Theoretical and computational studies of vectorial processes in biomolecular systems

Efficient vectorial processes such as the transduction of bioenergy and signals are characteristics that strikingly distinguish living systems from inanimate materials. Recent developments in biophysical and biochemical techniques have provided new information about the structure, dynamics and interaction of biomolecules involved in vectorial life processes at multiple length and temporal scales. This wealth of data makes it possible to carry out theoretical and computational studied of key mechanistic questions associated with complex life processes at an unprecedented level. Using two “vectorial biomolecular machines”, myosin and cytochrome c oxidase, as examples, we discuss the identification of interesting and biologically relevant questions that require thorough theoretical analysis. Technical challenges and recent progress related to these theoretical investigations are briefly summarized     

BNCT优化网格设计及相关算法研究

用MCNP蒙特卡罗程序模拟了硼中子俘获治疗(BNCT)3种国际基准网格模型, 并与 修正的Snyder椭球模型进行了比较. 在此基础上, 给出了一种保质量守恒、内存量少、易于产生输入文件的4种基本材料成分的BNCT网格模型. 计算结果表明, 在4mm网格下, 新模型可以达到基准模型的精度; 根据解析模型剂量随深度的变化规律, 研究构造了多网格组合模型, 在重要区域计算精度不损失的条件下, 计算时间大大缩短. 最后研究给出了一个既保证精度、又在可接受的时间内完成剂量计算的模型、样本数和相应的算法, 它基本上满足临床BNCT的要求.     

Combinational simulations of free energy of polymer solution

It is conceptually proposed that the total entropy of polymer solution is contributed from two distinct parts: the positional and the oomformational. The former can be represented analytically, while the latter can be simulated with the random self-avoiding walk model on the simple cubic lattice for multichain systems. The obtained results indicated that both the conformational entropy and the mixing heat are consistent with the scaling laws wry well.     

The Modified Group Expansions for Construction of Solutions to the BBGKY Hierarchy

A solution to the BBGKY hierarchy for nonequilibrium distribution functions is obtained within modified boundary conditions. The boundary conditions take into account explicitly both the nonequilibrium one-particle distribution function as well as local conservation laws. As a result, modified group expansions are proposed. On the basis of these expansions, a generalized kinetic equation for hard spheres and a generalized Bogolubov–Lenard–Balescu kinetic equation for a dense electron gas are derived within the polarization approximation.     

Calorimetric analysis of the ethanolysis of 1,2-epoxybutane

Polyethers, which are produced by alcoholysis of oxiranes, are often used as solvents in chemical plants. The spectra of the products can be influenced by the choice of the catalyst (acid or base). The results of the base-catalyzed ethanolysis of 1,2-epoxybutane are displayed. The reaction was investigated calorimetrically by varying the molar ratio between ethanol and 1,2-epoxybutane, the starting temperature and the concentration of the catalyst sodium hydroxide. Additionally, the influence of the used alcohol will be shown in one example. To determine the activation parameters, the experiments were evaluated by the nonlinear software package TA-kin v3.3.     

Kinetic limit of a conservative lattice gas dynamics showing long-range correlations

An anisotropic lattice gas dynamics is investigated for which particles on ^d jump to empty nearest neighbor sites with (fast) rate ^–2 in a specified direction and some particular configuration-dependent rates in the other directions. The model is translation and reflection invariant and is particle conserving. The space coordinate in the fast-rate direction is rescaled by ^–1. It follows that the density field converges in probability, as 0, to the corresponding solution of a nonlinear diffusion-type equation. The microscopic fluctuations about the deterministic macroscopic evolution are determined explicitly and it is found that the stationary fluctuations decay via a power law (1/r ^d ) with the direction dependence of a quadrupole field.     

High-precision Monte Carlo test of the conformai-invariance predictions for two-dimensional mutually avoiding walks

Let _l be the critical exponent associated with the probability thatl independentN-step ordinary random walks, starting at nearby points, are mutually avoiding. Using Monte Carlo methods combined with a maximum-likelihood data analysis, we find that in two dimensions ₂=0.6240±0.0005±0.0011 and ₃=1.4575±0.0030±0.0052, where the first error bar represents systematic error due to corrections to scaling (subjective 95% confidence limits) and the second error bar represents statistical error (classical 95% confidence limits). These results are in good agreement with the conformal-invariance predictions ₂=5/8 and ₃=35/24.     

Branched polymers in a wedge geometry in three dimensions

We investigate the statistical and dimensional properties of uniform star polymers attached by the branching vertex of degreef in a wedge geometry in three dimensions and described by the wedge angles and. We show that the growth constant is equal to ^f , where is the self-avoiding walk limit. Thef and (, ) dependences of the corresponding critical exponent _f (, ) are studied using Monte Carlo techniques. In the casef=1, our results are compared with existing predictions obtained from series expansion and renormalization group methods. We have also estimated the amplitudes for the mean square radius of gyration and the mean square end-to-end branch length. Our results for the ratio of the mean square radius of gyration of anf-star to that of a linear polymer of the same degree of polymerization attached in a similar wedge, and the analogous ratio for the mean square end-to-end branch length, are consistent with these ratios being lattice-independent quantities.     

Superdegenerate point in FCC phase diagram: CVM and Monte Carlo investigations

We investigate the topology of the phase diagram of binary alloys on the fee lattice with first-neighbor antiferromagnetic interactions around the superdegenerate point, where the L1₀ and L1₂ phases meet. We treat the system as a hard-constraint lattice gas, following a procedure previously described by Lebowitzet al. We perform cluster variation method calculations in theT0 limit and Monte Carlo simulations directly atT=0 K on the ground states of the superdegenerate point. We find that: (i) there is no disordered phase in the neighborhood of this point; (ii) a phase L for which two of the four cubic sublattices have the same average occupancy and each of the two others are different appears between L1₀ and L1₂; (iii) the transition L/L1₂ is of first order.     

Likelihood estimation of soft-core interaction potentials for Gibbsian point patterns

The likelihood method is developed for the analysis of socalled regular point patterns. Approximating the normalizing factor of Gibbs canonical distribution, we simultaneously estimate two parameters, one for the scale and the other which measures the softness (or hardness), of repulsive interactions between points. The approximations are useful up to a considerably high density. Some real data are analyzed to illustrate the utility of the parameters for characterizing the regular point pattern.