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Free energy calculation of single molecular interaction using Jarzynski's identity method:the case of HIV-1 protease inhibitor system

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Acta Mechanica Sinica 2012年第3期28卷 891-903页

作者： de-chang Li Bao-Hua Ji Biomechanics and Biomaterials Lab Department of Applied MechanicsBeijing Institute of TechnologyKey Laboratory.of Dynamics and Control of Flight VehicleMinistry of Education100081 BeijingChina

Jarzynski＇ identity （JI） method was suggested a promising tool for reconstructing free energy landscape of biomolecular interactions in numerical simulations and ex- periments. However, JI method has not yet been well tested in complex systems such as ligand-receptor molecular pairs. In this paper, we applied a huge number of steered molec- ular dynamics （SMD） simulations to dissociate the protease of human immunodeficiency type I virus （HIV-1 protease） and its inhibitors. We showed that because of intrinsic com- plexity of the ligand-receptor system, the energy barrier pre- dicted by JI method at high pulling rates is much higher than experimental results. However, with a slower pulling rate and fewer switch times of simulations, the predictions of JI method can approach to the experiments. These results sug- gested that the JI method is more appropriate for reconstruct- ing free energy landscape using the data taken from experi- ments, since the pulling rates used in experiments are often much slower than those in SMD simulations. Furthermore, we showed that a higher loading stiffness can produce higher precision of calculation of energy landscape because it yields a lower mean value and narrower bandwidth of work distri- bution in SMD simulations.

关键词： Molecular dynamics simulation. Single molecu-lar interaction ~ Molecular biomechanics ~ Steered moleculardynamics ~ Free energy calculation

Numerical simulation of solidification morphologies of Cu-0.6Cr casting alloy using modified cellular automaton model

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Transactions of Nonferrous Metals Society of China 2010年第6期20卷 1072-1077页

作者： TSAI de-chang HWANG Weng-sing department of Materials Science and Engineering National Cheng Kung University

The purpose of this study is to predict the morphologies in the solidification process for Cu-0.6Cr(mass fraction,%)alloy by vacuum continuous casting(VCC)and verify its accuracy by the observed experimental *** numerical simulation aspect, finite difference(FD)method and modified cellular automaton(MCA)model were used to simulate the macro-temperature field, micro-concentration field,nucleation and grain growth of Cu-0.6Cr alloy using real data from actual casting *** the observed casting experiment,the preliminary grain morphologies are the directional columnar grains by the VCC *** solidification morphologies by MCAFD model are in agreement with the result of actual casting experiment well.

关键词： Cu-Cr alloy vacuum continuous casting solidification morphology simulation modified cellular automaton model finite difference method

The love of a beloved hapatologist,Dr. Rudi Schmid

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World Journal of Gastroenterology 2007年第48期13卷 6612-6613页

作者： You-de chang World Journal of Gastroenterology The WJG Press and Beijing Baishideng BioMed Scientific Co. Ltd. Room 903 Building D Ocean Intemational Center No.62 Dongsihuan Zhonglu Chaoyang District Beijing 100025 China

Dr. Schmid was a former dean of the University of California, San Francisco School of Medicine and a liver specialist whose early studies of porphyrins led to several significant fundamental discoveries. He was the first to demonstrate that there were different forms of porphyria. He also developed the first experimental model for hepatic porphyria, a model that for many years was used for most of the work in this field and cited in hundreds of papers. His contributions were recognized when he was awarded the 1990 Friedenwald Medal by the American Gastroenterological Association, its most coveted award for lifetime achievement.

关键词： Gastroenterology

Science news release and its benefi ts to your research

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World Journal of Gastroenterology 2007年第45期13卷 6120-6121页

作者： You-de chang World Journal of Gastroenterology The WJGPress PO Box 2345 Beijing 100023 China

News release to the latest science f indings is benef icial to both researchers and their served institutions as well as the public. It will help to set a bridge of communication between researchers, the public and media, and publishers, making the latest research findings well known to the public. World Journal of Gastroenterology has currently freely opened the News Release Service System (WJG-NRSS) for original articles with potential signifi cance and novelty for news release to mass media to broaden the f indings to the public.

关键词： Gastroenterology

Low-density Ferromagnetism in the Hubbard Model

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Chinese Physics Letters 2001年第1期18卷 109-110页

作者： AN Jin GONG chang-de National Laboratory of Solid State Microstructures and department of Physics Nanjing UniversityNanjing 210093 Chinese Center of Advanced Science and Technology(World Laboratory) P.O.Box 8730Beijing 100080

We study analytically the stability of the saturated ferromagnetic ground state(the Nagaoka state)of the Hubbard model in the low electron density limit with the mean-field *** find that the critical U_(c) is just 4πt,where t is the hopping integral between the nearest neighbours,i.e.,when U is larger than 4πt,the paramagnetic state is unstable with respect to the ferromagnetic state,and vice versa.

关键词： Hubbard ferromagnetic saturated

Joint parameter estimation of DOD/DOA/polarization for bistatic MIMO radar

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The Journal of China Universities of Posts and Telecommunications 2010年第5期17卷 32-37页

作者： JIANG Hong WANG de-fa LIU chang College of Communication Engineering Jilin University Changchun 130012 China

In the paper,polarization-sensitive array is exploited at the receiver of multiple input multiple output （MIMO） radar system,a novel method is proposed for joint estimation of direction of departure （DOD）,direction of arrival （DOA） and polarization parameters for bistatic MIMO radars.A signal model of polarimetric MIMO radar is developed,and the multi-parameter estimation algorithm for target localization is described by exploiting polarization array processing and the invariance property in both transmitter array and receiver *** making use of polarization diversity techniques,the proposed method has advantages over traditional localization algorithms for bistatic MIMO *** show that the performance of DOD and DOA estimation is greatly enhanced when different states of polarization of echoes is fully ***,when two targets are closely spaced and cannot be well separated in spatial domain,the estimation resolution of traditional algorithms will be greatly *** the proposed algorithm can work well and achieve high-resolution identification and accurate localization of multiple targets.

关键词： MIMO radar joint parameter estimation polarization direction of arrival direction of departure

Evidence of Phase Separation in the Hubbard Model

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Chinese Physics Letters 2000年第5期17卷 365-366页

作者： LUAN Bin-Quan GONG chang-de National Key Laboratory of Solid States of Microstructure and department of Physics Nanjing UniversityNanjing 210093

We examine theoretically the possibility of phase separation due to bole aggregation in the background of anti-ferromagneticallyr ordered CuO_(2) *** results which are calculated within a self-consistent mean-field-type approximation give obvious evidence of phase *** conclusions agree with previous numerical results(from exact diagonalization).

关键词： Hubbard ferromagnetic separation

Instability of the Random Fixed Point of Renormalization Group for the Spin Systems with Quenched Disorder

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Chinese Physics Letters 1997年第3期14卷 165-168页

作者： WU Xin-tian GONG chang-de department of Physics and National Laboratory of Solid State Microstructure Nanjing UniversityNanjing 210093 Chinese Center of Advanced Science and Technology(World Laboratory) P.O.Box 8370Beijing 100080 department of Physics Nanjing UniversityNanjing 210093

The replica trick used in the renormalization group(RG)for the disordered spin systems is *** recursion relations of RG are derived in a more general situation in which the coupling constants can have arbitrary symmetry to the replica *** is shown that the random fixed point found by Luther,Grinstein and Lubensky is *** instability implies that the replica symmetry should be broken in the RG for the disordered systems.

关键词： symmetry disordered Fixed

Some Properties for the Largest Component of Random Geometric Graphs with Applications in Sensor Networks

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Acta Mathematicae Applicatae Sinica 2009年第4期25卷 579-592页

作者： Ge Chen Tian-de Guo chang-long Yao School of Mathematical Science Graduate University of Chinese Academy of Sciences Beijing 100049 China

In this paper we consider the standard Poisson Boolean model of random geometric graphs G（Hλ,s; 1） in Rd and study the properties of the order of the largest component L1 （G（Hλ,s; 1）） . We prove that ElL1 （G（Hλ,s; 1））] is smooth with respect to A, and is derivable with respect to s. Also, we give the expression of these derivatives. These studies provide some new methods for the theory of the largest component of finite random geometric graphs （not asymptotic graphs as s - co） in the high dimensional space （d 〉 2）. Moreover, we investigate the convergence rate of E[L1（G（Hλ,s; 1））]. These results have significance for theory development of random geometric graphs and its practical application. Using our theories, we construct and solve a new optimal energy-efficient topology control model of wireless sensor networks, which has the significance of theoretical foundation and guidance for the design of network layout.

关键词： Random geometric graph the largest component wireless sensor networks topology control