Related papers: Internal water and microsecond dynamics in myoglob…
We report here a molecular dynamics simulation study on water and aqueous LiCl solutions confined in 1.6 nm cylindrical pores of silica to investigate a dynamical cross-over, observed earlier experimentally, wherein LiCl slows down confined…
Separation of salt ions from seawater using graphene oxide (GO) membrane is an emerging desalination method. Here, we investigate the dynamic behavior of water, sodium, and chloride ions inside GO membrane using a computational approach.…
Lipid bilayers forming biological membranes are known to behave as viscous 2D fluids on submicrometer scales; usually they contain a large number of active protein inclusions. Recently, it has been shown [Proc. Nat. Acad. Sci. USA 112,…
Collision cross sections and rate constants between two ground- state oxygen molecules are investigated theoretically at translational energies below $\sim 1$K and in zero magnetic field. We present calculations for elastic and spin-…
Among other improvements, the Martini 3 coarse-grained force field provides a more accurate description of the solvation of protein pockets and channels through the consistent use of various bead types and sizes. Here, we show that the…
Motivated by recent experiments of motile bacteria crossing liquid-liquid interfaces of isotropic- nematic coexistence (Cheon et al., Soft Matter 20: 7313-7320, 2024), we study the dynamics of prolate microswimmers traversing clean…
MAB phases (MABs) are atomically-thin laminates of ceramic/metallic-like layers, having made a breakthrough in the development of 2D materials. Though theoretically offering a vast chemical and phase space, relatively few MABs have yet been…
In this study, the thermal relaxation of the 20 naturally occurring amino-acids in water is investigated using transient non-equilibrium molecular-dynamics simulations. By modeling the thermal relaxation process, the relaxation times of the…
A low-temperature dynamical transition has been reported in several proteins. We provide the first observation of a `protein-like' dynamical transition in nonbiological aqueous environments. To this aim we exploit the popular colloidal…
We investigate whether an interpretation of water's thermodynamics [Science, 319, 582 (2008)] by using analogy with the binary metal alloys lambda-type ordering transition or buckminsterfullerene's orientational-ordering transition has…
Water's ability to self-dissociate into H$_3$O$^+$ and OH$^-$ ions is central to acid-base chemistry and bioenergetics. Recent experimental advances have enabled the confinement of water down to the nanometre scale, even to the…
By performing molecular dynamics simulations with up to 132 million coarse-grained particles in half-micron sized boxes, we show that hydrodynamics quantitatively explains the finite-size effects on diffusion of lipids, proteins, and carbon…
Swimming droplets are a class of active particles whose motility changes as a function of time due to shrinkage and self-avoidance of their trail. Here we combine experiments and theory to show that our non-Markovian droplet (NMD) model,…
The zero point kinetic energy of protons in water is large on the scale of chemical interaction energies(29 Kj/mol in bulk room temperature water). Its value depends upon the structure of the hydrogen bond network, and can change as the…
Water molecules on lipid membrane surfaces are known to contribute to membrane stability by connecting lipid molecules and acting as a water bridge. Although the number of water molecules near the membrane fluctuates dynamically, the…
The normal modes and relaxation rates of weak colloidal gels are investigated in computations employing different models of the hydrodynamic interactions between colloids. The eigenspectrum is computed for freely draining,…
Microorganisms are rarely found in Nature swimming freely in an unbounded fluid. Instead, they typically encounter other organisms, hard walls, or deformable boundaries such as free interfaces or membranes. Hydrodynamic interactions between…
We numerically investigate the hydrodynamics and membrane dynamics of multicomponent vesicles in two strongly confined geometries. This serves as a simplified model for red blood cells undergoing large deformations while traversing narrow…
An efficient simulation method is presented for Brownian fiber suspensions, which includes both uncrossability of the fibers and hydrodynamic interactions between the fibers mediated by a mesoscopic solvent. To conserve hydrodynamics,…
Motivated by the implications of the complex and dynamic modular geometry of an enzyme on its motion, we investigate the effect of combining long-range internal and external hydrodynamic interactions due to thermal fluctuations with…