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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 Theoretical Biology, peking university, beijing 100871, china 2 School of physics, peking university, beijing 100871, china 3 BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, peking university, beijing 100871, china 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

Target-Scarching on Percolation

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Communications in Theoretical physics 2005年第9期44卷 431-434页

作者： YANG Shi--Jie department of physics, beijing Normal university, beijing 100875, china

We study target-searching processes on a percolation, on which a hunter tracks a target by smelling odorsit emits. The odor intensity is supposed to be inversely proportional to the distance it propagates. The Monte Carlosimulation is performed on a 2-dimensional bond-percolation above the threshold. Having no idea of the location of thetarget, the hunter determines its moves only by random attempts in each direction. For lager percolation connectivityP0.90, it reveals a scaling law for the searching time versus the distance to the position of the target. The scalingexponent is dependent on the sensitivity of the hunter. For smaller P, the scaling law is broken and the prohability offinding out the target significantly reduces. The hunter seems trapped in the cluster of the percolation and can hardlyreach the goal.

关键词： percolation searching scaling law

Multiuser detection algorithm based on belief propagation in multiple-input multiple-output systems

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Science in china(Series F) 2004年第3期47卷 384-393页

作者： JIANG Wei XIANG Haige department of Electronics, peking university, beijing 100871, china 1. department of Electronics Peking University 100871 Beijing China

In MIMO (multiple-input, multiple-output) systems, signals from differenttransmitting antennas interfere at each receiving antenna and multiuser detection (MUD)algorithms may be adopted to improve the system performance. This paper proposes anovel multiuser detection algorithm in MIMO systems based on the idea of 'beliefpropagation' which has achieved great accomplishment in decoding of low-densityparity-check codes. The proposed algorithm has a low computation complexityproportional to the square of transmitting/receiving antenna number. Simulation resultsshow that under low signal-to-noise ratio (SNR) circumstances, the proposed algorithmoutperforms the traditional linear minimum mean square error (MMSE) detector while itencounters a 'floor' of bit error rate under high SNR circumstances. So the proposedalgorithm is applicable to MIMO systems with channel coding and decoding. Although inthis paper the proposed algorithm is derived in MIMO systems, obviously it can be appliedto ordinary code-division multiple access (CDMA) systems.

关键词： multiple-input multiple-output belief propagation multiuser detection

New evidence for lack of CMB power on large scales

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Science china(physics,Mechanics & Astronomy) 2010年第3期53卷 567-570页

作者： LIU Hao1 & LI TiPei1,2,3 1 Key Laboratory of Particle Astrophysics, Institute of High Energy physics, Chinese Academy of Sciences, beijing 100049, china 2 department of physics & Center for Astrophysics, Tsinghua university, beijing 100084, china 3.department of Engineering physics & Center for Astrophysics, Tsinghua university, beijing 100084, china 1. Key Laboratory of Particle Astrophysics Institute of High Energy Physics Chinese Academy of Sciences Beijing 100049 China2. Department of Physics & Center for Astrophysics Tsinghua University Beijing 100084 China3. Department of Engineering Physics & Center for Astrophysics Tsinghua University Beijing 100084 China

A digitalized temperature map is recovered from the first light sky survey image published by the Planck team, from which an angular power spectrum of the cosmic microwave background (CMB) is derived. The amplitudes of the low multipoles (low-l) measured from the preliminary Planck power spectrum are significantly lower than those reported by the WMAP team. Possible systematical effects are far from enough to explain the observed low-l differences.

关键词： cosmology cosmic microwave background data analysis

Shape phase transitions in nuclei:Effective order parameters and trajectories

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Science china(physics,Mechanics & Astronomy) 2011年第S1期54卷 88-97页

作者： ZHANG Yu1,2, HOU ZhanFeng2 & LIU YuXin2,3 1department of physics, Liaoning Normal university, Dalian 116029, china 2department of physics and the State Key Laboratory of Nuclear physics and Technology, peking university, beijing 100871, china 3Center of Theoretical Nuclear physics, National Laboratory of Heavy Ion Accelerator, Lanzhou 720000, china 1. department of physics Liaoning Normal University Dalian 116029 China2. Department of Physics and the State Key Laboratory of Nuclear Physics and Technology Peking University Beijing 100871 China3. Center of Theoretical Nuclear Physics National Laboratory of Heavy Ion Accelerator Lanzhou 720000 China

We analyze systematically the effective order parameters in nuclear shape phase transition both in experiments and in the interacting boson model. We find that energy ratios and B(E2) ratios can distinguish the first from the second-order phase transition in theory above a certain boson number N (about 50), but in experiments, only those quantities, such as E(L1+)/E(02+) and B(E2; (L+2)1 → L1)/B(E2; 21 → 01), etc., of which the monotonous transitional behavior in the second-order phase transition is broken in the first order phase transition independent of N, are qualified as the effective order parameters. By implementing the originally proposed effective order parameters and the new ones, we find that the isotones with neutron number Nn = 62 are a trajectory of the second order phase transition. In addition, we predict that the transitional behavior of isomer shifts of Xe, Ba isotopes and Nn = 62 isotones is approximately monotonous due to the finiteness of nuclear system.

关键词： nuclear shape phase transition interacting boson model effective order parameter finite particle number effect transition trajectory

Effects of diffusion time and diffusion gradient strength on the mean diffusivity of water molecules in healthy human brain

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Progress in Natural Science:Materials International 2006年第7期16卷 706-711页

作者： GAO Song, WANG Xiaoying and BAO Shanglian ( Laboratory of Medical physics & Engineering, peking university, beijing 100871, china department of Radiology, The First Affiliated Hospital of peking university, beijing 100034, china) peking Univ Lab Med Phys & Engn Beijing 100871 Peoples R China peking Univ Affiliated Hosp 1 Dept Radiol Beijing 100034 Peoples R China

Diffusion time and diffusion gradient strength are two important parameters of pulsed gradient spin echo (PGSE) that is the most commonly used method in diffusion-weighted magnetic resonance imaging. However, the effects of the diffusion time on the mean diffusivity (MD) in previous studies are controversial. In this study, a new experimental protocol was designed to evaluate the effects of the two parameters on the results of PGSE. It was found that MD decreased significantly with the increased diffusion time or increased diffusion gradient strength, which cannot be explained by the previous theories. Through theoretical analysis, we found the flaw in the pulsed gradient spin echo (PGSE) method, which is the explanation for the controversial results of diffusion time obtained by oth- ers.

关键词： diffusion time diffusion gradient strength diffusion-weighted imaging diffusion tensor imaging mean diffusivity.

The localization of 1-cohomology of transitive Lie algebroids

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Science china Mathematics 2006年第2期49卷 277-288页

作者： CHEN Zhuo & LIU Zhangju department of Mathematics, Capital Normal university, beijing 100037, china School of Mathematical Science, peking university, beijing 100871, china 1. department of Mathematics Capital Normal University Beijing 100037 China 2. School of Mathematical Science Peking University Beijing 100871 China

For a transitive Lie algebroid A on a connected manifold M and its representation on a vector bundle F, we define a morphism of cohomology groups rk: Hk(A,F) → Hk(Lx,Fx), called the localization map, where Lx is the adjoint algebra at x ∈ M. The main result in this paper is that if M is simply connected, or H (LX,FX) is trivial, then T is injective. This means that the Lie algebroid 1-cohomology is totally determined by the 1-cohomology of its adjoint Lie algebra in the above two cases.

关键词： transitive Lie algebroid representation cohomology localization.

Electrical Properties of Expanded Graphite Intercalation Compounds

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Journal of Materials Science & Technology 2001年第3期17卷 371-374页

作者： Xiuyun CHUAN department of Geology, peking university, beijing 100871, china Daizhang CHEN and Xunruo ZHOU department of Materials Science, china university of Geosciences, beijing 100083, china E-mail: cxyljhcj@*** peking Univ Dept Geol Beijing 100871 Peoples R China china Univ Geosci Dept Mat Sci Beijing 100083 Peoples R China

The intercalation compounds of CuCl2 were synthesized with expanded graphite, whose magnitude of the electrical conductivity is about 10(3)S(.)cm(-1). Their electrical conductivity is 3 similar to6 times as high as that of the expanded graphite, and about 10 times as high as that of GIC made of the non-expanded graphite. The microanalysis results of chemical compounds by X-ray energy spectrum scanning of TEM testified that the atomic ratio of chloride and cupric is nonstoichoimetric. The multivalence and exchange of electrovalence of the cupric ion was confirmed by the XPS-ESCA. Vacancy of chlorine anion increases the concentration of charge carrier. The special stage structure, made of graphite and chloride, produces a weak chemical bond belt and provides a carrier space in the direction of GIC layer. These factors develop the electrical properties.

关键词： In Ph Electrical Properties of Expanded Graphite Intercalation Compounds Graphite ESCA

On the Abundance of Chaotic Behavior for Generic One-Parameter Families of Maps

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Acta Mathematica Sinica,English Series 1996年第4期12卷 398-412页

作者： Zheng Zhiming department of Mathematics peking university beijing, 100871 china department of Mathematics Peking University Beijing China

In this paper, we want to show the abundance of chaotic systems with absolutely continuous probability measures in the generic regular family with perturbable points. More precisely, we prove that if fa:I→I, a∈P is a regular family satisfying some conditions described in the next section, then there exists a Borel set Ω(?)P of positive Lebesgue measure such that for every a∈Ω, fa admits an absolutely continuous invariant probability measure w.r.t. the Lebesgue measure. The idea of proof in this paper, as compared with that shown in [1] and [7], follows a similar line.

关键词： Chaos Generic regular family Probability measure