Alexander V. Yakubovich

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 systems energy, to optimize molecular structure as well as to consider the molecular and random walk dynamics. MBN Explorer allows to use a broad variety of interatomic potentials, to model different molecular systems, such as atomic clusters, fullerenes, nanotubes, polypeptides, proteins, DNA, composite systems, nanofractals, and so on. A distinct feature of the program, which makes it significantly different from the existing codes, is its universality and applicability to the description of a broad range of problems involving different molecular systems. Most of the existing codes are developed for particular classes of molecular systems and do not permit multiscale approach while MBN Explorer goes beyond these drawbacks. On demand, MBN Explorer allows to group particles in the system into rigid fragments, thereby significantly reducing the number of dynamical degrees of freedom. Despite the universality, the computational efficiency of MBN Explorer is comparable (and in some cases even higher) than the computational efficiency of other software packages, making MBN Explorer a possible alternative to the available codes.

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 ions linear energy transfer, estimate the radius from the ions path, within which DNA damage by the shock wave mechanism is dominant. At much smaller values of linear energy transfer, the shock waves turn out to be instrumental in propagating reactive species formed close to the ions path to large distances, successfully competing with diffusion.

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. Calculations have been carried out within the ab initio theoretical framework based on the density functional theory and accounting for all the electrons in the system. We have determined stable conformations and calculated the energy barriers for transitions between them. Using a thermodynamic approach, we have estimated the times of characteristic transitions between these conformations. The results of our calculations have been compared with those obtained by other theoretical methods and with the available experimental data extracted from the Protein Data Base. This comparison demonstrates a reasonable correspondence of the most prominent minima on the calculated potential energy surfaces to the experimentally measured angles and for alanine chains appearing in native proteins. We have also investigated the influence of the secondary structure of polypeptide chains on the formation of the potential energy landscape. This analysis has been performed for the sheet and the helix conformations of chains of six amino acids.

Atomic and Molecular Data Needs for Radiation Damage Modeling: Multiscale Approach

We present a brief overview of the multiscale approach towards understanding of the processes responsible for the radiation damage caused by energetic ions. This knowledge is very important, because it can be utilized in the ion‐beam cancer therapy, which is one of the most advanced modern techniques to cure certain type of cancer. The central element of the multiscale approach is the theoretical evaluation and quantification of the DNA damage within cell environment. To achieve this goal one needs a significant amount of data on various atomic and molecular processes involved into the cascade of events starting with the ion entering and propagation in the biological medium and resulting in the DNA damage. The discussion of the follow up biological processes are beyond the scope of this brief overview. We consider different paths of the DNA damage and focus on the the illustration of the thermo‐mechanical effects caused by the propagation of ions through the biological environment and in particular on the...

Ab initio theory of helix↔coil phase transition

Abstract.In this paper, we suggest a theoretical method based on the statistical mechanics for treating the α-helix↔random coil transition in alanine polypeptides. We consider this process as a first-order phase transition and develop a theory which is free of model parameters and is based solely on fundamental physical principles. It describes essential thermodynamical properties of the system such as heat capacity, the phase transition temperature and others from the analysis of the polypeptide potential energy surface calculated as a function of two dihedral angles, responsible for the polypeptide twisting. The suggested theory is general and with some modification can be applied for the description of phase transitions in other complex molecular systems (e.g. proteins, DNA, nanotubes, atomic clusters, fullerenes).

Kinetics of liquid-solid phase transition in large nickel clusters

In this paper we have explored computationally the solidification process of large nickel clusters. This process has the characteristic features of the first order phase transition occurring in a finite system. The focus of our research is placed on the elucidation of correlated dynamics of a large ensemble of particles in the course of the nanoscale liquid-solid phase transition through the computation and analysis of the results of molecular dynamics (MD) simulations with the corresponding theoretical model. This problem is of significant interest and importance, because the controlled dynamics of systems on the nanoscale is one of the central topics in the development of modern nanotechnologies. MD simulations in large molecular systems are rather computer power demanding. Therefore, in order to advance with MD simulations we have used modern computational methods based on the graphics processing units (GPU). The advantages of the use of GPUs for MD simulations in comparison with the CPUs are demonstrated and benchmarked. The reported speedup reaches factors greater than 400. This work opens a path towards exploration with the use of MD of a larger number of scientific problems inaccessible earlier with the CPU based computational technology.

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.

Molecular dynamics simulation of nanoindentation of nickel-titanium crystal

We present the results of molecular dynamics simulations of nanoindentation of a bimetallic nickel-titanium crystal in the austenitic (cubic) B2 phase. By considering three different types of indenters, namely of square, conical and spherical shapes, we observe the dependence of deformations of the crystalline structure on the type of the indenter. Various load-displacement curves are observed for different indenter types. We perform the molecular dynamics simulations of a full indentation cycle, which includes the loading and unloading stages. On the basis of such simulations we evaluate mechanical properties of the material, namely we calculate hardness and reduced Youngs modulus. We observe variation of the calculated parameters depending on the indenter type and discuss the origin of occurring discrepancies.

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.

Studying Phase Transition in Nanocarbon Structures

We investigate phase transitions in C60 and present a novel theoretical approach for the description of its fragmentation and formation. This theoretical approach consists of a statistical mechanics model combined with a topologically‐constrained forcefield which was developed to describe the formation and fragmentation of C60 within a specific C60↔30C2 channel. Based on this forcefield, we conduct molecular dynamics simulations where we demonstrate that at the phase transition temperature, both the cage and gaseous phases were found to coexist and the system continuously oscillates between the two phases, i.e. the fullerene repeats its fragmentation and reassembly within a single molecular dynamics trajectory. Combining the results of the molecular dynamics simulations and the statistical mechanics approach, we obtain a phase transition temperature of 3800–4200 K at pressures of 10–100 kPa, in good correspondence with carbon‐arc discharge experiments. Furthermore, we also conduct molecular dynamics simul...