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The design and implementation of a new framework for adaptive mesh refinement (AMR) calculations is described. It is intended primarily for applications in astrophysical fluid dynamics, but its flexible and modular design enables its use…
Ensuring a satisfactory statistical convergence of anharmonic thermodynamic properties requires sampling of many atomic configurations, however the methods to obtain those necessarily produce correlated samples, thereby reducing the…
Alumina and aluminum oxyhydroxides underpin chemical-engineering technologies from heterogeneous catalysis, corrosion protection, functional coatings, energy-storage devices, to biomedical components. Yet molecular models that predictively…
Alchemical Grid Dock (AlGDock) is open-source software designed to compute the binding potential of mean force (BPMF) - the binding free energy between a flexible ligand and a rigid receptor - for a small organic ligand and a biological…
We present Entropy Adaptive Decoding (EAD), a novel approach for efficient language model inference that dynamically switches between different-sized models based on prediction uncertainty. By monitoring rolling entropy in model logit…
Ultrafast, time-resolved spectroscopies enable the direct observation of non-equilibrium processes in condensed-phase systems and have revealed key insights into energy transport, hydrogen-bond dynamics, and vibrational coupling. While ab…
Often gaining insight into the functioning of biomolecular systems requires to follow their dynamics along a microscopic reaction coordinate (RC) on a macroscopic time scale, which is beyond the reach of current all atom molecular dynamics…
Understanding how different classes of molecules move across biological membranes is a prerequisite to predicting a solute's permeation rate, which is a critical factor in the fields of drug design and pharmacology. We use biased Molecular…
The exact and phaseless variants of Auxiliary-Field Quantum Monte Carlo (AFQMC) have been shown to be capable of producing accurate ground-state energies for a wide variety of systems including those which exhibit substantial electron…
For optimal control problems that involve planning and following a trajectory, two degree of freedom (2DOF) controllers are a ubiquitously used control architecture that decomposes the problem into a trajectory generation layer and a…
In this study, we introduce a novel open-source chemistry model for OpenFOAM to speed-up the reactive computational fluid dynamics (CFD) simulations using finite-rate chemistry. First, a dynamic load balancing model called DLBFoam is…
Interpolating scattered CFD datasets onto a uniform Cartesian grid can distort the true geometry, producing a convex-hull type envelope and activating nonphysical regions. This work presents a reconstruction framework that recovers…
We propose a computationally efficient approach to the nonadiabatic time-dependent density functional theory (TDDFT) which is based on a representation of the frequency-dependent exchange correlation kernel as a response of a set of damped…
We present an energy-preserving mechanic formulation for dynamic quasi-brittle fracture in an Eulerian-Lagrangian formulation, where a second-order phase-field equation controls the damage evolution. The numerical formulation adapts in…
Quantum computing has made tremendous progress in recent years, providing potentialities for breaking the bottleneck of computing power in the field of scientific computing, like computational fluid dynamics. To reduce computational costs…
We have developed a thorough and accurate method of determining anharmonic free energies, the temperature dependent effective potential technique (TDEP). It is based on \emph{ab initio} molecular dynamics followed by a mapping onto a model…
The augmented Lagrangiam method (ALM), widely used in quantum chemistry constrained optimization problems, is applied in the context of the nuclear Density Functional Theory (DFT) in the self-consistent constrained Skyrme…
We prove the convergence of an adaptive mixed finite element method (AMFEM) for (nonsymmetric) convection-diffusion-reaction equations. The convergence result holds from the cases where convection or reaction is not present to convection-or…
In conventional well-known derivation methods for the adaptive Thouless-Anderson-Palmer (TAP) free energy, special assumptions that are difficult to mathematically justify except in some mean-field models, must be made. Here, we present a…
We present Q-AMOEBA (CF), an enhanced version of the Q-AMOEBA polarizable model that integrates a geometry-dependent charge flux (CF) term while designed for an explicit treatment of nuclear quantum effects (NQE). The inclusion of CF…