Derivatives of molecular surface area and volume: simple and exact analytical formulas

The computational effort of biomolecular simulations can be significantly reduced by means of implicit solvent models in which the energy generally contains a correction depending on the surface area and/or the volume of the molecule. In this article, we present simple derivation of exact, easy-to-use analytical formulas for these quantities and their derivatives with respect to atomic coordinates. In addition, we provide an efficient, linear-scaling algorithm for the construction of the power diagram required for practical implementation of these formulas. Our approach is implemented in a C++ header-only template library.     

Transition network based on equilibrium sampling: a new method for extracting kinetic information from Monte Carlo simulations of protein folding

We propose a new type of transition network for modeling of protein dynamics. The nodes of the network correspond to the conformations taken from random sampling of equilibrium ensemble available, e.g., by Monte Carlo simulations. Although this approach does not provide absolute values of folding/unfolding rates, it allows identification of reaction pathways, transition state ensemble, and, eventually, intermediates. The new method is verified by a comparison with direct molecular dynamic simulations performed for a coarse-grained Gō-like model of proteins. As an illustrative example, we analyze kinetics of formation of a small β-hairpin (Trp zipper 1) in the all-atom representation.     

Ten microseconds in the life of a superhelix

Dynamic light scattering measurement data of DNA topoisomers are compared with two different computer models: a Monte Carlo model and a Brownian dynamics model. First results on the kinetics of formation of a superhelix and on the influence of curved sequences on the dynamics of superhelical DNA are reported.To whom correspondence should be addressed     

Conformational changes of a polyelectrolyte in mixtures of water and acetone

Samples of a polyelectrolyte poly(methacryloylethyl trimethylammonium methylsulfate), PMETMMS, with molar masses M_w = 22−25 × 10⁶ were examined with viscosity, static light scattering, and conductivity measurements in a water–acetone solvent. Because acetone is a nonsolvent for this polymer the measurements were performed to determine the influence of the solvent composition, the polymer concentration, and the presence of added ions on the conformation of the polyelectrolyte in mixed solvents. The possible influence of a hydrodynamic field on the polymer conformation was also studied. The viscosity of the polymer solutions as a function of polymer concentration, as well as of the solvent composition, was studied using a broad range of shear rates. When the mass fraction of acetone in the solvent, γ, is below 0.5, the solutions show a usual polyelectrolyte behavior. When γ ≥ 0.80, the polymer adopts a compact conformation. This is observed as a decrease of the radius of gyration, R_g, second virial coefficient, A₂, the viscosity, and also as a change in the conductivity of the solution. The change in the polymer conformation may be induced also by dilution. When 0.60 ≤ γ < 0.80, a gradual decrease in the polymer concentration leads to a sudden decrease of the reduced viscosity, which indicates a decrease in the particle size. The values of M_w measured by static light scattering were constant in all experiments. © 1998 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 36: 1107–1114, 1998     

Directional Synthesis of Hybrid Polymers from 2- and 4-Vinylpyridines

Formation of hybrid three-dimensional structures by treatment of copolymers of 2- and 4-vinylpyridine with butyllithium, followed by grafting of tert-butyl acrylate molecules, was studied by mass-spectrometric thermal analysis and ¹³C NMR spectroscopy.     

Investigation of Neutron Generation upon Irradiation of Deuterated Crystalline Structures with an Electron Beam

Physics of Atomic Nuclei - The possibility of neutron generation by irradiating deuterated crystalline structures with an electron beam with an energy of 20–40 keV was studied. As targets,...     

Facilitated diffusion of DNA-binding proteins: efficient simulation with the method of excess collisions

In this paper, a new method to efficiently simulate diffusion controlled second order chemical reactions is derived and applied to site-specific DNA-binding proteins. The protein enters a spherical cell and propagates via two competing modes, a free diffusion and a DNA-sliding mode, to search for its specific binding site in the center of the cell. There is no need for a straightforward simulation of this process. Instead, an alternative and exact approach is shown to be essentially faster than explicit random walk simulations. The speed-up of this novel simulation technique is rapidly growing with system size.     

Relationships of graft polymerization of vinyl monomers onto cellulose. Reaction kinetics and polymer structure

Graft polymerization of acrylamide and sulfuric salt of 2-methyl-5 vinylpyridine onto cellulose using CO(III) salts was studied. It was shown that graft polymerisation of water-soluble polymers can be described by general relationships of radical reaction. The relation between elementary reaction constants of the formation and termination of active centers in cellulose, as well as relation between constants of the propagation, transfer and termination of chains were determined for different cellulose materials and monomers. The translational diffusion, sedimentation, viscosity, and flow birefringence of copolymers have been investigated in different solvents. Experimental data showed that the copolymers obtained are graft copolymers with two to five grafted chains onto macromolecules. The minimum distance between the branch points is 100 ± 20 glucoside units. The peculiarity of these copolymers is relatively low polydispersity. The conformation of macromolecules of such copolymers in solution depends on the compatibility of the copolymer components and the thermodynamic properties of the solvent.