Related papers: Practical guide to replica exchange transition int…
Computer simulations have become an important tool across the biomedical sciences and beyond. For many important problems several different models or hypotheses exist and choosing which one best describes reality or observed data is not…
Interest in equilibrium-based sampling methods has grown with recent advances in computational hardware and Markov state modeling (MSM) methods, yet outstanding questions remain that hinder widespread adoption. Namely, how do sampling…
We introduce a path sampling method for obtaining statistical properties of an arbitrary stochastic dynamics. The method works by decomposing a trajectory in time, estimating the probability of satisfying a progress constraint, modifying…
This article presents a multi-physics methodology for the numerical simulation of physical systems that involve the non-linear interaction of multi-phase reactive fluids and elastoplastic solids, inducing high strain-rates and high…
Few-Shot Instance Segmentation (FSIS) requires detecting and segmenting novel classes with limited support examples. Existing methods based on Region Proposal Networks (RPNs) face two issues: 1) Overfitting suppresses novel class objects;…
Frequently, the design of physicochemical processes requires screening of large numbers of alternative designs with complex geometries. These geometries may result in conformal meshes which introduce stability issues, significant…
We introduce a method for predicting RNA folding pathways, with an application to the most important RNA tetraloops. The method is based on the idea that ensembles of three-dimensional fragments extracted from high-resolution crystal…
Distinguishing between reconfigurable intelligent surface (RIS) assisted paths and non-line-of-sight (NLOS) paths is a fundamental problem for RIS-assisted integrated sensing and communication. In this work, we propose a pattern alternation…
System dynamics is a popular approach in many fields of science and technology, but it has not been investigated for cell signaling pathways yet. It is a well formulated methodology used to analyze the components of a system considering the…
We perform a systematic comparison of various numerical schemes for the approximation of interface problems. We consider unfitted approaches in view of their application to possibly moving configurations. Particular attention is paid to the…
With the increased penetrations of distributed energy resources (DERs), the need for integrated transmission and distribution system analysis (T&D) is imperative. This paper presents an integrated unbalanced T&D analysis framework using an…
Simulation experiments are typically conducted repeatedly during the model development process, for example, to re-validate if a behavioral property still holds after several model changes. Approaches for automatically reusing and…
We investigate a generic, parallel replica-exchange framework for Monte Carlo simulations based on the Wang-Landau method. To demonstrate its advantages and general applicability for massively parallel simulations of complex systems, we…
Accurate representation of interfaces and flux exchange is vital for coupled multiphysics simulations across a broad range of applications. Currently, coupling approaches are limited by the underlying discretization or to specific physical…
Molecular dynamics simulations have become essential in many areas of atomistic modelling from drug discovery to materials science. They provide critical atomic-level insights into key dynamical events experiments cannot easily capture.…
The explosion of data throughout the biomedical sciences provides unprecedented opportunities to learn about the dynamics of evolution and disease progression, but harnessing these large and diverse datasets remains challenging. Here, we…
We propose a new method for molecular dynamics and Monte Carlo simulations, which is referred to as the replica-permutation method (RPM), to realize more efficient sampling than the replica-exchange method (REM).In RPM not only exchanges…
Normal molecular dynamics simulations are usually unable to simulate chemical reactions due to the low probability of forming the transition state. Therefore, enhanced sampling methods are implemented to accelerate the occurrence of…
We present a molecular simulation method to simultaneously find multiple transition pathways, and their associated free-energy profiles. The scheme extends path-metadynamics (PMD) [Phys. Rev. Lett. 109, 020601 (2012)] with multiple paths…
Temporal point processes are powerful generative models for event sequences that capture complex dependencies in time-series data. They are commonly specified using autoregressive models that learn the distribution of the next event from…