Related papers: A Simplified Approach to Simulating Raman Spectra …
LAMMPS is a widely popular classical Molecular Dynamics package. It was designed for materials modeling but it is well prepared for simulations in Soft Matter. The use packages like LAMMPS has advantages and disadvantages. The main…
Chemical potential of species in solution is essential for understanding various chemical processes at interfaces. Molecular dynamics (MD) simulations, constrained by fixed compositions, cannot satisfy a constant chemical potential…
In this paper we demonstrate how asymmetric molecular rotational spectra may be introduced to students both "pictorially" and with simple formulae. It is shown that the interpretation of such spectra relies heavily upon pattern recognition.…
Molecules are the most demanding quantum systems to be simulated by quantum computers because of their complexity and the emergent role of quantum nature. The recent theoretical proposal of Huh et al. (Nature Photon., 9, 615 (2015)) showed…
A novel approach to simulate simple protein-ligand systems at large time- and length-scales is to couple Markov state models (MSMs) of molecular kinetics with particle-based reaction-diffusion (RD) simulations, MSM/RD. Currently, MSM/RD…
We describe an approach based on non-equilibrium molecular dynamics (NEMD) simulations to calculate the ionic mobility of solid ion conductors such as solid electrolytes from first-principles. The calculations are carried out in finite…
The dissociation of ligands from proteins and other biomacromolecules occurs over a wide range of timescales. For most pharmaceutically relevant inhibitors, these timescales are far beyond those that are accessible by conventional molecular…
Accelerated molecular dynamics (MD) simulations are implemented to model the sliding process of AFM experiments at speeds close to those found in experiment. In this study the hyperdynamics method, originally devised to extend MD time…
Vibrational spectra of condensed and gas-phase systems containing light nuclei are influenced by their quantum-mechanical behaviour. The quantum dynamics of light nuclei can be approximated by the imaginary time path integral (PI)…
This work combines for the first time ab initio molecular dynamics (AIMD) within the Born-Oppenheimer approximation, with a global natural orbital functional (GNOF), an approximate functional of the one-particle reduced density matrix. The…
We present a new reduced-order computational method for the molecular dynamics simulation of entangled polymer systems. The polymer chains are modeled as continuous Gaussian chains. Our algorithm is based on the application of the molecular…
A general method for rotational microwave spectroscopy and control of polar molecular ions via direct microwave addressing is considered. Our method makes use of spatially varying AC Stark shifts, induced by far off-resonant, focused laser…
We present a novel approach to model ultrafast time-dependent nonlinear optical polarization sensitive signals emitted from randomly-oriented molecules. By projecting the laboratory-frame analyzer polarization axis into the molecular frame…
Context: Radiation-MHD simulations have become a standard tool to investigate the physics of solar and stellar atmospheres. Aims: The aim of this paper to present a method that allows efficient and accurate analysis of flows in such…
In most cases the ultrafast dynamics of resonantly excited molecules are considered, and almost always computed in the molecular frame, while experiments are carried out in the laboratory frame. Here we provide a formalism in terms of a lab…
An iterative method is derived for image reconstruction. Among other attributes, this method allows constraints unrelated to the radiation measurements to be incorporated into the reconstructed image. A comparison is made with the widely…
A brief introduction to the projector augmented wave method is given and recent developments are reviewed. The projector augmented wave method is an all-electron method for efficient ab-initio molecular dynamics simulations with the full…
We develop a model reduction technique for non-smooth dynamical systems using spectral submanifolds. Specifically, we construct low-dimensional, sparse, nonlinear and non-smooth models on unions of slow and attracting spectral submanifolds…
The estimation of the direction of electromagnetic (EM) waves from a radio source using electrically short antennas is one of the challenging problems in the field of radio astronomy. In this paper we have developed an algorithm which…
Simulations are vital for understanding and predicting the evolution of complex molecular systems. However, despite advances in algorithms and special purpose hardware, accessing the timescales necessary to capture the structural evolution…