Related papers: Molecular Dynamics with Conformationally Dependent…
The application of a matrix-based reconstruction protocol for obtaining Molecular Frame (MF) photoelectron angular distributions (MFPADs) from laboratory frame (LF) measurements (LFPADs) is explored. Similarly to other recent works on the…
Classical empirical force fields have dominated biomolecular simulation for over 50 years. Although widely used in drug discovery, crystal structure prediction, and biomolecular dynamics, they generally lack the accuracy and transferability…
Chemically-active colloids modify the concentration of chemical solutes surrounding them in order to self-propel. In doing so, they generate long-ranged hydrodynamic flows and chemical gradients that modify the trajectories of other…
This dissertation presents an investigation into the electrical properties of two types of G4-DNA and several DNA-based molecules, targeting them as candidates for molecular wires and devices. Atomic force microscopy (AFM) and electrostatic…
The Cellular Potts Model (CPM) is a robust, cell-level methodology for simulation of biological tissues and morphogenesis. Both tissue physiology and morphogenesis depend on diffusion of chemical morphogens in the extra-cellular fluid or…
In this manuscript, we undertake an examination of a classical plasma deployed on two finite co-planar surfaces: a circular region $\Omega_{in}$ into an annular region $\Omega_{out}$ with a gap in between. It is studied both from the point…
In the molecular dynamics calculations for the free energy of ions and ionic molecules, we often encounter wet charged molecular systems where electrical neutrality condition is broken. This causes a problem in the evaluation of…
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…
We propose a method for multi-scale hybrid simulations of molecular dynamics (MD) and computational fluid dynamics (CFD). In the method, usual lattice-mesh based simulations are applied for CFD level, but each lattice is associated with a…
Simulating the molecular dynamics (MD) using classical or semi-classical trajectories provides important details for the understanding of many chemical reactions, protein folding, drug design, and solvation effects. MD simulations using…
The molecular dipole moment ($\boldsymbol{\mu}$) is a central quantity in chemistry. It is essential in predicting infrared and sum-frequency generation spectra, as well as induction and long-range electrostatic interactions. Furthermore,…
Accurate simulations of a condensed system of ions or polar molecules are concerned with proper handlings of the involved electrostatics. For such a Coulomb system at a charged planar interface, the Coulomb interaction averaged over the…
The influence of nearest-neighbor diffusion on the decay of a metastable low-coverage phase (monolayer adsorption) in a square lattice-gas model of electrochemical metal deposition is investigated by kinetic Monte Carlo simulations. The…
The analysis of the damage on plasma facing materials (PFM), due to its direct interaction with the plasma environment, is needed to build the next generation of nuclear machines, where tungsten has been proposed as a candidate. In this…
Molecular fragment or embedding methods are powerful techniques for overcoming scalability limitations in electronic structure theory by dividing large molecular systems into individual units that are small enough to be treated using…
This paper introduces a new approach for simulating magnetic properties of nanocomposites comprising magnetic particles embedded in a non-magnetic matrix, taking into account the 3D structure of the system in which particles' positions…
Molecular Density Functional Theory (MDFT) offers an efficient implicit- solvent method to estimate molecule solvation free-energies whereas conserving a fully molecular representation of the solvent. Even within a second order ap-…
We present a machine learning (ML) method for predicting electronic structure correlation energies using Hartree-Fock input.The total correlation energy is expressed in terms of individual and pair contributions from occupied molecular…
In this work, we analytically examine the validity of molecular dynamics for a soft potential system by considering a simple one-dimensional system with a piecewise continuous linear repulsive potential wall having a constant slope $a$. We…
Interfaces between molecules and 2D materials exhibit energy-driven functionalities, wherein charge transfer directs molecular motion. Unlike equilibrium systems, where molecular assemblies settle into static configurations, continuous…