相关论文: A methodology of quantifying membrane permeability…
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…
This Feature Article presents an overview of the current status of Ring Polymer Molecular Dynamics (RPMD) rate theory. We first analyze the RPMD approach and its connection to quantum transition-state theory. We then focus on its practical…
The thermodynamic (TD) properties of biological membranes play a central role for living systems. It has been suggested, for instance, that nonlinear pulses such as action potentials (APs) can only exist if the membrane state is in vicinity…
Peripheral membrane proteins can reversibly and specifically bind to biological membranes to carry out functions such as cell signalling, enzymatic activity, or membrane remodelling. Structures of these proteins and of their lipid-binding…
In our recent work on concentrated suspensions of uniformly porous colloidal spheres with excluded volume interactions, a variety of short-time dynamic properties were calculated, except for the rotational self-diffusion coefficient. This…
We explored the composition dependence of a rather comprehensive set of properties of liquid water-ethanol mixtures by using the isobaric-isothermal molecular dynamics computer simulations. The united atom non-polarizable model from the…
Sediment transport over an erodible sediment bed is studied by particle resolved simulations with a hybrid parallel approach. To overcome the challenges of load imbalance in the traditional domain decomposition method when encountering…
The oxidation of human sebum, a lipid mixture covering our skin, generates a range of volatile and semi-volatile carbonyl compounds that contribute largely to indoor air pollution in crowded environments. Kinetic models have been developed…
The interaction between nano- or micro-sized particles and cell membranes is of crucial importance in many biological and biomedical applications such as drug and gene delivery to cells and tissues. During their cellular uptake, the…
We have investigated thermodynamic and dynamic properties as well as the dielectric constant of water-metha\-nol model mixtures in the entire range of composition by using constant pressure molecular dynamics simulations at ambient…
Water management is a key factor that limits PEFC's performance. We show how insights into this problem can be gained from pore-scale simulations of water invasion in a model fibrous medium. We explore the influence of contact angle on the…
Failure of amorphous materials is characterized by the emergence of dissipation. The connection between particle dynamics, dissipation, and overall material rheology, however, has still not been elucidated. Here, we take a new approach…
The effects of the hydration mechanism on continental crust recycling are analyzed through a 2D finite element thermo-mechanical model. Oceanic slab dehydration and consequent mantle wedge hydration are implemented using a dynamic method.…
Ring polymer molecular dynamics (RPMD) has proven to be an accurate approach for calculating thermal rate coefficients of various chemical reactions. For wider application of this methodology, efficient ways to generate the underlying…
We present a simple and computationally efficient coarse-grained and solvent-free model for simulating lipid bilayer membranes. In order to be used in concert with particle-based reaction-diffusion simulations, the model is purely based on…
In many biological systems, the movement of individual agents is commonly characterized as having multiple qualitatively distinct behaviors that arise from various biophysical states. This is true for vesicles in intracellular transport,…
We measure the flow of water through mixed packings of glass spheres and soft swellable hydrogel grains, at constant sample volume. Permeability values are obtained at constant sample volume and at porosities smaller than random close…
We consider subdiffusion in a system which consists of two media separated by a thin membrane. The subdiffusion parameters may be different in each of the medium. Using the new method presented in this paper we derive the probabilities (the…
In this paper, we show that the permeability of a porous {material} and that of a bubbly fluid are limiting cases of the complexified version of the two-fluid models posed in {Lipton_Avellaneda_1990}. We assume the viscosity of the…
In this work, we developed an interatomic potential for saturated hydrocarbons using the modified embedded-atom method (MEAM), a reactive semi-empirical many-body potential based on density functional theory and pair potentials. We…