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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

A-site ordered quadruple perovskite oxides AA'3B4O12

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Chinese Physics B 2016年第7期25卷 62-74页

作者：龙有文 Beijing National Laboratory for condensed matter Physics Institute of Physics Chinese Academy of Sciences Collaborative Innovation Center of Quantum matter

The A-site ordered perovskite oxides with chemical formula AA’BOdisplay many intriguing physical properties due to the introduction of transition metals at both A and B sites. Here, research on the recently discovered intermetallic charge transfer occurring between A-site Cu and B-site Fe ions in La CuFeOand its analogues is reviewed, along with work on the magnetoelectric multiferroicity observed in La MnCrOwith cubic perovskite structure. The Cu–Fe intermetallic charge transfer(LaCuFeO→ LaCuFeO) leads to a first-order isostructural phase transition accompanied by drastic variations in magnetism and electrical transport properties. The La MnCrOis a novel spindriven multiferroic system with strong magnetoelectric coupling effects. The compound is the first example of cubic perovskite multiferroics to be found. It opens up a new arena for studying unexpected multiferroic mechanisms.

关键词： high-pressure synthesis A-site ordered perovskite charge transfer multiferroicity

Frequency dependence of quantum path interference in non-collinear high-order harmonic generation

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Chinese Physics B 2016年第2期25卷 129-134页

作者：钟诗阳贺新奎滕浩叶蓬汪礼锋何鹏魏志义 Beijing National Laboratory for condensed matter Physics Institute of Physics Chinese Academy of Sciences

High-order harmonic generation（HHG） driven by two non-collinear beams including a fundamental and its weak second harmonic is numerically studied. The interference of harmonics from adjacent electron quantum paths is found to be dependent on the relative delay of the driving pulse, and the dependences are different for different harmonic *** frequency dependence of the interference is attributed to the spatial frequency chirp in the HHG beam resulting from the harmonic dipole phase, which in turn provides a potential way to gain an insight into the generation of high-order harmonics. As an example, the intensity dependent dipole phase coefficient α is retrieved from the interference fringe.

关键词： high harmonic generation non-collinear dipole phase ultrafast optics

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

Monte Carlo simulation on backward steps of single kinesin molecule

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Chinese Physics B 2008年第4期17卷 1513-1517页

作者：王宏张勇窦硕星王鹏业 Laboratory of Soft matter Physics Beijing National Laboratory for Condensed Matter PhysicsInstitute of PhysicsChinese Academy of Science

Kinesin is a stepping molecular motor travelling along the microtubule. It moves primarily in the plus end direction of the microtubule and occasionally in the minus-end, backward, direction. Recently, the backward steps of kinesin under different loads and temperatures start to attract interests, and the relations among them are revealed. This paper aims to theoretically understand these relations observed in experiments. After introducing a backward pathway into the previous model of the ATPase cycle of kinesin movement, the dependence of the backward movement on the load and the temperature is explored through Monte Carlo simulation. Our results agree well with previous experiments.

关键词： kinesin backward steps Monte Carlo ATPase cycle

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

A review of the growth and structures of silicene on Ag(111)

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Chinese Physics B 2015年第8期24卷 15-24页

作者：吴克辉 Beijing National Laboratory for condensed matter Physics and institute of Physics Chinese Academy of Sciences Collaborative Innovation Center of Quantum matter

Ag(111) is currently the most often used substrate for growing silicene films. Silicene forms a variety of different phases on the Ag(111) substrate. However, the structures of these phases are still not fully understood so far. In this brief review we summarize the growth condition and resulting silicene phases on Ag(111), and discuss the most plausible structural model and electronic property of individual phases. The existing debates on silicene on Ag(111) system are clarified as mush as possible.

关键词： silicene scanning tunneling microscopy surface structure Dirac fermion

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

Visualizing temperature-dependent phase stability in high

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npj Computational Materials 2021年第1期7卷 1375-1383页

作者： Daniel Evans Jiadong Chen George Bokas Wei Chen Geoffroy Hautier Wenhao Sun Department of Materials Science and Engineering University of MichiganAnn ArborMIUSA institute of condensed matter and nanosciences(IMCN) UCLouvainLouvain-La-NeuveBelgium Thayer School of Engineering Dartmouth CollegeHanoverNHUSA

High entropy alloys(HEAs)contain near equimolar amounts of five or more elements and are a compelling space for materials *** the design of HEAs,great emphasis is placed on identifying thermodynamic conditions for single-phase and multi-phase stability regions,but this process is hindered by the difficulty of navigating stability relationships in high-component *** phase diagrams use barycentric coordinates to represent composition axes,which require(N–1)spatial dimensions to represent an N-component system,meaning that HEA systems with N>4 components cannot be readily ***,we propose forgoing barycentric composition axes in favor of two energy axes:a formation-energy axis and a‘reaction energy’*** Inverse Hull Webs offer an information-dense 2D representation that successfully captures complex phase stability relationships in N≥5 component *** use our proposed diagrams to visualize the transition of HEA solid-solutions from high-temperature stability to metastability upon quenching,and identify important thermodynamic features that are correlated with the persistence or decomposition of metastable HEAs.

关键词： stability phase thermodynamic