Related papers: Water drives peptide conformational transitions
We perform lengthy molecular dynamics simulations of the SPC/E model of water to investigate the dynamics under pressure at many temperatures and compare with experimental measurements. We calculate the isochrones of the diffusion constant…
Water hydrating phospholipid membranes determine their stability and function, as well as their interaction with other molecules. In this article we study, using all-atom molecular dynamics simulations, the rotational and translational…
Wettability is a pore-scale property that impacts the relative movement and distribution of fluids in a porous medium. There are reservoir fluids that provoke the surface within pores to undergo a wettability change. This wettability…
Both molecular mechanical and quantum mechanical calculations play an important role in describing the behavior and structure of molecules. In this work, we compare for the same peptide systems the results obtained from folding molecular…
Dissipative particle dynamics (DPD) is a novel particle method for mesoscale modeling of complex fluids. DPD particles are often thought to represent packets of real atoms, and the physical scale probed in DPD models are determined by the…
We study chemically driven running droplets on a partially wetting solid substrate by means of coupled evolution equations for the thickness profile of the droplets and the density profile of an adsorbate layer. Two models are introduced…
Protein-peptide interactions play essential roles in many cellular processes and their structural characterization is the major focus of current experimental and theoretical research. Two decades ago, it was proposed to employ the steered…
Efficient water transport through nanostructure membranes is essential for advancing filtration and desalination technologies. In this study, we investigate the flow of water through molybdenum disulfide (MoS$_{2}$) nanopores of varying…
Understanding what happens inside the rippling and dancing surface of a liquid remains one of the great challenges of fluid dynamics. Using molecular dynamics (MD) we can pick apart the interface structure and understand surface tension. In…
Recent experiments on liquid water show collective dipole orientation fluctuations dramatically slower then expected (with relaxation time $>$ 50 ns) [D. P. Shelton, Phys. Rev. B {\bf 72}, 020201(R) (2005)]. Molecular dynamics simulations…
The purpose of this work is to use active particles to study the effect of facilitation on supercooled liquids. To this end we investigate the behavior of a model supercooled liquid doped with intermittently active and intermittently slowed…
Water plays a fundamental role in protein stability. However, the effect of the properties of water on the behaviour of proteins is only partially understood. Several theories have been proposed to give insight into the mechanisms of cold…
Molecular search phenomena are observed in a variety of chemical and biological systems. During the search the participating particles frequently move in complex inhomogeneous environments with random transitions between different dynamic…
A very early start up time of the hydrodynamic evolution is needed in order to reproduce observations from relativistic heavy-ion collisions experiments. At such early times the systems is still not locally equilibrated. Another source of…
It is well-known that wettability exerts fundamental control over multiphase flow in porous media, which has been extensively studied in uniform-wet porous media. In contrast, multiphase flow in porous media with heterogeneous wettability…
Molecular dynamics simulations of ultrathin water film confined between atomically flat rigid diamond plates are described. Films with thickness of one and two molecular diameters are concerned and TIP4P model is used for water molecules.…
In this paper, we use the cell dynamics method to study the dynamics of phase transformation when three phases exist. The system we study is a two-dimensional system. The system is able to achieve three phases coexistence, which for…
The dynamic transition between the ordered flow and the plastic flow is studied for a two-dimensional driven vortex lattice, in the presence of sharp and dense pinning centers, from numerical simulations. For this system, which does not…
The self-propelled motion of microscopic bodies immersed in a fluid medium is studied using molecular dynamics simulation. The advantage of the atomistic approach is that the detailed level of description allows complete freedom in…
Protein conformational changes are activated processes essential for protein functions. Activation in a protein differs from activation in a small molecule in that it involves directed and systematic energy flows through preferred channels…