Exploring the Origin of Power Law Distribution in Single-Molecule Conformation Dynamics: Energy Landscape Perspectives

We explored the origin of power law distribution observed in single-molecule conformational dynamics experiments. By establishing a kinetic master equation approach to study statistically the microscopic state dynamics, we show that the underlying landscape with exponentially distributed density of states leads to power law distribution of kinetics. The exponential density of states emerges when the system becomes glassy and landscape becomes rough with significant trapping.

Kinetics and Statistical Distributions of Single-Molecule Conformational Dynamics

We developed a coarse-grained yet microscopic detailed model to study the statistical fluctuations of single-molecule protein conformational dynamics of adenylate kinase. We explored the underlying conformational energy landscape and found that the system has two basins of attractions, open and closed conformations connected by two separate pathways. The kinetics is found to be nonexponential, consistent with single-molecule conformational dynamics experiments. Furthermore, we found that the statistical distribution of the kinetic times for the conformational transition has a long power law tail, reflecting the exponential density of state of the underlying landscape. We also studied the joint distribution of the two pathways and found memory effects.

Vortex dynamics in the studies of looping in tropical cyclone tracks

This paper proposes criteria for predicting the tendency of looping in tropical cyclone tracks using the approach of vortex dynamics. We model the asymmetric structure of a cyclone by a system of vortex patches. The evolution of such system of vortices is simulated by the method of contour dynamics. A new set of exact analytic formulas for contour dynamics calculations is derived, which is shown to be more computationally effective. Based on point-vortex models, we derive analytic formulas for the criteria of looping in a cyclone track. From numerical experiments, the simulated trajectories obtained from the point-vortex system and vortex patch system agree quite well. Hence, the looping criteria obtained from the point-vortex system can be applied by forecasters to stay alert for tendency of looping in a cyclone track. To demonstrate the applicability of the proposed criteria, the trajectory of Typhoon Yancy (9012), whose field data are available from ''TCM-90'', is simulated. The case study shows that the asymmetric structure similar to the pattern of a beta gyre is responsible for its recurvature when Yancy landed Fujian Province, China on 20 August 1990.

Fast simulation of the forward tracking detector of HPLUS

The necessity of installing a forward tracking detector stack is discussed for the Hadron Physics LanzhoU Spectrometer(HPLUS). A local tracker is developed to solve the multi-track finding problem. The track candidates are searched iteratively via Hough Transform. The fake tracks are removed by a least square fitting process. With this tracker we have studied the feasibility of pp -> pp + phi(-> K+K-), a typical physical channel proposed on HPLUS. The single track momentum resolution due to the uncertainty of the positioning in FTD is 1.3%. The multiple scattering effect contributes about 20% to the momentum resolution in the FTD coverage. The width and the signal-to-background ratio of the reconstructed phi are 1.51 MeV and 4.36, respectively, taking into account the direct Kaon channel pp -> pp + K+K- as background. The geometry coverage of FTD for phi events is about 85.4%. Based on the current fast simulation and estimation, the geometrical configuration of FTD meets the physical requirement of HPLUS under the current luminosity and multiplicity conditions. The tracker is applicable in the full simulation coming next and is extendable to other tracking component of HPLUS.

Dominant kinetic paths on biomolecular binding-folding energy landscape

The identification of kinetic pathways is a central issue in understanding the nature of flexible binding. A new approach is proposed here to study the dynamics of this binding-folding process through the establishment of a path integral framework on the underlying energy landscape. The dominant kinetic paths of binding and folding can be determined and quantified. In this case, the corresponding kinetic paths of binding are shown to be intimately correlated with those of folding and the dynamics becomes quite cooperative. The kinetic time can be obtained through the contributions from the dominant paths and has a U-shape dependence on temperature.

Effects of chain flexibility on polymer conformation in dilute solution studied by lattice Monte Carlo simulation

Effects of chain flexibility on the conformation of homopolymers in good solvents have been investigated by Monte Carlo simulation. Bond angle constraint coupled with persistence length of polymer chains has been introduced in the modified eight-site bond fluctuation simulation model. The study about the effects of chain flexibility on polymer sizes reveals that the orientation of polymer chains under confinement is driven by the loss of conformation entropy. The conformation of polymer chains undergoing a gradual change from spherical iso-diametric ellipsoid to rodlike iso-diametric ellipsoid with the decrease of polymer chain flexibility in a wide region has been clearly illustrated from several aspects. Furthermore, a comparison of the freely jointed chain (FJC) model and the wormlike chain (WLC) model has also been made to describe the polymer sizes in terms of chain flexibility and quasi-quantitative boundary toward the suitability of the models.

履带式移动机器人行动规划技术的研究

本文以８６３－５１２型号项目为背景，从运动特性、运动描述、运动控制以及运动规划等几个方面研究履带式移动机器人的行动规划技术；首先从理论上分析了履带式移动机器人的内在运动传递机理，指出了其区别于轮式移动载体的独特的运动特性，尤其是在其转向特性方面，得出了履带式移动机器人运动角速度几乎不可控原理、原地转弯转不准问题、以及履带式车辆行动规划时所要遵循的规则等重要结论，针对履带式移动机器人的纵向运动控制问题，讨论了其速度控制模型，提出了一种速度测量与控制的简单、准确、可靠的方法。在磺向运动方面，提出了一种基于ＦＭ－ＬＩＫＥ和ＡＭ－ＬＩＫＥ相结合的复合控制技术，解决了难度较大的方向控制问题。最后提供了实验结果，证明了上述方法与结论的正确性。上述方法与结论，作为８６３－５１２某型号任务的一部分，业已通过验收。

A Molecular Dynamics Simulation: the Effect of Finite Size on the Thermal Conductivity in a Single Crystal Silicon

Non-equilibrium molecular dynamics (NEMD) simulations are performed to calculate thermal conductivity. The environment-dependent interatomic potential (EDIP) potential on crystal silicon is adopted as a model system. The issues are related to nonlinear response, local thermal equilibrium and statistical averaging. The simulation results by non-equilibrium molecular dynamics show that the calculated thermal conductivity decreases almost linearly as the film thickness reduced at the nanometre scale. The effect of size on the thermal conductivity is also obtained by a theoretic analysis of the kinetic theory and formulas of the heat capacity. The analysis reveals that the contributions of phonon mean free path (MFP) and phonon number in a finite cell to thermal conductivity are very important.

Spin dynamics in the second subband of a quasi-two-dimensional system studied in a single-barrier heterostructure by time-resolved Kerr rotation

Spin dynamics in the first and second subbands have been examined simultaneously by time resolved Kerr rotation in a single-barrier heterostructure of a 500 nm thick GaAs absorption layer. By scanning the wavelengths of the probe and pump beams towards the short wavelength in the zero magnetic field, the spin coherent time T-2(1)* in the 1st subband E-1 decreases in accordance with the D'yakonov-Perel' (DP) spin decoherence mechanism. Meanwhile, the spin coherence time T-2(2)* in the 2nd subband E-2 remains very low at wavelengths longer than 810 nm, and then is dramatically enhanced afterwards. At 803 nm, T-2(2)* (450 ps) becomes ten times longer than T-2(1)* (50 ps). A new feature has been discovered at the wavelength of 811nm under the bias of -0.3V (807nm under the bias of -0.6V) that the spin coherence times (T-2(1)* and T-2(2)*) and the effective g* factors (vertical bar g*(E-1)vertical bar and vertical bar g*(E-2)vertical bar) all display a sudden change, presumably due to the "resonant" spin exchange coupling between two spin opposite bands. Copyright (C) EPLA, 2008.

Controlling electronic structures by irradiation in single-walled SiC nanotubes: a first-principles molecular dynamics study

Using first-principles molecular dynamics simulations, the displacement threshold energy and defect configurations are determined in SiC nanotubes. The simulation results reveal that a rich variety of defect structures (vacancies, Stone-Wales defects and antisite defects) are formed with threshold energies from 11 to 64 eV. The threshold energy shows an anisotropic behavior and exhibits a dramatic decrease with decreasing tube diameter. The electronic structure can be altered by the defects formed by irradiation, which suggests that the electron irradiation may be a way to use defect engineering to tailor electronic properties of SiC nanotubes.

Chiral symmetry analysis and rigid rotational invariance for the lattice dynamics of single-wall carbon nanotubes

We provide a detailed expression of the vibrational potential for the lattice dynamics of single-wall carbon nanotubes (SWCNT's) satisfying the requirements of the exact rigid translational as well as rotational symmetries, which is a nontrivial generalization of the valence force model for the planar graphene sheet. With the model, the low-frequency behavior of the dispersion of the acoustic modes as well as the flexure mode can be precisely calculated. Based upon a comprehensive chiral symmetry analysis, the calculated mode frequencies (including all the Raman- and infrared-active modes), velocities of acoustic modes, and the polarization vectors are systematically fitted in terms of the chiral angle and radius, where the restrictions of various symmetry operations of SWCNT's are fulfilled.

Exploring the mechanism of flexible biomolecular recognition with single molecule dynamics

Combining a single-molecule study of protein binding with a coarse grained molecular dynamics model including solvent (water molecules) effects, we find that biomolecular recognition is determined by flexibilities in addition to structures. Our single-molecule study shows that binding of CBD (a fragment of Wiskott-Aldrich syndrome protein) to Cdc42 involves bound and loosely bound states, which can be quantitatively explained in our model as a result of binding with large conformational changes. Our model identified certain key residues for binding consistent with mutational experiments. Our study reveals the role of flexibility and a new scenario of dimeric binding between the monomers: first bind and then fold.

Single molecule dynamics and statistical fluctuations of gene regulatory networks: A repressilator

The authors developed a time dependent method to study the single molecule dynamics of a simple gene regulatory network: a repressilator with three genes mutually repressing each other. They quantitatively characterize the time evolution dynamics of the repressilator. Furthermore, they study purely dynamical issues such as statistical fluctuations and noise evolution. They illustrated some important features of the biological network such as monostability, spirals, and limit cycle oscillation. Explicit time dependent Fano factors which describe noise evolution and show statistical fluctuations out of equilibrium can be significant and far from the Poisson distribution. They explore the phase space and the interrelationships among fluctuations, order, amplitude, and period of oscillations of the repressilators. The authors found that repressilators follow ordered limit cycle orbits and are more likely to appear in the lower fluctuating regions. The amplitude of the repressilators increases as the suppressing of the genes decreases and production of proteins increases. The oscillation period of the repressilators decreases as the suppressing of the genes decreases and production of proteins increases.

Diffusion and single molecule dynamics on biomolecular interface binding energy landscape

We propose a new approach to study the diffusion dynamics on biomolecular interface binding energy landscape. The resulting mean first passage time (MFPT) has 'U'curve dependence on the temperature. It is shown that the large specificity ratio of gap to roughness of the underlying binding energy landscape not only guarantees the thermodynamic stability and the specificity [P.A. Rejto, G.M. Verkhivker, in: Proc. Natl. Acad. Sci. 93 (1996) 8945; C.J. Tsai, S. Kumar, B. Ma, R. Nussinov, Protein Sci. 8 (1999) 1181; G.A. Papoian, P.G. Wolynes, Biopolymers 68 (2003) 333; J. Wang, G.M. Verkhivker, Phys. Rev. Lett. 90 (2003) 198101] but also the kinetic accessibility. The complex kinetics and the associated fluctuations reflecting the structures of the binding energy landscape emerge upon temperature changes. The theory suggests a way of connecting the models/simulations with single molecule experiments by analysing the kinetic trajectories.