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Modeling the intracellular dynamics for Vif-APO mediated HIV-1 virus infection

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Chinese science Bulletin 2010年第22期55卷 2329-2340页

作者： WANG Yi1,2.& LAI LuHua1,3.1 center for {2. Biology, Peking University, beijing 100871, {3. 2.School of physics, Peking University, beijing 100871, {3. 3.BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, beijing 100871, {3. center for theoretical Biology Peking University Beijing 100871 China School of physics Peking University Beijing 100871 China BNLMS State Key Laboratory for Structural Chemistry of Unstable and Stable Species College of Chemistry and Molecular Engineering Peking University Beijing 100871 China

The viral infectivity factor (Vif) was found to be essential for controlling HIV-1 virus infectivity. It targets cellular antiviral proteins in APOBEC family (APO) to trigger its fast degradation and inhibits APO packaging into nascent virion. In the present study, we propose a mathematical model to quantitatively study the intracellular dynamics of these typical virus-host interactions. Four sets of published experimental data were compared with simulation results to justify the model. Systematic parameter sensitivity and perturbation analysis showed that parameters related to APO are crucial to the infectivity of newly synthesized HIV-1 virus. Interestingly, we discovered that the synthesis rate of the viral structure protein Gag and the required number per nascent virion are optimized to achieve high virion production with minimal level of packaged APO, and large portion of model parameters are beneficial to virus only within a relatively small range. Furthermore, minor variations in several parameters related to viral protein Tat, the activator of viral RNA synthesis, were found to induce switch-like behaviors on both incorporated Vif and APO. These findings may provide new insights for understanding the high mutation rate of HIV-1 virus and its latency, as well as help identify key targets for therapeutic design.

关键词：病毒感染载脂蛋白 HIV 细胞内动力学抗病毒蛋白建模介导

Dynamics of morphological changes for mitochondrial fission and fusion

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science china({2.,Mechanics & Astronomy) 2010年第4期53卷 680-689页

作者： WANG ShiQi 1,2.4 , FU ChangLiang 1,2., ZHANG Yan 1,2., CHEN Quan 3.& LONG Mian 1,2.1 Key Laboratory of Microgravity (National Microgravity Laboratory), beijing 100190, {2. 2.center for Biomechanics and Bioengineering, Institute of Mechanics, Chinese Academy of {3., beijing 100190, {2. 3.State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of {3., beijing 100101, {2. 4 Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of {3., beijing 100044, {2. 1. Key Laboratory of Microgravity (National Microgravity Laboratory) Beijing 100190 China2. Center for Biomechanics and Bioengineering Institute of Mechanics Chinese Academy of Sciences Beijing 100190 China4. Institute of Vertebrate Paleontology and Paleoanthropology Chinese Academy of Sciences Beijing 100044 China3. State Key Laboratory of Biomembrane and Membrane Biotechnology Institute of Zoology Chinese Academy of Sciences Beijing 100101 China

Mitochondria experience continuous fusion and fission in a living cell, but their dynamics remains poorly quantified. Here a theoretical model was developed, upon a simplified population balance equation (PBE), to predict the morphological changes induced by mitochondrial fission and fusion. Assuming that both fission and fusion events are statistically independent, the survival probability of mitochondria staying in the fission or fusion state was formulated as an exponentially-decayed function with time, which depended on the time-dependent distribution of the mitochondrial volume and the fission and fusion rates. Parametric analysis was done for two typical volume distributions. One was Gamma distribution and the other was Gaussian distribution, derived from the measurements of volume distribution for individual mitochondria in a living cell and purified mitochondria in vitro. The predictions indicated that the survival probability strongly depended on morphological changes of individual mitochondria and was inversely correlated to the fission and fusion rates. This work provided a new insight into quantifying the mitochondrial dynamics via monitoring the evolution of the mitochondrial volume.

关键词： mitochondria morphology fission fusion dynamics modeling

A possible proton pygmy resonance in ^(17)Ne

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science china({2.,Mechanics & Astronomy) 2011年第S1期54卷 49-52页

作者： MA ZhongYu1,2.& TIAN Yuan1 1 china Institute of Atomic Energy, beijing 102.1{2. china 2.{{2. of theoretical Nuclear physics, National Laboratory of Heavy Collision, Lanzhou 7{2.000, china 1. china Institute of Atomic Energy Beijing 102413 China2. Center of Theoretical Nuclear Physics National Laboratory of Heavy Collision Lanzhou 730000 China

The low-lying electric dipole strengths in proton-rich nuclei 17F and 17Ne, which can be produced at HIRFL-CSR in Lanzhou, are investigated. In the framework of the covariant density functional theory the self-consistent relativistic Hartree Bogoliubov model and the relativistic quasiparticle random phase approximation with the NL3.parameter set and Gogny pairing interaction are adopted in the calculations. A pronounced dipole peak appears below 10 MeV in17Ne, but does not occur in 17F. The prop erties of this low-lying E1 excitation in 17Ne are studied, which may correspond to a proton pygmy resonance with different characteristics from those of giant dipole resonance.

关键词： proton pygmy resonance relativistic Hartree-Bogoliubov model relativistic quasiparticle random phase approximation

How random are matrix elements of the nuclear shell model Hamiltonian?

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science china({2.,Mechanics & Astronomy) 2009年第10期52卷 1477-1481页

作者： SHEN JiaJie1 & ZHAO YuMing1,2.3.4 1 Department of physics,Shanghai Jiao Tong University,Shanghai 2.02.0,{2. 2.center of {3. Nuclear physics,National Laboratory of Heavy Ion Accelerator,Lanzhou 73.000,{2. 3.Nishina center,Institute of Physical Chemical Research(RIKEN),Hirosawa 2.1,Wako-shi,Saitama 3.1-0198,Japan 4 CCAST,World Laboratory,beijing 100080,{2. Department of physics Shanghai Jiao Tong University Shanghai 200240 China center of theoretical Nuclear {2. National Laboratory of Heavy Ion Accelerator Lanzhou 730000 China Nishina center Institute of Physical Chemical Research (RIKEN) Hirosawa 2-1 Wako-shi Saitama 351-0198 Japan World Laboratory CCAST Beijing 100080 China

In this paper we study the general behavior of matrix elements of the nuclear shell model *** find that nonzero off-diagonal elements exhibit a regular pattern,if one sorts the diagonal matrix elements from smaller to larger *** correlation between eigenvalues and diagonal matrix elements for the shell model Hamiltonian is more remarkable than that for random matrices with the same distribution unless the dimension is small.

关键词： nuclear shell model geometry property linear correlation randomize

Ab-initio molecular dynamics simulation on nano-system under external pressure

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science china Mathematics 2004年第z1期47卷 92-100页

作者： Jl Min, SUN Deyan & GONG XingaoSurface physics Laboratory and Department of physics, Fudan University, Shanghai 2.04{2., china Institute of Solid State physics, Chinese Academy of sciences, Hefei 2.2.0{2., china Interdisciplary center for theoretical studies, Chinese Academy of sciences, {12. 100080, china Fudan Univ Surface Phys Lab Shanghai 200433 Peoples R China Fudan Univ Dept Phys Shanghai 200433 Peoples R China Chinese Acad Sci Inst Solid State Phys Hefei 230031 Peoples R China Chinese Acad Sci Interdisciplinary Ctr Theoret Studies Beijing 100080 Peoples R China

A new constant-pressure molecular dynamics (MD) method is developed to simulate the dynamic behavior and structure transition of finite system under external pressure. In this method, no artificial parameter is introduced and the computation overheads are very small. As an application, a hard-soft transition of single wall carbon nanotube (SWCNT) under external pressure is found, which is in agreement with the experiments.

关键词： phase transition, simulation, nano-particles

Topological Structure of Vortex Solution in Jackiw-Pi Model

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Communications in theoretical physics 2007年第7期48卷 143-146页

作者： LI Xi-Guo LIU Zi-Yu LI Yong-Qing GAO Yuan GUO Yan-Rui XIAO Guo-Qing1 Institute of Modern physics,the Chinese Academy of sciences,P.O.Box {2.,Lanzhou 7{2.000,china2.Graduate School,the Chinese Academy of sciences,beijing 100049,china{2.center of theoretical Nuclear physics,National Laboratory of Heavy Ion Collisions,Lanzhou 7{2.000,china Institute of Modern physics the Chinese Academy of Sciences P.O. Box 31 Lanzhou 730000 China

By using φ-mapping method,we discuss the topological structure of the self-duality solution in Jackiw-Pimodel in terms of gauge potential *** set up relationship between Chern-Simons vortex solution andtopological number,which is determined by Hopf index and Brouwer *** also give the quantization of flux inthis ***,we study the angular momentum of the vortex,which can be expressed in terms of,the flux.

关键词： topological structure vortex Jackiw-Pi model

A quantification model for apoptosis in mouse embryos in the early stage of fetation

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science china(Life {2.) 2009年第10期52卷 922-927页

作者： WANG PengFei1, FU JianHua1, MA WanYun1, CHEN DieYan1, Lü DanYu2.& BAI WenJia3.1 Key Laboratory for Atomic and Molecular Nanosciences of Education Ministry, Department of {2., Tsinghua University, beijing 100084, {3. 2.Department of Anatomy & Histology and Embryology, School of Basic Medical sciences Peking University Health science center, beijing 100083. {3. 3.Department of Automation, Tsinghua University, beijing 100084, {3. 1. Key Laboratory for Atomic and Molecular Nanosciences of Education Ministry Department of Physics Tsinghua University Beijing 100084 China 2. Department of Anatomy & Histology and Embryology School of Basic Medical Sciences Peking University Health Science Center Beijing 100083 China 3. Department of Automation Tsinghua University Beijing 100084 China

Apoptosis is the most important inducement and modulator for embryos in the early stage of fetation, i.e. after the 8-cell stage, mostly the morula and blastula stage, to proceed to the stage of nonlinear development. Using a two-photon laser scanning microscopy (TPLSM) system, we obtained 3.dimensional (3.) fluorescent images of preimplantation mouse embryos. A model for quantification was established. The statistical results for the spatial location of apoptosis bodies in embryos was obtained following image processing, as well as investigation of the kinetics of apoptosis. It was found that most (70%) apoptosis occurred in the trophectoderm, and the departure between the centroid and geometric {2. of embryos had a step transition when embryos developed into the 3.-cell stage, which was consistent with the theoretical prediction that the blastocele would induce a symmetry break of the distribution of cells in embryos.

关键词： apoptosis preimplantation mouse embryo TPLSM quantification model

Probing Nuclear Symmetry Energy with Giant Dipole Resonances in Finite Nuclei

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原子核物理评论 2009年第S1期26卷 181-184页

作者： CAO Li-gang1,3.MA Zhong-yu2.3.(1 Institute of Modern {2.,Chinese Academy of sciences,Lanzhou 73.000,china 2.china Institute of Atomic Energy,beijing 102.13.china 3.center of {12. Nuclear {2.,National Laboratory of Heavy Ion Research Facility in Lanzhou,Lanzhou 73.000,china) Institute of Modern physics Chinese Academy of SciencesLanzhou 730000China center of theoretical Nuclear {2. National Laboratory of Heavy Ion Research Facility in LanzhouLanzhou 730000China china Institute of Atomic Energy Beijing 102413China center of theoretical Nuclear {2. National Laboratory of Heavy Ion Research Facility in LanzhouLanzhou 730000China

The relationship between the centroid energies of the isovector giant dipole resonance of finite nuclei and the symmetry energy has been studied. It is found the excitation energies of the dipole resonance in finite nuclei are correlated linearly with the symmetry energy at and below the saturation density. This linear correlation leads to the symmetry energy at the saturation density at the interval 3..0 MeV ≤ S(ρ0) ≤ 3..0 MeV,and the symmetry energy at ρ = 0.1 fm-3.at the interval 2..2.2..5 MeV. It is proposed that a precise measurement of the dipole mode in nuclei could set up an important constraint on the equation of state for nuclear matter.

关键词： symmetry energy dipole resonance Pygmy resonance

The theoretical research of basic function method in incompressible viscous flow and its simulations in three-dimensional aneurysms

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science china({2.,Mechanics & Astronomy) 2009年第6期52卷 909-918页

作者： SHEN Fang1 & WU WangYi2.1 State Key Laboratory for Space Weather, center for Space science and Applied Research, Chinese Academy of {2., {3. 100190, china 2.State Key Laboratory of Turbulence and Complex Systems & Department of Mechanics and Engineering science, Peking University, {3. 100871, china 1. State Key Laboratory for Space Weather Center for Space Science and Applied Research Chinese Academy of Sciences Beijing 100190 China 2. State Key Laboratory of Turbulence and Complex Systems & Department of Mechanics and Engineering science Peking University Beijing 100871 China

Basic function method is developed to treat the incompressible viscous flow. Artificial compressibility coefficient, the technique of flux splitting method and the combination of central and upwind schemes are applied to construct the basic function scheme of trigonometric function type for solving three-dimensional incompressible Navier-Stokes equations numerically. To prove the method, flows in finite-length-pipe are calculated, the velocity and pressure distribution of which solved by our method quite coincide with the exact solutions of Poiseuille flow except in the areas of entrance and exit. After the method is proved elementary, the hemodynamics in two-and three-dimensional aneurysms is researched numerically by using the basic function method of trigonometric function type and unstructured grids generation technique. The distributions of velocity, pressure and shear force in steady flow of aneurysms are calculated, and the influence of the shape of the aneurysms on the hemodynamics is studied.

关键词： basic function unstructured grid aneurysm viscous incompressible flow artificial compressibility flux splitting