Kinetics and Statistical Distributions of Single-Molecule Conformational Dynamics

We developed a coarse-grained yet microscopic detailed model to study the statistical fluctuations of single-molecule protein conformational dynamics of adenylate kinase. We explored the underlying conformational energy landscape and found that the system has two basins of attractions, open and closed conformations connected by two separate pathways. The kinetics is found to be nonexponential, consistent with single-molecule conformational dynamics experiments. Furthermore, we found that the statistical distribution of the kinetic times for the conformational transition has a long power law tail, reflecting the exponential density of state of the underlying landscape. We also studied the joint distribution of the two pathways and found memory effects.

Statistical distributions obtained from the compression of monodisperse, soft and frictionless particles

The cyclic compression of several granular systems has been simulated with a molecular dynamics code. All the samples consisted of bidimensional, soft, frictionless and equal-sized particles that were initially arranged according to a squared lattice and were compressed by randomly generated irregular walls. The compression protocols can be described by some control variables (volume or external force acting on the walls) and by some dimensionless factors, that relate stiffness, density, diameter, damping ratio and water surface tension to the external forces, displacements and periods. Each protocol, that is associated to a dynamic process, results in an arrangement with its own macroscopic features: volume (or packing ratio), coordination number, and stress; and the differences between packings can be highly significant. The statistical distribution of the force-moment state of the particles (i.e. the equivalent average stress multiplied by the volume) is analyzed. In spite of the lack of a theoretical framework based on statistical mechanics specific for these protocols, it is shown how the obtained distributions of mean and relative deviatoric force-moment are. Then it is discussed on the nature of these distributions and on their relation to specific protocols.

Matrix-Variate Statistical Distributions and Fractional Calculus

MSC 2010: 15A15, 15A52, 33C60, 33E12, 44A20, 62E15 Dedicated to Professor R. Gorenflo on the occasion of his 80th birthday

Statistical distribution of depth-integrated local horizontal momentum for second-order random ocean waves in finite water depth

Based on the second-order random wave solutions of water wave equations in finite water depth, statistical distributions of the depth- integrated local horizontal momentum components are derived by use of the characteristic function expansion method. The parameters involved in the distributions can be all determined by the water depth and the wave-number spectrum of ocean waves. As an illustrative example, a fully developed wind-generated sea is considered and the parameters are calculated for typical wind speeds and water depths by means of the Donelan and Pierson spectrum. The effects of nonlinearity and water depth on the distributions are also investigated.

On the Statistical Distribution of Object-Oriented System Properties

The statistical distributions of different software properties have been thoroughly studied in the past, including software size, complexity and the number of defects. In the case of object-oriented systems, these distributions have been found to obey a power law, a common statistical distribution also found in many other fields. However, we have found that for some statistical properties, the behavior does not entirely follow a power law, but a mixture between a lognormal and a power law distribution. Our study is based on the Qualitas Corpus, a large compendium of diverse Java-based software projects. We have measured the Chidamber and Kemerer metrics suite for every file of every Java project in the corpus. Our results show that the range of high values for the different metrics follows a power law distribution, whereas the rest of the range follows a lognormal distribution. This is a pattern typical of so-called double Pareto distributions, also found in empirical studies for other software properties.

Frequency distributions of passenger cars by weight and wheelbase by state: July 1, 1976.

Mode of access: Internet.

Robust control of nonlinear stochastic systems by modelling conditional distributions of control signals

We introduce a novel inversion-based neuro-controller for solving control problems involving uncertain nonlinear systems that could also compensate for multi-valued systems. The approach uses recent developments in neural networks, especially in the context of modelling statistical distributions, which are applied to forward and inverse plant models. Provided that certain conditions are met, an estimate of the intrinsic uncertainty for the outputs of neural networks can be obtained using the statistical properties of networks. More generally, multicomponent distributions can be modelled by the mixture density network. In this work a novel robust inverse control approach is obtained based on importance sampling from these distributions. This importance sampling provides a structured and principled approach to constrain the complexity of the search space for the ideal control law. The performance of the new algorithm is illustrated through simulations with example systems.

Role of free volume in strain softening of as-cast and annealed bulk metallic glass

Plasticity in amorphous alloys is associated with strain softening, induced by the creation of additional free volume during deformation. In this paper, the role of free volume, which was a priori in the material, on work softening was investigated. For this, an as-cast Zr-based bulk metallic glass (BMG) was systematically annealed below its glass transition temperature, so as to reduce the free volume content. The bonded-interface indentation technique is used to generate extensively deformed and well defined plastic zones. Nanoindentation was utilized to estimate the hardness of the deformed as well as undeformed regions. The results show that the structural relaxation annealing enhances the hardness and that both the subsurface shear band number density and the plastic zone size decrease with annealing time. The serrations in the nanoindentation load-displacement curves become smoother with structural relaxation. Regardless of the annealing condition, the nanohardness of the deformed regions is similar to 12-15% lower, implying that the prior free volume only changes the yield stress (or hardness) but not the relative flow stress (or the extent of strain softening). Statistical distributions of the nanohardness obtained from deformed and undeformed regions have no overlap, suggesting that shear band number density has no influence on the plastic characteristics of the deformed region.

Influence of viscoelastic nature on the intermittent peel-front dynamics of adhesive tape

We investigate the influence of viscoelastic nature of the adhesive on the intermittent peel front dynamics by extending a recently introduced model for peeling of an adhesive tape. As time and rate-dependent deformation of the adhesives are measured in stationary conditions, a crucial step in incorporating the viscoelastic effects applicable to unstable intermittent peel dynamics is the introduction of a dynamization scheme that eliminates the explicit time dependence in terms of dynamical variables. We find contrasting influences of viscoelastic contribution in different regions of tape mass, roller inertia, and pull velocity. As the model acoustic energy dissipated depends on the nature of the peel front and its dynamical evolution, the combined effect of the roller inertia and pull velocity makes the acoustic energy noisier for small tape mass and low-pull velocity while it is burstlike for low-tape mass, intermediate values of the roller inertia and high-pull velocity. The changes are quantified by calculating the largest Lyapunov exponent and analyzing the statistical distributions of the amplitudes and durations of the model acoustic energy signals. Both single and two stage power-law distributions are observed. Scaling relations between the exponents are derived which show that the exponents corresponding to large values of event sizes and durations are completely determined by those for small values. Th scaling relations are found to be satisfied in all cases studied. Interestingly, we find only five types of model acoustic emission signals among multitude of possibilities of the peel front configurations.

Dependence of shear yield strain and shear transformation zone on the glass transition temperature in thin film metallic glasses

The dependence of shear yield strain, the activation energy and volume of shear transformation zone on the glass transition temperature was investigated through the analysis of statistical distributions of the first pop-in events during spherical indentation of four different thin film metallic glasses. Only the Cu-Zr metallic glass exhibits a bimodal distribution of the first pop-in loads, whereas W-Ru-B, Zr-Cu-Ni-Al and La-Co-Al metallic glasses show an unimodal distribution. Results show that shear yield strain and activation energy of shear transformation zone decrease whereas the volume of shear transformation zone increases with increasing homologous temperature, indicating that it is the activation energy rather than the volume of shear transformation zone that controls shear yield strain. (C) 2015 Elsevier B.V. All rights reserved.

Towards understanding the mixing characteristics of turbulent buoyant flows

This work proposes a new simulation methodology in which variable density turbulent flows can be studied in the context of a mixing layer with or without the presence of gravity. Specifically, this methodology is developed to probe the nature of non-buoyantly-driven (i.e. isotropically-driven) or buoyantly-driven mixing deep inside a mixing layer. Numerical forcing methods are incorporated into both the velocity and scalar fields, which extends the length of time over which mixing physics can be studied. The simulation framework is designed to allow for independent variation of four non-dimensional parameters, including the Reynolds, Richardson, Atwood, and Schmidt numbers. Additionally, the governing equations are integrated in such a way to allow for the relative magnitude of buoyant energy production and non-buoyant energy production to be varied.

The computational requirements needed to implement the proposed configuration are presented. They are justified in terms of grid resolution, order of accuracy, and transport scheme. Canonical features of turbulent buoyant flows are reproduced as validation of the proposed methodology. These features include the recovery of isotropic Kolmogorov scales under buoyant and non-buoyant conditions, the recovery of anisotropic one-dimensional energy spectra under buoyant conditions, and the preservation of known statistical distributions in the scalar field, as found in other DNS studies.

This simulation methodology is used to perform a parametric study of turbulent buoyant flows to discern the effects of varying the Reynolds, Richardson, and Atwood numbers on the resulting state of mixing. The effects of the Reynolds and Atwood numbers are isolated by looking at two energy dissipation rate conditions under non-buoyant (variable density) and constant density conditions. The effects of Richardson number are isolated by varying the ratio of buoyant energy production to total energy production from zero (non-buoyant) to one (entirely buoyant) under constant Atwood number, Schmidt number, and energy dissipation rate conditions. It is found that the major differences between non-buoyant and buoyant turbulent flows are contained in the transfer spectrum and longitudinal structure functions, while all other metrics are largely similar (e.g. energy spectra, alignment characteristics of the strain-rate tensor). Also, despite the differences noted between fully buoyant and non-buoyant turbulent fields, the scalar field, in all cases, is unchanged by these. The mixing dynamics in the scalar field are found to be insensitive to the source of turbulent kinetic energy production (non-buoyant vs. buoyant).

Extended bidirectional reflectance distribution function for polarized light scattering from subsurface defects under a smooth surface

By introducing the scattering probability of a subsurface defect (SSD) and statistical distribution functions of SSD radius, refractive index, and position, we derive an extended bidirectional reflectance distribution function (BRDF) from the Jones scattering matrix. This function is applicable to the calculation for comparison with measurement of polarized light-scattering resulting from a SSD. A numerical calculation of the extended BRDF for the case of p-polarized incident light was performed by means of the Monte Carlo method. Our numerical results indicate that the extended BRDF strongly depends on the light incidence angle, the light scattering angle, and the out-of-plane azimuth angle. We observe a 180 degrees symmetry with respect to the azimuth angle. We further investigate the influence of the SSD density, the substrate refractive index, and the statistical distributions of the SSD radius and refractive index on the extended BRDF. For transparent substrates, we also find the dependence of the extended BRDF on the SSD positions. (c) 2006 Optical Society of America.

基底微缺陷对介质薄膜光学性能影响的理论研究

基于非均匀膜理论提出一种存在微缺陷的介质基底的折射率分层模型，将基底依次分为表面层、亚表面层和体材料层，其中表面层和亚面层分别等效为折射率服从统计分布的非均匀膜，将它们分别再次细分为N1和N2个子层，每一子层均视为均匀介质膜．应用光学薄膜特征矩阵法对其进行理论分析，并对单层介质膜的光学性能进行数值计算．研究结果表明：基底的表面和亚表面微缺陷改变了薄膜和基底的等效折射率，导致了准Brewster角和组合反射率与理想情形的偏离．同时这些微缺陷也改变了光在薄膜和基底中的传播特性，因此反射相移和相位差均偏离理想情

Theoretical analysis of optical properties of dielectric coatings dependence on substrate subsurface defects

A model for refractive index of stratified dielectric substrate was put forward according to theories of inhomogeneous coatings. The substrate was divided into surface layer, subsurface layer and bulk layer along the normal direction of its surface. Both the surface layer (separated into N-1 sublayers of uniform thickness) and subsurface layer (separated into N-2 sublayers of uniform thickness), whose refractive indices have different statistical distributions, are equivalent to inhomogeneous coatings, respectively. And theoretical deduction was carried Out by employing characteristic matrix method of optical coatings. An example of mathematical calculation for optical properties of dielectric coatings had been presented. The computing results indicate that substrate subsurface defects can bring about additional bulk scattering and change propagation characteristic in thin film and Substrate. Therefore, reflectance, reflective phase shift and phase difference of an assembly of coatings and substrate deviate from ideal conditions. The model will provide some beneficial theory directions for improving optical properties of dielectric coatings via substrate surface modification. (c) 2005 Elsevier B.V. All rights reserved.

Estimativa do recurso contingente dos folhelhos oleígenos da Formação Tremembé, Bacia de Taubaté, na região de Tremembé-Pindamonhangaba, SP

Esta dissertação tem como objetivo apresentar uma estimativa preliminar do volume de recurso contingente não-convencionais de folhelhos oleígenos (oil shale) na Formação Tremembé através de métodos probabilísticos aplicados à informações compiladas de bibliografias existentes sobre a bacia. Como base para esta estimativa utilizou-se informações obtidas através de sísmica 2D, poços existentes na área e perfis geoquímicos. Através da interpretação dos mesmos foram gerados os valores de inputs para os parâmetros utilizados no cálculo, como: espessura econômica, densidade do minério e valor de Ensaio Fisher (Litros de óleo por tonelada de rocha). Para a análise foi construída uma planilha Excel no qual já descrito cada parâmetro do cálculo. Foi utilizado o software @Risk, da Palisade Inc., que é capaz de atribuir distribuições estatísticas a parâmetros utilizados no cálculo obtendo, a partir do método Monte Carlo, distribuições dos possíveis resultados. A metodologia apresentada se demonstra mais adequada ao caso em estudo que o método determinístico, devido a restrição e ausência da precisão dos dados o que aumentaria as incertezas e as chances de erro no cálculo do volume, podendo impossibilitar uma avaliação, no caso do segundo. A metodologia probabilística ao mesmo tempo em que permite uma avaliação preliminar na ausência de dados precisos, ela gera cenários probabilísticos de resultados, possibilitando a antecipação da tomada de decisões em um projeto, permitindo sua continuação ou abandono.