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Three coarse-grained molecular dynamics (MD) models are investigated with the aim of developing and analyzing multiscale methods which use MD simulations in parts of the computational domain and (less detailed) Brownian dynamics (BD)…
We investigate the translocation of stiff polymers in the presence of binding particles through a nanopore by two-dimensional Langevin dynamics simulations. We find that the mean translocation time shows a minimum as a function of the…
We revisit the classical problem of flow of electrolyte solutions through charged capillary nanopores or nanotubes as described by the capillary pore model (also called "space charge" theory). This theory assumes very long and thin pores…
In recent years, molecular dynamics (MD) simulations have emerged as a pivotal tool for understanding the structure, dynamics, and phase behavior in charged soft matter systems. To explore phenomena across greater length and time scales in…
Selective ion transport is a hallmark of biological ion channel behavior but is a major challenge to engineer into artificial membranes. Here, we demonstrate, with all-atom molecular dynamics simulations, that bare graphene nanopores yield…
In charged nanopores, ionic diffusion current reflects the ionic selectivity and ionic permeability of nanopores which determines the performance of osmotic energy conversion, i.e. the output power and efficiency. Here, theoretical…
Many single molecule experiments for molecular motors comprise not only the motor but also large probe particles coupled to it. The theoretical analysis of these assays, however, often takes into account only the degrees of freedom…
The study of the ability of drug molecules to enter cells through the membrane is of vital importance in the field of drug delivery. In cases where the transport of the drug molecules through the membrane is not easily accomplishable, other…
Throughout our history, we, humans, have sought to better control and understand our environment. To this end, we have extended our natural senses with a host of sensors-tools that enable us to detect both the very large, such as the…
We study the transport of paramagnetic colloidal particles on a patterned magnetic substrate with kinetic Monte Carlo and Brownian dynamics computer simulations. The planar substrate is decorated with point dipoles in either parallel or…
We present an analytical model of salt- and water-ion transport across an ion-selective interface based on an assumption of local equilibrium of the water-dissociation reaction. The model yields current-voltage characteristics and curves of…
In this letter we perform an experimental study of ionic transport and current fluctuations inside individual Carbon Nanotubes (CNT). The conductance exhibits a power law behavior at low salinity, with an exponent close to 1/3 versus the…
We combine quantum-chemical calculations and molecular dynamics simulations to consider aqueous ion flow across non-axisymmetric nanopores in monolayer graphene and MoS$_2$. When the pore-containing membrane is subject to uniaxial tensile…
We consider a class of systems where, due to the large mismatch of dielectric constants, the Coulomb interaction is approximately one-dimensional. Examples include ion channels in lipid membranes and water filled nanopores in silicon or…
Approach-to-equilibrium molecular dynamics simulations have been used to study thermal transport in nanocrystalline graphene sheets. Nanostructured graphene has been created using an iterative process for grain growth from initial seeds…
A versatile and transferable coarse-grained (CG) model was developed to investigate the self-assembly of two ubiquitous methacrylate-based copolymers: poly(ethylene oxide-b-methylmethacrylate) (PEO-b-PMMA) and poly(ethylene…
We perform extensive coarse-grained (CG) Langevin dynamics simulations of intrinsically disordered proteins (IDPs), which possess fluctuating conformational statistics between that for excluded volume random walks and collapsed globules.…
Using a variational field theory, we show that an electrolyte confined to a neutral cylindrical nanopore traversing a low dielectric membrane exhibits a first-order ionic liquid-vapor pseudo-phase-transition from an ionic-penetration…
In this work, we develop a two-component coarse-grained molecular dynamics (CGMD) model for simulating the erythrocyte membrane. This proposed model possesses the key feature of combing the lipid bilayer and the erythrocyte cytoskeleton,…
The properties of polymer liquids on hard and soft substrates are investigated by molecular dynamics simulation of a coarse-grained bead-spring model and dynamic single-chain-in-mean-field (SCMF) simulations of a soft, coarse-grained…