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To assist the design of novel, highly efficient molecular junctions, a deep understanding of the precise charge transport mechanisms through these devices is of prime importance. In the present contribution, we describe a procedure to…
We present an efficient method for evaluating current-induced forces in nanoscale junctions, which naturally integrates into the non-equilibrium Green's function formalism implemented within density functional theory. This allows us to…
In living organisms, information is processed in interconnected symphonies of ionic currents spiking through protein ion channels. As a result of dynamically switching their conductive states, ion channels exhibit a variety of…
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…
A comprehensive description of molecular electron transfer reactions is essential for our understanding of fundamental phenomena in bio-energetics and molecular electronics. Experimental studies of molecular systems in condensed-phase…
We investigate the dynamics of water confined in soft ionic nano-assemblies, an issue critical for a general understanding of the multi-scale structure-function interplay in advanced materials. We focus in particular on hydrated…
We present a new, nucleotide-level model for RNA, oxRNA, based on the coarse-graining methodology recently developed for the oxDNA model of DNA. The model is designed to reproduce structural, mechanical and thermodynamic properties of RNA,…
Cells control the size and organization of biomolecular condensates formed by liquid-liquid phase separation (LLPS), but multiple mechanisms likely contribute to this control and remain to be fully elucidated. Here we propose a…
The requirement to boost the resolution of nanopore-based biosequencing devices necessitates the integration of novel biosensing techniques with reduced sensitivity to background noise. In this article, we probe the signatures of…
Accurate calculations of electrostatic potentials and treatment of substrate polarizability are critical for predicting the permeation of ions inside water-filled nanopores. The {\it ab initio} molecular dynamics method (AIMD), based on…
The number of precise conductance measurements in nanopores is quickly growing. In order to clarify the dominant mechanisms at play and facilitate the characterization of such systems for which there is still no clear consensus, we propose…
Nanopores spanning synthetic membranes have been used as key components in proof-of-principle nanofluidic applications, particularly those involving manipulation of biomolecules or sequencing of DNA. The only practical way of manipulating…
We have proposed an efficient parameterization method for a recent variant of the Gay-Berne potential for dissimilar and biaxial particles and demonstrated it for a set of small organic molecules. Compared to the previously proposed…
We expand iterative numerically-exact influence functional path-integral tools and present a method capable of following the nonequilibrium time evolution of subsystems coupled to multiple bosonic and fermionic reservoirs simultaneously.…
Molecules in molecular junctions are subject to current-induced forces that can break chemical bonds, induce reactions, destabilize molecular geometry, and halt the operation of the junction. Theories behind current-driven molecular…
To acquire the ability to numerically study the rheology of particulate two-phase flows that lack scale separation, we present a general method to average or coarse-grain the equations of motion of a mixture of a continuous fluid of…
We coarse-grain a model of closely-packed ellipses that can vary their aspect ratio to derive continuum equations for materials comprising confluent deformable particles such as epithelial cell layers. We show that contractile nearest…
In modern applications of heterogeneous liquid-phase nanocatalysis, the catalysts (e.g., metal nanoparticles) need to be typically affixed to a colloidal carrier system for stability and easy handling. "Passive carriers" (e.g., simple…
Ionic Liquids feature thermophysical properties that are of interest in solvents, energy storage materials and tenable lubrication applications. Recently, a series of coarse grained (CG) models was developed to investigate…
Under many conditions, macroscopic grains flow like a fluid; kinetic theory pred icts continuum equations of motion for this granular fluid. In order to test the theory, we perform event driven molecular simulations of a two-dimensional gas…