Related papers: Lambda-ABF: Simplified, Portable, Accurate and Cos…
This study presents a novel optimisation technique for atomic structure calculations using the Flexible Atomic Code, focussing on complex multielectron systems relevant to $r$-process nucleosynthesis and kilonova modelling. We introduce a…
Inverse problems are ubiquitous because they formalize the integration of data with mathematical models. In many scientific applications the forward model is expensive to evaluate, and adjoint computations are difficult to employ; in this…
A time-fractional Allen-Cahn equation with volume constraint is first proposed by introducing a nonlocal time-dependent Lagrange multiplier. Adaptive linear second-order energy stable schemes are developed for the proposed model by…
The Lagrange multiplier method has proven highly effective for mitigating the ill-conditioning of full waveform inversion (FWI), enabling robust and computationally efficient algorithms that converge to accurate velocity models even from…
This article describes nonequilibrium techniques for the calculation of free energies of solids using molecular dynamics (MD) simulations. These methods provide an alternative to standard equilibrium thermodynamic integration methods and…
In this report, we propose a divergence-free preserving mixed finite element method (FEM) for the system of nonlinear fourth-order thermally driven active fluid equations. By introducing two auxiliary variables, we lower the complexity of…
We introduce a powerful iterative algorithm to compute protein folding pathways, with realistic all-atom force fields. Using the path integral formalism, we explicitly derive a modified Langevin equation which samples directly the ensemble…
Meshless methods are often used in numerical simulations of systems of partial differential equations (PDEs), particularly those which involve complex geometries or free surfaces. Here we present a novel compact scheme based on the local…
We present Active Learning for Accelerated Bayesian Inference (\texttt{alabi}): an open-source Python package for performing Bayesian inference with computationally expensive models. Given a forward model and observational data to construct…
We introduce force-kernel extended-system adaptive biasing force (FK-eABF), a force-based kernel reformulation of eABF that replaces the histogram-based mean-force accumulator of conventional eABF with a sparse population of Gaussian…
This paper introduces an open-source software for distributed and decentralized non-convex optimization named ALADIN-$\alpha$. ALADIN-$\alpha$ is a MATLAB implementation of tailored variants of the Augmented Lagrangian Alternating Direction…
We report the results of our participation in the SAMPL8 GDCC Blind Challenge for host-guest binding affinity predictions. Absolute binding affinity prediction is of central importance to the biophysics of molecular association and…
The calculation of the interfacial free energy between two thermodynamic phases is crucial across various fields, including materials science, chemistry, and condensed matter physics. In this study, we apply an existing thermodynamic…
We introduce the self-Relative Binding Free Energy (self-RBFE) approach to evaluate the intrinsic statistical variance of dual-topology alchemical binding free energy estimators. The self-RBFE is the relative binding free energy between a…
This study employed an artificial intelligence-enhanced molecular simulation framework to enable efficient Path Integral Molecular Dynamics (PIMD) simulations. Owing to its modular architecture and high-throughput capabilities, the…
The promise of active learning (AL) is to reduce labelling costs by selecting the most valuable examples to annotate from a pool of unlabelled data. Identifying these examples is especially challenging with high-dimensional data (e.g.…
We propose a path cover adaptive algebraic multigrid (PC-$\alpha$AMG) method for solving linear systems of weighted graph Laplacians and can also be applied to discretized second order elliptic partial differential equations. The…
A simple, efficient, and accurate method is proposed to map multi-dimensional free energy landscapes. The method combines the temperature-accelerated molecular dynamics (TAMD) proposed in [Maragliano & Vanden-Eijnden, Chem. Phys. Lett. 426,…
We propose an ab-initio molecular dynamics method, capable to reduce dramatically the autocorrelation time required for the simulation of classical and quantum particles at finite temperature. The method is based on an efficient…
This work introduces a novel adaptive mesh refinement (AMR) method that utilizes dominant balance analysis (DBA) for efficient and accurate grid adaptation in computational fluid dynamics (CFD) simulations. The proposed method leverages a…