In Silico Investigation of Potential Applications of Gamma Carbonic Anhydrases as Catalysts of CO2 Biomineralization Processes: A Visit to the Thermophilic Bacteria Persephonella hydrogeniphila,Persephonella marina,Thermosulfidibacter takaii,and Thermus thermophilus

Carbonic anhydrases (CAs) have been identified as ideal catalysts for CO₂ sequestration. Here, we report the sequence and structural analyses as well as the molecular dynamics (MD) simulations of four γ-CAs from thermophilic bacteria. Three of these, Persephonella marina, Persephonella hydrogeniphila, and Thermosulfidibacter takaii originate from hydrothermal vents and one, Thermus thermophilus HB8, from hot springs. Protein sequences were retrieved and aligned with previously characterized γ-CAs, revealing differences in the catalytic pocket residues. Further analysis of the structures following homology modeling revealed a hydrophobic patch in the catalytic pocket, presumed important for CO₂ binding. Monitoring of proton shuttling residue His69 (P. marina γ-CA numbering) during MD simulations of P. hydrogeniphila and P. marina’s γ-CAs (γ-PhCA and γ-PmCA), showed a different behavior to that observed in the γ-CA of Escherichia coli, which periodically coordinates Zn²⁺. This work also involved the search for hotspot residues that contribute to interface stability. Some of these residues were further identified as key in protein communication via betweenness centrality metric of dynamic residue network analysis. T. takaii’s γ-CA showed marginally lower thermostability compared to the other three γ-CA proteins with an increase in conformations visited at high temperatures being observed. Hydrogen bond analysis revealed important interactions, some unique and others common in all γ-CAs, which contribute to interface formation and thermostability. The seemingly thermostable γ-CA from T. thermophilus strangely showed increased unsynchronized residue motions at 423 K. γ-PhCA and γ-PmCA were, however, preliminarily considered suitable as prospective thermostable CO₂ sequestration agents.     

Chemical-Shift Perturbations Reflect Bile Acid Binding to Norovirus Coat Protein: Recognition Comes in Different Flavors

Bile acids have been reported as important cofactors promoting human and murine norovirus (NoV) infections in cell culture. The underlying mechanisms are not resolved. Through the use of chemical shift perturbation (CSP) NMR experiments, we identified a low-affinity bile acid binding site of a human GII.4 NoV strain. Long-timescale MD simulations reveal the formation of a ligand-accessible binding pocket of flexible shape, allowing the formation of stable viral coat protein–bile acid complexes in agreement with experimental CSP data. CSP NMR experiments also show that this mode of bile acid binding has a minor influence on the binding of histo-blood group antigens and vice versa. STD NMR experiments probing the binding of bile acids to virus-like particles of seven different strains suggest that low-affinity bile acid binding is a common feature of human NoV and should therefore be important for understanding the role of bile acids as cofactors in NoV infection.     

金刚石膜的计算机虚拟制备技术中的分子动力学模拟

综述了近年来金刚石薄膜形成过程的分子动力学（Molecular Dynamics，简称MD）模拟研究，详细地阐述了原子间相互作用势的选取，总结了不同沉积条件下MD的计算模型和几种典型情况下的模拟结果。研究表明：在原子尺度上，MD方法能较全面地提供有关膜生长的信息，对进一步了解金刚石膜形成的微观机制以及为细观层次仿真提供基本信息均具有重要意义。     

基于双因子认证技术的网络身份识别

本文提出了一种基于动态双因子认证技术的网络身份识别方法,用户每次登录的口令是利用系统时间和用户ID通过MD5加密算法计算得到,其通过MD5加密后生成的登录口令是随机的,这将进一步提高开放网络环境下身份识别的可靠性和安全性。同时,本文还提出网络身份识别技术可以应用到各类网站的服务器上,用来完成对用户身份的识别,以提高网络系统的安全性。     

A PROTOTYPE GRID FRAMEWORK FOR THE CHEMICAL PROCESS INDUSTRIES

This article presents a GRID framework for distributed computations in the chemical process industries. We advocate a generic agent-based GRID environment in which chemical processes can be represented, simulated, and optimized as a set of autonomous, collaborative software agents. The framework features numerous advantages in terms of scalability, software reuse, security, and distributed resource discovery and utilization. It is a novel example of how advanced distributed techniques and paradigms can be elegantly applied in the area of chemical engineering to support distributed computations and discovery functions in chemical process engineering. A prototype implementation of the proposed framework for chemical process design is presented to illustrate the concepts.     

Interactive simulated patient—an advanced tool for student-activated learning in medicine and healthcare

An advanced learning system for interactive simulation of patient cases (ISP) is described. The system was designed to meet specific pedagogical needs where student activation and problem orientation were two of the key issues. The system includes features such as video based illness history-taking function using free text input, highly interactive physiological examination procedures, extensive laboratory tests and detailed user feedback. The system was constructed mainly in Authorware Professional, starting more than 10 years ago, and it is now available in refined versions in different languages. Twelve pedagogical and three technical features were initially defined for the project. All of these aims were fulfilled. The ISP system has been successfully used in education, and in international collaboration, including three applicability field tests. The system is also a powerful research tool for studying for instance medical decision-making.     

RSA数字签名技术在信息化工程监理流程E化中的研究

提出的信息化工程监理流程的E化过程就是将监理流程通过现有的IT技术进行重新梳理、再造,达到电子化、网络化。将对在E化过程中数字签名的应用进行研究,以应对E化容易出现的伪造这一网络安全问题。主要讲述hash签名技术中单向散列函数对文件进行摘要处理,然后使用RSA公钥加密算法对摘要进行加密。也会对签名过程和验证过程给予解说。     

Molecular Dynamics Simulations Based on 1-Phenyl-4-Benzoyl-1-Hydro-Triazole ERRα Inverse Agonists

Estrogen-related receptor α (ERRα), which is overexpressed in a variety of cancers has been considered as an effective target for anticancer therapy. ERRα inverse agonists have been proven to effectively inhibit the migration and invasion of cancer cells. As few crystalline complexes have been reported, molecular dynamics (MD) simulations were carried out in this study to deepen the understanding of the interaction mechanism between inverse agonists and ERRα. The binding free energy was analyzed by the MM-GBSA method. The results show that the total binding free energy was positively correlated with the biological activity of an inverse agonist. The interaction of the inverse agonist with the hydrophobic interlayer composed of Phe328 and Phe495 had an important impact on the biological activity of inverse agonists, which was confirmed by the decomposition of energy on residues. As Glu331 flipped and formed a hydrogen bond with Arg372 in the MD simulation process, the formation of hydrogen bond interaction with Glu331 was not a necessary condition for the compound to act as an inverse agonist. These rules provide guidance for the design of new inverse agonists.     

基于IPv6的视频资源服务平台构建

介绍了基于IPv6视频资源服务平台的工作原理和关键技术,设计并开发了基于IPv6的视频资源服务平台,该平台能实现视频教学、影视娱乐、交流答疑、视频直播、视频点播等功能。     

ATOMISTIC MOLECULAR DYNAMICS SIMULATIONS OF GAS DIFFUSION AND SOLUBILITY IN RUBBERY AMORPHOUS HYDROCARBON POLYMERS

Diffusion coefficients D of H 2 , He, O 2 , N 2 , and CO 2 in different rubbery amorphous polymeric matrices were estimated by atomistic molecular dynamics simulations at 298 K using the Einstein relationship, and compared with the relevant experimental values, where available. The simulated diffusion coefficients D of all the gases in all polymers considered almost regularly decreased with increasing molecular gas volumes and increasing polymer glass transition temperature. Further, solubility coefficients and heats of solution were obtained for all gases from Grand Canonical Monte Carlo simulations, which were also used to calculate sorption isotherms. In general, there is a good agreement between experimental and simulated values of diffusion and solubility coefficients for all gases considered.