Development and testing of new force fields for molecular dynamics simulations

Recent progress in modeling of protein folding in Dr. Shaw laboratory has been achieved only after some improvements of potentials of covalent forces, taken from the standard AMBER force field; and still, the force field used is not quite satisfactory to reproduce folded structures of some larger proteins, having significant, about 5A, RMS deviation between the computed and experimentally determined 3D structures. The objective of this research is to develop and test new polarizable atomic force fields (FFs) for "in-vacuum" and "in-water" non-bonded interactions based on AMBER ff99SBILDN force fields, improved by inclusion of new terms. FFs parameter optimization will be done using our set of molecular crystals with crystallographic data from the Cambridge Structural Database and sublimation/solvation thermodynamics characteristics from various sources

Operator method in solving non-linear equations of the Hartree-Fock type

The operator method is used to construct the solutions of the problem of the polaron in the strong coupling limit and of the helium atom on the basis of the Hartree-Fock equation. $E_0=-0.1085128052\alpha^2$ is obtained for the polaron ground-state energy. Energies for 2s- and 3s-states are also calculated. The other excited states are briefly discussed.Comment: 7 page

Dynamics of Soliton-Like Excitations in a Chain of a Polymer Crystal: Influence of Neighbouring Chains Mobility

We investigate influence of mobility of neighbouring chains on dynamics of soliton-like excitations in a chain of the simplest polymer crystal (polyethylene in the “united atoms ” approximation) using molecular dynamics simulation. We present results for point-like structural defects: static and moving at low, medium and high velocities; and examine howthe structure of a crystal will affect them. 1Introduction The present work is concerned with the behaviour of a system presumed to be close to an integrable one, namely Sine-Gordon system. Sine-Gordon equation is well known to be the simplest continual one-dimensional model of a dislocation in a crystal (the well known Frenkel–Kontorova model). It can be equally used to describe nonlinear dynamics of a directed macromolecular chain subjected to a periodic potential [1, 2]. Because it is a periodic potential which is generated by immobile neighbouring chains in a polymer crystal, it was supposed that one can identify topological solitons of Sine-Gordon type with point defects in a polymer chain (vacancies and inclusions) which are caused by loca

Collisional dynamics simulation of grafted polymer brushes consisting of anisotropic Monomers

Наведено результати комп’ютерного моделювання методом динйміки зіткнєнь двох типів полімерних щіток: перший тип містить ланцюжки ізотропних мономерів ("гнучка щітка"), тоді як другий тип відповідає анізотропії мономерів ("анізотропна щітка"). Досліджено як незбурені щітки, так і щітки під впливом стаціонарного зсувного потоку. Довжина, висота та нахил щітки, а також параметр порядку обчислені при різних щільностях пришивки. Результати збігаються з теоретичними завбаченнями, що маються.We present results of a collisional dynamics simulations of two types of polymer brushes: one containing chains consisting of isotropic monomers ("flexible" brush) and another with large anisotropy of monomers ("anisotropic" brush). Both unperturbed brushes and brushes under shear deformation at constant shear rates were studied. The height of the brush, the elongation and the inclination of the polymer chains in the brush as well as order parameter were calculated at different grafting densities and shear rates. The results are in accordance with available theoretical predictions.Представлены результаты компьютерного моделирования методом столкновительной динамики двух типов полимерных щёток: первый тип содержит цепочки, состоящие из изотропных мономеров ("гибкая щётка"), тогда как второй тип соответствует сильной анизотропии мономеров ("анизотропная щётка"). Исследованы как невозмущённые щётки, так и щётки под воздействием стационарного сдвигового потока. Длина, высота и наклон щётки, а также параметр порядка вычислены при различных плотностях пришивки. Результаты согласуются с имеющимися теоретическими предсказаниями

Insight into the Structure of Polybutylcarbosilane Dendrimer Melts via Extensive Molecular Dynamics Simulations

Extensive molecular dynamics simulations of polybutylcarbosilane dendrimer melts were performed in a wide temperature range from 300 to 600 K. The melt macroscopic and structural characteristics were analyzed for the third up to the eighth generation dendrimers for the systems consisting of 8 and 27 dendrimer molecules in the simulation box. For every system, averaging was performed over 8 independent simulation runs and along equilibrium time trajectories of up to 5 ns. Calculated values of the thermal expansion coefficients, heat capacity, and self-diffusion coefficients are in a good agreement with experimental observations. Analysis of the molecular mass dependence of the gyration radius and shape factor, detailed radial density distributions of dendrimer structural units, mobility of the branching points, and intermolecular interaction energy allowed to shed light on the basics of distinction in behavior of low and high generation dendrimer melts and formulate the directions of further research

Computer Simulation of Gas-Phase Neutralization of Electrospray-Generated Protein Macroions

The process of neutralizing hydrated multicharged gas-phase protein ions with small counterions was simulated using a molecular dynamics (MD) technique. Hen egg white lysozyme (HEWL) molecules with different numbers of positive charges, both dry and solvated by up to 1500 water molecules, were first equilibrated. Simulations revealed that the hydration layer over a highly charged protein surface adapted a spiny structure with water protrusions composed of oriented water dipoles. MD simulations of the neutralization process showed that the impact of a small dehydrated single-charged counterion with a dehydrated HEWL ion bearing eight uncompensated charges resulted in a short local increase in temperature by 600–1000 K, which quickly (in 3–5 ps) dissipated over the whole protein molecule, increasing its average temperature by 20–25 K. When the protein ion was solvated, no drastic local increase in the temperature of the protein atoms was observed, because the impact energy was dissipated among the water molecules near the collision site

Computer Simulation of Gas-Phase Neutralization of Electrospray-Generated Protein Macroions

The process of neutralizing hydrated multicharged gas-phase protein ions with small counterions was simulated using a molecular dynamics (MD) technique. Hen egg white lysozyme (HEWL) molecules with different numbers of positive charges, both dry and solvated by up to 1500 water molecules, were first equilibrated. Simulations revealed that the hydration layer over a highly charged protein surface adapted a spiny structure with water protrusions composed of oriented water dipoles. MD simulations of the neutralization process showed that the impact of a small dehydrated single-charged counterion with a dehydrated HEWL ion bearing eight uncompensated charges resulted in a short local increase in temperature by 600–1000 K, which quickly (in 3–5 ps) dissipated over the whole protein molecule, increasing its average temperature by 20–25 K. When the protein ion was solvated, no drastic local increase in the temperature of the protein atoms was observed, because the impact energy was dissipated among the water molecules near the collision site

COMPARISON OF THE TEST RESULTS OF MATHEMATIC UNDERSTANDING IN THE TOWNS OF SVERDLOVSK REGION WITH THE HELP OF STATISTICAL METHODS

The aim of the study is to compare the results of diagnosing of mathematic understanding in two towns of Sverdlovsk region (Novouralsk and Verkhnyaya Pyshma) with a comparable level of school education. Research methods: conducting diagnostics at general schools among pupils of grades 5–11 and comparison of obtained results. Conclusions: the diagnostic of understanding of basics in mathematics provides an opportunity to identify the pupils’ problem areas; the diagnostic results in both towns vary significantly; many students have a poor understanding of some basic issues in mathematics.Цель исследования – сравнение результатов диагностики понимания математики в двух городах Свердловской области с сопоставимым уровнем школьного образования (Новоуральск и Верхняя Пышма). Методы исследования: проведение диагностики в общеобразовательных школах среди учащихся 5–11 классов; сравнение полученных результатов. Выводы: диагностика понимания основ математики даёт возможность выявить проблемные зоны учащихся; результаты диагностики в обоих городах существенно различаются; многие учащиеся слабо понимают некоторые из основных положений математики