Local elevation: A method for improving the searching properties of molecular dynamics simulation

Summary The concept of memory has been introduced into a molecular dynamics algorithm. This was done so as to persuade a molecular system to visit new areas of conformational space rather than be confined to a small number of low-energy regions. The method is demonstrated on a simple model system and the 11-residue cyclic peptide cyclosporin A. For comparison, calculations were also performed using simulated temperature annealing and a potential energy annealing scheme. Although the method can only be applied to systems with a small number of degrees of freedom, it offers the chance to generate a multitude of different low-energy structures, where other methods only give a single one or few. This is clearly important in problems such as drug design, where one is interested in the conformational spread of a system.     

多晶顺磁共振谱的拟合

对电子自旋1/2≤S<3.5,核自旋1/2≤I<4.5和配体少于10个的顺磁体系的多晶EPR谱的拟合进行研究。在VAX-11/785计算机上用FORTRAN语言建立EPR谱模拟程序包,计算了多个例子,获得较为满意的结果。     

Multistage Electrochemical Reactions with the Transfer of Intermediates between Near-Electrode Layer and Bulk Solution: Analysis of a Kinetic Model and Computer-Aided Modeling

Kinetic equations for a multistage electrode process complicated by the transfer of intermediates between the near-electrode layer and bulk solution are derived and analyzed. Computer-aided modeling of the kinetics of processes of this kind is performed. Conditions under which the share of diffused intermediates is no longer vanishingly small are determined. Effect of various factors on the individual stages is established. Techniques of processing experimental data for determining kinetic parameters of separate stages are suggested.     

Modeling Studies of the Formation and Destruction of NO in Pulsed Barrier Discharges in Nitrogen and Air

This paper presents the results of modeling studies on the formation and destruction of NO in pulsed barrier discharges in nitrogen and air. The goals of this work are to identify the major processes involved in the formation and destruction of NO in air discharges, to distinguish between oxidative and reductive paths for NO destruction, to explore the potential importance of excited state reactions, to evaluate the role of water in such systems, and to identify the final products in the absence of heterogeneous processes. In all cases, the systems were modeled with 100×10^–4% (100 ppm) of added NO, with and without 3% added water. The focus in all of this work is chemistry in the post-pulse regime.     

Phenomenological and neural-network modeling of cephalosporin C production bioprocess

Cephalosporin C production process withCephalosporium acremonium ATCC 48272 in synthetic medium was investigated and the experimental results allowed the development of a mathematical model describing the process behavior. The model was able to explain fairly well the diauxic phenomenon, higher growth rate during the glucose-consumption phase, and the production occurring only in the sucrose-consumption phase. Moreover, the process was simulated utilizing the neural-networks technique. Two feed-forward neural-networks with one hidden layer were employed. Both models, phenomenological and neural-networks based, satisfactorily describe the bioprocess. The difficulties in determining kinetic parameters are avoided when neural networks are utilized.     

Molecular modeling study of the differential ligand–receptor interaction at the μ, δ and κ opioid receptors

3D models of the opioid receptors , and were constructed using BUNDLE, an in-house program to build de novo models of G-protein coupled receptors at the atomic level. Once the three opioid receptors were constructed and before any energy refinement, models were assessed for their compatibility with the results available from point-site mutations carried out on these receptors. In a subsequent step, three selective antagonists to each of three receptors (naltrindole, naltrexone and nor-binaltorphamine) were docked onto each of the three receptors and subsequently energy minimized. The nine resulting complexes were checked for their ability to explain known results of structure-activity studies. Once the models were validated, analysis of the distances between different residues of the receptors and the ligands were computed. This analysis permitted us to identify key residues tentatively involved in direct interaction with the ligand.     

A Three-Dimensional Two-Phase Model for Thermal Plasma Chemical Vapor Deposition with Liquid Feedstock Injection

In this paper, a comprehensive model for thermal plasma chemical vapor deposition (TPCVD) with liquid feedstock injection is documented. The gas flow is assumed to be steady, of a single temperature. Radiation and charged species contributions are excluded, but extensive homogeneous and heterogeneous chemistry is included. The liquid phase is traced by considering individual droplets. Discussion on the model's application to diamond production from acetone in a hydrogen–argon plasma is included. The major conclusions are: (1) Liquid injection possesses a capability to deliver the hydrocarbon precursor directly onto the deposition target. (2) For the case of complete evaporation of the droplet before reaching the substrate, the deposition rate is similar to that obtained with gaseous precursors. (3) The computational results compare well with experimental data. The modeling results can be used to optimize the injection parameters with regard to the deposition rate.     

分子筛模型中非骨架离子位置的研究

从理论上研究了非骨架阳离子可能的分布位置．计算了分子筛晶体基本结构单元在整个空间的静电势分布，找出空间中静电势的各个极小点．在静电势最低点逐个放置钠离子，优化，重新计算模型分子筛的电势分布．研究了阳离子放置过程中静电势变化的趋势．