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New expression of bimodal phase distributions in direct-method phasing of protein single-wavelength anomalous diffraction data

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Chinese Physics B 2010年第8期19卷 8-13页

作者：张涛古元新郑朝德范海福 Research Institute of Magnetic Materials School of Physical Sciences and TechnologyLanzhou University National laboratory for Condensed matter Physics and Key laboratory of Soft matter Physics Institute of PhysicsChinese Academy of Sciences Beijing National laboratory for Condensed matter Physics and Key laboratory of Soft matter Physics Institute of PhysicsChinese Academy of Sciences

One of the essential points of the direct-method single-wavelength anomalous diffraction （SAD） phasing for proteins is to express the bimodal SAD phase distribution by the sum of two Gaussian functions peaked respectively at φh″＋｜△φh｜ and φh″-｜△φh｜. The probability for △φh being positive （P＋） can be derived based on the Cochran distribution in direct methods. Hence the SAD phase ambiguity can be resolved by multiplying the Gaussian function peaked at φh″＋｜△φh｜ with P＋ and multiplying the Gaussian function peaked at φh″-｜△φh｜ with P_ （=1- P＋）. The direct-method SAD h phasing has been proved powerful in breaking SAD phase ambiguities, in particular when anomalous-scattering signals are weak. However, the approximation of bimodal phase distributions by the sum of two Gaussian functions introduces considerable errors. In this paper we show that a much better approximation can be achieved by replacing the two Gaussian functions with two von Mises distributions. Test results showed that this leads to significant improvement on the efficiency of direct-method SAD-phasing.

关键词： direct methods single-wavelength anomalous diffraction OASIS program proteins

OASIS4.0—a new version of the program OASIS for phasing protein diffraction data

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Chinese Physics B 2010年第8期19卷 474-482页

The program OASIS4.0 has been released. Apart from the improved single-wavelength anomalous diffraction （SAD） phasing algorithm described in a separate paper, an important new feature in this version is the automation of the iterative phasing and model-building process in solving protein structures. A new graphical user＇s interface （GUI） is provided for controlling and real-time monitoring the dual-space iterative process. The GUI is discussed in detail in the present paper.

关键词： program OASIS4.0 automatic dual-space fragment extension proteins

Growth of Pb S nanoclusters on specific sites of programmed oligodeoxynucleotides

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Chinese Physics B 2015年第1期24卷 398-403页

作者：陆颖滕翠娟李颖王惠徐春华胡书新李明 Beijing National laboratory for Condensed matter Physics and Key laboratory of Soft matter Physics Institute of PhysicsChinese Academy of Sciences

We develope a method to synthesize Pb S nanoclusters（NCs） using guanine-containing oligodeoxynucleotides（ODNs）as templates. The NCs on the ODNs are ultra small（ranging from ～ 0.5 nm to 2.1 nm） and luminescent in the visible region. They are characterized by photoluminescence（PL） spectra, transmission electron microscopy（TEM）, and X-ray powder diffraction（XRD）. The ODN–NC complexes can be used as customer-designed fluorophores which do not have the problem of multiple conjugations. The same method enables us to fabricate Pb S quantum dot molecules and connect them into nanowires, expanding their potential applications in molecule electronics and quantum computing.

关键词： Pb S nanoclusters quantum dot molecules oligodeoxynucleotides photoluminescence

Brownian dynamics simulation of the cross-talking effect among modified histones on conformations of nucleosomes

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Chinese Physics B 2010年第4期19卷 461-468页

作者：段兆文李伟谢平窦硕星王鹏业 Key laboratory of Soft matter Physics Beijing National Laboratory for Condensed Matter PhysicsInstitute of PhysicsChinese Academy of Sciences

Using Brownian dynamics simulation, we studied the effect of histone modifications On conformations of an array of nucleosomes in a segment of chromatin. The simulation demonstrated that the segment of chromatin shows the dynamic behaviour that its conformation can switch between a state with nearly all of the histones being wrapped by DNA and a state with nearly all of the histones being unwrapped by DNA, thus involving the ＂cross-talking＂ interactions among the histones. Each state can stay for a sufficiently long time. These conformational states are essential for gene expression or gene silence. The simulation also shows that these conformational states can be inherited by the daughter DNAs during DNA replication, giving a theoretical explanation of the epigenetic phenomenon.

关键词： nucleosome histone modification DNA Brownian dynamics

Effective temperature and fluctuation-dissipation theorem in athermal granular systems:A review

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Chinese Physics B 2014年第7期23卷 73-78页

作者：陈琼厚美瑛 Key laboratory of Soft matter Physics Beijing National Laboratory for Condensed Matter Physics Institute of PhysicsChinese Academy of Sciences

The definition and the previous measurements of a dynamics-relevant temperature-like quantity in granular media are reviewed for slow and fast particle systems. Especially, the validity of the fluctuation-dissipation theorem in such an athermal system is explored. Experimental evidences for the fluctuation-dissipation theorem relevant effect temperature support the athermal statistical mechanics, which has been widely explored in recent years by physicists. Difficulties encountered in defining temperature or establishing thermodynamics or statistical mechanics in non-equilibrium situations are discussed.

关键词： granular systems fluctuation-dissipation relation non-equilibrium thermodynamics

DEM simulation of granular segregation in two-compartment system under zero gravity

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Chinese Physics B 2017年第4期26卷 238-244页

作者：王文广周志刚宗谨厚美瑛 Key laboratory of Soft matter Physics Beijing National Laboratory for Condense Matter PhysicsInstitute of PhysicsChinese Academy of Sciences School of Physical sciences University of Chinese Academy of Sciences

In this paper,granular segregation in a two-compartment cell in zero gravity is studied numerically by DEM *** the simulation using a virtual window method we find a non-monotonic flux,a function which governs the segregation.A parameter is used to quantify the *** effect of three parameters：the total number of particles N,the excitation strength F,and the position of the window coupling the two compartments,on the segregation and the waiting time%are *** is found that the segregation observed in zero gravity exists and does not depend on the excitation strength *** waiting time T,however,depends strongly on F：the higher the F,the lower the waiting time V,The simulation results are important in guiding the SJ-10 satellite microgravity experiments.

关键词： DEM simulation granular gas microgravity segregation

Synchronous Measurement of Ultrafast Anisotropy Decay of the B850 in Bacterial LH2 Complex

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Chinese Physics Letters 2015年第2期32卷 48-51页

作者：王云鹏都鲁超朱刚贝王专翁羽翔 laboratory of Soft matter Physics and Beijing National Laboratory for Condensed Matter PhysicsInstitute of PhysicsChinese Academy of Sciences

Ultrafast anisotropic decay is a prominent parameter revealing ultrafast energy and electron transfer; however, it is dimcult to be determined reliably owing to the requirement of a simultaneous availability of the parallel and perpendieular polarized decay kinetics. Nowadays, any measurement of anisotropic decay is a kind of approach to the exact simultaneity. Here we report a novel method for a synchronous ultrafast anisotropy decay measurement, which can well determine the anisotropy, even at a very early time, as the rising phase of the excitation laser pulse. The anisotropic decay of the B850 in bacteriM light harvesting antenna complex LH2 of rhodobacter sphaeroides in solution at room temperature with coherent excitation is detected by this method, which shows a polarization response time of 30 fs, and the energy transfer from the initial excitation to the bacteriochlorophylls in B850 ring takes about 7Ors. The anisotropic decay that is probed at the red side of the absorption spectrum, such as 880 nm, has an initial value of 0.4, corresponding to simulated emission, while the blue side with an anisotropy of 0.1 contributes to the ground-state bleaching. Our results show that the coherent excitation covering the whole ring might not be realized owing to the symmetry breaking of LH2： from C9 symmetry in membrane to C2 symmetry in solution.

关键词： Synchronous Measurement of Ultrafast Anisotropy Decay of the B850 in Bacterial LH2 Complex LH

Model for Unidirectional Movement of Axonemal and Cytoplasmic Dynein Molecules

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Acta Biochimica et Biophysica Sinica 2006年第10期38卷 711-724页

作者： Ping XIE* Shuo-Xing DOU Peng-Ye WANG laboratory of Soft matter Physics,Beijing National laboratory for Condensed matter Physics,Institute of Physics,Chinese Academy of sciences,Beijing 100080,China laboratory of Soft matter Physics Beijing National Laboratory for Condensed Matter Physics Institute of Physics Chinese Academy of SciencesBeijing 100080 China

A model for the unidirectional movement of dynein is presented based on the structuralobservations and biochemical experimental results *** this model,the binding affinity of dynein formicrotubule (MT) is independent of its nucleotide state and the change between strong and weak MT-bindingis determined naturally by the variation of relative orientation between the stalk and MT,as the stalk rotatesfollowing nucleotide-state *** the enigmatic communication from the adenosine triphosphate(ATP)-binding site in the globular domain to the far MT-binding site in the tip of the stalk,which is aprerequisite in conventional models,is not *** the present model,the previous experimentalresults such as the effect of ATP and adenosine diphosphate (ADP) bindings on dissociation of dynein fromMT,the movement of single-headed axonemal dyneins at saturating ATP concentration,the load dependenceof step-size for the movement of two-headed cytoplasmic dyneins and the dependence of stall force on ATPconcentration can be well explained.

关键词： dynein mechanism mechanochemistry molecular motor

Electronic structure and nematic phase transition in superconducting multiple-layer FeSe films grown by pulsed laser deposition method

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Chinese Physics B 2017年第7期26卷 363-372页

作者：沈兵冯中沛黄建伟胡勇高强李聪徐煜刘国东俞理赵林金魁周兴江 National laboratory for Superconductivity Beijing National Laboratory for Condensed Matter Physics Institute of PhysicsChinese Academy of Sciences University of Chinese Academy of sciences Collaborative Innovation Center of Quantum matter

We report comprehensive angle-resolved photoemission investigations on the electronic structure of single crystal multiple-layer FeSe films grown on CaF_2 substrate by pulsed laser deposition（PLD） method. Measurements on FeSe/CaF_2 samples with different superconducting transition temperatures T_c of 4 K, 9 K, and 14 K reveal electronic difference in their Fermi surface and band structure. Indication of the nematic phase transition is observed from temperature-dependent measurements of these samples; the nematic transition temperature is 140-160 K, much higher than ~90 K for the bulk FeSe. Potassium deposition is applied onto the surface of these samples; the nematic phase is suppressed by potassium deposition which introduces electrons to these FeSe films and causes a pronounced electronic structure change. We compared and discussed the electronic structure and superconductivity of the FeSe/CaF_2 films by PLD method with the FeSe/SrTiO_3 films by molecular beam epitaxy（MBE） method and bulk FeSe. The PLD-grown multilayer FeSe/CaF_2 is more hole-doped than that in MBE-grown multiple-layer FeSe films. Our results on FeSe/CaF_2 films by PLD method establish a link between bulk FeSe single crystal and FeSe/SrTiO_3 films by MBE method, and provide important information to understand superconductivity in FeSe-related systems.

关键词： iron-based superconductor FeSe film ARPES electronic structure