme (AdResS). The spatially adaptive molecular resolution procedure allows for changing from a…
We present an Adaptively Biased Molecular Dynamics (ABMD) method for the computation of the free energy surface of a reaction coordinate using non-equilibrium dynamics. The ABMD method belongs to the general category of umbrella sampling…
Predicting how materials behave under realistic conditions requires understanding the statistical distribution of atomic configurations on crystal lattices, a problem central to alloy design, catalysis, and the study of phase transitions.…
Computing reaction rates in biomolecular systems is a common goal of molecular dynamics simulations. The reactions considered often involve conformational changes in the molecule, either changes in the structure of a protein or the relative…
Surfaces serve as highly efficient catalysts for a vast variety of chemical reactions. Typically, such surface reactions involve billions of molecules which diffuse and react over macroscopic areas. Therefore, stochastic fluctuations are…
Numerical simulations of two-phase flow and fluid structure interaction problems are of great interest in many environmental problems and engineering applications. To capture the complex physical processes involved in these problems, a high…
Ensuring the safety of autonomous vehicles (AVs) requires both accurate estimation of their performance and efficient discovery of potential failure cases. This paper introduces Bayesian adaptive multifidelity sampling (BAMS), which…
When numerically solving partial differential equations, for a given problem and operating condition, adaptive mesh refinement (AMR) has proven its efficiency to automatically build a discretization achieving a prescribed accuracy at low…
A stable added-mass partitioned (AMP) algorithm is developed for fluid-structure interaction (FSI) problems involving viscous incompressible flow and compressible elastic solids. Deforming composite grids are used to effectively handle the…