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The design of hybrid peptide-solid interfaces for nanotechnological applications such as biomolecular nanoarrays requires a deep understanding of the basic mechanisms of peptide binding and assembly at solid substrates. Here we show by…
We developed a multiscale approach (MultiSCAAL) that integrates the potential of mean force (PMF) obtained from all-atomistic molecular dynamics simulations with a knowledge-based energy function for coarse-grained molecular simulations in…
In the last decade, advances in molecular dynamics (MD) and Markov State Model (MSM) methodologies have made possible accurate and efficient estimation of kinetic rates and reactive pathways for complex biomolecular dynamics occurring on…
Accurately determining a change in protein binding affinity upon mutations is important for the discovery and design of novel therapeutics and to assist mutagenesis studies. Determination of change in binding affinity upon mutations…
We present a new method that enables the identification and analysis of both transition and metastable conformational states from atomistic or coarse-grained molecular dynamics (MD) trajectories. Our algorithm is presented and studied by…
Molecular dynamics (MD)-based path sampling algorithms are a very important class of methods used to study the energetics and kinetics of rare (bio)molecular events. They sample the highly informative but highly unlikely reactive…
Path-integral molecular dynamics (PIMD) simulations are crucial for accurately capturing nuclear quantum effects in materials. However, their computational intensity and reliance on multiple software packages often limit their applicability…
The biological function of proteins is encoded in their structure and expressed through the mediation of their dynamics. Local fluctuations are known to initiate biologically relevant pathways as they cooperatively enhance the dynamics in…
We investigate membrane-mediated interactions between transmembrane proteins using coarse-grained models. We compare the effective potential of mean force (PMF) between two proteins, which are always aligned parallel to the z-axis of the…
Molecular Dynamics - Green's Functions Reaction Dynamics (MD-GFRD) is a multiscale simulation method for particle dynamics or particle-based reaction-diffusion dynamics that is suited for systems involving low particle densities. Particles…
We utilize a multiscale modeling framework to study the effect of shape, size and ligand composition on the efficacy of binding of a ligand-coated-particle to a substrate functionalized with the target receptors. First, we show how…
Understanding the complex behavior of molecular systems is fundamental to fields such as physics, materials science, and biology. Molecular dynamics (MD) simulations are crucial tools for studying atomic-level dynamics. This work focuses on…
The native structures of proteins, except for notable exceptions of intrinsically disordered proteins, in general take their most stable conformation in the physiological condition to maintain their structural framework so that their…
In this work, we study the damage in crystalline molybdenum material samples due to neutron bombardment in a primary knock-on atom range of 0.5-10 keV at room temperature. We perform machine learned molecular dynamics (MD) simulations with…
This chapter describes the application of constrained geometric simulations for prediction of antibody structural dynamics. We utilize constrained geometric simulations method FRODAN, which is a low computational complexity alternative to…
Confinement can substantially alter the physicochemical properties of materials by breaking translational isotropy and rendering all physical properties position-dependent. Molecular dynamics (MD) simulations have proven instrumental in…
A novel combination of discontinuous molecular dynamics and the Langevin equation, together with an intermediate-resolution model, are used to carry out long (several $\mu$s) simulation and study folding transition and transport of proteins…
We consider the problem of estimating parameter sensitivities for stochastic models of multiscale reaction networks. These sensitivity values are important for model analysis, and, the methods that currently exist for sensitivity estimation…
Molecular dynamics simulations have been performed to understand true atomic resolution, which has been observed on the Si(111)-7$\times$7 surface by dynamic force microscopy in ultra high vacuum(UHV). Stable atomic-scale contrast is…
We propose a framework for describing the dynamics associated with the adsorption of small molecules to liquid-vapor interfaces, using an intermediate resolution between traditional continuum theories that are bereft of molecular detail and…