Modified Nosé–Hoover thermostat for solid state for constant temperature molecular dynamics simulation

Nosé–Hoover (NH) thermostat methods incorporated with molecular dynamics (MD) simulation have been widely used to simulate the instantaneous system temperature and feedback energy in a canonical ensemble. The method simply relates the kinetic energy to the system temperature via the particles’ momenta based on the ideal gas law. However, when used in a tightly bound system such as solids, the method may suffer from deriving a lower system temperature and potentially inducing early breaking of atomic bonds at relatively high temperature due to the neglect of the effect of the potential energy of atoms based on solid state physics.     

Extensive Numerical Tests of Leapfrog Integrator in Middle Thermostat Scheme in Molecular Simulations

Accurate and efficient integration of the equations of motion is indispensable for molecular dynamics (MD) simulations. Despite the massive use of the conventional leapfrog (LF) integrator in modern computational tools within the framework of MD propagation, further development for better performance is still possible. The alternative version of LF in the middle thermostat scheme (LF-middle) achieves a higher order of accuracy and efficiency and maintains stable dynamics even with the integration time stepsize extended by several folds. In this work, we perform a benchmark test of the two integrators (LF and LF-middle) in extensive conventional and enhanced sampling simulations, aiming at quantifying the time-stepsize-induced variations of global properties (e.g., detailed potential energy terms) as well as of local observables (e.g., free energy changes or bond-lengths) in practical simulations of complex systems. The test set is composed of six chemically and biologically relevant systems, including the conformational change of dihedral flipping in the N-methylacetamide and an AT (Adenine-Thymine) tract, the intra-molecular proton transfer inside malonaldehyde, the binding free energy calculations of benzene and phenol targeting T4 lysozyme L99A, the hydroxyl bond variations in ethaline deep eutectic solvent, and the potential energy of the blue-light using flavin photoreceptor. It is observed that the time-step-induced error is smaller for the LF-middle scheme. The outperformance of LF-middle over the conventional LF integrator is much more significant for global properties than local observables. Overall, the current work demonstrates that the LF-middle scheme should be preferably applied to obtain accurate thermodynamics in the simulation of practical chemical and biological systems.     

Applications of periodic orbit theory toN-particle systems

In recent years a number of new techniques have become available in nonequilibrium statistical mechanics, all derived from dynamical system theory, especially from the thermodynamic formalism of Ruelle. We focus here on periodic orbit theory, and we compare it with a novel approach proposed by Evans, Cohen, and Morriss, and developed further by Gallavotti and Cohen. We argue that the two approaches based on such theories are equivalent for systems of many particles if the underlying dynamics is similar to that of Anosov systems, and that such equivalence should remain in more general situations. We extend our previous explanation of irreversibility in the thermostatted Lorentz gas toN-particle diffusion and shearing systems.     

Optimization of direct whole blood PCR amplification with applications on a static thermostat chip

In this paper, direct whole blood PCR amplifications on a static chip thermostat without sample purifications are demonstrated; in these amplifications, problems such as cross-interferences and contaminations could be avoided. The amplification conditions, such as the compositions of reagents and thermal programs, were investigated systematically by a GeneAmp PCR system with a native p53 gene segment (about543 bp) of human genome and an exterior lambda DNA segment (about 500 bp) as targets. Direct amplifications of p53 and K-ras (about 157 bp) gene segments from 0.5 μL blood samples were successfully demonstrated by a static PCR chip with an indium tin oxide glass substrate. The chip thermostat has a typical size of 25 mm × 25 mm, and a polyethylene tube was used as the PCR vial on the glass surface of the chip. Fuzzy proportional integration–differentiation algorithms were adopted in temperature controls of the chip with an aid of a micro-Pt100 sensor. In the direct PCR with the thermostat chip, the whole process only involves automatic thermal programs. This work demonstrated that a chip PCR for field test without desktop facilities is possible either for a point of care test or for forensic analysis. Figure Photo of the glass static thermostat chip with 2 PCR reaction vials Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

基于集中式智能控制系统上位机数据采集算法

将集中式控制系统是将常用的二层结构改进为智能化三层结构的设计方案,即传感器、智能巡检仪和上位机。上位机既可以直接读取传感器的数据也可读取智能巡检仪的采集数据。此方案较好地解决了二层结构所出现的问题,并且也适合较大规模的其它类型的控制系统。但这种设计方案存在当传感器数量规模较大时上位机所采集数据出现丢失现象。为此提出了利用数据库的历史数据及工艺控制曲线的线性特征的数据采集补赏算法,较好地解决了数据丢失的问题。并以温控系统为例仿真了在较大规模控制环境下的算法性能,试验结果达到了研究目的。     

Derivation of the linear and nonlinear non-Markov fluctuation-dissipation relations of the first kind for a dynamical model

A dynamical system consisting of a subsystem having the variablesz=(q,p) and of another dynamical system (thermostat) is considered in the nonquantum case. Using a dynamical equation, it is shown that the linear and quadratic non-Markov fluctuation-dissipation relations (FDRs) of the first kind are valid in the first nonvanishing approximation in interaction constants. Applying these FDRs, one can determine the statistical properties of the fluctuations when the form of the nonlinear phenomenological equation is known. The non-Markov FDRs of the first kind are the direct generalization (to the inertial case) of the Markov FDRs that are the consequence of detailed balance.     

Behavior of Mercury Vapor Upon Irradiation by a Mercury Lamp in an Inert Gas

Abstract

The behavior of mercury vapor during irradiation by a mercury lamp is investigated. Using the flameless atomic absorption technique for mercury determination, it was found that when mercury vapor in an inert gas is irradiated by a mercury lamp, the atomic absorption signal of mercury is decreased rapidly and the signal may be restored by heating to 70°C. These phenomena indicate that the irradiation products of mercury vapor in the quartz tube are deposited on the tube, and are dissociated into the mono-atomic state of mercury upon heating.     

The Nosé-Hoover Thermostat in Molecular Dynamics for Nuclear Matter

In this work we present a calculation of the hamiltonian variables solving the molecular dynamics equations of motion for a system of nuclear matter kept at fixed temperature by using the Nosé-Hoover Thermostat and interacting via a semiclassical potential depending on both positions and momenta.     

热超构材料十年简史

文章简要介绍了热超构材料自2008年以来的十年发展历程。作者挑选了24篇文章按照出版时间的先后顺序,逐一点评,在呈现新物理和新应用的同时,亦述及人文思想。期望此举有助读者快速了解该领域的全貌及未来发展趋势。     

On the use of mass scaling for stable and efficient simulated tempering with molecular dynamics

Simulated tempering (ST) is a generalized‐ensemble algorithm that employs trajectories exploring a range of temperatures to effectively sample rugged energy landscapes. When implemented using the molecular dynamics method, ST can require the use of short time steps for ensuring the stability of trajectories at high temperatures. To address this shortcoming, a mass‐scaling ST (MSST) method is presented in which the particle mass is scaled in proportion to the temperature. Mass scaling in the MSST method leads to velocity distributions that are independent of temperature and eliminates the need for velocity scaling after the accepted temperature updates that are required in conventional ST simulations. The homogeneity in time scales with changing temperature improves the stability of simulations and allows for the use of longer time steps at high temperatures. As a result, the MSST is found to be more efficient than the standard ST method, particularly for cases in which a large temperature range is employed. © 2016 Wiley Periodicals, Inc.