相关论文: The low-density/high-density liquid phase transiti…
Due to efficient scaling with electron number N, density functional theory (DFT) is widely used for studies of large molecules and solids. Restriction of an exact mean-field theory to local potential functions has recently been questioned.…
We explore the microstructure and phase behavior of confined soft colloids which can actively switch their interactions at a predefined kinetic rate. For this, we employ a reaction-diffusion approach based on a reactive dynamical…
The phase transition of confined fluids in mesoporous materials deviates from that of bulk fluids due to the interactions with the surrounding heterogeneous structure. For example, adsorbed fluids in metal-organic-frameworks (MOFs) have…
Evaluating accessible conformational space is computationally expensive and thermal motions are partly neglected in computer models of molecular interactions. This produces error into the estimates of binding strength. We introduce a method…
To sample rare events, dissipation-corrected targeted molecular dynamics (dcTMD) applies a constant velocity constraint along a one-dimensional reaction coordinate $s$, which drives an atomistic system from an initial state into a target…
A charged Yukawa liquid confined in a slit nanopore is studied in order to understand excluded volume effects in the interaction force between the pore walls. A previously developed self-consistent scheme (S. Buyukdagli el al., J. Stat.…
The elliptic flow for $Z\le2$ particles in heavy ion collisions at energies from several tens to several hundreds MeV per nucleon is investigated by means of transport model,i.e. a new version of the Improved Quantum Molecular Dynamics…
We revisit the equilibrium statistical mechanics of a classical fluid of point-like particles with repulsive power-law pair interactions, focusing on density and energy fluctuations at finite temperature. Such long-range interactions,…
We construct a new mesoscopic model for granular media using Dynamical Density Functional Theory (DDFT). The model includes both a collision operator to incorporate inelasticity and the Helmholtz free energy functional to account for…
Folding and aggregation of proteins, the interaction between proteins and membranes, as well as the adsorption of organic soft matter to inorganic solid substrates belong to the most interesting challenges in understanding structure and…
We investigate membrane-mediated interactions between transmembrane proteins using coarse-grained models. We compare the effective potential of mean force (PMF) between two proteins, which are always aligned parallel to the z-axis of the…
We report a joint simulation and theoretical study of the liquid-vapor phase behaviour of a fluid in which polydispersity in the particle size couples to the strength of the interparticle interactions. Attention is focussed on the case in…
Simulations on a Lennard-Jones computer glass are performed to study effects arising from defects in glasses at low temperatures. The numerical analysis reveals that already a low concentration of defects may dramatically change the low…
Molecular dynamics simulation is used for studying the contact angle of nanoscale sessile drops on a planar solid wall in a system interacting via the truncated and shifted Lennard-Jones potential. The entire range between total wetting and…
We present a theoretical study of the folding of small proteins inside confining potentials. Proteins are described in the framework of an effective potential model which contains the Ramachandran angles as degrees of freedom and does not…
It is shown that diffusion-limited classical nucleation theory (CNT) can be recovered as a simple limit of the recently proposed dynamical theory of nucleation based on fluctuating hydrodynamics (Lutsko, JCP 136, 034509 (2012)). The same…
We introduce a simple spherical model whose structural properties are similar to the ones generated by models with directional interactions, by employing a binary mixture of large and small hard spheres, with a square-well attraction acting…
Excluded-volume effects can play an important role in determining transport properties in diffusion of particles. Here, the diffusion of finite-sized hard-core interacting particles in two or three dimensions is considered systematically…
Using molecular dynamics simulations we study the slow dynamics of a colloidal fluid annealed within a matrix of obstacles quenched from an equilibrated colloidal fluid. We choose all particles to be of the same size and to interact as hard…
Unlike their model membrane counterparts, biological membranes are richly decorated with a heterogeneous assembly of membrane proteins. These proteins are so tightly packed that their excluded area interactions can alter the free energy…