Accurate Vapor Pressure Prediction for Large Organic Molecules: Application to Materials Utilized in Organic Light-Emitting Diodes.

We present a theoretical method based on molecular dynamics (MD) simulations for the prediction of saturated vapor pressure of liquids constituting of large organic molecules at various temperatures. The approach is based on free energy calculations at a fixed temperature and a subsequent Gibbs-Duhem integration over the interval of temperatures. Results of the theoretical approach are compared with experimental measurements for a set of six molecules utilized in organic light-emitting diodes (OLEDs).

Molecular dynamics simulation of self-diffusion processes in titanium in bulk material, on grain junctions and on surface.

The process of self-diffusion of titanium atoms in a bulk material, on grain junctions and on surface is explored numerically in a broad temperature range by means of classical molecular dynamics simulation. The analysis is carried out for a nanoscale cylindrical sample consisting of three adjacent sectors and various junctions between nanocrystals. The calculated diffusion coefficient varies by several orders of magnitude for different regions of the sample.

Biodamage via shock waves initiated by irradiation with ions.

Radiation damage following the ionising radiation of tissue has different scenarios and mechanisms depending on the projectiles or radiation modality. We investigate the radiation damage effects due to shock waves produced by ions. We analyse the strength of the shock wave capable of directly producing DNA strand breaks and, depending on the ion's linear energy transfer, estimate the radius from the ion's path, within which DNA damage by the shock wave mechanism is dominant.

MesoBioNano Explorer--a universal program for multiscale computer simulations of complex molecular structure and dynamics.

We present a multipurpose computer code MesoBioNano Explorer (MBN Explorer). The package allows to model molecular systems of varied level of complexity. In particular, MBN Explorer is suited to compute system's energy, to optimize molecular structure as well as to consider the molecular and random walk dynamics.

Micromechanics of base pair unzipping in the DNA duplex.

All-atom molecular dynamics (MD) simulations of DNA duplex unzipping in a water environment were performed. The investigated DNA double helix consists of a Drew-Dickerson dodecamer sequence and a hairpin (AAG) attached to the end of the double-helix chain. The considered system is used to examine the process of DNA strand separation under the action of an external force.

Two-center-multipole expansion method: application to macromolecular systems.

We propose a theoretical method for the calculation of the interaction energy between macromolecular systems at large distances. The method provides a linear scaling of the computing time with the system size and is considered as an alternative to the well-known fast multipole method. Its efficiency, accuracy, and applicability to macromolecular systems is analyzed and discussed in detail.

Ab initio study of alanine polypeptide chain twisting.

We have investigated the potential energy surfaces for alanine chains consisting of three and six amino acids. For these molecules we have calculated potential energy surfaces as a function of the Ramachandran angles and , which are widely used for the characterization of the polypeptide chains. These particular degrees of freedom are essential for the characterization of the proteins folding process.