Related papers: Translational Mobilities of Proteins in Nanochanne…
We employ a three-dimensional molecular dynamics to simulate translocation of a polymer through a nanopore driven by an external force. The translocation is investigated for different three pore diameter and two different external forces.…
The translocation of a polymer through a pore in a membrane separating fluids of different viscosities is studied via several computational approaches. Starting with the polymer halfway, we find that as a viscosity difference across the…
In fluid transport across nanopores, there is a fundamental dissipation that arises from the connection between the pore and the macroscopic reservoirs. This entrance effect can hinder the whole transport in certain situations, for short…
This paper presents experimental results about transport of dilute suspensions of nano-objects in silicon-glass micrometric and sub-micrometric channels. Two kinds of objects are used: solid, rigid latex beads and spherical capsule-shaped,…
Protein adsorption/desorption upon nanoparticle surfaces is an important process to understand for developing new nanotechnology involving biomaterials, while atomistic picture of the process and its coupling with protein conformational…
We investigate proteins within heterogeneous cell membranes where non-equilibrium phenomena arises from spatial variations in concentration and temperature. We develop simulation methods building on non-equilibrium statistical mechanics to…
The remaining dynamical degrees of freedom of molecular fluids confined into capillaries of nano to sub-nanometer diameter are of fundamental relevance for future developments in the field of nanofluidics. These properties cannot be simply…
The influence of spatial confinement on the thermally excited stochastic cation dynamics of the room-temperature ionic liquid 1-N-butylpyridinium bis-((trifluoromethyl)sulfonyl)imide ([BuPy][Tf_2N]) inside porous carbide-derived carbons…
We consider the dynamics of pore-driven polymer translocation through a nanopore to semi-infinite space when the chain is initially confined and equilibrated in a narrow channel. To this end, we use Langevin dynamics (LD) simulations and…
We present a coarse-grained model for evaluation of interactions of globular proteins with nanoparticles. The protein molecules are represented by one bead per aminoacid and the nanoparticle by a homogeneous sphere that interacts with the…
We evaluate the thermal conductivity of a model nanofluid at various volume fractions of nanoparticles with equilibrium (EMD) and non-equilibrium (NEMD) molecular dynamics simulations. The Green-Kubo formalism is used for the EMD…
Developing accurate and efficient coarse-grained representations of proteins is crucial for understanding their folding, function, and interactions over extended timescales. Our methodology involves simulating proteins with molecular…
The origin of the dramatic slowdown of dynamics near the glass transition temperature (Tg) remains a long-standing fundamental and unresolved issue in soft condensed matter. While single-molecule (SM) experiments using fluorescent probes…
We study translational and rotational diffusion of anisotropic gold nanoparticles (NPs) dispersed in the bulk of a nematic liquid crystal fluid host. Experimental data reveal strong anisotropy of translational diffusion with respect to the…
Recent studies have suggested that the Nuclear Pore Complex (NPC) plays a significant role in mechanotransduction. When a force is exerted, the NPC's diameter widens, leading to an increased molecular flux into the nucleus. In this study,…
Using Langevin dynamics simulations, we investigate the dynamics of polymer translocation into a circular nanocontainer through a nanopore under a driving force $F$. We observe that the translocation probability initially increases and then…
Coarse-graining (CG) accelerates molecular simulations of protein dynamics by simulating sets of atoms as singular beads. Backmapping is the opposite operation of bringing lost atomistic details back from the CG representation. While…
Enzyme-based systems have been shown to undergo directional motion in response to their substrate gradient. Here, we formulate a kinetic model to analyze the directional movement of an ensemble of protein molecules in response to a gradient…
Translational motion of neurotransmitter receptors is key for determining receptor number at the synapse and hence, synaptic efficacy. We combine live-cell STORM superresolution microscopy of nicotinic acetylcholine receptor (nAChR) with…
This paper series aims to establish a complete correspondence between fine-grained (FG) and coarse-grained (CG) dynamics by way of excess entropy scaling (introduced in Paper I). While Paper II successfully captured translational motions in…