Polarizational bremsstrahlung in collisions of slow atomic particles

The polarizational bremsstrahlung problem is considered in collisions of slow atomic particles. It is demonstrated that the polarizational bremsstrahlung dominates in the region of high impact parameters and small photon frequencies over the well-known molecular orbital X-ray emission. The contribution of the polarizational bremsstrahlung to the total radiation spectrum is significant over a wide frequency range.     

α-helix↔random coil phase transition: analysis of ab initio theory predictions

In the present paper we present results of calculations obtained with the use of the theoretical method described in our preceding paper [Eur. Phys. J. D, DOI: 10.1140/epjd/e2007-00328-9] and perform detail analysis of α-helix↔random coil transition in alanine polypeptides of different length. We have calculated the potential energy surfaces of polypeptides with respect to their twisting degrees of freedom and construct a parameter–free partition function of the polypeptide using the suggested method [Eur. Phys. J. D, DOI: 10.1140/epjd/e2007-00328-9]. From the build up partition function we derive various thermodynamical characteristics for alanine polypeptides of different length as a function of temperature. Thus, we analyze the temperature dependence of the heat capacity, latent heat and helicity for alanine polypeptides consisting of 21, 30, 40, 50 and 100 amino acids. Alternatively, we have obtained same thermodynamical characteristics from the use of molecular dynamics simulations and compared them with the results of the new statistical mechanics approach. The comparison proves the validity of the statistical mechanic approach and establishes its accuracy.     

Finslerian N-Spinors: Algebra

New mathematical objects called Finslerian N-spinors are discussed. The Finslerian N-spinor algebra is developed. It is found that Finslerian N-spinors are associated with an N²-dimensional flat Finslerian space. A generalization of the epimorphism SL(2, ) O ₊ (1, 3) to a case of the group SL(N,) is constructed. Particular examples of Finslerian N-spinors for N = 2, 3 are considered in detail.     

Electrical transport and magnetic ordering in R 2Ti3Ge4 (R=Dy, Ho and Er) compounds

New R ₂Ti₃Ge₄ (R=Dy, Ho and Er) intermetallic compounds have been synthesized and characterized by X-ray diffraction and low temperature ac magnetic susceptibility, electrical resistivity and thermoelectric power measurements were carried out. The compounds crystallize in the parent, Sm₅Ge₄-type orthorhombic structure (space group Pnma) and lanthanide contraction is observed as one moves along the rare-earth series. The changeover from paramagnetic to antiferromagnetic phase happens at low temperatures and the ordering temperature scales with the de Gennes factor. The electrical resistivity is metallic with a negative curvature above 100 K. Thermopower displays a weak maximum at temperatures less than 50 K signifying the possible phonon and magnon drag effects.     

Modeling the effect of ion-induced shock waves and DNA breakage with the reactive CHARMM force field

Ion-induced DNA damage is an important effect underlying ion beam cancer therapy. This article introduces the methodology of modeling DNA damage induced by a shock wave caused by a projectile ion. Specifically it is demonstrated how single- and double strand breaks in a DNA molecule could be described by the reactive CHARMM (rCHARMM) force field implemented in the program MBN Explorer. The entire workflow of performing the shock wave simulations, including obtaining the crucial simulation parameters, is described in seven steps. Two exemplary analyses are provided for a case study simulation serving to: (a) quantify the shock wave propagation and (b) describe the dynamics of formation of DNA breaks. The article concludes by discussing the computational cost of the simulations and revealing the possible maximal computational time for different simulation set-ups.     

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. This process occurs in vivo and now is being intensively investigated in experiments with single molecules. The DNA dodecamer duplex is consequently unzipped pair by pair by means of the steered MD. The unzipping trajectories turn out to be similar for the duplex parts with G·C content and rather distinct for the parts with A·T content. It is shown that during the unzipping each pair experiences two types of motion: relatively quick rotation together with all the duplex and slower motion in the frame of the unzipping fork. In the course of opening, the complementary pair passes through several distinct states: (i) the closed state in the double helix, (ii) the metastable preopened state in the unzipping fork and (iii) the unbound state. The performed simulations show that water molecules participate in the stabilization of the metastable states of the preopened base pairs in the DNA unzipping fork.     

Efficient 3D kinetic monte carlo method for modeling of molecular structure and dynamics

Self‐assembly of molecular systems is an important and general problem that intertwines physics, chemistry, biology, and material sciences. Through understanding of the physical principles of self‐organization, it often becomes feasible to control the process and to obtain complex structures with tailored properties, for example, bacteria colonies of cells or nanodevices with desired properties. Theoretical studies and simulations provide an important tool for unraveling the principles of self‐organization and, therefore, have recently gained an increasing interest. The present article features an extension of a popular code MBN Explorer (MesoBioNano Explorer) aiming to provide a universal approach to study self‐assembly phenomena in biology and nanoscience. In particular, this extension involves a highly parallelized module of MBN Explorer that allows simulating stochastic processes using the kinetic Monte Carlo approach in a three‐dimensional space. We describe the computational side of the developed code, discuss its efficiency, and apply it for studying an exemplary system. © 2014 Wiley Periodicals, Inc.