Related papers: Molecular Dynamics with Conformationally Dependent…
Globular proteins undergo thermal fluctuations in solution, while maintaining an overall well-defined folded structure. In particular, studies have shown that the core structure of globular proteins differs in small, but significant ways…
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…
This review describes recent advances by the authors and others on the topic of incorporating experimental data into molecular simulations through maximum entropy methods. Methods which incorporate experimental data improve accuracy in…
Analytical expressions for the elastic and dynamic form factors (FFs) are derived in the shell model (SM) with a potential well of finite depth. The consideration takes into account the motion of the target-nucleus center of mass (CM).…
Heterogeneous multiscale methods (HMM) combine molecular accuracy of particle-based simulations with the computational efficiency of continuum descriptions to model flow in soft matter liquids. In these schemes, molecular simulations…
Partial atomic charges belong to key concepts of computational chemistry. In some cases, however, they fail in describing the electrostatics of molecules. One such example is the $\sigma$-hole, a region of positive electrostatic potential…
The physical foundations of the dissipation of energy and the associated heating in weakly collisional plasmas are poorly understood. Here, we compare and contrast several measures that have been used to characterize energy dissipation and…
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…
We propose a hybrid deterministic and stochastic approach to achieve extended time scales in atomistic simulations that combines the strengths of molecular dynamics (MD) and Monte Carlo (MC) simulations in an easy-to-implement way. The…
Atomic displacement parameters (ADPs) are crystallographic information that describe the statistical distribution of atoms around an atom site. Anisotropic ADPs by atom were directly derived from classical molecular dynamics (MD)…
The molecular polarizability describes the tendency of a molecule to deform or polarize in response to an applied electric field. As such, this quantity governs key intra- and inter-molecular interactions such as induction and dispersion,…
The trend to fabricate electrical circuits on nanoscale dimensions has led to impressive progress in the field of molecular electronics in the last decade. A theoretical description of molecular contacts as the building blocks of future…
We push the boundaries of electronic structure-based \textit{ab-initio} molecular dynamics (AIMD) beyond 100 million atoms. This scale is otherwise barely reachable with classical force-field methods or novel neural network and machine…
This paper extends the Lorentz-Abraham model of an electron (i.e. the equations of motion for a small spherical shell of charge, which is rigid in its proper frame) to treat a small spherically symmetric charge distribution, allowing for…
We provide a theory of the deflection of polar and non-polar rotating molecules by inhomogeneous static electric field. Rainbow-like features in the angular distribution of the scattered molecules are analyzed in detail. Furthermore, we…
Field emission coupled with molecular dynamics simulation (FEcMD) software package is a computational tool for studying the electron emission characteristics and the atomic structure evolution of micro- and nano-protrusions made of pure…
Structure, function and dynamics of many biomolecular systems can be characterized by the energetic variational principle and the corresponding systems of partial differential equations (PDEs). This principle allows us to focus on the…
Atom-centered point charge model of the molecular electrostatics---a major workhorse of the atomistic biomolecular simulations---is usually parameterized by least-squares (LS) fitting of the point charge values to a reference electrostatic…
Diffusion Monte Carlo (DMC) based on fixed-node approximation has enjoyed significant developments in the past decades and become one of the go-to methods when accurate ground state energy of molecules and materials is needed. The remaining…
Measuring bipartite fluctuations of a conserved charge, such as the particle number, is a powerful approach to understanding quantum systems. When the measured region has sharp corners, the bipartite fluctuation receives an additional…