The slow-scale stochastic simulation algorithm

Reactions in real chemical systems often take place on vastly different time scales, with "fast" reaction channels firing very much more frequently than "slow" ones. These firings will be interdependent if, as is usually the case, the fast and slow reactions involve some of the same species. An exact stochastic simulation of such a system will necessarily spend most of its time simulating the more numerous fast reaction events. This is a frustratingly inefficient allocation of computational effort when dynamical stiffness is present, since in that case a fast reaction event will be of much less importance to the system's evolution than will a slow reaction event. For such situations, this paper develops a systematic approximate theory that allows one to stochastically advance the system in time by simulating the firings of only the slow reaction events. Developing an effective strategy to implement this theory poses some challenges, but as is illustrated here for two simple systems, when those challenges can be overcome, very substantial increases in simulation speed can be realized.     

Fast heavy ion induced photon emission from organic solids and plasma desorption mass spectrometry

Fission fragments from a ²⁵²Cf source have been used to study fast heavy ion induced desorption of ions and luminescence in the wavelength region 200–680 nm from samples of Csl, the amino acids valine, isoleucine and tyrosine, and of the peptide substance P. All samples emit photons under fast heavy ion bombardment. Most of the emission is confined to the near-UV region and within narrow time profiles. Analysis of the fast decay regions of the time profiles show that all the compounds have at least a fast and a slow decay component, both in the nanosecond region. The use of such narrow photon signals as start time markers for time-of-flight measurements (TOF) has been demonstrated. As the photon signal is derived directly from the desorption event it gives the true number of starts for a secondary ion TOF spectrum. Characteristics of the photon emission from a CsI target together with correlation studies between the desorbed secondary ions and the photon signal indicate that the light emission is from the bulk of the material and not correlated with the secondary ions.     

Non-Fickian interdiffusion of dynamically asymmetric species: a molecular-dynamics study

We use molecular dynamics combined with dissipative particle dynamics to construct a model of a binary mixture where the two species differ only in their dynamic properties (friction coefficients). For an asymmetric mixture of slow and fast particles we study the interdiffusion process. The relaxation of the composition profile is investigated in terms of its Fourier coefficients. While for weak asymmetry we observe Fickian behavior, a strongly asymmetric system exhibits clear indications of anomalous diffusion, which occurs in a crossover region between cases I (Fickian) and II (sharp front moving with constant velocity), and is close to the case II limit.     

Time-of-flight secondary ion mass spectrometry of matrix-diluted oligo- and polypeptides bombarded with slow and fast projectiles: Positive and negative matrix and analyte ion yields, background signals, and sample aging

Human angiotensin II, chain B of bovine insulin, and porcine insulin were determined by time-of-flight secondary ion mass spectrometry under impact of approximately 25 keV Xe+ and SF5+ ion beams and approximately 100 MeV 252Cf fission fragments. Matrix-embedded samples, dissolved in a large surplus of alpha-cyano-4-hydroxycinnamic acid, were prepared by nebulizer spray deposition, neat samples by the droplet technique. It is shown that the status of the sample can be assessed by evaluating the matrix-specific features of the mass spectra. The beneficial effect of matrix isolation was small for angiotensin but large for the insulin samples, which did not show parent peaks from neat material. Negative ion yields under SF5+ impact were up to a factor of 50 higher than with Xe+. For positive secondary ions, the enhancement was much smaller. The mass spectra produced by slow ion beams or fast fission fragments were qualitatively similar. Quantitative differences include the following: with fast projectiles the yields were about 10-30 times higher than with slow ions, but similar for negative ion emission under SF5+ bombardment; the analyte-to-matrix yield ratios were higher with slow ions and up to 250 times higher than the molar analyte concentration; for analyte ions the peak-to-background ratios were higher using slow projectiles; the fraction of carbon-rich collisionally formed molecular ions was much higher with fast projectiles. Sample aging in vacuum for up to five weeks strongly reduced the yield of protonated analyte molecules ejected by slow ion impact, but not of deprotonated species. Hence protonation seems to correlate with sample "wetness" or the presence of volatile proton-donating additives.     

Transport mechanisms in capillary condensation of water at a single-asperity nanoscopic contact

Transport mechanisms involved in capillary condensation of water menisci in nanoscopic gaps between hydrophilic surfaces are investigated theoretically and experimentally by atomic force microscopy (AFM) measurements of capillary force. The measurements showed an instantaneous formation of a water meniscus by coalescence of the water layers adsorbed on the AFM tip and sample surfaces, followed by a time evolution of meniscus toward a stationary state corresponding to thermodynamic equilibrium. This dynamics of the water meniscus is indicated by time evolution of the meniscus force, which increases with the contact time toward its equilibrium value. Two water transport mechanisms competing in this meniscus dynamics are considered: (1) Knudsen diffusion and condensation of water molecules in the nanoscopic gap and (2) adsorption of water molecules on the surface region around the contact and flow of the surface water toward the meniscus. For the case of very hydrophilic surfaces, the dominant role of surface water transportation on the meniscus dynamics is supported by the results of the AFM measurements of capillary force of water menisci formed at sliding tip-sample contacts. These measurements revealed that fast movement of the contact impedes on the formation of menisci at thermodynamic equilibrium because the flow of the surface water is too slow to reach the moving meniscus.     

Robust alignment of chromatograms by statistically analyzing the shifts matrix generated by moving window fast Fourier transform cross‐correlation

Retention time shift is one of the most challenging problems during the preprocessing of massive chromatographic datasets. Here, an improved version of the moving window fast Fourier transform cross‐correlation algorithm is presented to perform nonlinear and robust alignment of chromatograms by analyzing the shifts matrix generated by moving window procedure. The shifts matrix in retention time can be estimated by fast Fourier transform cross‐correlation with a moving window procedure. The refined shift of each scan point can be obtained by calculating the mode of corresponding column of the shifts matrix. This version is simple, but more effective and robust than the previously published moving window fast Fourier transform cross‐correlation method. It can handle nonlinear retention time shift robustly if proper window size has been selected. The window size is the only one parameter needed to adjust and optimize. The properties of the proposed method are investigated by comparison with the previous moving window fast Fourier transform cross‐correlation and recursive alignment by fast Fourier transform using chromatographic datasets. The pattern recognition results of a gas chromatography mass spectrometry dataset of metabolic syndrome can be improved significantly after preprocessing by this method. Furthermore, the proposed method is available as an open source package at https://github.com/zmzhang/MWFFT2 .     

有机液体的慢极化介电谱

高绝缘液体存在一种特殊类型的极化响应; 其性质很不同于普通的介电极化响应。后者可用频域方法描述, 称为快响应;前者不能用频域而只能用时域方法描述, 故区别地称为慢响应。在微分时域介电谱中, 每种快或慢极化机构贡献一个峰。苯的时域谱有一个快峰和两个慢峰。室温下石蜡只有一个快峰和一个慢峰; 在加热熔解过程中慢峰分裂为两个峰。慢极化响应和液体中分子的局部束缚空间电荷有关; 慢极化介电谱可以给出分子动力的许多信息。     

A new method for measuring the diffusion coefficient in a gas phase

A new and fast method for measuring the diffusion coefficients of binary gas mixtures using ion mobility spectrometry (IMS) has been developed. In this method, the sample is injected as a short pulse into the flowing drift gas, forming a Gaussian concentration profile inside the drift region. This Gaussian cloud is irradiated with a fast moving swarm of electrons to create negative ions. The flash of electrons is so short that the negative ions do not move much during the exposure time. The ions then drift toward the detector, where they are collected. The collected ion signal pattern reflects the spatial distribution of the sample inside the cloud at the time of exposure. This is repeated in intervals of 300-400 ms to monitor the spatial spreading of the molecules in the drift region. Consecutive IMS spectra show the evolution of the cloud over time. The collected spectra are fit to Gaussian functions to extract diffusion coefficients. Using this method, the diffusion coefficient of O(2), CHCl(3), and C(2)H(2)Cl(2) were measured, and the results are in good agreement with the previously reported experimental data.     

固态电解质中锂离子传输机理研究进展

固态电解质在室温下表现出非凡的离子导电性,使其有潜力应用于全固态锂离子电池.开发新的高性能固态电解质需要对锂离子传输机理及其规律进行深入研究.本文论述了近期研究中锂离子传输机理方面的研究进展,包括离子传输理论基础的概述;总结Li10GeP2S12、Li7La3Zr2O12和Li1+xAlxTi2-x(PO4)3固态电解...     

Anomalous lithium ion diffusion into CeO2·TiO2 thin film by film thickness variations

CeO₂·TiO₂ thin film is considered as an excellent candidate for a passive ion storage layer due to its good electrochemical stability and comparatively great charge capacitance. When cerium-titanium oxide thin film is adopted as an ion storage layer against cathodic tungsten oxide layer, the electrochromic device shows long term durability and cyclability. Therefore, many researchers investigated the composition and crystallinity effects to the charge density. In our study, we prepared CeO₂·TiO₂ thin by sol–gel dip-coating method, varying thickness by controlling withdrawal speeds. As investigating results of cyclic voltammetry and chronocoulometry, we found that there are three regions in the film thicknesses: (1) fast lithium ion diffusion region under 100 nm, (2) slow diffusion region in the range of 100 to 150 nm, and (3) fast and great charge capacitance region over 150 nm. In region 1, lithium ions diffuse very fast and reach into indium-tin oxide (ITO) layers, and slow diffusion region follows in region 2, probably due to the remains or impurities within the film, and in region 3, lithium ion diffusion gets fast again, accompanied with charge capacitance increase with thickness.     

Analysis of the approximate slow invariant manifold method for reactive flow equations

The Approximate Slow Invariant Manifold method of Singh, Powers and Paolucci is a useful method for addressing model reduction in systems of reactive flow equations. It exploits separations of time scales between slow and fast species, and it generalizes the Intrinsic Low-Dimensional Manifold method, which was developed for model reduction in the context of reaction kinetics, to systems with diffusive and active transport. In this article, we present a mathematical analysis of the Approximate Slow Invariant Manifold method in the context of systems of reaction–diffusion equations with slow and fast reaction kinetics. Beginning with systems of two species (one slow and one fast), and then treating general systems with multiple slow and fast species, we explicitly determine the accuracy of the Approximate Slow Invariant Manifold method. We find that it is correct up to and including the terms of first order in the small parameter that measures the separation of the kinetics time scales, and that it captures many of the terms at second order, as well. Our analysis includes precise statements of the errors at second order, and we find that these are proportional to the slow components of the reaction–diffusion equation, as well as to the curvature of the critical manifold. We illustrate the results analytically on two prototypical examples, the Michaelis–Menten–Henri model with diffusion of the slow species and the Davis–Skodje model in which both the slow and fast species diffuse.     

Electrophoretic analysis of electrically trained skeletal muscle.

Sheep latissimus dorsi muscle was electrically trained, thereby inducing fast-to-slow fibre-type transformation. Using a combination of one- and two-dimensional gel electrophoresis techniques with computer analysis, we have analysed altered expression of contractile protein isoforms at protein and mRNA level over a time course of electrical training extending to 5 months. Myosin heavy chain and regulatory myosin light chain analysis showed predominant expression of their slow isoforms (86% and 92%, respectively) after 3 months of training. At the same time point, however, tropomyosin analysis revealed that the slow isoform of the alpha-subunit accounted for 64% of the total alpha expression. Troponin T isoform switching proceeded more slowly over the same time course than tropomyosin and the thick filament proteins studied. Troponin T analysis revealed 5 fast and 2 slow isoforms in the sheep, of which the second slow isoform only became clearly visible after 5 months' training. At this time point the two slow isoforms were more predominant than their fast counterparts. This suggests that a wide heterogeneity of fast and slow isoform combinations are possible in the thin filament of skeletal muscle.     

Ring closure reaction dynamics of diarylethene derivatives in solution

Photochromic ring closure reaction dynamics of 1,2-bis(2-methylbenzo[b]thiophen-3-yl)hexafluoro cyclopentene and its derivatives in solution has been studied by femtosecond time-resolved fluorescence. Time-resolved spontaneous fluorescence of the open isomer reveals a fast component of around 1 ps and a slow component on the order of 100 ps. Fluorescence time profiles, reaction quantum yields, and relative populations of the parallel (C(s) symmetry) and antiparallel (C(2) symmetry) conformations indicate that both time components are attributable mostly to the C(2) conformer that undergoes the ring closure reaction. The fast component is assigned to the direct ring closure reaction, and the slow component is assigned to the reaction through conformation change. Time constants of the slow component for the derivatives are inversely proportional to the reaction quantum yields, suggesting that the rate of the conformational dynamics is comparable to the rate of other population relaxation processes. The relative amplitude and exact time constant of the fast component depend on the detection wavelength displaying a higher relative amplitude with shorter time constant at longer wavelengths. The results allow us to propose a conformational inhomogeneity model, in which a broad distribution of conformations of the open isomers in the ground state is projected into two minima in the excited electronic potential surface to lead to the slow and the fast reaction pathways.     

Electrospray ionization-voltage sweep-Ion mobility spectrometry for biomolecules and complex samples

Voltage Sweep Ion Mobility Spectrometry (VSIMS) has been applied to complex samples using electrospray ionization (ESI). The usable range of VSIMS has been extended from that obtained in previous studies where only volatile compounds were investigated. Using ESI, VSIMS was evaluated with compounds with reduced mobility values as low as 0.3 V²cm^?1 s^?1. The primary advantage of VSIMS is to enable a drift time ion mobility spectrometer (DTIMS) to detect both fast and slow moving ions at optimal resolving power, thus improving the peak capacity. In this work ESI-VSIMS was applied to a series of small peptides and drugs spanning a large range of reduced mobility values in order to demonstrate ESI-VSIMS to separation. To demonstrate improved peak capacity of IMS with voltage scan operation, oligomers of silicone oil provided a series of evenly-spaced peaks, ranging in reduced mobility values from 0.85 to 0.3 V²cm^?1 s^?1. The peak capacity of 61 for a standard IMS was improved to 102 when voltage sweep operation was employed. In addition, VSIMS increased the average resolving power of the DTIMS from 66 to 106 for silicone oil.     

Cation selective ion channels formed by macrodiolide antibiotic elaiophylin in lipid bilayer membranes

The macrodiolide antibiotic elaiophylin (1) forms stable, long-lasting cation selective ion channels in planar lipid bilayer membranes prepared from soybean phosphatidylcholine. Current of the single ion channel displayed two sublevels corresponding to the two substates of the channel conductance: a slow substate, with about 5 s of mean dwell time in the open state at 40% level of the total amplitude conductance, and a fast substate of higher conductance with dwell times in the open and closed state of about 0.1 s. Amplitude conductances of the single ion channels in 200 mM of LiCl, NaCl, KCl, RbCl and CsCl were 75, 140, 220, 240 and 226 pS, and the conductance was linear function of the electrolyte concentration. Ratios of cation to anion permeabilities of the channel for NaCl and KCl were 8+/-2 and >24, respectively. A molecular model of the channel structure is suggested.     

Solvent dynamics effect in condensed-phase electron-transfer reactions

Channel-based reaction-diffusion equations are solved analytically for two electron transfer (ET) models, where the fast inner-sphere coordinate leads to an ET reaction treated by Fermi's golden rule, and the slow solvent coordinate moves via diffusion. The analytic solution has let us derive an ET rate constant that modifies the Marcus-Jortner formula by adding a constant alpha which we call a dynamic correction factor. The dynamic correction factor measures the effect of solvent friction. When the relaxation of solvent dynamics is fast, the dynamic correction can be neglected and the ET rate constant reduces to the traditional Marcus-Jortner formula. If the solvent dynamic relaxation is slow, the dynamic correction can be very large and the ET rate can be reduced by orders of magnitude. Using a generalized Zusman-Sumi-Marcus model as a starting point, we introduce two variants, GZSM-A and GZSM-B, where in model A, only one quantum mode is considered for inner-sphere motion and in model B, a classical mode for inner-sphere motion is added. By comparing the two models with experimental data, it is shown that model B is better than model A. For the solvents that have a relaxation time ranging between 0 and 5 ps, our result agrees fairly well with experimental data; for the solvents that have a relaxation time ranging between 5 and 40 ps, our result deviates from the experimental values. After introducing an adjustable scaling index in the effective time correlation function of the reaction coordinate, good agreement is achieved between the experiment and the theory for model B for all of the solvents studied in this paper.     

Efficient multiple time scale molecular dynamics: Using colored noise thermostats to stabilize resonances

Multiple time scale molecular dynamics enhances computational efficiency by updating slow motions less frequently than fast motions. However, in practice, the largest outer time step possible is limited not by the physical forces but by resonances between the fast and slow modes. In this paper we show that this problem can be alleviated by using a simple colored noise thermostatting scheme which selectively targets the high frequency modes in the system. For two sample problems, flexible water and solvated alanine dipeptide, we demonstrate that this allows the use of large outer time steps while still obtaining accurate sampling and minimizing the perturbation of the dynamics. Furthermore, this approach is shown to be comparable to constraining fast motions, thus providing an alternative to molecular dynamics with constraints.     

铵根离子在水溶液中的跳跃转动机理

铵根离子的动力学行为与生命体内的生物和化学过程密切相关.依据流体力学理论,由于铵根离子与水分子之间存在多个强氢键,其转动应较慢,但实验结果并非如此,其转动的微观机理尚不清晰.本文分子动力学模拟研究表明,水溶液中铵根离子主要以快速、大角度的跳跃方式进行转动,像水分子一样遵从扩展分子跳跃转动模型.通过微观转动模式的分解和两种转动弛豫时间的比较发现,相对其氢键骨架的扩散转动,跳跃转动对其转动速率贡献更大,并随浓度增大不断强化.与水分子氢键交换方式相比,铵根离子更倾向于在非氢键相连的水分子间发生交换.     

Purine N-oxides—XLI : The 3-acyloxypurine 8-substitution reaction: On the mechanism of the reaction

The 3-acyloxypurine 8-substitution reaction involves elimination of the 3-acyloxy group and nucleophilic substitution at C-8 to yield 8-substituted xanthines or guanines. In aqueous solutions the reaction of 3-acetoxyxanthine proceeds slowly below pH 2, but is greatly accelerated with an increase of the pH from 3 to 7. It is proposed that the slow reaction involves heterolytic cleavage of the 3-acetoxy moiety from 3-acetoxyxanthine to yield a nitrenium ion at N-3 followed by intermolecular nucleophilic substitution of the incipient carbonium ion at the allylic C-8 position, also the most probable mechanism in polar aprotic solvents. The beginning of the fast reaction coincides with the beginning of ionization of the imidazole hydrogen of 3-acetoxyxanthine. It is proposed that this ionization induces a similar but more rapid departure of the 3-acetoxy group from the anion of 3-acetoxyxanthine to produce dehydroxanthine. The latter, upon protonation, yields the same reactive carbonium ion at C-8 that is formed in the slow reaction. Some reduction of 3-acetoxyxanthine to xanthine accompanies the fast reaction. That reduction has the characteristics of a free-radical mediated reaction. It is proposed that reduction results from a homolytic cleavage of the NO bond in the 3-acetoxyxanthine anion to produce a radical-anion, which abstracts hydrogen from water to yield xanthine. These reaction mechanisms and possible alternatives are evaluated.     

Approximation of slow attracting manifolds in chemical kinetics by trajectory-based optimization approaches

Many common kinetic model reduction approaches are explicitly based on inherent multiple time scales and often assume and directly exploit a clear time scale separation into fast and slow reaction processes. They approximate the system dynamics with a dimension-reduced model after eliminating the fast modes by enslaving them to the slow ones. The corresponding restrictive assumption of full relaxation of fast modes often renders the resulting approximation of slow attracting manifolds inaccurate as a representation of the reduced model and makes the numerical solution of the nonlinear "reduction equations" particularly difficult in many cases where the gap in intrinsic time scales is not large enough. We demonstrate that trajectory optimization approaches can avoid such severe restrictions by computing numerical solutions that correspond to "maximally relaxed" dynamical modes in a suitable sense. We present a framework of trajectory-based optimization for model reduction in chemical kinetics and a general class of reduction criteria characterizing the relaxation of chemical forces along reaction trajectories. These criteria can be motivated geometrically exploiting ideas from differential geometry and fundamental physics and turn out to be highly successful in example applications. Within this framework, we provide results for the computational approximation of slow attracting low-dimensional manifolds in terms of families of optimal trajectories for a six-component hydrogen combustion mechanism.