相关论文: Implementing Reactivity in Molecular Dynamics Simu…
The direct-forcing immersed boundary method (DF-IBM) algorithm previously developed by the authors is extended by coupling the Navier-Stokes equations with the Newton-Euler equations for rigid body dynamics within the DF-IBM framework. This…
By performing an ensemble of molecular dynamics simulations, the model-dependent ionisation state is computed for strongly interacting systems self-consistently. This is accomplished through a free energy minimisation framework based on the…
The quality of biomolecular simulations critically depends on the accuracy of the force field used to calculate the potential energy of the molecular configurations. Currently, most simulations employ non-polarisable force fields, which…
Electronic structure methods offer in principle accurate predictions of molecular properties, however, their applicability is limited by computational costs. Empirical methods are cheaper, but come with inherent approximations and are…
Atomic force microscopy (AFM) enables high-resolution imaging and quantitative force measurement, which is critical for understanding nanoscale mechanical, chemical, and biological interactions. In dynamic AFM modes, however, interaction…
As computational chemistry methods evolve, dynamic effects have been increasingly recognized to govern chemical reaction pathways in both organic and inorganic systems. Here, we introduce a committor-based workflow that integrates a…
Contact-rich tasks present significant challenges for robotic manipulation policies due to the complex dynamics of contact and the need for precise control. Vision-based policies often struggle with the skill required for such tasks, as…
Interatomic-force measurements are regularly performed using frequency-modulation atomic force microscopy. This requires conversion of the observed shift in the resonant frequency of a force-sensing cantilever, to the actual force…
The advances of machine-learned force fields have opened up molecular dynamics (MD) simulations for compounds for which ab-initio MD is too resource-intensive and phenomena for which classical force fields are insufficient. Here we describe…
We present GridFF, an efficient method for simulating molecules on rigid substrates, derived from techniques used in protein-ligand docking in biochemistry. By projecting molecule-substrate interactions onto precomputed spatial grids with…
Small mechanical forces play important functional roles in many crucial cellular processes, including in the dynamical behavior of the cytoskeleton and in the regulation of osmotic pressure through membrane-bound proteins. Molecular…
Coarse-grained (CG) molecular simulations have become a standard tool to study molecular processes on time- and length-scales inaccessible to all-atom simulations. Parameterizing CG force fields to match all-atom simulations has mainly…
The dynamics of dissipative soft-sphere gases obeys Newton's equation of motion which are commonly solved numerically by (force-based) Molecular Dynamics schemes. With the assumption of instantaneous, pairwise collisions, the simulation can…
The development and implementation of increasingly accurate methods for electronic structure calculations mean that, for many atomistic simulation problems, treating light nuclei as classical particles is now one of the most serious…
Machine learning interatomic potentials (MLIPs) offer an efficient and accurate framework for large-scale molecular dynamics (MD) simulations, effectively bridging the gap between classical force fields and \textit{ab initio} methods. In…
Molecular dynamics (MD) simulation techniques are widely used for various natural science applications. Increasingly, machine learning (ML) force field (FF) models begin to replace ab-initio simulations by predicting forces directly from…
The interaction of condensed phase systems with external electric fields is crucial in myriad processes in nature and technology ranging from the field-directed motion of cells (galvanotaxis), to energy storage and conversion systems…
The development of computational models for the numerical simulation of chemically reacting flows operating in the turbulent regime requires the solution of partial differential equations that represent the balance of mass, linear momentum,…
We present a general mathematical procedure to handle interactions described by a Morse potential in the presence of a strong harmonic excitation. We account for permanent and field-induced terms and their gradients in the dipole moment…
Despite the intense activity at the electronic and atomistic resolutions, coarse grained (CG) modeling of MOFs remains largely unexplored. One of the main reasons for this is the lack of adequate CG force fields. In this work, we present…