Electromagnetic retarded interaction and symmetry violation of time reversal in high order stimulated radiation and absorption processes of light

It has been proved that when the retarded effect (or multiple moment effect) of radiation fields is taken into account, the high order stimulated radiation and stimulated absorption probabilities of light are not the same so that time reversal symmetry would be violated, though the Hamiltonian of electromagnetic interaction is still unchanged under time reversal. The reason to cause time reversal symmetry violation is that certain filial or partial transition processes of bound atoms are forbidden or cannot be achieved due to the law of energy conservation and the special states of atoms themselves. These restrictions would cause the symmetry violation of time reversal of other filial or partial transition processes which can be actualized really. The symmetry violation is also relative to the asymmetry of initial states of bound atoms before and after time reversal. For the electromagnetic interaction between non-bound atoms and radiation field, there is no such kind of symmetry violation of time reversal. In this way, the current formula on the parameters of stimulated radiation and absorption of light with time reversal symmetry should be revised. A more reliable foundation can be established for the theories of laser and nonlinear optics in which non-equilibrium processes are involved.     

Exact Mean-Field Solutions of the Asymmetric Random Average Process

We consider the asymmetric random average process (ARAP) with continuous mass variables and parallel discrete time dynamics studied recently by Krug/Garcia and Rajesh/Majumdar [both J. Statist. Phys. 99 (2000)]. The model is defined by an arbitrary state-independent fraction density function (r) with support on the unit interval. We examine the exactness of mean-field steady-state mass distributions in dependence of and identify as a conjecture based on high order calculations the class of density functions yielding product measure solutions. Additionally the exact form of the associated mass distributions P(m) is derived. Using these results we show examplary the exactness of the mean-field ansatz for monomial fraction densities (r)=(n–1) r ^n–2 with n2. For verification we calculate the mass distributions P(m) explicitly and prove directly that product measure holds. Furthermore we show that even in cases where the steady state is not given by a product measure very accurate approximants can be found in the class .     

Efficient use of nonequilibrium measurement to estimate free energy differences for molecular systems

A promising method for calculating free energy differences DeltaF is to generate nonequilibrium data via "fast-growth" simulations or by experiments--and then use Jarzynski's equality. However, a difficulty with using Jarzynski's equality is that DeltaF estimates converge very slowly and unreliably due to the nonlinear nature of the calculation--thus requiring large, costly data sets. The purpose of the work presented here is to determine the best estimate for DeltaF given a (finite) set of work values previously generated by simulation or experiment. Exploiting statistical properties of Jarzynski's equality, we present two fully automated analyses of nonequilibrium data from a toy model, and various simulated molecular systems. Both schemes remove at least several k(B)T of bias from DeltaF estimates, compared to direct application of Jarzynski's equality, for modest sized data sets (100 work values), in all tested systems. Results from one of the new methods suggest that good estimates of DeltaF can be obtained using 5-40-fold less data than was previously possible. Extending previous work, the new results exploit the systematic behavior of bias due to finite sample size. A key innovation is better use of the more statistically reliable information available from the raw data.     

A New Approach to Metal Surface Nitriding Using Dielectric Barrier Discharge at Atmospheric Pressure

A new approach to metal surface nitriding using dielectric barrier discharge (DBD) plasma at atmospheric pressure is presented in this paper. Results of the study show that the plasma nitriding at atmospheric pressure using DBDs is realizable. Harder and thicker compound layer and diffusion layer on the treated surface has been formed in shorter treatment time comparing with the conventional vacuum plasma nitriding, Increasing the applied voltage will facilitate the formation of a thicker nitrided layer using the DBD. The nitrided layer acquired by this new approach is mainly composed of ɛ phase and γ′ phase, and the crystal grains of the ɛ phase is fine and has high dislocations density.     

Influence of grain boundary state on electrical resistivity of ultrafine grained aluminium

An ultrafine grained (UFG) structure has been obtained in commercial purity Al by high-pressure torsion (HPT). Changes in microhardness and electrical resistivity of the UFG material after annealing at various temperatures within a range of 363–673 K have been investigated in correlation with the microstructure evolution. It has been shown that annealing at 363 K leads to substantial decrease in the electrical resistivity while keeping high microhardness level and approximately the same average grain size. The contributions from the various microstructural units (vacancies, dislocations, grain boundaries (GBs)) to the electrical resistivity were analysed. It was shown for the first time that a non-equilibrium state associated with strain-distorted grain boundary (GB) structure strongly affects electrical resistivity of UFG Al. The resistivity of non-equilibrium GBs in UFG structure formed by HPT was evaluated to be at least 50% higher than the resistivity of the thermally equilibrium GBs in a coarse-grained structure.     

准静态颗粒介质的弹性势能弛豫分析

颗粒体系是典型的多体相互作用体系, 具有多重的能量亚稳态. 对于准静态颗粒体系, 引入构型颗粒温度T_c描述弹性势能涨落. 本文认为平衡的体系具有一定的构型颗粒温度T_a, 其量值反映了其结构特征. 当外界扰动激发的构型颗粒温度超出T_a时, 产生不可逆过程. 通过对应力松弛过程的分析, 发现(T_c-T_a)激发了弹性弛豫, 且(T_c-T_a)越大则松弛过程中应力变化越大, 最终构型颗粒温度T_c→T_a时,宏观应力松弛结束,体系达到新的能量亚稳态.     

DNA-Topology Simplification by Topoisomerases

The topological properties of DNA molecules, supercoiling, knotting, and catenation, are intimately connected with essential biological processes, such as gene expression, replication, recombination, and chromosome segregation. Non-trivial DNA topologies present challenges to the molecular machines that process and maintain genomic information, for example, by creating unwanted DNA entanglements. At the same time, topological distortion can facilitate DNA-sequence recognition through localized duplex unwinding and longer-range loop-mediated interactions between the DNA sequences. Topoisomerases are a special class of essential enzymes that homeostatically manage DNA topology through the passage of DNA strands. The activities of these enzymes are generally investigated using circular DNA as a model system, in which case it is possible to directly assay the formation and relaxation of DNA supercoils and the formation/resolution of knots and catenanes. Some topoisomerases use ATP as an energy cofactor, whereas others act in an ATP-independent manner. The free energy of ATP hydrolysis can be used to drive negative and positive supercoiling or to specifically relax DNA topologies to levels below those that are expected at thermodynamic equilibrium. The latter activity, which is known as topology simplification, is thus far exclusively associated with type-II topoisomerases and it can be understood through insight into the detailed non-equilibrium behavior of type-II enzymes. We use a non-equilibrium topological-network approach, which stands in contrast to the equilibrium models that are conventionally used in the DNA-topology field, to gain insights into the rates that govern individual transitions between topological states. We anticipate that our quantitative approach will stimulate experimental work and the theoretical/computational modeling of topoisomerases and similar enzyme systems.     

Capturing the Polarization Response of Solvated Proteins under Constant Electric Fields in Molecular Dynamics Simulations

We capture and compare the polarization response of a solvated globular protein ubiquitin to static electric (E-fields) using atomistic molecular dynamics simulations. We collectively follow E-field induced changes, electrical and structural, occurring across multiple trajectories using the magnitude of the protein dipole vector ( P _p ). E-fields antiparallel to P _p induce faster structural changes and more facile protein unfolding relative to parallel fields of the same strength. While weak E-fields (0.1–0.5 V/nm) do not unfold ubiquitin and produce a reversible polarization, strong E-fields (1–2 V/nm) unfold the protein through a pathway wherein the helix:β-strand interactions rupture before those for the β1-β5 clamp. Independent of E-field direction, high E-field induced structural changes are also reversible if the field is switched off before P _p exceeds 2 times its equilibrium value. We critically examine the dependence of water properties, protein rotational diffusion and E-field induced protein unfolding pathways on the thermostat/barostat parameters used in our simulations.     

Viscosity and normal stress forces of Lennard-Jones chains using reverse non-equilibrium molecular dynamics

Reverse non-equilibrium molecular dynamics was applied for the calculation of the viscosity for different chain lengths. Each chain consisted of m tangent spherical sites, where m was 1, 2, 4, 8 or 16, respectively. From these results, shear thinning was observed at high shear rates. The normal stress forces were also estimated via the calculation of the total stress tensor, and they were related to the shear thinning effect depending on the length of the chain. Furthermore, a power law equation was used to fit the rheological curves of each chain, making possible the calculation of the viscoelasticity as a function of the sites involved in the chains.