Numerical modeling of magnetic drug targeting

A special focused magnet, designed for the use in the magnetic targeted drug delivery system, was constructed. The theoretical calculation of the adhesion condition for a magnetic fluid drop in magnetic field with obtained design showed that the constructed focused magnet generates a sufficient magnetic force for the capture of a magnetic drop on the vessel wall and can be used 1.5–2 cm deeper in an organism compared with the prism permanent magnet, which can enable non-invasivity of the magnetic drug targeting procedure. The maximal values for magnetic field and gradient of magnetic field are 0.38 T and 101 T/m, respectively.     

Two-photon ultrashort nonlinear dynamics of coherent bosonic quasiparticles in condensed media

We present a theoretical study of the ultrashort nonlinear dynamics of bosonic quasiparticles in condensed media participating in two-photon quantum transitions. In the resonance approximation we obtain exact solutions in the form of elliptic functions. We show that allowing for antiresonant terms in the Hamiltonian of the interaction of the electromagnetic field and the quasiparticles leads to an entirely new phenomenon: the development of ultrashort chaos. The dynamical stochasticity of the quasiparticles is due to the disintegration of constants of motion of the system. Finally, we predict the effect of nonlinear tunneling from one potential well to another. Zh. éksp. Teor. Fiz. 113, 2065–2080 (June 1998)     

Random sequences with power-law correlations exhibit proteinlike behavior

We use a replica approach to investigate the thermodynamic properties of the random heteropolymers with persistent power-law correlations in monomer sequence. We show that this type of sequences possess proteinlike properties. In particular, we show that they can fold into stable unique three-dimensional structure (the "native" structure, in protein terminology) through two different types of pathways. One is a fast folding pathway and leads directly to the native structure. Another one, a more slower pathway, passes through the microphase separated (MPS) state and includes a number of intermediate glassy states. The scale and the magnitude of the MPS are calculated. The frozen state can be reached only by sequences with weak long-range correlations. The critical value for the correlation exponent is found, above which (strong correlations) freezing is impossible.     

Multicanonical parallel simulations of proteins with continuous potentials

The determination of the three‐dimensional (3D) structure of a protein or peptide is a very important research problem in biological and medical sciences. Anfinsen's experiments (Science 1973, 181, 223) on renaturation of denatured proteins have shown that the native 3D structure of a (small) protein at low (room) temperatures is uniquely determined by its amino acid sequence, which suggests that it might be possible to determine the 3D structure of a protein from its amino acid sequence by pure computations. As a step toward that goal, in this article we present a simple approach for parallelization of multicanonical Monte Carlo simulations of proteins with continuous potentials. Our method is based on the parallel calculation of the protein energy function. The algorithm is tested by simulated annealing and multicanonical simulations of two small peptides, and known results are reproduced accurately. An acceptable degree of parallelization can be achieved in the simulation of Protein L using up to 30 PCs. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1287–1296, 2001     

The appearance of structures of excitons, photons, and biexcitons, regular and chaotic in time, in direct-band semiconductors

The dynamic properties of excitons and biexcitons in a ring cavity are studied. The nonlinearity of the problem is due to the direct binding of two excitons into a biexciton by virtue of the Coulomb attraction between them. A bifurcation analysis is carried out, revealing the points of Hopf bifurcations and period doubling. The effect of the cavity Q factor on the switching times is investigated. The possibility of experimental observation of the phenomena under study is discussed.     

Photoconduction spectroscopy of p-type GaSb films

Excess carrier lifetimes (77 K) have been measured as function of the absorbed flux density in undoped p-type gallium antimonide films (GaSb/GaAs) using steady state photoconductivity measurements with the illumination wavelength of 1.1 μm. Using the results from Hall effect measurements along with the relations describing the lifetimes of the excess minority carriers in the bulk of the films and at the surface, the theoretical values of the effective excess carrier lifetime in the materials were also calculated. Discrepancies between the experimental and theoretical results were described using a two-layer model, by considering the variation in the charge distribution within the layer due to the presence of surface states, as well as the band offset between the layer and the substrate. Theoretical modeling of the experimental result yields values of different parameters such as band bending at the surface, minimum value of Shockley–Read–Hall lifetime and maximum value of the surface recombination velocity.     

Efficient combination of Wang-Landau and transition matrix Monte Carlo methods for protein simulations

An efficient combination of the Wang-Landau and transition matrix Monte Carlo methods for protein and peptide simulations is described. At the initial stage of simulation the algorithm behaves like the Wang-Landau algorithm, allowing to sample the entire interval of energies, and at the later stages, it behaves like transition matrix Monte Carlo method and has significantly lower statistical errors. This combination allows to achieve fast convergence to the correct values of density of states. We propose that the violation of TTT identities may serve as a qualitative criterion to check the convergence of density of states. The simulation process can be parallelized by cutting the entire interval of simulation into subintervals. The violation of ergodicity in this case is discussed. We test the algorithm on a set of peptides of different lengths and observe good statistical convergent properties for the density of states. We believe that the method is of general nature and can be used for simulations of other systems with either discrete or continuous energy spectrum.     

Formation of the five-membered zirconacyclocumulene Cp2Zr(η4-ButC4But) and the binuclear zirconocene butatrienyl complex Cp2(Bun)Zr(ButC4But)Zr(Bun)Cp2 in the reaction of the Negishi reagent with 1,4-di(tert-butyl)butadiyne

Russian Chemical Bulletin -     

Enveloping triangulation method for detecting internal cavities in proteins and algorithm for computing their surface areas and volumes

Detection and quantitative characterization of the internal cavities in proteins remain an important topic in studying protein structure and function. Here we propose a new analytical method for detecting the existence of cavities in proteins. The method is based on constructing the special enveloping triangulation enclosing the cavities. Based on this method, we develop an algorithm and a fortran package, CAVE, for computing volumes and surface areas of cavities in proteins. We first test our method and algorithm in some artificial systems of spheres and find that the calculated results are consistent with exact results. Then we apply the package to compute volumes and surface areas of cavities for some protein structures in the Protein Data Bank. We compare our calculated results with those obtained by some other methods and find that our approach is reliable.