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Electric Field-Induced Fluid Velocity Field Distribution in DNA Solution

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Chinese physics Letters 2008年第10期25卷 3818-3821页

作者：张凌云王鹏业 laboratory of Soft matter physics Beijing National Laboratory for Condensed Matter Physics Institute of Physics Beijing 100190

We present an analytical solution for fluid velocity field distribution of polyelectrolyte DNA. Both the electric field force and the viscous force in the DNA solution are considered under a suitable boundary condition. The solution of electric potential is analytically obtained by using the linearized Poisson-Boltzmann equation. The fluid velocity along the electric field is dependent on the cylindrical radius and concentration. It is shown that the electric field-induced fluid velocity will be increased with the increasing cylindrical radius, whose distribution also varies with the concentration

关键词： the power-law exponents precipitation durative abrupt precipitation change

2277-W continuous-wave diode-pumped heat capacity laser

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Chinese Optics Letters 2007年第4期5卷 226-228页

作者：杨晓冬薄勇彭钦军崔前进耿爱丛崔大复许祖彦 beijing national laboratory for condensed matter physics Institute of physics Chinese Academy of Sciences beijing national laboratory for condensed matter physics Institute of Physic Chinese Academy of Sciences

A high power continuous-wave （CW） diode-pumped Nd：YAG laser operated in heat capacity mode is demonstrated by use of two identical highly efficient diode-pumped laser heads placed in a plane-plane resonator. The laser heads are uniformly pumped with a five-fold symmetrical side-pumping configuration, and each head is able to output maximum output power of 2200 W at 808 nm. Under a total pump power of 4290 W, the output power of the laser at 1064 nm is up to 2277 W, corresponding to an optical-to-optical efficiency of 53.1%.

关键词： Continuous wave lasers Optically pumped lasers Specific heat

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

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

An intermediate state of T7 RNA polymerase provides another pathway of nucleotide selection

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Chinese physics B 2017年第10期26卷 12-27页

作者：王展峰刘玉如王鹏业谢平 Key laboratory of Soft matter physics Beijing National Laboratory for Condensed Matter Physics Institute of PhysicsChinese Academy of Science

Phage T7 RNA polymerase is a single-subunit transcription enzyme, transcribing template DNA to RNA. Nucleoside triphosphate （NTP） selection and translocation are two critical steps of the transcription elongation. Here, using all-atom molecular dynamics simulations, we found that between pre- and post-translocation states of T7 RNA polymerase an intermediate state exists, where the O helix C-terminal residue tyrosine 639, which plays important roles in translocation, locates between its pre- and post-translocation positions and the side chain of the next template DNA nucleotide has moved into the active site. NTP selection in this intermediate state was studied, revealing that the selection in the intermediate state can be achieved relying on the effect of Watson-Crick interaction between NTP and template DNA nucleotide, effect of stability of the components near the active site such as the nascent DNA-RNA hybrid and role of tyrosine 639. This indicates that another NTP-selection pathway can also exist besides the main pathway where NTP selection begins at the post-translocation state upon the entry of NTE

关键词： RNA polymerase transcription elongation fidelity control molecular dynamics simulation

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

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

Unified nonequilibrium dynamical theory for exchange bias and training effects

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Chinese physics B 2009年第9期18卷 3960-3965页

作者：张开成刘邦贵 Institute of physics Chinese Academy of Sciences beijing national laboratory for condensed matter physics

We have investigated the exchange bias and training effect in the ferromagnetic/antiferromagnetic （FM/AF） heterostructures using a unified Monte Carlo dynamical approach. The magnetization of the uncompensated AF layer is still open after the first field cycling is finished. Our simulated results show obvious shift of hysteresis loops （exchange bias） and cycling dependence of exchange bias （training effect） when the temperature is below 45 K. The exchange bias field decreases with decreasing cooling rate or increasing temperature and the number of the field cycling. Essentially, these two effects can be explained on the basis of the microscopical coexistence of both reversible and irreversible moment reversals of the AF domains. Our simulations are useful to understand the real magnetization dynamics of such magnetic heterostructures.

关键词： ferromagnetic/antiferromagnetic bilayers hysteresis exchange bias training

Effects of energy dissipation on anisotropic materials

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Chinese physics B 2015年第7期24卷 378-383页

作者：张凌云 beijing national laboratory for condensed matter physics Institute of PhysicsChinese Academy of Sciences

A model and its simulations are presented to describe the effects of energy dissipation on anisotropic systems. When the current electromigration is constant, energy dissipation depends on lattice constants, resistivity, and the angles along the longitudinal and transversal directions. It is shown that an orientation variation of the grain can significantly influence the energy dissipation for some anisotropic materials. Based on calculations for the grain model, the mechanism of grain growth and microstructure evolution under electromigration is explained. Theoretical implications about material selection and reliability are derived.

关键词： electromigration energy dissipation