A coarse-grained model of the effective interaction for charged amino acid residues and its application to formation of GCN4-pLI tetramer

ABSTRACT

We present a simple coarse-grained model of the effective interaction for charged amino acid residues, such as Glu and Lys, in a water solvent. The free-energy profile as a function of the distance between two charged amino acid side-chain analogues in an explicit water solvent is calculated with all-atom molecular dynamics simulation and thermodynamic integration method. The calculated free-energy profile is applied to the coarse-grained potential of the effective interaction between two amino acid residues. The Langevin dynamics simulations with our coarse-grained potential are performed for association of a small protein complex, GCN4-pLI tetramer. The tetramer conformation reproduced by our coarse-grained model is similar to the X-ray crystallographic structure. We show that the effective interaction between charged amino acid residues stabilises association and orientation of protein complex. We also investigate the association pathways of GCN4-pLI tetramer.     

A staggered-grid finite-difference method with perfectly matched layers for poroelastic wave equations.

A particle velocity-strain, finite-difference (FD) method with a perfectly matched layer (PML) absorbing boundary condition is developed for the simulation of elastic wave propagation in multidimensional heterogeneous poroelastic media. Instead of the widely used second-order differential equations, a first-order hyperbolic leap-frog system is obtained from Biot's equations. To achieve a high accuracy, the first-order hyperbolic system is discretized on a staggered grid both in time and space. The perfectly matched layer is used at the computational edge to absorb the outgoing waves. The performance of the PML is investigated by calculating the reflection from the boundary. The numerical method is validated by analytical solutions. This FD algorithm is used to study the interaction of elastic waves with a buried land mine. Three cases are simulated for a mine-like object buried in "sand," in purely dry "sand" and in "mud." The results show that the wave responses are significantly different in these cases. The target can be detected by using acoustic measurements after processing.     

Nonlinear interferometric vibrational imaging

Coherent anti-Stokes Raman scattering (CARS) processes are "coherent," but the phase of the anti-Stokes radiation is lost by most incoherent spectroscopic CARS measurements. We propose a Raman microscopy imaging method called nonlinear interferometric vibrational imaging, which measures Raman spectra by obtaining the temporal anti-Stokes signal through nonlinear interferometry. With a more complete knowledge of the anti-Stokes signal, we show through simulations that a high-resolution Raman spectrum can be obtained of a molecule in a single pulse using broad band radiation. This could be useful for identifying the three-dimensional spatial distribution of molecular species in tissue.     

采用加权直方图分析和蒙特卡洛重采样法对自由能级的校正研究

本文采用加权直方图分析方法和蒙特卡洛重采样方法进行自由基校正研究. 生成的自由能表面几乎可以收敛到具有足够采样情况的精准表面,并且比常规的加权直方图分析校正方法能更稳定地处理采样不足的情况,为检测能级校正表面的不确定性提供指南,并且定义了明确的标准用以确定能改善其视觉效果的自由能表面平滑程度. 本文通过水中的丙氨酸二肽和KillerRed蛋白质子转移的自由能图证明该方法的优势,说明蒙特卡洛重采样法可以作为在产生自由能表面实际的系统中的实用工具.     

“Thought-experiments” by molecular dynamics

A method for studying the dynamical properties of liquids by molecular dynamics simulation is described. Its basis is the measurement of the response to a weak applied field of appropriate character. The explicit form of the mechanical perturbation is worked out in several cases, and details are given of the numerical techniques used in implementing the method.     

Using piecewise polynomials for faster potential function evaluation

In many molecular dynamics simulation software packages and hardware implementations, piecewise polynomials are used to represent and compute pairwise potential functions efficiently. In this paper, we present three modifications applicable to most interpolations to increase their accuracy. The increased accuracy reduces the amount of data that needs to be stored for each interaction potential, making such interpolations more suitable for architectures with limited memory and/or cache or hardware implementations.     

Temperature and solvent influence on the fluorescence spectrum of anthracene and anthracene-diethylaniline exciplex

By studying the modifications of the fluorescence and excitation bands of anthracene (A) both under the influence of the solvent and temperature, we concluded that these changes are due to the different contributions, both to emission and absorption, of certain molecular species, which appear by the deformation of the anthracene molecule. The influence of solvent and temperature upon the frequency of the maximum of emission of the exciplex anthracene-diethylaniline (DEA) can be explained by the fact that the A molecular species which are connected to the molecules of DEA are changed under the influence of the temperature and solvent.     

C(60) molecular bearings and the phenomenon of nanomapping

Inspired by suggestions of C(60) "nanobearings," we have measured sliding friction on fixed and rotating C(60) layers to explore whether a lubricating effect is present. We refer to this general phenomenon as "nanomapping," whereby macroscopic attributes are mapped in a one on one fashion to nanoscale entities. Our measurements are the first to directly link friction to a documented molecular rotation state. Friction is, however, observed to be higher for rotating layers, in defiance of the ball-bearing analogy. Thus, no direct mapping of macro- to nanoscale attributes can be established.     

First-principles calculations of SO<Subscript>2</Subscript> sensing with Si nanowires

High chemical reactivity and large surface-to-volume ratio have recently led to growinginterest in the employment of silicon nanowires (SiNWs) in sensing applications forchemical species detection. The working principle of SiNWs sensors resides in thepossibility to induce modifications in their electronic properties via molecularinteraction. A detailed analysis of the interaction of Si with molecular compounds is thenrequired to design and optimize NW-based sensors. Here we study the mechanisms ofadsorption on SiNWs of SO₂, an air pollutant with pernicious effects on humans.First-principles density-functional calculations are performed to calculate the electronicstructure of a SO₂molecule adsorbed at a silicon surface in case of undoped substrate and in presence ofsubstitutional subsurface and deep boron impurities. Comparing the results with the caseof NO₂ adsorption –a similar molecule that, nonetheless has a very different interaction with a Si surface –,we show the specific traits of SO₂ interaction: formation of localized states in theband-gap and absence of reactivation of pre-existing and passivated sub-surfaceimpurities. A connection between the modifications in the system electronic structure andthe strength of the molecular interaction is discussed.     

分子线电子输运特性的第一性原理研究

从第一性原理出发 ,利用密度泛函理论研究了SH -C8H16-SH分子和金表面的相互作用 ,并利用分子前线轨道理论和微扰理论定量地确定了该相互作用能常数 ,然后 ,利用弹性散射格林函数方法研究了该分子与金表面形成的分子线的伏 安特性 .研究结果表明 ,当含有硫氢官能团的有机分子化学吸附于金表面时 ,硫原子将与金原子形成以共价键为主的混和键 ,此时 ,扩展的分子轨道使分子线的电导呈现出欧姆特性 ,而对于局域的分子轨道 ,电子的输运只能通过隧道效应来实现 .对分子线伏 安特性的计算结果显示 ,在零偏压附近 ,存在一个电流禁区 ,随着偏压的增加 ,分子线的电导呈现出平台特征 .     

A low diffusion particle method for simulating compressible inviscid flows

A new particle method is presented for the numerical simulation of compressible inviscid gas flows, through procedures which involve relatively small modifications to an existing direct simulation Monte Carlo (DSMC) algorithm. Implementation steps are outlined for simulations involving various grid geometries and for gas mixtures comprising an arbitrary number of species. The proposed method is compared with other numerical schemes through a series of one-dimensional and two-dimensional test cases, and is shown to provide a significant reduction in both artificial diffusion and statistical scatter effects relative to existing DSMC-based equilibrium particle methods.     

Perceived sound quality of sound-reproducing systems.

Perceived sound quality of loudspeakers, headphones, and hearing aids was investigated by multivariate techniques from experimental psychology with the purpose (a) to find out and interpret the meaning of relevant dimensions in perceived sound quality, (b) find out the positions of the investigated systems in these dimensions, (c) explore the relations between the perceptual dimensions and the physical characteristics of the systems, and (d) explore the relations between the perceptual dimensions and overall evaluations of the systems. The resulting dimensions were interpreted as "clearness/distinctness," "sharpness/hardness softness," "brightness-darkness," "fullness-thinness," "feeling of space," "nearness," "disturbing sounds," and "loudness." Their relations to physical variables were explored by studying the positions of the investigated systems in the respective dimensions. Their relations to overall evaluations were studied, and the implications of the investigations for continued research are discussed.     

基于深度张量神经网络预测有机分子的相互作用能

分子的相互作用在分子动力学模拟过程中起着关键的作用. 受限于计算资源,大分子的长时间尺度的相互作用能无法通过量化计算实现. 本文采用一种深度学习框架-深度张量神经网络来预测三个有机分子相关体系中量化精度的相互作用能. 其中,分子的几何结构和原子类型作为网络的输入用于预测相互作用能. 通过分层生成的数据集合实现了网络中隐层参数的优化和训练. 相互作用能的预测结果显示,深度张量神经网络可以在较短的时间内,在1 kcal/mol的平均绝对误差的范围内准确预测分子间的相互作用能. 这一过程提高了计算效率,并为计算相互作用能提供了可靠的计算框架.     

On the construction of a bias potential for atomic system simulation by the hyperdynamics method

Hyperdynamics is the method of accelerated molecular dynamics simulation based on lowering energy barriers while performing the dynamic simulation of a nano/atomic system. A system with reduced energy barriers between different states is obtained by changing the potential of interaction, namely, by constructing the so-called bias potential. An approach allowing a bias potential to be obtained is considered. To demonstrate this method, the hyperdynamics simulation of the diffusion of an atom, adsorbed on a 2D crystal surface, and a vacancy, located in its bulk, is carried out. The results are compared with relevant results obtained by molecular dynamics. It is shown that the hyperdynamics approach makes it possible to obtain statistical results, similar to those provided by molecular dynamics. This allows the accelerated simulation of atomic systems to be conducted with minor losses in the accuracy of results.     

基于气体动理论的二维Karman涡街数值模拟

基于从稀薄流到连续流的跨流域气体动理论统一算法(gas-kinetic unified algorithm,GKUA),通过数值求解考虑转动自由度激发的Boltzmann-Rykov模型方程,得到了一种跨流域非定常流动数值模拟的方法.该求解方法以Boltzmann模型方程为控制方程,在常温状态下如果考虑转动能激发的情况...     

纳米孔壁面作用对蛋白质过孔影响的粗粒化分子动力学模拟

基于粗粒化分子动力学方法模拟电驱动蛋白质过孔过程,研究纳米孔-水/纳米孔-蛋白质相互作用对电泳迁移率的影响;用操控式分子动力学模拟分析蛋白质在不同相互作用下过孔摩擦系数和摩擦阻力.研究发现：蛋白质黏附纳米孔壁面对其过孔特性影响并不明显,而纳米孔-水相互作用对蛋白质过孔电泳迁移率和摩擦系数影响较大.随纳米孔-水相互作用增强,纳米孔壁面与蛋白质附近水分子运动差异显现,蛋白质过孔摩擦阻力显著增大,过孔摩擦系数随之增大,进而影响蛋白质过孔电泳迁移率.所得结果可为纳米孔材料设计提供理论指导.     

Targeting of Kolmogorov-Arnold-Moser Orbits by the Bailout Embedding Method in Two Coupled Standard Maps

A bailout embedding method for controlling chaos can make the chaotic orbits targeting into Kolmogorov- Arnold-Moser orbits. We apply this method to a high-dimensional system with two coupled standard maps. The numerical simulation shows that this method could obtain target islands in order and hence could be used to control chaos. Moreover, it is robust in the presence of weak external noise.     

Particle-in-cell modeling of relativistic laser–plasma interaction with the adjustable-damping,direct implicit method

Implicit particle-in-cell codes offer advantages over their explicit counterparts in that they suffer weaker stability constraints on the need to resolve the higher frequency modes of the system. This feature may prove particularly valuable for modeling the interaction of high-intensity laser pulses with overcritical plasmas, in the case where the electrostatic modes in the denser regions are of negligible influence on the physical processes under study. To this goal, we have developed the new two-dimensional electromagnetic code ELIXIRS (standing for ELectromagnetic Implicit X-dimensional Iterative Relativistic Solver) based on the relativistic extension of the so-called Direct Implicit Method [D. Hewett, A.B. Langdon, Electromagnetic direct implicit plasma simulation, J. Comput. Phys. 72 (1987) 121–155]. Dissipation-free propagation of light waves into vacuum is achieved by an adjustable-damping electromagnetic solver. In the high-density case where the Debye length is not resolved, satisfactory energy conservation is ensured by the use of high-order weight factors. In this paper, we first derive the electromagnetic direct implicit method as a simplified Newton scheme. Its linear properties are then investigated through numerically solving the relation dispersions obtained for both light and plasma waves, accounting for finite space and time steps. Finally, our code is successfully benchmarked against explicit particle-in-cell simulations for two kinds of physical problems: plasma expansion into vacuum and relativistic laser–plasma interaction. In both cases, we will demonstrate the robustness of the implicit solver for crude discretizations, as well as the gains in efficiency which can be realized over standard explicit simulations.     

An electromagnetic simulation assisted small signal modeling method for InP double-heterojunction bipolar transistors

We present a convenient and practical electromagnetic (EM) assisted small-signal model extraction method for InP double-heterojunction bipolar transistors (DHBTs). Parasitic parameters of pad and electrode fingers are extracted by means of 3D EM simulation. The simulations with a new excitation scheme are closer to the actual on-wafer measurement conditions. Appropriate simulation settings are calibrated by comparing measurement and simulation of OPEN and SHORT structures. A simpler $\pi $-type topology is proposed for the intrinsic model, in which the base-collector resistance $R_\mu$, output resistance $R_{\rm ce}$ are deleted, and a capacitance $C_{\rm ce}$ is introduced to characterize the capacitive parasitic caused by the collector finger and emitter ground bar. The intrinsic parameters are all extracted by exact equations that are derived from rigorous mathematics. The method is characterized by its ease of implementation and the explicit physical meaning of extraction procedure. Experimental validations are performed at four biases for three InGaAs/InP HBT devices with $0.8\times 7 $μm, 0$.8\times 10 $μm and $0.8\times 15 $μm emitter, and quite good fitting results are obtained in the range of 0.1-50 GHz.