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Along with recent progress in structural biology and genome biology, structural dynamics of molecular systems including nucleic acids has attracted attention in the context of gene regulation. Structure-function relationship is an important…
We have revisited the composition dependence of principal properties of liquid water-DMSO mixtures by using the isobaric-isothermal molecular dynamics computer simulations. A set of non-polarizable semi-flexible models for the DMSO molecule…
Conformations of a single-component bottle-brush polymer with a fully flexible backbone under poor solvent conditions are studied by molecular-dynamics simulations, using a coarse-grained bead-spring model with side chains of up to N=40…
Acid solutions exhibit a variety of complex structural and dynamical features arising from the presence of multiple interacting reactive proton defects and counterions. However, disentangling the transient structural motifs of proton…
Recent experiments have identified peptides with adhesion affinity for GaAs and Si surfaces. Here we use all-atom Monte Carlo (MC) simulations with implicit solvent to investigate the behavior in aqueous solution of four such peptides, all…
We investigate the dynamical motion of particles on a two-dimensional symmetric periodic substrate in the presence of both a dc drive along a symmetry direction of the periodic substrate and an additional circular ac drive. For large enough…
Sophorolipids are well-known scaled-up microbial glycolipid biosurfactants with a strong potential for commercialization due to their biological origin and mildness in contact with the skin and the environment compared to classical…
Investigation of dynamics in dense granular media is challenging. Here we present a setup that facilitates gas fluidization of dense granular media in microgravity. The dynamics is characterized using diffusing wave spectroscopy. We…
In molecular liquids such as water, time-delayed influences between microscopic or mesoscopic variables are typically probed using time-correlation functions, which are symmetric under detailed balance and therefore blind to dynamical…
Structure-based virtual screening aims to identify high-affinity ligands by estimating binding free energies between proteins and small molecules. However, the conformational flexibility of both proteins and ligands challenges conventional…
Molecular dynamics simulations have been performed on pure liquid water, aqueous solutions of sodium chloride, and polymer solutions exposed to a strong external electric field with the goal to gain molecular insight into the structural…
Cellulose nanocrystals (CNCs) are rodlike biosourced colloidal particles used as key building blocks in a growing number of materials with innovative mechanical or optical properties. While CNCs form stable suspensions at low volume…
Understanding of the molecular interaction between asphaltenes and other molecules, which may act as its solvents, provides insights into the nature of its stability in petroleum fluids and its phase transitions. Molecular dynamics…
To evaluate shear viscosity of ethylene glycol oligomers (EGO)/water binary mixture by means of coarse-grained molecular dynamics (CG-MD) simulations, we proposed the self-diffusion-coefficient-based parameterization of non-bonded…
The dynamics of a folded protein is studied in water and glycerol at a series of temperatures below and above their respective dynamical transition. The system is modeled in two distinct states whereby the protein is decoupled from the bulk…
An articulated body is defined as a finite number of rigid bodies connected by a set of arbitrary constraints that limit the relative motion between pairs of bodies. Such a general definition encompasses a wide variety of situations in the…
Stokesian Dynamics (SD) is a numerical framework used for simulating hydrodynamic interactions in particle suspensions at low Reynolds number. It combines far-field approximations with near-field lubrication corrections, offering a balance…
We have developed x-ray diffraction measurements with high energy-resolution and accuracy to study water structure at three different temperatures (7, 25 and 66 C) under normal pressure. Using a spherically curved Ge crystal an energy…
The dynamics of membranes, shells and capsules in fluid flow has become an active research area in computational physics and computational biology. The small thickness of these elastic materials enables their efficient approximation as a…
Low Reynolds number direct simulations of large populations of hydrodynamically interacting swimming particles confined between planar walls are performed. The results of simulations are compared with a theory that describes dilute…