Related papers: Polarizable Multipolar Molecular Dynamics Using Di…
Accounting for geometry-induced changes in the electronic distribution in molecular simulation is important for capturing effects such as charge flow, charge anisotropy and polarization. Multipolar force fields have demonstrated their…
The impact of targeted replacement of individual terms in empirical force fields is quantitatively assessed for pure water, dichloromethane (DCM), and solvated K$^+$ and Cl$^-$ ions. For the electrostatics, point charges (PCs) and machine…
We present an implementation of the fast multipole method for computing coulombic electrostatic and polarization forces from polarizable force-fields based on induced point dipole moments. We demonstrate the expected $O(N)$ scaling of that…
Accurate modelling of electrostatic interactions and charge transfer is fundamental to computational chemistry, yet most machine learning interatomic potentials (MLIPs) rely on local atomic descriptors that cannot capture long-range…
Molecular dynamics simulations of biomolecules have been widely adopted in biomedical studies. As classical point-charge models continue to be used in routine biomolecular applications, there have been growing demands on developing…
A machine learning (ML) based equivariant neural network for constructing distributed charge models (DCMs) of arbitrary resolution, DCM-net, is presented. DCMs efficiently and accurately model the anisotropy of the molecular electrostatic…
Quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations have been developed to simulate molecular systems, where an explicit description of changes in the electronic structure is necessary. However, QM/MM MD…
A proper treatment of electrostatic interactions is crucial for the accurate calculation of forces in computer simulations. Electrostatic interactions are typically modeled using Ewald based methods, which have become one of the…
A new pairwise hybrid machine-learning/molecular mechanics (ML/MM) potential is introduced that is conceived for application to large, heterogeneous condensed-phase systems. The PhysNet ML method describes monomers and short-range dimer…
We introduce a general framework for many-body force field models, the Completely Multipolar Model (CMM), that utilizes multipolar electrical moments modulated by exponential decay of electron density as a common functional form for all…
A kernel-based method (kernelized minimal distributed charge model - kMDCM) to represent the molecular electrostatic potential (ESP) in terms of off-center point charges whose positions adapts to the molecular geometry. Using Gaussian…
Electronic polarization and dispersion are decisive actors in determining interaction energies between molecules. These interactions have a particularly profound effect on excitation energies of molecules in complex environments, especially…
In recent years, molecular dynamics (MD) simulations have emerged as a pivotal tool for understanding the structure, dynamics, and phase behavior in charged soft matter systems. To explore phenomena across greater length and time scales in…
Point multipole expansions are widely used to gain physical insight into complex distributions of charges and to reduce the cost of computing interactions between such distributions. However, practical applications that typically retain…
This review summarizes recent progress in investigating polymer systems by using Differential dynamic microscopy (DDM), a rapidly emerging approach that transforms a commercial microscope by combining real-space information with the…
A molecular dynamics (MD) simulation is used to quantitatively analyze the induced membrane potential for an applied external field varied between 0.4 V/nm to 2.0 V/nm. The change in the electrostatic potential in the DPPC is directly…
We present a general procedure to introduce electronic polarization into classical Molecular Dynamics (MD) force-fields using a Neural Network (NN) model. We apply this framework to the simulation of a solid-liquid interface where the…
The dynamics of the electrons for a molecule in solution is coupled to the dynamics of its polarizable environment, i.e., the solvent. To theoretically investigate such electronic dynamics, we have recently developed equations of motion…
Accurate, yet computationally efficient energy functions are essential for state-of-the art molecular dynamics (MD) studies of condensed phase systems. Here, a generic workflow based on a combination of machine learning-based and empirical…
The issues of electronic polarizability in molecular dynamics simulations are discussed. We argue that the charges of ionized groups in proteins, and charges of ions in conventional non-polarizable force fields such as CHARMM, AMBER,…