A Generalized Markov Sampler

A recent development of the Markov chain Monte Carlo (MCMC) technique is the emergence of MCMC samplers that allow transitions between different models. Such samplers make possible a range of computational tasks involving models, including model selection, model evaluation, model averaging and hypothesis testing. An example of this type of sampler is the reversible jump MCMC sampler, which is a generalization of the Metropolis–Hastings algorithm. Here, we present a new MCMC sampler of this type. The new sampler is a generalization of the Gibbs sampler, but somewhat surprisingly, it also turns out to encompass as particular cases all of the well-known MCMC samplers, including those of Metropolis, Barker, and Hastings. Moreover, the new sampler generalizes the reversible jump MCMC. It therefore appears to be a very general framework for MCMC sampling. This paper describes the new sampler and illustrates its use in three applications in Computational Biology, specifically determination of consensus sequences, phylogenetic inference and delineation of isochores via multiple change-point analysis.     

Time-Reversed Dynamical Entropy and Irreversibility in Markovian Random Processes

A concept of time-reversed entropy per unit time is introduced in analogy with the entropy per unit time by Shannon, Kolmogorov, and Sinai. This time-reversed entropy per unit time characterizes the dynamical randomness of a stochastic process backward in time, while the standard entropy per unit time characterizes the dynamical randomness forward in time. The difference between the time-reversed and standard entropies per unit time is shown to give the entropy production of Markovian processes in nonequilibrium steady states.     

Fe(phen)32+与DNA作用的荧光光度法研究

为了考察金属配合物Fe(phen)32+与DNA 的作用模式, 应用荧光光度法对Fe(phen)32+与DNA及DNA-EB的作用进行了研究,结果表明Fe(phen)32+是主要以共轭平面插入形式与DNA作用的, 并计算出稳定常数等一系列热力学数据.     

A new VOF‐based numerical scheme for the simulation of fluid flow with free surface. Part II: application to the cavity filling and sloshing problems

Finite element analysis of fluid flow with moving free surface has been performed in 2‐D and 3‐D. The new VOF‐based numerical algorithm that has been proposed by the present authors (Int. J. Numer. Meth. Fluids, submitted) was applied to several 2‐D and 3‐D free surface flow problems. The proposed free surface tracking scheme is based on two numerical tools; the orientation vector to represent the free surface orientation in each cell and the baby‐cell to determine the fluid volume flux at each cell boundary. The proposed numerical algorithm has been applied to 2‐D and 3‐D cavity filling and sloshing problems in order to demonstrate the versatility and effectiveness of the scheme. The proposed numerical algorithm resolved successfully the free surfaces interacting with each other. The simulated results demonstrated applicability of the proposed numerical algorithm to the practical problems of large free surface motion. It has been also demonstrated that the proposed free surface tracking scheme can be easily implemented in any irregular non‐uniform grid systems and can be extended to 3‐D free surface flow problems without additional efforts. Copyright © 2003 John Wiley & Sons, Ltd.     

Quantum-Chemical Study of the Profiles of Reactions that Form Pyrrole Anion N-Adducts with CS<Subscript>2</Subscript> and CO<Subscript>2</Subscript>

The profiles of reactions leading to pyrrole anion N-adducts with CO₂ and CS₂ have been studied by the ab initio (RHF/6-31+G*, MP2/6-31+G*) and density functional (B3LYP/6-31+G*) methods. Addition of the pyrrole anion to the carbon disulfide molecule is accompanied by the appearance of a minimum corresponding to a pre-reaction complex. The transformation of the complex to the N-pyrrolyldithiocarboxylate anion occurs via a low activation barrier, which is due to repolarization of the C=S bonds. The profile of the reaction leading to the pyrrole anion N-adduct with CO₂ does not contain any intermediate stationary points throughout the whole route from reagents to products.Original Russian Text Copyright © 2004 by V. B. Kobychev, N. M. Vitkovskaya, I. L. Zaitseva, and B. A. Trofimov__________Translated from Zhurnal Strukturnoi Khimii, Vol. 45, No. 6, pp. 990–993, November–December, 2004.     

Novel route to synthesis of allyl starch and biodegradable hydrogel by copolymerizing allyl‐modified starch with methacrylic acid and acrylamide

Maize starch was modified by allyl chloride adopting an interfacial reaction technique with cetyltrimethyl ammonium bromide as a phase‐transfer catalyst and pyridine as an acid acceptor. The degree of substitution was determined from an increasing carbon content of the modified starch. The percentage of carbon and hydrogen of the allyl‐modified starch was estimated by elemental analysis (C, H, and N), and the product characterization was done through ¹H NMR and ¹³C NMR analyses. The allyl‐modified starch was then copolymerized with methacrylic acid and a combination of methacrylic acid and acrylamide at 50 and 70 °C with potassium persulfate as an initiator. The copolymer thus formed swelled in distilled water after neutralization with sodium carbonate. The percentage of absorption capacity of the hydrogels was determined with distilled water and 0.9% NaCl solution. The highest percentage of absorption, 6500%, was achieved for the developed hydrogel containing allyl starch and acrylic monomer in a 1.7:1 w/w ratio and acrylic monomer, namely, methacrylic acid and acrylamide in a 3.2:1 w/w ratio. The study on biodegradability of the developed hydrogel showed that the hydrogel is degradable in the presence of diastase (amylase). © 2003 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 41: 1650–1658, 2003     

Determination of the rheological behavior of epoxy–amine thermosets by dynamic mechanical analysis: Isothermal methods versus nonisothermal methods

The reticulation process of an epoxy resin using an amine as a cure agent was studied at different temperatures and concentrations of the cure agent with dynamic mechanical thermal analysis. The study was performed under both isothermal and nonisothermal conditions, and a temperature–time–transformation diagram was obtained. The measurements from the two modes gave similar results, although the nonisothermal mode required fewer experiments. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 1965–1977, 2003     

Dihydroboronium derivatives of (S,S)-1,2-bis(t-butylmethylphosphino)ethane as convenient chiral ligand precursors

Dihydroboronium derivatives of (S,S)-1,2-bis(t-butylmethylphosphino)ethane (t-Bu-BisP*) were prepared and used as chiral diphosphine ligand precursors in Rh-catalyzed asymmetric hydrogenation of methyl (Z)-acetamidocinnamate to afford the hydrogenation product in up to 94% enantioselectivity.     

GM(1,1)改进模型及其应用

根据 GM( 1 ,1 )灰色模型的指数特性 ,通过在区间上求积分给出了关于背景值的一个比较确切的计算公式 ,讨论了由此建立的 GM( 1 ,1 )改进模型的适用范围和预测精度 .结果表明改进模型比原 GM( 1 ,1 )模型适用性要强、模拟和预测精度要高 ,不仅适用于低增长序列、也适用于高增长序列 ,不仅适用于短期预测 ,同样也适用于中、长期预测     

Relative intensity noise of mode-locked fiber grating external cavity semiconductor lasers

The noise of hybrid soliton pulse source (HSPS) with linearly chirped Gaussian apodized fiber Bragg grating is analyzed by couple-mode equations including spontaneous emission noise when the HSPS is mode-locked. Relative intensity noise is calculated using numerical solutions of these equations. It is shown that transform limited pulses are generated over a wide tuning range around the fundamental mode-locking frequency with low spontaneous noise. However, a high noise level affects the operation of device, and therefore transform-limited pulses are not obtainable over a wide tuning range. It is also shown that noise is extremely sensitive to the RF and DC currents, linewidth enhancement factor, gain saturation parameter and spontaneous coupling factor.