AC relaxation in the iron(8) molecular magnet

Science.gov (United States)

Rose, Geordie

2000-11-01

We investigate the low energy magnetic relaxation characteristics of the ``iron eight'' (Fe8) molecular magnet. Each molecule in this material contains a cluster of eight Fe 3+ ions surrounded by organic ligands. The molecules arrange themselves into a regular lattice with triclinic symmetry. At sufficiently low energies, the electronic spins of the Fe3+ ions lock together into a ``quantum rotator'' with spin S = 10. We derive a low energy effective Hamiltonian for this system, valid for temperatures less than Tc ~ 360 mK , where Tc is the temperature at which the Fe8 system crosses over into a ``quantum regime'' where relaxation characteristics become temperature independent. We show that in this regime the dominant environmental coupling is to the environmental spin bath in the molecule. We show how to explicitly calculate these couplings, given crystallographic information about the molecule, and do this for Fe8. We use this information to calculate the linewidth, topological decoherence and orthogonality blocking parameters. All of these quantities are shown to exhibit an isotope effect. We demonstrate that orthogonality blocking in Fe8 is significant and suppresses coherent tunneling. We then use our low energy effective Hamiltonian to calculate the single-molecule relaxation rate in the presence of an external magnetic field with both AC and DC components by solving the Landau-Zener problem in the presence of a nuclear spin bath. Both sawtooth and sinusoidal AC fields are analyzed. This single-molecule relaxation rate is then used as input into a master equation in order to take into account the many-molecule nature of the full system. Our results are then compared to quantum regime relaxation experiments performed on the Fe8 system.

Reliable Approximation of Long Relaxation Timescales in Molecular Dynamics

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Wei Zhang

2017-07-01

Full Text Available Many interesting rare events in molecular systems, like ligand association, protein folding or conformational changes, occur on timescales that often are not accessible by direct numerical simulation. Therefore, rare event approximation approaches like interface sampling, Markov state model building, or advanced reaction coordinate-based free energy estimation have attracted huge attention recently. In this article we analyze the reliability of such approaches. How precise is an estimate of long relaxation timescales of molecular systems resulting from various forms of rare event approximation methods? Our results give a theoretical answer to this question by relating it with the transfer operator approach to molecular dynamics. By doing so we also allow for understanding deep connections between the different approaches.

Stability and suppression of turbulence in relaxing molecular gas flows

CERN Document Server

Grigoryev, Yurii N

2017-01-01

This book presents an in-depth systematic investigation of a dissipative effect which manifests itself as the growth of hydrodynamic stability and suppression of turbulence in relaxing molecular gas flows. The work describes the theoretical foundations of a new way to control stability and laminar turbulent transitions in aerodynamic flows. It develops hydrodynamic models for describing thermal nonequilibrium gas flows which allow the consideration of suppression of inviscid acoustic waves in 2D shear flows. Then, nonlinear evolution of large-scale vortices and Kelvin-Helmholtz waves in relaxing shear flows are studied. Critical Reynolds numbers in supersonic Couette flows are calculated analytically and numerically within the framework of both linear and nonlinear classical energy hydrodynamic stability theories. The calculations clearly show that the relaxation process can appreciably delay the laminar-turbulent transition. The aim of the book is to show the new dissipative effect, which can be used for flo...

Influence of Tertiary paleoenvironmental changes on the diversification of South American mammals: a relaxed molecular clock study within xenarthrans

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Vizcaíno Sergio F

2004-04-01

Full Text Available Abstract Background Comparative genomic data among organisms allow the reconstruction of their phylogenies and evolutionary time scales. Molecular timings have been recently used to suggest that environmental global change have shaped the evolutionary history of diverse terrestrial organisms. Living xenarthrans (armadillos, anteaters and sloths constitute an ideal model for studying the influence of past environmental changes on species diversification. Indeed, extant xenarthran species are relicts from an evolutionary radiation enhanced by their isolation in South America during the Tertiary era, a period for which major climate variations and tectonic events are relatively well documented. Results We applied a Bayesian approach to three nuclear genes in order to relax the molecular clock assumption while accounting for differences in evolutionary dynamics among genes and incorporating paleontological uncertainties. We obtained a molecular time scale for the evolution of extant xenarthrans and other placental mammals. Divergence time estimates provide substantial evidence for contemporaneous diversification events among independent xenarthran lineages. This correlated pattern of diversification might possibly relate to major environmental changes that occurred in South America during the Cenozoic. Conclusions The observed synchronicity between planetary and biological events suggests that global change played a crucial role in shaping the evolutionary history of extant xenarthrans. Our findings open ways to test this hypothesis further in other South American mammalian endemics like hystricognath rodents, platyrrhine primates, and didelphid marsupials.

Bayesian non- and semi-parametric methods and applications

CERN Document Server

Rossi, Peter

2014-01-01

This book reviews and develops Bayesian non-parametric and semi-parametric methods for applications in microeconometrics and quantitative marketing. Most econometric models used in microeconomics and marketing applications involve arbitrary distributional assumptions. As more data becomes available, a natural desire to provide methods that relax these assumptions arises. Peter Rossi advocates a Bayesian approach in which specific distributional assumptions are replaced with more flexible distributions based on mixtures of normals. The Bayesian approach can use either a large but fixed number

BEAST: Bayesian evolutionary analysis by sampling trees

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Drummond Alexei J

2007-11-01

Full Text Available Abstract Background The evolutionary analysis of molecular sequence variation is a statistical enterprise. This is reflected in the increased use of probabilistic models for phylogenetic inference, multiple sequence alignment, and molecular population genetics. Here we present BEAST: a fast, flexible software architecture for Bayesian analysis of molecular sequences related by an evolutionary tree. A large number of popular stochastic models of sequence evolution are provided and tree-based models suitable for both within- and between-species sequence data are implemented. Results BEAST version 1.4.6 consists of 81000 lines of Java source code, 779 classes and 81 packages. It provides models for DNA and protein sequence evolution, highly parametric coalescent analysis, relaxed clock phylogenetics, non-contemporaneous sequence data, statistical alignment and a wide range of options for prior distributions. BEAST source code is object-oriented, modular in design and freely available at http://beast-mcmc.googlecode.com/ under the GNU LGPL license. Conclusion BEAST is a powerful and flexible evolutionary analysis package for molecular sequence variation. It also provides a resource for the further development of new models and statistical methods of evolutionary analysis.

Effect of holographic grating period on its relaxation in a molecular glassy film

International Nuclear Information System (INIS)

Ozols, A; Augustovs, P; Kokars, V; Traskovskis, K; Saharov, D

2013-01-01

Holographic grating (HG) relaxation has been experimentally studied in 5,5,5-triphenylpentyl 4-((4-(bis(5,5,5-triphenylpentyl)amino) phenyl) diazenyl) benzoate molecular glassy film for HG periods (Λ) of 0.50, 2.0 and 8.6 μm. A strong effect of HG period on its relaxation is found manifesting itself differently in the volume and on the surface. The volume part of HG is fairly stable during 40 days if Λ > 0.50μm whereas the surface part of HG (most probably, surface relief grating) exhibits relaxational self-enhancement which is maximal at Λ = 8.6μm. It is proposed that thermostimulated directional mass transfer in the process of relaxation can be responsible for this relaxational self-enhancement. Weak HG recording and relatively fast HG decay takes place at Λ=0.50 μm. Therefore, effective chromophore photoorientation domain of about 0.2 μm is supposed

Simulations of vibrational relaxation in dense molecular fluids

International Nuclear Information System (INIS)

Holian, B.L.

1985-07-01

In the understanding of high-temperatre and -pressure chemistry in explosives, first step is the study of the transfer of energy from translational degrees of freedom into internal vibrations of the molecules. We present new methods using nonequilibrium molecular dynamics (NEMD) for measuring vibrational relaxation in a diatomic fluid, where we expect a classical treatment of many-body collisions to be relevant because of the high densities (2 to 3 times compressed compared to the normal fluid) and high temperatures (2000 to 4000 K) involved behind detonation waves. NEMD techniques are discussed, including their limitations, and qualitative results presented

Selective excitation, relaxation, and energy channeling in molecular systems

International Nuclear Information System (INIS)

Rhodes, W.C.

1993-08-01

Research involves theoretical studies of response, relaxation, and correlated motion in time-dependent behavior of large molecular systems ranging from polyatomic molecules to protein molecules in their natural environment. Underlying theme is subsystem modulation dynamics. Main idea is that quantum mechanical correlations between components of a system develop with time, playing a major role in determining the balance between coherent and dissipative forces. Central theme is interplay of coherence and dissipation in determining the nature of dynamic structuring and energy flow in molecular transformation mechanisms. Subsystem equations of motion are being developed to show how nonlinear, dissipative dynamics of a particular subsystem arise from correlated interactions with the rest of the system (substituent groups, solvent, lattice modes, etc.); one consequence is resonance structures and networks. Quantum dynamics and thermodynamics are being applied to understand control and energy transfer mechanisms in biological functions of protein molecules; these mechanisms are both global and local. Besides the above theory, the research deals with phenomenological aspects of molecular systems

Expectation propagation for large scale Bayesian inference of non-linear molecular networks from perturbation data.

Science.gov (United States)

Narimani, Zahra; Beigy, Hamid; Ahmad, Ashar; Masoudi-Nejad, Ali; Fröhlich, Holger

2017-01-01

Inferring the structure of molecular networks from time series protein or gene expression data provides valuable information about the complex biological processes of the cell. Causal network structure inference has been approached using different methods in the past. Most causal network inference techniques, such as Dynamic Bayesian Networks and ordinary differential equations, are limited by their computational complexity and thus make large scale inference infeasible. This is specifically true if a Bayesian framework is applied in order to deal with the unavoidable uncertainty about the correct model. We devise a novel Bayesian network reverse engineering approach using ordinary differential equations with the ability to include non-linearity. Besides modeling arbitrary, possibly combinatorial and time dependent perturbations with unknown targets, one of our main contributions is the use of Expectation Propagation, an algorithm for approximate Bayesian inference over large scale network structures in short computation time. We further explore the possibility of integrating prior knowledge into network inference. We evaluate the proposed model on DREAM4 and DREAM8 data and find it competitive against several state-of-the-art existing network inference methods.

Inhomogeneous Relaxation of a Molecular Layer on an Insulator due to Compressive Stress

Science.gov (United States)

Bocquet, F.; Nony, L.; Mannsfeld, S. C. B.; Oison, V.; Pawlak, R.; Porte, L.; Loppacher, Ch.

2012-05-01

We discuss the inhomogeneous stress relaxation of a monolayer of hexahydroxytriphenylene (HHTP) which adopts the rare line-on-line (LOL) coincidence on KCl(001) and forms moiré patterns. The fact that the hexagonal HHTP layer is uniaxially compressed along the LOL makes this system an ideal candidate to discuss the influence of inhomogeneous stress relaxation. Our work is a combination of noncontact atomic force microscopy experiments, density functional theory and potential energy calculations, and a thorough interpretation by means of the Frenkel-Kontorova model. We show that the assumption of a homogeneous molecular layer is not valid for this organic-inorganic heteroepitaxial system since the best calculated energy configuration correlates with the experimental data only if inhomogeneous relaxations of the layer are taken into account.

Anisotropic Rotational Diffusion Studied by Nuclear Spin Relaxation and Molecular Dynamics Simulation: An Undergraduate Physical Chemistry Laboratory

Science.gov (United States)

Fuson, Michael M.

2017-01-01

Laboratories studying the anisotropic rotational diffusion of bromobenzene using nuclear spin relaxation and molecular dynamics simulations are described. For many undergraduates, visualizing molecular motion is challenging. Undergraduates rarely encounter laboratories that directly assess molecular motion, and so the concept remains an…

A study of internal energy relaxation in shocks using molecular dynamics based models

International Nuclear Information System (INIS)

Li, Zheng; Parsons, Neal; Levin, Deborah A.

2015-01-01

Recent potential energy surfaces (PESs) for the N 2 + N and N 2 + N 2 systems are used in molecular dynamics (MD) to simulate rates of vibrational and rotational relaxations for conditions that occur in hypersonic flows. For both chemical systems, it is found that the rotational relaxation number increases with the translational temperature and decreases as the rotational temperature approaches the translational temperature. The vibrational relaxation number is observed to decrease with translational temperature and approaches the rotational relaxation number in the high temperature region. The rotational and vibrational relaxation numbers are generally larger in the N 2 + N 2 system. MD-quasi-classical trajectory (QCT) with the PESs is also used to calculate the V-T transition cross sections, the collision cross section, and the dissociation cross section for each collision pair. Direct simulation Monte Carlo (DSMC) results for hypersonic flow over a blunt body with the total collision cross section from MD/QCT simulations, Larsen-Borgnakke with new relaxation numbers, and the N 2 dissociation rate from MD/QCT show a profile with a decreased translational temperature and a rotational temperature close to vibrational temperature. The results demonstrate that many of the physical models employed in DSMC should be revised as fundamental potential energy surfaces suitable for high temperature conditions become available

Dual reorientation relaxation routes of water molecules in oxyanion’s hydration shell: A molecular geometry perspective

Energy Technology Data Exchange (ETDEWEB)

Xie, Wen Jun; Yang, Yi Isaac; Gao, Yi Qin, E-mail: gaoyq@pku.edu.cn [Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering and Biodynamic Optical Imaging Center, Peking University, Beijing 100871 (China)

2015-12-14

In this study, we examine how complex ions such as oxyanions influence the dynamic properties of water and whether differences exist between simple halide anions and oxyanions. Nitrate anion is taken as an example to investigate the hydration properties of oxyanions. Reorientation relaxation of its hydration water can occur through two different routes: water can either break its hydrogen bond with the nitrate to form one with another water or switch between two oxygen atoms of the same nitrate. The latter molecular mechanism increases the residence time of oxyanion’s hydration water and thus nitrate anion slows down the translational motion of neighbouring water. But it is also a “structure breaker” in that it accelerates the reorientation relaxation of hydration water. Such a result illustrates that differences do exist between the hydration of oxyanions and simple halide anions as a result of different molecular geometries. Furthermore, the rotation of the nitrate solute is coupled with the hydrogen bond rearrangement of its hydration water. The nitrate anion can either tilt along the axis perpendicularly to the plane or rotate in the plane. We find that the two reorientation relaxation routes of the hydration water lead to different relaxation dynamics in each of the two above movements of the nitrate solute. The current study suggests that molecular geometry could play an important role in solute hydration and dynamics.

Dual reorientation relaxation routes of water molecules in oxyanion’s hydration shell: A molecular geometry perspective

International Nuclear Information System (INIS)

Xie, Wen Jun; Yang, Yi Isaac; Gao, Yi Qin

2015-01-01

In this study, we examine how complex ions such as oxyanions influence the dynamic properties of water and whether differences exist between simple halide anions and oxyanions. Nitrate anion is taken as an example to investigate the hydration properties of oxyanions. Reorientation relaxation of its hydration water can occur through two different routes: water can either break its hydrogen bond with the nitrate to form one with another water or switch between two oxygen atoms of the same nitrate. The latter molecular mechanism increases the residence time of oxyanion’s hydration water and thus nitrate anion slows down the translational motion of neighbouring water. But it is also a “structure breaker” in that it accelerates the reorientation relaxation of hydration water. Such a result illustrates that differences do exist between the hydration of oxyanions and simple halide anions as a result of different molecular geometries. Furthermore, the rotation of the nitrate solute is coupled with the hydrogen bond rearrangement of its hydration water. The nitrate anion can either tilt along the axis perpendicularly to the plane or rotate in the plane. We find that the two reorientation relaxation routes of the hydration water lead to different relaxation dynamics in each of the two above movements of the nitrate solute. The current study suggests that molecular geometry could play an important role in solute hydration and dynamics

Bayesian screening for active compounds in high-dimensional chemical spaces combining property descriptors and molecular fingerprints.

Science.gov (United States)

Vogt, Martin; Bajorath, Jürgen

2008-01-01

Bayesian classifiers are increasingly being used to distinguish active from inactive compounds and search large databases for novel active molecules. We introduce an approach to directly combine the contributions of property descriptors and molecular fingerprints in the search for active compounds that is based on a Bayesian framework. Conventionally, property descriptors and fingerprints are used as alternative features for virtual screening methods. Following the approach introduced here, probability distributions of descriptor values and fingerprint bit settings are calculated for active and database molecules and the divergence between the resulting combined distributions is determined as a measure of biological activity. In test calculations on a large number of compound activity classes, this methodology was found to consistently perform better than similarity searching using fingerprints and multiple reference compounds or Bayesian screening calculations using probability distributions calculated only from property descriptors. These findings demonstrate that there is considerable synergy between different types of property descriptors and fingerprints in recognizing diverse structure-activity relationships, at least in the context of Bayesian modeling.

A Bayesian Nonparametric Approach to Factor Analysis

DEFF Research Database (Denmark)

Piatek, Rémi; Papaspiliopoulos, Omiros

2018-01-01

This paper introduces a new approach for the inference of non-Gaussian factor models based on Bayesian nonparametric methods. It relaxes the usual normality assumption on the latent factors, widely used in practice, which is too restrictive in many settings. Our approach, on the contrary, does no...

Bayesian analysis in plant pathology.

Science.gov (United States)

Mila, A L; Carriquiry, A L

2004-09-01

ABSTRACT Bayesian methods are currently much discussed and applied in several disciplines from molecular biology to engineering. Bayesian inference is the process of fitting a probability model to a set of data and summarizing the results via probability distributions on the parameters of the model and unobserved quantities such as predictions for new observations. In this paper, after a short introduction of Bayesian inference, we present the basic features of Bayesian methodology using examples from sequencing genomic fragments and analyzing microarray gene-expressing levels, reconstructing disease maps, and designing experiments.

Genomic-Enabled Prediction Based on Molecular Markers and Pedigree Using the Bayesian Linear Regression Package in R

Directory of Open Access Journals (Sweden)

Paulino Pérez

2010-09-01

Full Text Available The availability of dense molecular markers has made possible the use of genomic selection in plant and animal breeding. However, models for genomic selection pose several computational and statistical challenges and require specialized computer programs, not always available to the end user and not implemented in standard statistical software yet. The R-package BLR (Bayesian Linear Regression implements several statistical procedures (e.g., Bayesian Ridge Regression, Bayesian LASSO in a unified framework that allows including marker genotypes and pedigree data jointly. This article describes the classes of models implemented in the BLR package and illustrates their use through examples. Some challenges faced when applying genomic-enabled selection, such as model choice, evaluation of predictive ability through cross-validation, and choice of hyper-parameters, are also addressed.

Non-monotonic behaviour in relaxation dynamics of image restoration

International Nuclear Information System (INIS)

Ozeki, Tomoko; Okada, Masato

2003-01-01

We have investigated the relaxation dynamics of image restoration through a Bayesian approach. The relaxation dynamics is much faster at zero temperature than at the Nishimori temperature where the pixel-wise error rate is minimized in equilibrium. At low temperature, we observed non-monotonic development of the overlap. We suggest that the optimal performance is realized through premature termination in the relaxation processes in the case of the infinite-range model. We also performed Markov chain Monte Carlo simulations to clarify the underlying mechanism of non-trivial behaviour at low temperature by checking the local field distributions of each pixel

Corroborative evidences of TV γ -scaling of the α-relaxation originating from the primitive relaxation/JG β relaxation

Science.gov (United States)

Ngai, K. L.; Paluch, M.

2017-12-01

Successful thermodynamic scaling of the structural alpha-relaxation time or transport coefficients of glass-forming liquids determined at various temperatures T and pressures P means the data conform to a single function of the product variable TVgamma, where V is the specific volume and gamma is a material specific constant. In the past two decades we have witnessed successful TVgamma-scaling in many molecular, polymeric, and even metallic glass-formers, and gamma is related to the slope of the repulsive part of the intermolecular potential. The advances made indicate TVgamma-scaling is an important aspect of the dynamic and thermodynamic properties of glass-formers. In this paper we show the origin of TVgamma-scaling is not from the structural alpha-relaxation time. Instead it comes from its precursor, the Johari-Goldstein beta-relaxation or the primitive relaxation of the Coupling Model and their relaxation times or tau_0 respectively. It is remarkable that all relaxation times are functions of TVgamma with the same gama, as well as the fractional exponent of the Kohlrausch correlation function of the structural alpha-relaxation. We arrive at this conclusion convincingly based on corroborative evidences from a number of experiments and molecular dynamics simulations performed on a wide variety of glass-formers and in conjunction with consistency with the predictions of the Coupling Model.

Second-order Monte Carlo wave-function approach to the relaxation effects on ringing revivals in a molecular system interacting with a strongly squeezed coherent field

International Nuclear Information System (INIS)

Nakano, Masayoshi; Kishi, Ryohei; Nitta, Tomoshige; Yamaguchi, Kizashi

2004-01-01

We investigate the relaxation effects on the quantum dynamics in a two-state molecular system interacting with a single-mode strongly amplitude-squeezed coherent field using the second-order Monte Carlo wave-function method. The molecular population inversion (collapse-revival behavior of Rabi oscillations) is known to show the echoes after each revival, which are referred to as ringing revivals, in the case of strongly squeezed coherent fields with oscillatory photon-number distributions due to the phase-space interference effect. Two types of relaxation effects, i.e., cavity relaxation (the dissipation of an internal single mode to outer mode) and molecular coherent (phase) relaxation caused by nuclear vibrations on ringing revivals are investigated from the viewpoint of the quantum-phase dynamics using the quasiprobability (Q function) distribution of a single-mode field and the off-diagonal molecular density matrix ρ elec1,2 (t). It turns out that the molecular phase relaxation attenuates both the entire revival-collapse behavior and the increase in ρ elec1,2 (t) during the quiescent region, whereas a very slight cavity relaxation particularly suppresses the echoes in ringing revivals more significantly than the first revival but hardly changes a primary variation in envelope of ρ elec1,2 (t) in the nonrelaxation case

Molecular motion of micellar solutes: a 13C NMR relaxation study

International Nuclear Information System (INIS)

Stark, R.E.; Kasakevich, M.L.; Granger, J.W.

1982-01-01

A series of simple NMR relaxation experiments have been performed on nitrobenzene and aniline dissolved in the ionic detergents sodium dodecyl sulfate (SDS) and hexadecyltrimethylammonium bromide (CTAB). Using 13 C relaxation rates at various molecular sites, and comparing data obtained in organic media with those for micellar solutions, the viscosity at the solubilization site was estimated and a detailed picture of motional restrictions imposed by the micellar enviroment was derived. Viscosities of 8 to 17 cp indicate a rather fluid environment for solubilized nitrobenzene; both additives exhibit altered motional preferences in CTAB solutions only. As an aid in interpretation of the NMR data, quasi-elastic light scattering and other physical techniques have been used to evaluate the influence of organic solutes on micellar size and shape. The NMR methods are examined critically in terms of their general usefulness for studies of solubilization in detergent micelles. 48 references

Simple molecular mechanism of heat transfer: Debye relaxation versus power-law

International Nuclear Information System (INIS)

Gall, M.; Kutner, R.

2005-01-01

We study a simple molecular model (at coarse-grain level) as a basis of irreversible heat transfer through a diathermic partition. The partition separates into two adjacent parts a box containing ideal point particles that communicate only though this partition. We provide the basic mechanism of energy transfer between the left- and right-hand side gas samples by assuming equipartition of kinetic energy of all outgoing particles colliding with the partition at a given time. We analyse and compare two essentially different cases (A) the reference one, where we assume that the border walls of the box and the diathermic partitions can randomize the direction of motion of rebounding particles, and (B) the case where we assume the mirror collisions of particles with the border walls and the partition. In both cases the rebounding of the particles from border walls is elastic. The above introduced assumptions allow us to numerically simulate and analytically consider, for example, the relaxation of temperatures of both gas samples and the entropy of the system. However, in both cases the long-time relaxation is essentially different since in case (A) it is an exponential one, while in case (B) it seems to be a power-law relaxation. The obtained results well agree in case (A) with the predictions of the phenomenological, linear theory of irreversible theory had to be developed which assumes time-dependence of heat conductivity; it describes the relaxation of the system far from equilibrium. The explanation of the results obtained in this case is, nevertheless, an intriguing problem. (author)

Relaxed Poisson cure rate models.

Science.gov (United States)

Rodrigues, Josemar; Cordeiro, Gauss M; Cancho, Vicente G; Balakrishnan, N

2016-03-01

The purpose of this article is to make the standard promotion cure rate model (Yakovlev and Tsodikov, ) more flexible by assuming that the number of lesions or altered cells after a treatment follows a fractional Poisson distribution (Laskin, ). It is proved that the well-known Mittag-Leffler relaxation function (Berberan-Santos, ) is a simple way to obtain a new cure rate model that is a compromise between the promotion and geometric cure rate models allowing for superdispersion. So, the relaxed cure rate model developed here can be considered as a natural and less restrictive extension of the popular Poisson cure rate model at the cost of an additional parameter, but a competitor to negative-binomial cure rate models (Rodrigues et al., ). Some mathematical properties of a proper relaxed Poisson density are explored. A simulation study and an illustration of the proposed cure rate model from the Bayesian point of view are finally presented. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Stress relaxation of bi-disperse polystyrene melts

DEFF Research Database (Denmark)

Hengeller, Ludovica; Huang, Qian; Dorokhin, Andriy

2016-01-01

We present start-up of uniaxial extension followed by stress relaxation experiments of a bi-disperse 50 % by weight blend of 95k and 545k molecular weight polystyrene. We also show, for comparison, stress relaxation measurements of the polystyrene melts with molecular weight 95k and 545k, which...... are the components of the bi-disperse melt. The measurements show three separated relaxation regimes: a fast regime, a transition regime, and a slow regime. In the fast regime, the orientation of the long chains is frozen and the stress relaxation is due to stretch relaxation of the short chains primarily....... Conversely in the slow regime, the long chains have retracted and undergo relaxation of orientation in fully relaxed short chains....

Comparison of different strategies for using fossil calibrations to generate the time prior in Bayesian molecular clock dating.

Science.gov (United States)

Barba-Montoya, Jose; Dos Reis, Mario; Yang, Ziheng

2017-09-01

Fossil calibrations are the utmost source of information for resolving the distances between molecular sequences into estimates of absolute times and absolute rates in molecular clock dating analysis. The quality of calibrations is thus expected to have a major impact on divergence time estimates even if a huge amount of molecular data is available. In Bayesian molecular clock dating, fossil calibration information is incorporated in the analysis through the prior on divergence times (the time prior). Here, we evaluate three strategies for converting fossil calibrations (in the form of minimum- and maximum-age bounds) into the prior on times, which differ according to whether they borrow information from the maximum age of ancestral nodes and minimum age of descendent nodes to form constraints for any given node on the phylogeny. We study a simple example that is analytically tractable, and analyze two real datasets (one of 10 primate species and another of 48 seed plant species) using three Bayesian dating programs: MCMCTree, MrBayes and BEAST2. We examine how different calibration strategies, the birth-death process, and automatic truncation (to enforce the constraint that ancestral nodes are older than descendent nodes) interact to determine the time prior. In general, truncation has a great impact on calibrations so that the effective priors on the calibration node ages after the truncation can be very different from the user-specified calibration densities. The different strategies for generating the effective prior also had considerable impact, leading to very different marginal effective priors. Arbitrary parameters used to implement minimum-bound calibrations were found to have a strong impact upon the prior and posterior of the divergence times. Our results highlight the importance of inspecting the joint time prior used by the dating program before any Bayesian dating analysis. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Critical thickness and strain relaxation in molecular beam epitaxy-grown SrTiO3 films

International Nuclear Information System (INIS)

Wang, Tianqi; Ganguly, Koustav; Marshall, Patrick; Xu, Peng; Jalan, Bharat

2013-01-01

We report on the study of the critical thickness and the strain relaxation in epitaxial SrTiO 3 film grown on (La 0.3 Sr 0.7 )(Al 0.65 Ta 0.35 )O 3 (001) (LSAT) substrate using the hybrid molecular beam epitaxy approach. No change in the film's lattice parameter (both the in-plane and the out-of-plane) was observed up to a film thickness of 180 nm, which is in sharp contrast to the theoretical critical thickness of ∼12 nm calculated using the equilibrium theory of strain relaxation. For film thicknesses greater than 180 nm, the out-of-plane lattice parameter was found to decrease hyperbolically in an excellent agreement with the relaxation via forming misfit dislocations. Possible mechanisms are discussed by which the elastic strain energy can be accommodated prior to forming misfit dislocations leading to such anomalously large critical thickness

Bayesian estimation of multicomponent relaxation parameters in magnetic resonance fingerprinting.

Science.gov (United States)

McGivney, Debra; Deshmane, Anagha; Jiang, Yun; Ma, Dan; Badve, Chaitra; Sloan, Andrew; Gulani, Vikas; Griswold, Mark

2018-07-01

To estimate multiple components within a single voxel in magnetic resonance fingerprinting when the number and types of tissues comprising the voxel are not known a priori. Multiple tissue components within a single voxel are potentially separable with magnetic resonance fingerprinting as a result of differences in signal evolutions of each component. The Bayesian framework for inverse problems provides a natural and flexible setting for solving this problem when the tissue composition per voxel is unknown. Assuming that only a few entries from the dictionary contribute to a mixed signal, sparsity-promoting priors can be placed upon the solution. An iterative algorithm is applied to compute the maximum a posteriori estimator of the posterior probability density to determine the magnetic resonance fingerprinting dictionary entries that contribute most significantly to mixed or pure voxels. Simulation results show that the algorithm is robust in finding the component tissues of mixed voxels. Preliminary in vivo data confirm this result, and show good agreement in voxels containing pure tissue. The Bayesian framework and algorithm shown provide accurate solutions for the partial-volume problem in magnetic resonance fingerprinting. The flexibility of the method will allow further study into different priors and hyperpriors that can be applied in the model. Magn Reson Med 80:159-170, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

Characteristic imsets for learning Bayesian network structure

Czech Academy of Sciences Publication Activity Database

Hemmecke, R.; Lindner, S.; Studený, Milan

2012-01-01

Roč. 53, č. 9 (2012), s. 1336-1349 ISSN 0888-613X R&D Projects: GA MŠk(CZ) 1M0572; GA ČR GA201/08/0539 Institutional support: RVO:67985556 Keywords : learning Bayesian network structure * essential graph * standard imset * characteristic imset * LP relaxation of a polytope Subject RIV: BA - General Mathematics Impact factor: 1.729, year: 2012 http://library.utia.cas.cz/separaty/2012/MTR/studeny-0382596.pdf

Extended Thermodynamics of Rarefied Polyatomic Gases: 15-Field Theory Incorporating Relaxation Processes of Molecular Rotation and Vibration

Directory of Open Access Journals (Sweden)

Takashi Arima

2018-04-01

Full Text Available After summarizing the present status of Rational Extended Thermodynamics (RET of gases, which is an endeavor to generalize the Navier–Stokes and Fourier (NSF theory of viscous heat-conducting fluids, we develop the molecular RET theory of rarefied polyatomic gases with 15 independent fields. The theory is justified, at mesoscopic level, by a generalized Boltzmann equation in which the distribution function depends on two internal variables that take into account the energy exchange among the different molecular modes of a gas, that is, translational, rotational, and vibrational modes. By adopting the generalized Bhatnagar, Gross and Krook (BGK-type collision term, we derive explicitly the closed system of field equations with the use of the Maximum Entropy Principle (MEP. The NSF theory is derived from the RET theory as a limiting case of small relaxation times via the Maxwellian iteration. The relaxation times introduced in the theory are shown to be related to the shear and bulk viscosities and heat conductivity.

Relaxation Dynamics of Nanoparticle-Tethered Polymer Chains

KAUST Repository

Kim, Sung A

2015-09-08

© 2015 American Chemical Society. Relaxation dynamics of nanoparticle-tethered cis-1,4-polyisoprene (PI) are investigated using dielectric spectroscopy and rheometry. A model system composed of polymer chains densely grafted to spherical SiO2 nanoparticles to form self-suspended suspensions facilitates detailed studies of slow global chain and fast segmental mode dynamics under surface and geometrical confinement-from experiments performed in bulk materials. We report that unentangled polymer molecules tethered to nanoparticles relax far more slowly than their tethered entangled counterparts. Specifically, at fixed grafting density we find, counterintuitively, that increasing the tethered polymer molecular weight up to values close to the entanglement molecular weight speeds up chain relaxation dynamics. Decreasing the polymer grafting density for a fixed molecular weight has the opposite effect: it dramatically slows down chain relaxation, increases interchain coupling, and leads to a transition in rheological response from simple fluid behavior to viscoelastic fluid behavior for tethered PI chains that are unentangled by conventional measures. Increasing the measurement temperature produces an even stronger elastic response and speeds up molecular relaxation at a rate that decreases with grafting density and molecular weight. These observations are discussed in terms of chain confinement driven by crowding between particles and by the existence of an entropic attractive force produced by the space-filling constraint on individual chains in a self-suspended material. Our results indicate that the entropic force between densely grafted polymer molecules couples motions of individual chains in an analogous manner to reversible cross-links in associating polymers.

Nuclear spin-lattice relaxation in carbon nanostructures

Energy Technology Data Exchange (ETDEWEB)

Panich, A.M., E-mail: pan@bgu.ac.i [Department of Physics, Ben-Gurion University of the Negev, P.O. Box 653, Beer Sheva 84105 (Israel); Sergeev, N.A. [Institute of Physics, University of Szczecin, 70-451 Szczecin (Poland)

2010-04-15

Interpretation of nuclear spin-lattice relaxation data in the carbon nanostructures is usually based on the analysis of fluctuations of dipole-dipole interactions of nuclear spins and anisotropic electron-nuclear interactions responsible for chemical shielding, which are caused by molecular dynamics. However, many nanocarbon systems such as fullerene and nanotube derivatives, nanodiamonds and carbon onions reveal noticeable amount of paramagnetic defects with unpaired electrons originating from dangling bonds. The interaction between nuclear and electron spins strongly influences the nuclear spin-lattice relaxation, but usually is not taken into account, thus the relaxation data are not correctly interpreted. Here we report on the temperature dependent NMR spectra and spin-lattice relaxation measurements of intercalated fullerenes C{sub 60}(MF{sub 6}){sub 2} (M=As and Sb), where nuclear relaxation is caused by both molecular rotation and interaction between nuclei and unpaired electron spins. We present a detailed theoretical analysis of the spin-lattice relaxation data taking into account both these contributions. Good agreement between the experimental data and calculations is obtained. The developed approach would be useful in interpreting the NMR relaxation data in different nanostructures and their intercalation compounds.

Vibrational relaxation of a triatomic molecular impurity: D2O in vitreous As2S3

International Nuclear Information System (INIS)

Rella, C.W.; Schwettman, H.A.; Engholm, J.R.

1995-01-01

Measurements of the relaxation of the D 2 O stretch mode in vitreous As 2 S 3 are presented. Because the bending mode of the molecule offers an intra-molecular decay channel for the stretch mode, the decay scheme of the D 2 O molecule is more complex than that of diatomic molecules. The asymmetric stretch mode of D 2 O has a frequency of 2680 cm -1 . To study the relaxation of this mode we applied a pump-probe technique, using intense psec; pulses of the Stanford Free Electron Laser. Due to the small cross-section of the vibrational mode, successful efforts were made to improve the signal to noise ratio by using a laser stabilization system and a tightly focused beam to increase the intensity, by averaging the signal with a kHz repetition rate and by using samples with an optimized D 2 O concentration. A rapid relaxation rate on the order of 5 x 10 9 sec -1 at low temperature is found that increases with temperature. Recalling that the bending mode of the D 2 O molecule has a frequency of 1170 cm -1 , one would expect a decay in a third order process, involving two quanta of the bending mode plus a vibrational host quanta with a frequency of 340 cm -1 , which coincides with a fundamental frequency of the pyramidal building blocks of the glassy As 2 S 3 host. Instead, we find from the temperature dependence of the relaxation rate that the D 2 O stretching mode relaxes in a higher order process. This indicates that the relaxation dynamics of small molecules is more complex than generally assumed

Structure-based bayesian sparse reconstruction

KAUST Repository

Quadeer, Ahmed Abdul

2012-12-01

Sparse signal reconstruction algorithms have attracted research attention due to their wide applications in various fields. In this paper, we present a simple Bayesian approach that utilizes the sparsity constraint and a priori statistical information (Gaussian or otherwise) to obtain near optimal estimates. In addition, we make use of the rich structure of the sensing matrix encountered in many signal processing applications to develop a fast sparse recovery algorithm. The computational complexity of the proposed algorithm is very low compared with the widely used convex relaxation methods as well as greedy matching pursuit techniques, especially at high sparsity. © 1991-2012 IEEE.

Local spin dynamics at low temperature in the slowly relaxing molecular chain [Dy(hfac)3{NIT(C6H4OPh)}]: A μ+ spin relaxation study

Science.gov (United States)

Arosio, Paolo; Corti, Maurizio; Mariani, Manuel; Orsini, Francesco; Bogani, Lapo; Caneschi, Andrea; Lago, Jorge; Lascialfari, Alessandro

2015-05-01

The spin dynamics of the molecular magnetic chain [Dy(hfac)3{NIT(C6H4OPh)}] were investigated by means of the Muon Spin Relaxation (μ+SR) technique. This system consists of a magnetic lattice of alternating Dy(III) ions and radical spins, and exhibits single-chain-magnet behavior. The magnetic properties of [Dy(hfac)3{NIT(C6H4OPh)}] have been studied by measuring the magnetization vs. temperature at different applied magnetic fields (H = 5, 3500, and 16500 Oe) and by performing μ+SR experiments vs. temperature in zero field and in a longitudinal applied magnetic field H = 3500 Oe. The muon asymmetry P(t) was fitted by the sum of three components, two stretched-exponential decays with fast and intermediate relaxation times, and a third slow exponential decay. The temperature dependence of the spin dynamics has been determined by analyzing the muon longitudinal relaxation rate λinterm(T), associated with the intermediate relaxing component. The experimental λinterm(T) data were fitted with a corrected phenomenological Bloembergen-Purcell-Pound law by using a distribution of thermally activated correlation times, which average to τ = τ0 exp(Δ/kBT), corresponding to a distribution of energy barriers Δ. The correlation times can be associated with the spin freezing that occurs when the system condenses in the ground state.

Local spin dynamics at low temperature in the slowly relaxing molecular chain [Dy(hfac)3(NIT(C6H4OPh))]: A μ+ spin relaxation study

International Nuclear Information System (INIS)

Arosio, Paolo; Orsini, Francesco; Corti, Maurizio; Mariani, Manuel; Bogani, Lapo; Caneschi, Andrea; Lago, Jorge; Lascialfari, Alessandro

2015-01-01

The spin dynamics of the molecular magnetic chain [Dy(hfac) 3 (NIT(C 6 H 4 OPh))] were investigated by means of the Muon Spin Relaxation (μ + SR) technique. This system consists of a magnetic lattice of alternating Dy(III) ions and radical spins, and exhibits single-chain-magnet behavior. The magnetic properties of [Dy(hfac) 3 (NIT(C 6 H 4 OPh))] have been studied by measuring the magnetization vs. temperature at different applied magnetic fields (H = 5, 3500, and 16500 Oe) and by performing μ + SR experiments vs. temperature in zero field and in a longitudinal applied magnetic field H = 3500 Oe. The muon asymmetry P(t) was fitted by the sum of three components, two stretched-exponential decays with fast and intermediate relaxation times, and a third slow exponential decay. The temperature dependence of the spin dynamics has been determined by analyzing the muon longitudinal relaxation rate λ interm (T), associated with the intermediate relaxing component. The experimental λ interm (T) data were fitted with a corrected phenomenological Bloembergen-Purcell-Pound law by using a distribution of thermally activated correlation times, which average to τ = τ 0 exp(Δ/k B T), corresponding to a distribution of energy barriers Δ. The correlation times can be associated with the spin freezing that occurs when the system condenses in the ground state

Dielectric relaxation spectra of liquid crystals in relation to molecular structure

International Nuclear Information System (INIS)

Wrobel, S.

1986-07-01

The dielectric spectra obtained for some members of two homologous series, i.e. for di-alkoxyazoxybenzenes and penthyl-alkoxythiobenzoates, are discussed qualitatively on the basis of the Nordio-Rigatti-Segre diffusion model. It is additionally assumed that the molecular reorientations take place about the principal axes of the inertia tensor. The distribution of correlation times, which is strongly temperature dependent in the vicinity of the clearing point, is interpreted as being caused by fluctuations of the principal axes frame which are due to conformation changes inside the end chains. The Bauer equation is used to describe both principal molecular reorientations, i.e. the reorientations about the long and short axis, observed in liquid crystalline structure by means of dielectric relaxation methods. The energies and entropies of activation have been computed for both principal reorientations. The differences between the high frequency limit of the dielectric permittivity and the refractive index squared of liquid crystals are explained in terms of two librational motions of the molecules observed by other experimental techniques, viz. far infra-red, Raman and inelastic neutron scattering spectroscopies, and found in this work on the basis of dielectrically measured energy barriers. It has been shown qualitatively that intramolecular libratory motions greatly effect the high frequency dielectric spectrum. Finally, molecular motions in liquid crystals are divided into two types: coherent and incoherent. 127 refs., 56 figs., 17 tabs. (author)

Water interactions with varying molecular states of bovine casein: 2H NMR relaxation studies

International Nuclear Information System (INIS)

Kumosinski, T.F.; Pessen, H.; Prestrelski, S.J.; Farrell, H.M. Jr.

1987-01-01

The caseins occur in milk as spherical colloidal complexes of protein and salts with an average diameter of 1200 A, the casein micelles. Removal of Ca2+ is thought to result in their dissociation into smaller protein complexes stabilized by hydrophobic interactions and called submicelles. Whether these submicelles actually occur within the micelles as discrete particles interconnected by calcium phosphate salt bridges has been the subject of much controversy. A variety of physical measurements have shown that casein micelles contain an inordinately high amount of trapped water (2 to 7 g H 2 O/g protein). With this in mind it was of interest to determine if NMR relaxation measurements could detect the presence of this trapped water within the micelles, and to evaluate whether it is a continuum with picosecond correlation times or is associated in part with discrete submicellar structures with nanosecond motions. For this purpose the variations in 2 H NMR longitudinal and transverse relaxation rates of water with protein concentration were determined for bovine casein at various temperatures, under both submicellar and micellar conditions. D 2 O was used instead of H 2 O to eliminate cross-relaxation effects. From the protein concentration dependence of the relaxation rates, the second virial coefficient of the protein was obtained by nonlinear regression analysis. Using either an isotropic tumbling or an intermediate asymmetry model, degrees of hydration, v, and correlation times, tau c, were calculated for the caseins; from the latter parameter the Stokes radius, r, was obtained. Next, estimates of molecular weights were obtained from r and the partial specific volume. Values were in the range of those published from other methodologies for the submicelles

Investigation of effective impact parameters in electron-ion temperature relaxation via Particle-Particle Coulombic molecular dynamics

Science.gov (United States)

Zhao, Yinjian

2017-09-01

Aiming at a high simulation accuracy, a Particle-Particle (PP) Coulombic molecular dynamics model is implemented to study the electron-ion temperature relaxation. In this model, the Coulomb's law is directly applied in a bounded system with two cutoffs at both short and long length scales. By increasing the range between the two cutoffs, it is found that the relaxation rate deviates from the BPS theory and approaches the LS theory and the GMS theory. Also, the effective minimum and maximum impact parameters (bmin* and bmax*) are obtained. For the simulated plasma condition, bmin* is about 6.352 times smaller than the Landau length (bC), and bmax* is about 2 times larger than the Debye length (λD), where bC and λD are used in the LS theory. Surprisingly, the effective relaxation time obtained from the PP model is very close to the LS theory and the GMS theory, even though the effective Coulomb logarithm is two times greater than the one used in the LS theory. Besides, this work shows that the PP model (commonly known as computationally expensive) is becoming practicable via GPU parallel computing techniques.

Resonances in field-cycling NMR on molecular crystals. (reversible) Spin dynamics or (irreversible) relaxation?; Resonanzen in Field-Cycling-NMR an Molekuelkristallen. (reversible) Spindynamik oder (irreversible) Relaxation?

Energy Technology Data Exchange (ETDEWEB)

Tacke, Christian

2015-07-01

Multi spin systems with spin 1/2 nuclei and dipolar coupled quadrupolar nuclei can show so called ''quadrupolar dips''. There are two main reasons for this behavior: polarization transfer and relaxation. They look quite alike and without additional research cannot be differentiated easily in most cases. These two phenomena have quite different physical and theoretical backgrounds. For no or very slow dynamics, polarization transfer will take place, which is energy conserving inside the spin system. This effect can entirely be described using quantum mechanics on the spin system. Detailed knowledge about the crystallography is needed, because this affects the relevant hamiltonians directly. For systems with fast enough dynamics, relaxation takes over, and the energy flows from the spin system to the lattice; thus a more complex theoretical description is needed. This description has to include a dynamic model, usually in the form of a spectral density function. Both models should include detailed modelling of the complete spin system. A software library was developed to be able to model complex spin systems. It allows to simulate polarization transfer or relaxation effects. NMR measurements were performed on the protonic conductor K{sub 3}H(SO{sub 4}){sub 2}. A single crystal shows sharp quadrupolar dips at room temperature. Dynamics could be excluded using relaxation measurements and literature values. Thus, a polarization transfer analysis was used to describe those dips with good agreement. As a second system, imidazolium based molecular crystals were analyzed. The quadrupolar dips were expected to be caused by polarization transfer; this was carefully analyzed and found not to be true. A relaxation based analysis shows good agreement with the measured data in the high temperature area. It leverages a two step spectral density function, which indicates two distinct dynamic processes happening in this system.

A Robust Bayesian Truth Serum for Small Populations

OpenAIRE

Parkes, David C.; Witkowski, Jens

2012-01-01

Peer prediction mechanisms allow the truthful elicitation of private signals (e.g., experiences, or opinions) in regard to a true world state when this ground truth is unobservable. The original peer prediction method is incentive compatible for any number of agents n >= 2, but relies on a common prior, shared by all agents and the mechanism. The Bayesian Truth Serum (BTS) relaxes this assumption. While BTS still assumes that agents share a common prior, this prior need not be known to the me...

Molecular dissipation phenomena of nanoscopic friction in the heterogeneous relaxation regime of a glass former.

Science.gov (United States)

Sills, Scott; Gray, Tomoko; Overney, René M

2005-10-01

Nanoscale sliding friction involving a polystyrene melt near its glass transition temperature Tg (373 K) exhibited dissipation phenomena that provide insight into the underlying molecular relaxation processes. A dissipative length scale that shows significant parallelism with the size of cooperatively rearranging regions (CRRs) could be experimentally deduced from friction-velocity isotherms, combined with dielectric loss analysis. Upon cooling to approximately 10 K above Tg, the dissipation length Xd grew from a segmental scale of approximately 3 A to 2.1 nm, following a power-law relationship with the reduced temperature Xd approximately TR-phi. The resulting phi=1.89+/-0.08 is consistent with growth predictions for the length scale of CRRs in the heterogeneous regime of fragile glass formers. Deviations from the power-law behavior closer to Tg suggest that long-range processes, e.g., the normal mode or ultraslow Fischer modes, may couple with the alpha relaxation, leading to energy dissipation in domains of tens of nanometers.

Thermodynamic scaling of α-relaxation time and viscosity stems from the Johari-Goldstein β-relaxation or the primitive relaxation of the coupling model.

Science.gov (United States)

Ngai, K L; Habasaki, J; Prevosto, D; Capaccioli, S; Paluch, Marian

2012-07-21

By now it is well established that the structural α-relaxation time, τ(α), of non-associated small molecular and polymeric glass-formers obey thermodynamic scaling. In other words, τ(α) is a function Φ of the product variable, ρ(γ)/T, where ρ is the density and T the temperature. The constant γ as well as the function, τ(α) = Φ(ρ(γ)/T), is material dependent. Actually this dependence of τ(α) on ρ(γ)/T originates from the dependence on the same product variable of the Johari-Goldstein β-relaxation time, τ(β), or the primitive relaxation time, τ(0), of the coupling model. To support this assertion, we give evidences from various sources itemized as follows. (1) The invariance of the relation between τ(α) and τ(β) or τ(0) to widely different combinations of pressure and temperature. (2) Experimental dielectric and viscosity data of glass-forming van der Waals liquids and polymer. (3) Molecular dynamics simulations of binary Lennard-Jones (LJ) models, the Lewis-Wahnström model of ortho-terphenyl, 1,4 polybutadiene, a room temperature ionic liquid, 1-ethyl-3-methylimidazolium nitrate, and a molten salt 2Ca(NO(3))(2)·3KNO(3) (CKN). (4) Both diffusivity and structural relaxation time, as well as the breakdown of Stokes-Einstein relation in CKN obey thermodynamic scaling by ρ(γ)/T with the same γ. (5) In polymers, the chain normal mode relaxation time, τ(N), is another function of ρ(γ)/T with the same γ as segmental relaxation time τ(α). (6) While the data of τ(α) from simulations for the full LJ binary mixture obey very well the thermodynamic scaling, it is strongly violated when the LJ interaction potential is truncated beyond typical inter-particle distance, although in both cases the repulsive pair potentials coincide for some distances.

Local spin dynamics at low temperature in the slowly relaxing molecular chain [Dy(hfac)3(NIT(C6H4OPh))]: A μ{sup +} spin relaxation study

Energy Technology Data Exchange (ETDEWEB)

Arosio, Paolo, E-mail: paolo.arosio@guest.unimi.it; Orsini, Francesco [Department of Physics, Università degli Studi di Milano, and INSTM, Milano (Italy); Corti, Maurizio [Department of Physics, Università degli Studi di Pavia and INSTM, Pavia (Italy); Mariani, Manuel [Department of Physics and Astronomy, Università degli Studi di Bologna, Bologna (Italy); Bogani, Lapo [Physikalisches Institut, Universität Stuttgart, Stuttgart (Germany); Caneschi, Andrea [INSTM and Department of Chemistry, University of Florence, Firenze (Italy); Lago, Jorge [Departamento de Quimica Inorganica, Universidad del Pais Vasco, Bilbao (Spain); Lascialfari, Alessandro [Department of Physics, Università degli Studi di Milano, and INSTM, Milano (Italy); Centro S3, Istituto Nanoscienze - CNR, Modena (Italy)

2015-05-07

The spin dynamics of the molecular magnetic chain [Dy(hfac){sub 3}(NIT(C{sub 6}H{sub 4}OPh))] were investigated by means of the Muon Spin Relaxation (μ{sup +}SR) technique. This system consists of a magnetic lattice of alternating Dy(III) ions and radical spins, and exhibits single-chain-magnet behavior. The magnetic properties of [Dy(hfac){sub 3}(NIT(C{sub 6}H{sub 4}OPh))] have been studied by measuring the magnetization vs. temperature at different applied magnetic fields (H = 5, 3500, and 16500 Oe) and by performing μ{sup +}SR experiments vs. temperature in zero field and in a longitudinal applied magnetic field H = 3500 Oe. The muon asymmetry P(t) was fitted by the sum of three components, two stretched-exponential decays with fast and intermediate relaxation times, and a third slow exponential decay. The temperature dependence of the spin dynamics has been determined by analyzing the muon longitudinal relaxation rate λ{sub interm}(T), associated with the intermediate relaxing component. The experimental λ{sub interm}(T) data were fitted with a corrected phenomenological Bloembergen-Purcell-Pound law by using a distribution of thermally activated correlation times, which average to τ = τ{sub 0} exp(Δ/k{sub B}T), corresponding to a distribution of energy barriers Δ. The correlation times can be associated with the spin freezing that occurs when the system condenses in the ground state.

Rational extended thermodynamics of a rarefied polyatomic gas with molecular relaxation processes

Science.gov (United States)

Arima, Takashi; Ruggeri, Tommaso; Sugiyama, Masaru

2017-10-01

We present a more refined version of rational extended thermodynamics of rarefied polyatomic gases in which molecular rotational and vibrational relaxation processes are treated individually. In this case, we need a triple hierarchy of the moment system and the system of balance equations is closed via the maximum entropy principle. Three different types of the production terms in the system, which are suggested by a generalized BGK-type collision term in the Boltzmann equation, are adopted. In particular, the rational extended thermodynamic theory with seven independent fields (ET7) is analyzed in detail. Finally, the dispersion relation of ultrasonic wave derived from the ET7 theory is confirmed by the experimental data for CO2, Cl2, and Br2 gases.

Anomalous behavior of secondary dielectric relaxation in polypropylene glycols

Energy Technology Data Exchange (ETDEWEB)

Grzybowska, K; Grzybowski, A; Ziolo, J; Rzoska, S J; Paluch, M [Institute of Physics, Silesian University, Uniwersytecka 4, 40-007 Katowice (Poland)

2007-09-19

A surprising slow down in the dielectric secondary {gamma}-relaxation with temperature increasing near the glass transition is confirmed for several polypropylene glycols. The peculiar behavior diminishes as the molecular weight grows. The minimal model (Dyre and Olsen 2003 Phys. Rev. Lett. 91 155703) is applied successfully to describe the temperature dependences of the {gamma}-relaxation times. The minimal model parameters are analyzed for different molecular weights. A molecular explanation of the {gamma}-process anomaly for polypropylene glycols is proposed on the basis of the minimal model prediction.

Communication: High pressure specific heat spectroscopy reveals simple relaxation behavior of glass forming molecular liquid

DEFF Research Database (Denmark)

Roed, Lisa Anita; Niss, Kristine; Jakobsen, Bo

2015-01-01

The frequency dependent specific heat has been measured under pressure for the molecular glass forming liquid 5-polyphenyl-4-ether in the viscous regime close to the glass transition. The temperature and pressure dependences of the characteristic time scale associated with the specific heat...... is compared to the equivalent time scale from dielectric spectroscopy performed under identical conditions. It is shown that the ratio between the two time scales is independent of both temperature and pressure. This observation is non-trivial and demonstrates the existence of specially simple molecular...... liquids in which different physical relaxation processes are both as function of temperature and pressure/density governed by the same underlying “inner clock.” Furthermore, the results are discussed in terms of the recent conjecture that van der Waals liquids, like the measuredliquid, comply...

Stress relaxation in viscous soft spheres.

Science.gov (United States)

Boschan, Julia; Vasudevan, Siddarth A; Boukany, Pouyan E; Somfai, Ellák; Tighe, Brian P

2017-10-04

We report the results of molecular dynamics simulations of stress relaxation tests in athermal viscous soft sphere packings close to their unjamming transition. By systematically and simultaneously varying both the amplitude of the applied strain step and the pressure of the initial condition, we access both linear and nonlinear response regimes and control the distance to jamming. Stress relaxation in viscoelastic solids is characterized by a relaxation time τ* that separates short time scales, where viscous loss is substantial, from long time scales, where elastic storage dominates and the response is essentially quasistatic. We identify two distinct plateaus in the strain dependence of the relaxation time, one each in the linear and nonlinear regimes. The height of both plateaus scales as an inverse power law with the distance to jamming. By probing the time evolution of particle velocities during relaxation, we further identify a correlation between mechanical relaxation in the bulk and the degree of non-affinity in the particle velocities on the micro scale.

Study of local conformation and molecular movements of homo-polypeptides in aqueous solutions by using magnetic resonance and relaxation

International Nuclear Information System (INIS)

Perly, Bruno

1980-01-01

The objective of this research thesis is to study local conformations and mobilities of some typical homo-polypeptides by using techniques of magnetic resonance. By using these techniques, it is possible to make highly local observations of molecular elements which allows very efficient analysis of structural and dynamic properties of several biologically important compounds to be performed, and the study of their interactions. After a presentation of the general properties of the studied polypeptides, of magnetic resonance and of magnetic relaxation, the author presents some elements of macromolecular dynamics and movement models. Then, he reports the study of local conformations and structural transitions, applications of spin marking to the dynamic study of polypeptides, a dynamic study of the polypeptide skeleton under the form of statistic balls, the study of local movements of side chains by using nuclear relaxation, the study of the coupling of movements of main and side chains, and of the nuclear relaxation induced by a radical spin marker

On the field-induced switching of molecular organization in a biaxial nematic cell and its relaxation

Science.gov (United States)

Ricci, Matteo; Berardi, Roberto; Zannoni, Claudio

2015-08-01

We investigate the switching of a biaxial nematic filling a flat cell with planar homogeneous anchoring using a coarse-grained molecular dynamics simulation. We have found that an aligning field applied across the film, and acting on specific molecular axes, can drive the reorientation of the secondary biaxial director up to one order of magnitude faster than that for the principal director. While the π/2 switching of the secondary director does not affect the alignment of the long molecular axes, the field-driven reorientation of the principal director proceeds via a concerted rotation of the long and transversal molecular axes. More importantly, while upon switching off a (relatively) weak or intermediate field, the biaxial nematic liquid crystal is always able to relax to the initial surface aligned director state; this is not the case when using fields above a certain threshold. In that case, while the secondary director always recovers the initial state, the principal one remains, occasionally, trapped in a nonuniform director state due to the formation of domain walls.

Dielectric Relaxation Studies of Alkyl Methacrylate–Phenol Mixtures ...

African Journals Online (AJOL)

The Kirkwood correlation factor and the excess inverse relaxation time were determined and they yield information on the molecular interactions occurring in the systems. The values of the static permittivity and the relaxation time increase with an increase in the percentage of phenol in the mixtures. KEYWORDS: Dielectric ...

Impact of growth and annealing conditions on the parameters of Ge/Si(001) relaxed layers grown by molecular beam epitaxy

Energy Technology Data Exchange (ETDEWEB)

Yurasov, D. V., E-mail: Inquisitor@ipm.sci-nnov.ru [Russian Academy of Sciences, Institute for Physics of Microstructures (Russian Federation); Bobrov, A. I. [Lobachevsky State University of Nizhny Novgorod (Russian Federation); Daniltsev, V. M.; Novikov, A. V. [Russian Academy of Sciences, Institute for Physics of Microstructures (Russian Federation); Pavlov, D. A. [Lobachevsky State University of Nizhny Novgorod (Russian Federation); Skorokhodov, E. V.; Shaleev, M. V.; Yunin, P. A. [Russian Academy of Sciences, Institute for Physics of Microstructures (Russian Federation)

2015-11-15

Influence of the Ge layer thickness and annealing conditions on the parameters of relaxed Ge/Si(001) layers grown by molecular beam epitaxy via two-stage growth is investigated. The dependences of the threading dislocation density and surface roughness on the Ge layer thickness, annealing temperature and time, and the presence of a hydrogen atmosphere are obtained. As a result of optimization of the growth and annealing conditions, relaxed Ge/Si(001) layers which are thinner than 1 μm with a low threading dislocation density on the order of 10{sup 7} cm{sup –2} and a root mean square roughness of less than 1 nm are obtained.

Holographic grating relaxation technique for soft matter science

Energy Technology Data Exchange (ETDEWEB)

Lesnichii, Vasilii, E-mail: vasilii.lesnichii@physchem.uni-freiburg.de [Institute of Physical Chemistry, Albertstraße 21, Institute of Macromolecular Chemistry, Stefan-Meier-Str. 31, Albert-Ludwigs Universität, Freiburg im Breisgau 79104 (Germany); ITMO University, Kronverksky prospekt 49, Saint-Petersburg 197101 (Russian Federation); Kiessling, Andy [Institute of Physical Chemistry, Albertstraße 21, Institute of Macromolecular Chemistry, Stefan-Meier-Str. 31, Albert-Ludwigs Universität, Freiburg im Breisgau 79104 (Germany); Current address: Illinois Institute of Technology, 10 West 33rd Street, Chicago,IL60616 (United States); Bartsch, Eckhard [Institute of Physical Chemistry, Albertstraße 21, Institute of Macromolecular Chemistry, Stefan-Meier-Str. 31, Albert-Ludwigs Universität, Freiburg im Breisgau 79104 (Germany); Veniaminov, Andrey, E-mail: veniaminov@phoi.ifmo.ru [ITMO University, Kronverksky prospekt 49, Saint-Petersburg 197101 (Russian Federation)

2016-06-17

The holographic grating relaxation technique also known as forced Rayleigh scattering consists basically in writing a holographic grating in the specimen of interest and monitoring its diffraction efficiency as a function of time, from which valuable information on mass or heat transfer and photoinduced transformations can be extracted. In a more detailed view, the shape of the relaxation curve and the relaxation rate as a function of the grating period were found to be affected by the architecture of diffusing species (molecular probes) that constitute the grating, as well as that of the environment they diffuse in, thus making it possible to access and study spatial heterogeneity of materials and different modes of e.g., polymer motion. Minimum displacements and spatial domains approachable by the technique are in nanometer range, well below spatial periods of holographic gratings. In the present paper, several cases of holographic relaxation in heterogeneous media and complex motions are exemplified. Nano- to micro-structures or inhomogeneities comparable in spatial scale with holographic gratings manifest themselves in relaxation experiments via non-exponential decay (stepwise or stretched), spatial-period-dependent apparent diffusion coefficient, or unusual dependence of diffusion coefficient on molecular volume of diffusing probes.

Relationship between Structural and Stress Relaxation in a Block-Copolymer Melt

International Nuclear Information System (INIS)

Patel, Amish J.; Narayanan, Suresh; Sandy, Alec; Mochrie, Simon G. J.; Garetz, Bruce A.; Watanabe, Hiroshi; Balsara, Nitash P.

2006-01-01

The relationship between structural relaxation on molecular length scales and macroscopic stress relaxation was explored in a disordered block-copolymer melt. Experiments show that the structural relaxation time, measured by x-ray photon correlation spectroscopy is larger than the terminal stress relaxation time, measured by rheology, by factors as large as 100. We demonstrate that the structural relaxation data are dominated by the diffusion of intact micelles while the stress relaxation data are dominated by contributions due to disordered concentration fluctuations

Improved dynamical scaling analysis using the kernel method for nonequilibrium relaxation.

Science.gov (United States)

Echinaka, Yuki; Ozeki, Yukiyasu

2016-10-01

The dynamical scaling analysis for the Kosterlitz-Thouless transition in the nonequilibrium relaxation method is improved by the use of Bayesian statistics and the kernel method. This allows data to be fitted to a scaling function without using any parametric model function, which makes the results more reliable and reproducible and enables automatic and faster parameter estimation. Applying this method, the bootstrap method is introduced and a numerical discrimination for the transition type is proposed.

Relaxation dynamics following transition of solvated electrons

International Nuclear Information System (INIS)

Barnett, R.B.; Landman, U.; Nitzan, A.

1989-01-01

Relaxation dynamics following an electronic transition of an excess solvated electron in clusters and in bulk water is studied using an adiabatic simulation method. In this method the solvent evolves classically and the electron is constrained to a specified state. The coupling between the solvent and the excess electron is evaluated via the quantum expectation value of the electron--water molecule interaction potential. The relaxation following excitation (or deexcitation) is characterized by two time scales: (i) a very fast (/similar to/20--30 fs) one associated with molecular rotations in the first solvation shell about the electron, and (ii) a slower stage (/similar to/200 fs), which is of the order of the longitudinal dielectric relaxation time. The fast relaxation stage exhibits an isotope effect. The spectroscopical consequences of the relaxation dynamics are discussed

Nuclear magnetic relaxation induced by exchange-mediated orientational randomization: longitudinal relaxation dispersion for a dipole-coupled spin-1/2 pair.

Science.gov (United States)

Chang, Zhiwei; Halle, Bertil

2013-10-14

In complex biological or colloidal samples, magnetic relaxation dispersion (MRD) experiments using the field-cycling technique can characterize molecular motions on time scales ranging from nanoseconds to microseconds, provided that a rigorous theory of nuclear spin relaxation is available. In gels, cross-linked proteins, and biological tissues, where an immobilized macromolecular component coexists with a mobile solvent phase, nuclear spins residing in solvent (or cosolvent) species relax predominantly via exchange-mediated orientational randomization (EMOR) of anisotropic nuclear (electric quadrupole or magnetic dipole) couplings. The physical or chemical exchange processes that dominate the MRD typically occur on a time scale of microseconds or longer, where the conventional perturbation theory of spin relaxation breaks down. There is thus a need for a more general relaxation theory. Such a theory, based on the stochastic Liouville equation (SLE) for the EMOR mechanism, is available for a single quadrupolar spin I = 1. Here, we present the corresponding theory for a dipole-coupled spin-1/2 pair. To our knowledge, this is the first treatment of dipolar MRD outside the motional-narrowing regime. Based on an analytical solution of the spatial part of the SLE, we show how the integral longitudinal relaxation rate can be computed efficiently. Both like and unlike spins, with selective or non-selective excitation, are treated. For the experimentally important dilute regime, where only a small fraction of the spin pairs are immobilized, we obtain simple analytical expressions for the auto-relaxation and cross-relaxation rates which generalize the well-known Solomon equations. These generalized results will be useful in biophysical studies, e.g., of intermittent protein dynamics. In addition, they represent a first step towards a rigorous theory of water (1)H relaxation in biological tissues, which is a prerequisite for unravelling the molecular basis of soft

Regularities of intermediate adsorption complex relaxation

International Nuclear Information System (INIS)

Manukova, L.A.

1982-01-01

The experimental data, characterizing the regularities of intermediate adsorption complex relaxation in the polycrystalline Mo-N 2 system at 77 K are given. The method of molecular beam has been used in the investigation. The analytical expressions of change regularity in the relaxation process of full and specific rates - of transition from intermediate state into ''non-reversible'', of desorption into the gas phase and accumUlation of the particles in the intermediate state are obtained

Influence of E-beam irradiation on dielectric relaxation of recycled polypropylene

International Nuclear Information System (INIS)

Fazilova, Z.; Gafurov, U.; Tolstov, A.

2004-01-01

Full text: The dielectric relaxation connected with molecular groups and polymer chain mobility for un-irradiated and e-beam irradiated recycled polypropylene was investigated. It was studied films of samples produced from virgin (initial) and e- beam irradiated of the polymer granules (E-beam source with 5 MeV energy). The dielectric losses were measured with temperature increasing and decreasing regime. The losses were measured with E8-4 bridge help (the frequency is 1kH). Heating velocity was 2 grad/min. The dielectric losses did not appeared in minus temperature region for the initial polypropylene samples. The measurement in temperature increasing and decreasing shows that the relaxation peak at ∼ 35 o C for un-irradiated and ∼70 o C for irradiated polymer samples connected with macromolecular segments mobility with water molecular groups participation. The main relaxation peak (higher 100 o C) shifts after e-beam irradiation is result of the cross-links formation. ) The peak connected with macromolecular segments mobility in polymer amorphous regions (β-relaxation process). In irradiated polypropylene on IR spectroscopy data oxygen molecular groups is increased. The molecular groupings form inter-molecular hydrogen bonds. The intermolecular bonds also hindered molecular groups and macromolecular mobility. The e-beam stimulated cross-links formation was confirmed by method of sol-gel analyses. The work was supported by STCU Fund (Project No 3009)

String-like collective motion in the α- and β-relaxation of a coarse-grained polymer melt

Science.gov (United States)

Pazmiño Betancourt, Beatriz A.; Starr, Francis W.; Douglas, Jack F.

2018-03-01

Relaxation in glass-forming liquids occurs as a multi-stage hierarchical process involving cooperative molecular motion. First, there is a "fast" relaxation process dominated by the inertial motion of the molecules whose amplitude grows upon heating, followed by a longer time α-relaxation process involving both large-scale diffusive molecular motion and momentum diffusion. Our molecular dynamics simulations of a coarse-grained glass-forming polymer melt indicate that the fast, collective motion becomes progressively suppressed upon cooling, necessitating large-scale collective motion by molecular diffusion for the material to relax approaching the glass-transition. In each relaxation regime, the decay of the collective intermediate scattering function occurs through collective particle exchange motions having a similar geometrical form, and quantitative relationships are derived relating the fast "stringlet" collective motion to the larger scale string-like collective motion at longer times, which governs the temperature-dependent activation energies associated with both thermally activated molecular diffusion and momentum diffusion.

Vibrational and Rotational Energy Relaxation in Liquids

DEFF Research Database (Denmark)

Petersen, Jakob

Vibrational and rotational energy relaxation in liquids are studied by means of computer simulations. As a precursor for studying vibrational energy relaxation of a solute molecule subsequent to the formation of a chemical bond, the validity of the classical Bersohn-Zewail model for describing......, the vibrational energy relaxation of I2 subsequent to photodissociation and recombination in CCl4 is studied using classical Molecular Dynamics simulations. The vibrational relaxation times and the time-dependent I-I pair distribution function are compared to new experimental results, and a qualitative agreement...... is found in both cases. Furthermore, the rotational energy relaxation of H2O in liquid water is studied via simulations and a power-and-work analysis. The mechanism of the energy transfer from the rotationally excited H2O molecule to its water neighbors is elucidated, i.e. the energy-accepting degrees...

Magnetic relaxation in analytical, coordination and bioinorganic chemistry

International Nuclear Information System (INIS)

Mikhajlov, O.

1982-01-01

Nuclear magnetic relaxation is a special type of nuclear magnetic resonance in which the rate is measured of energy transfer between the excited nuclei and their molecular medium (spin-lattice relaxation) or the whole nuclear spin system (spin-spin relaxation). Nuclear magnetic relaxation relates to nuclei with a spin of 1/2, primarily H 1 1 , and is mainly measured in water solutions. It is suitable for (1) analytical chemistry because the relaxation time rapidly reduces in the presence of paramagnetic ions, (2) the study of complex compounds, (3) the study of biochemical reactions in the presence of different metal ions. It is also suitable for testing the composition of a flowing liquid. Its disadvantage is that it requires complex and expensive equipment. (Ha)

Universal Mechanism of Spin Relaxation in Solids

Science.gov (United States)

Chudnovsky, Eugene

2006-03-01

Conventional elastic theory ignores internal local twists and torques. Meantime, spin-lattice relaxation is inherently coupled with local elastic twists through conservation of the total angular momentum (spin + lattice). This coupling gives universal lower bound (free of fitting parameters) on the relaxation of the atomic or molecular spin in a solid [1] and on the relaxation of the electron spin in a quantum dot [2]. [1] E. M. Chudnovsky, D. A. Garanin, and R. Schilling, Phys. Rev. B 72, 094426 (2005). [2] C. Calero, E. M. Chudnovsky, and D. A. Garanin, Phys. Rev. Lett. 95, 166603 (2005).

Relaxation and transport properties of liquid n-triacontane

International Nuclear Information System (INIS)

Kondratyuk, N D; Lankin, A V; Norman, G E; Stegailov, V V

2015-01-01

Molecular modelling is used to calculate transport properties and to study relaxation of liquid n-triacontane (C 30 H 62 ). The problem is important in connection with the behavior of liquid isolators in a pre-breakdown state. Two all-atom models and a united-atom model are used. Shear viscosity is calculated using the Green-Kubo formula. The force fields are compared with each other using the following criteria: the required time for one molecular dynamics step, the compliance of the main physical and transport properties with experimental values. The problem of the system equilibration is considered. The united-atom potential is used to model the n-triacontane liquid with an initial directional orientation. The time of relaxation to the disordered state, when all molecules orientations are randomized, are obtained. The influence of the molecules orientations on the shear viscosity value and the shear viscosity relaxation are treated. (paper)

Charge Relaxation Dynamics of an Electrolytic Nanocapacitor

Science.gov (United States)

2015-01-01

Understanding ion relaxation dynamics in overlapping electric double layers (EDLs) is critical for the development of efficient nanotechnology-based electrochemical energy storage, electrochemomechanical energy conversion, and bioelectrochemical sensing devices as well as the controlled synthesis of nanostructured materials. Here, a lattice Boltzmann (LB) method is employed to simulate an electrolytic nanocapacitor subjected to a step potential at t = 0 for various degrees of EDL overlap, solvent viscosities, ratios of cation-to-anion diffusivity, and electrode separations. The use of a novel continuously varying and Galilean-invariant molecular-speed-dependent relaxation time (MSDRT) with the LB equation recovers a correct microscopic description of the molecular-collision phenomena and enhances the stability of the LB algorithm. Results for large EDL overlaps indicated oscillatory behavior for the ionic current density, in contrast to monotonic relaxation to equilibrium for low EDL overlaps. Further, at low solvent viscosities and large EDL overlaps, anomalous plasmalike spatial oscillations of the electric field were observed that appeared to be purely an effect of nanoscale confinement. Employing MSDRT in our simulations enabled modeling of the fundamental physics of the transient charge relaxation dynamics in electrochemical systems operating away from equilibrium wherein Nernst–Einstein relation is known to be violated. PMID:25678941

Bayesian methods for hackers probabilistic programming and Bayesian inference

CERN Document Server

Davidson-Pilon, Cameron

2016-01-01

Bayesian methods of inference are deeply natural and extremely powerful. However, most discussions of Bayesian inference rely on intensely complex mathematical analyses and artificial examples, making it inaccessible to anyone without a strong mathematical background. Now, though, Cameron Davidson-Pilon introduces Bayesian inference from a computational perspective, bridging theory to practice–freeing you to get results using computing power. Bayesian Methods for Hackers illuminates Bayesian inference through probabilistic programming with the powerful PyMC language and the closely related Python tools NumPy, SciPy, and Matplotlib. Using this approach, you can reach effective solutions in small increments, without extensive mathematical intervention. Davidson-Pilon begins by introducing the concepts underlying Bayesian inference, comparing it with other techniques and guiding you through building and training your first Bayesian model. Next, he introduces PyMC through a series of detailed examples a...

Dielectric relaxation studies of dilute solutions of amides

Energy Technology Data Exchange (ETDEWEB)

Malathi, M.; Sabesan, R.; Krishnan, S

2003-11-15

The dielectric constants and dielectric losses of formamide, acetamide, N-methyl acetamide, acetanilide and N,N-dimethyl acetamide in dilute solutions of 1,4-dioxan/benzene have been measured at 308 K using 9.37 GHz, dielectric relaxation set up. The relaxation time for the over all rotation {tau}{sub (1)} and that for the group rotation {tau}{sub (2)} of (the molecules were determined using Higasi's method. The activation energies for the processes of dielectric relaxation and viscous flow were determined by using Eyring's rate theory. From relaxation time behaviour of amides in non-polar solvent, solute-solvent and solute-solute type of molecular association is proposed.

Vogel-Fulcher dependence of relaxation rates in a nematic monomer and elastomer

Science.gov (United States)

Shenoy, D.; Filippov, S.; Aliev, F.; Keller, P.; Thomsen, D.; Ratna, B.

2000-12-01

Dielectric relaxation spectroscopy is used to study the relaxation processes in a nematic monomer and the corresponding cross-linked polymer nematic liquid crystal (elastomer). In the frequency window 10 mHz to 2 GHz the monomer liquid crystal shows a single relaxation whereas the polymer exhibits three relaxation processes, two of which are quantitatively analyzed. The temperature dependence of relaxation times in both the monomer and polymer follows a Vogel-Fulcher behavior. The relaxation processes are identified with specific molecular motions and activation energies are calculated in a linear approximation for comparison with literature data.

Green--Kubo formula for collisional relaxation

International Nuclear Information System (INIS)

Visscher, P.B.

1988-01-01

In this paper we generalize the Green--Kubo method (usually used for obtaining formulas for transport coefficients involving conserved densities) to relaxation processes occurring during collisions, such as the transfer of energy from vibrational to translational modes in a molecular fluid. We show that the relaxation rate can be calculated without evaluating time correlation functions over long times, and can in fact be written as a sum over collisions which makes the relation between the Green--Kubo method and approximate independent-collision models much clearer

A Bayesian approach to estimating hidden variables as well as missing and wrong molecular interactions in ordinary differential equation-based mathematical models.

Science.gov (United States)

Engelhardt, Benjamin; Kschischo, Maik; Fröhlich, Holger

2017-06-01

Ordinary differential equations (ODEs) are a popular approach to quantitatively model molecular networks based on biological knowledge. However, such knowledge is typically restricted. Wrongly modelled biological mechanisms as well as relevant external influence factors that are not included into the model are likely to manifest in major discrepancies between model predictions and experimental data. Finding the exact reasons for such observed discrepancies can be quite challenging in practice. In order to address this issue, we suggest a Bayesian approach to estimate hidden influences in ODE-based models. The method can distinguish between exogenous and endogenous hidden influences. Thus, we can detect wrongly specified as well as missed molecular interactions in the model. We demonstrate the performance of our Bayesian dynamic elastic-net with several ordinary differential equation models from the literature, such as human JAK-STAT signalling, information processing at the erythropoietin receptor, isomerization of liquid α -Pinene, G protein cycling in yeast and UV-B triggered signalling in plants. Moreover, we investigate a set of commonly known network motifs and a gene-regulatory network. Altogether our method supports the modeller in an algorithmic manner to identify possible sources of errors in ODE-based models on the basis of experimental data. © 2017 The Author(s).

Relaxation model of radiation-induced conductivity in polymers

Science.gov (United States)

Zhutayeva, Yu. R.; Khatipov, S. A.

1999-05-01

The paper suggests a relaxation model of radiation-induced conductivity (RIC) in polymers. According to the model, the transfer of charges generated in the polymer volume by ionizing radiation takes place with the participation of molecular relaxation processes. The mechanism of electron transport consists in the transfer of the charge directly between traps when they draw close to one another due to the rotation of macromolecule segments. The numerical solutions of the corresponding kinetic equations for different distribution functions Q( τ) of the times of molecular relaxation and for different functions of the probability P( τ, τ') of charge transfer in the `overlapping' regions of the diffusion spheres of the segments are analyzed. The relaxation model provides an explanation of the non-Arrhenius behavior of the RIC temperature dependence, the power dependence of RIC on the dose rate with a power index in the interval 0.5-1.0, the appearance of maxima in the curves of the RIC temporal dependence and their irreversible character in the region of large dose rates (more than 1 Gy/s). The model can be used for interpreting polymer RIC in conditions of kinetic mobility of macromolecules.

Thermal Fluctuations in the Magnetic Ground State of the Molecular Cluster Mn12O12 Acetate from μSR and Proton NMR Relaxation

International Nuclear Information System (INIS)

Lascialfari, A.; Borsa, F.; Carretta, P.; Jang, Z.H.; Borsa, F.; Gatteschi, D.

1998-01-01

Measurements of the spin-lattice relaxation rate are reported for muons and protons as a function of temperature for different values of the applied magnetic field in the Mn 12 O 12 molecular cluster. Strongly field dependent maxima in the relaxation rate versus temperature are observed below 50thinspthinspK. The results are explained in terms of thermal fluctuations of the total magnetization of the cluster among the different orientations with respect to the anisotropy axis. The lifetimes of the different m components of the total spin, S T =10 , of the molecule are obtained from the experiment and shown to be consistent with the ones expected from a spin-phonon coupling mechanism. No clear evidence for macroscopic quantum tunneling was observed in the field dependence of the proton relaxation rate at low T . copyright 1998 The American Physical Society

Rapid molecular evolution of human bocavirus revealed by Bayesian coalescent inference.

Science.gov (United States)

Zehender, Gianguglielmo; De Maddalena, Chiara; Canuti, Marta; Zappa, Alessandra; Amendola, Antonella; Lai, Alessia; Galli, Massimo; Tanzi, Elisabetta

2010-03-01

Human bocavirus (HBoV) is a linear single-stranded DNA virus belonging to the Parvoviridae family that has recently been isolated from the upper respiratory tract of children with acute respiratory infection. All of the strains observed so far segregate into two genotypes (1 and 2) with a low level of polymorphism. Given the recent description of the infection and the lack of epidemiological and molecular data, we estimated the virus's rates of molecular evolution and population dynamics. A dataset of forty-nine dated VP2 sequences, including also eight new isolates obtained from pharyngeal swabs of Italian patients with acute respiratory tract infections, was submitted to phylogenetic analysis. The model parameters, evolutionary rates and population dynamics were co-estimated using a Bayesian Markov Chain Monte Carlo approach, and site-specific positive and negative selection was also investigated. Recombination was investigated by seven different methods and one suspected recombinant strain was excluded from further analysis. The estimated mean evolutionary rate of HBoV was 8.6x10(-4)subs/site/year, and that of the 1st+2nd codon positions was more than 15 times less than that of the 3rd codon position. Viral population dynamics analysis revealed that the two known genotypes diverged recently (mean tMRCA: 24 years), and that the epidemic due to HBoV genotype 2 grew exponentially at a rate of 1.01year(-1). Selection analysis of the partial VP2 showed that 8.5% of sites were under significant negative pressure and the absence of positive selection. Our results show that, like other parvoviruses, HBoV is characterised by a rapid evolution. The low level of polymorphism is probably due to a relatively recent divergence between the circulating genotypes and strong purifying selection acting on viral antigens.

Electron spin relaxation in cryptochrome-based magnetoreception

DEFF Research Database (Denmark)

Kattnig, Daniel R; Solov'yov, Ilia A; Hore, P J

2016-01-01

The magnetic compass sense of migratory birds is thought to rely on magnetically sensitive radical pairs formed photochemically in cryptochrome proteins in the retina. An important requirement of this hypothesis is that electron spin relaxation is slow enough for the Earth's magnetic field to have...... this question for a structurally characterized model cryptochrome expected to share many properties with the putative avian receptor protein. To this end we combine all-atom molecular dynamics simulations, Bloch-Redfield relaxation theory and spin dynamics calculations to assess the effects of spin relaxation...... on the performance of the protein as a compass sensor. Both flavin-tryptophan and flavin-Z˙ radical pairs are studied (Z˙ is a radical with no hyperfine interactions). Relaxation is considered to arise from modulation of hyperfine interactions by librational motions of the radicals and fluctuations in certain...

Bayesian artificial intelligence

CERN Document Server

Korb, Kevin B

2010-01-01

Updated and expanded, Bayesian Artificial Intelligence, Second Edition provides a practical and accessible introduction to the main concepts, foundation, and applications of Bayesian networks. It focuses on both the causal discovery of networks and Bayesian inference procedures. Adopting a causal interpretation of Bayesian networks, the authors discuss the use of Bayesian networks for causal modeling. They also draw on their own applied research to illustrate various applications of the technology.New to the Second EditionNew chapter on Bayesian network classifiersNew section on object-oriente

Vibronic relaxation in molecular mixed crystals : Pentacene in naphthalene and p-terphenyl

NARCIS (Netherlands)

Hesselink, Wim H.; Wiersma, Douwe A.

1981-01-01

Picosecond photon echo techniques are used to measure directly vibronic relaxation times in the first excited singlet state of pentacene in naphthalene and p-terphenyl. In regions of low (< 300 cm–1) and high (> 1000 cm–1) vibrational energy, relaxation is fast (τ <2 ps) due to direct phonon

Bayesian Graphical Models

DEFF Research Database (Denmark)

Jensen, Finn Verner; Nielsen, Thomas Dyhre

2016-01-01

Mathematically, a Bayesian graphical model is a compact representation of the joint probability distribution for a set of variables. The most frequently used type of Bayesian graphical models are Bayesian networks. The structural part of a Bayesian graphical model is a graph consisting of nodes...

Nuclear spin relaxation due to chemical shift anisotropy of gas-phase 129Xe.

Science.gov (United States)

Hanni, Matti; Lantto, Perttu; Vaara, Juha

2011-08-14

Nuclear spin relaxation provides detailed dynamical information on molecular systems and materials. Here, first-principles modeling of the chemical shift anisotropy (CSA) relaxation time for the prototypic monoatomic (129)Xe gas is carried out, both complementing and predicting the results of NMR measurements. Our approach is based on molecular dynamics simulations combined with pre-parametrized ab initio binary nuclear shielding tensors, an "NMR force field". By using the Redfield relaxation formalism, the simulated CSA time correlation functions lead to spectral density functions that, for the first time, quantitatively determine the experimental spin-lattice relaxation times T(1). The quality requirements on both the Xe-Xe interaction potential and binary shielding tensor are investigated in the context of CSA T(1). Persistent dimers Xe(2) are found to be responsible for the CSA relaxation mechanism in the low-density limit of the gas, completely in line with the earlier experimental findings.

Bayesian artificial intelligence

CERN Document Server

Korb, Kevin B

2003-01-01

As the power of Bayesian techniques has become more fully realized, the field of artificial intelligence has embraced Bayesian methodology and integrated it to the point where an introduction to Bayesian techniques is now a core course in many computer science programs. Unlike other books on the subject, Bayesian Artificial Intelligence keeps mathematical detail to a minimum and covers a broad range of topics. The authors integrate all of Bayesian net technology and learning Bayesian net technology and apply them both to knowledge engineering. They emphasize understanding and intuition but also provide the algorithms and technical background needed for applications. Software, exercises, and solutions are available on the authors' website.

Inverse Bayesian inference as a key of consciousness featuring a macroscopic quantum logical structure.

Science.gov (United States)

Gunji, Yukio-Pegio; Shinohara, Shuji; Haruna, Taichi; Basios, Vasileios

2017-02-01

To overcome the dualism between mind and matter and to implement consciousness in science, a physical entity has to be embedded with a measurement process. Although quantum mechanics have been regarded as a candidate for implementing consciousness, nature at its macroscopic level is inconsistent with quantum mechanics. We propose a measurement-oriented inference system comprising Bayesian and inverse Bayesian inferences. While Bayesian inference contracts probability space, the newly defined inverse one relaxes the space. These two inferences allow an agent to make a decision corresponding to an immediate change in their environment. They generate a particular pattern of joint probability for data and hypotheses, comprising multiple diagonal and noisy matrices. This is expressed as a nondistributive orthomodular lattice equivalent to quantum logic. We also show that an orthomodular lattice can reveal information generated by inverse syllogism as well as the solutions to the frame and symbol-grounding problems. Our model is the first to connect macroscopic cognitive processes with the mathematical structure of quantum mechanics with no additional assumptions. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Lattice Distortion Mediated Paramagnetic Relaxation in High-Spin High-Symmetry Molecular Magnets

Science.gov (United States)

Garg, Anupam

1998-08-01

Field-dependent maxima in the relaxation rate of the magnetic molecules Mn12-Ac and Fe8-tacn have commonly been ascribed to some resonant tunneling phenomena. We argue instead that the relaxation is purely due to phonons. The rate maxima arise because of a Jahn-Teller-like distortion caused by the coupling of phonons to degenerate Zeeman levels of the molecule at the top of the barrier. The binding energy of the distorted intermediate states lowers the barrier height and increases the relaxation rate. A nonperturbative calculation of this effect is carried out for a model system. An approximate result for the field variation near a maximum is found to agree reasonably with experiment.

DPpackage: Bayesian Semi- and Nonparametric Modeling in R

Directory of Open Access Journals (Sweden)

Alejandro Jara

2011-04-01

Full Text Available Data analysis sometimes requires the relaxation of parametric assumptions in order to gain modeling flexibility and robustness against mis-specification of the probability model. In the Bayesian context, this is accomplished by placing a prior distribution on a function space, such as the space of all probability distributions or the space of all regression functions. Unfortunately, posterior distributions ranging over function spaces are highly complex and hence sampling methods play a key role. This paper provides an introduction to a simple, yet comprehensive, set of programs for the implementation of some Bayesian nonparametric and semiparametric models in R, DPpackage. Currently, DPpackage includes models for marginal and conditional density estimation, receiver operating characteristic curve analysis, interval-censored data, binary regression data, item response data, longitudinal and clustered data using generalized linear mixed models, and regression data using generalized additive models. The package also contains functions to compute pseudo-Bayes factors for model comparison and for eliciting the precision parameter of the Dirichlet process prior, and a general purpose Metropolis sampling algorithm. To maximize computational efficiency, the actual sampling for each model is carried out using compiled C, C++ or Fortran code.

Molecular theory for nuclear magnetic relaxation in protein solutions and tissue

International Nuclear Information System (INIS)

Kimmich, R.; Nusser, W.; Gneiting, T.

1990-01-01

A model theory is presented explaining a series of striking phenomena observed with nuclear magnetic relaxation in protein systems such as solutions or tissue. The frequency, concentration and temperature dependences of proton or deuteron relaxation times of protein solutions and tissue are explained. It is concluded that the translational diffusion of water molecules along the rugged surfaces of proteins and, to a minor degree, protein backbone fluctuations are crucial processes. The rate limiting factor of macromolecular tumbling is assumed to be given by the free water content in a certain analogy to the free-volume model of Cohen ad Turnbull. There are two characteristic water mass fractions indicating the saturation of the hydration shells and the onset of protein tumbling. A closed and relatively simple set of relaxation formulas is presented. The potentially fractal nature of the diffusion of water molecules on the protein surface is discussed. (author). 43 refs.; 4 figs

Low-relaxation spin waves in laser-molecular-beam epitaxy grown nanosized yttrium iron garnet films

Energy Technology Data Exchange (ETDEWEB)

Lutsev, L. V., E-mail: l-lutsev@mail.ru; Korovin, A. M.; Bursian, V. E.; Gastev, S. V.; Fedorov, V. V.; Suturin, S. M.; Sokolov, N. S. [Ioffe Physical-Technical Institute, Russian Academy of Sciences, 194021 St. Petersburg (Russian Federation)

2016-05-02

Synthesis of nanosized yttrium iron garnet (Y{sub 3}Fe{sub 5}O{sub 12}, YIG) films followed by the study of ferromagnetic resonance (FMR) and spin wave propagation in these films is reported. The YIG films were grown on gadolinium gallium garnet substrates by laser molecular beam epitaxy. It has been shown that spin waves propagating in YIG deposited at 700 °C have low damping. At the frequency of 3.29 GHz, the spin-wave damping parameter is less than 3.6 × 10{sup −5}. Magnetic inhomogeneities of the YIG films give the main contribution to the FMR linewidth. The contribution of the relaxation processes to the FMR linewidth is as low as 1.2%.

Bayesian Mediation Analysis

OpenAIRE

Yuan, Ying; MacKinnon, David P.

2009-01-01

This article proposes Bayesian analysis of mediation effects. Compared to conventional frequentist mediation analysis, the Bayesian approach has several advantages. First, it allows researchers to incorporate prior information into the mediation analysis, thus potentially improving the efficiency of estimates. Second, under the Bayesian mediation analysis, inference is straightforward and exact, which makes it appealing for studies with small samples. Third, the Bayesian approach is conceptua...

Introduction to Bayesian statistics

CERN Document Server

Bolstad, William M

2017-01-01

There is a strong upsurge in the use of Bayesian methods in applied statistical analysis, yet most introductory statistics texts only present frequentist methods. Bayesian statistics has many important advantages that students should learn about if they are going into fields where statistics will be used. In this Third Edition, four newly-added chapters address topics that reflect the rapid advances in the field of Bayesian staistics. The author continues to provide a Bayesian treatment of introductory statistical topics, such as scientific data gathering, discrete random variables, robust Bayesian methods, and Bayesian approaches to inferenfe cfor discrete random variables, bionomial proprotion, Poisson, normal mean, and simple linear regression. In addition, newly-developing topics in the field are presented in four new chapters: Bayesian inference with unknown mean and variance; Bayesian inference for Multivariate Normal mean vector; Bayesian inference for Multiple Linear RegressionModel; and Computati...

Excited-state relaxation of some aminoquinolines

Directory of Open Access Journals (Sweden)

2006-01-01

Full Text Available The absorption and fluorescence spectra, fluorescence quantum yields and lifetimes, and fluorescence rate constants ( k f of 2-amino-3-( 2 ′ -benzoxazolylquinoline (I, 2-amino-3-( 2 ′ -benzothiazolylquinoline (II, 2-amino-3-( 2 ′ -methoxybenzothiazolyl-quinoline (III, 2-amino-3-( 2 ′ -benzothiazolylbenzoquinoline (IV at different temperatures have been measured. The shortwavelength shift of fluorescence spectra of compounds studied (23–49 nm in ethanol as the temperature decreases (the solvent viscosity increases points out that the excited-state relaxation process takes place. The rate of this process depends essentially on the solvent viscosity, but not the solvent polarity. The essential increasing of fluorescence rate constant k f (up to about 7 times as the solvent viscosity increases proves the existence of excited-state structural relaxation consisting in the mutual internal rotation of molecular fragments of aminoquinolines studied, followed by the solvent orientational relaxation.

The relaxational behaviour of poly-(vinylidene fluoride) before and after gamma-irradiation

International Nuclear Information System (INIS)

Callens, A.

The main purpose of this work was to investigate how molecular chain reorganization may affect the physical property of polymers. This may be done by the analysis of the as received and post-irradiation relaxation spectra of the semi-crystalline linear chain polymer polyvinylidene fluoride (PVDF), which has been gamma-irradiated up to doses of 1 grad. The effects of the irradiation on the material are primarly main chain cross-linking production of unsaturated bonds and crystallite degradation. To reach a complete interpretation of the relaxation spectra, it is necessary to incorporate a third phase into the analysis besides the amorphous viscoelastic region (AVR) and the crystalline viscoelastic region (CVR), the intermediate phase. The amorphous phase (AVR) is at the origin of the relaxation effects occurring in the temperature region below room temperature. The saturation like behaviour of the cross-linking in the amorphous phase is at the origin of the intensity decrease, temperature shift and peak broadening of the beta relaxation. There is a large amount of evidence that in the neighbourhood of the beta relaxation, relaxation effects are created through irradiation, as mainly revealed by TSD-spectra (thermalloy stimulated depolarisation). The intensity of the gamma relaxation, gradually increases with dose, which has been attributed to the production of disordered chain from the debris of radiation enhanced crystallite destruction. The relaxation effect, occuring at the temperatures between AVR and CVR, is assigned to the long amorphous chain segments attached partly to the crystallites, mainly from the consideration of the similarity of the dose enhanced decrease in intensity of both beta and βsub(μ)-effects. The increase with dose of the intensity of the α1 relaxation, which has been classified within CVR, confirms the grainboundary hypothesis. The second component of CVR (α2 relaxation) is due to relaxation effects of molecular chains belonging to the

Relaxation of the magnetization in magnetic molecules

Science.gov (United States)

Carretta, S.; Bianchi, A.; Liviotti, E.; Santini, P.; Amoretti, G.

2006-04-01

Several mechanisms characterize the relaxation dynamics in magnetic molecules. We investigate two of them, spin-lattice coupling and incoherent quantum tunneling. The effect of the phonon heat bath is studied by analyzing the exponential time decay of the autocorrelation of the magnetization. We show that in ferromagnetic (Cu6) and antiferromagnetic (Fe6) molecular rings this decay is characterized by a single characteristic time. At very low temperature, relaxation through incoherent quantum tunneling may occur in nanomagnets such as Fe8 or Ni4. The mixing between levels with different values of the total spin (S mixing) greatly influences this mechanism. In particular, we demonstrate that a fourth-order anisotropy term O44, required to interpret experimental electron paramagnetic resonance and relaxation data in Ni4, naturally arises when S mixing is considered in calculations.

F19 relaxation in non-magnetic hexafluorides

International Nuclear Information System (INIS)

Rigny, P.

1969-01-01

The interesting properties of the fluorine magnetic resonance in the hexafluorides of molybdenum, tungsten and uranium, are very much due to large anisotropies of the chemical shift tensors. In the solid phases these anisotropies, the values of which are deduced from line shape studies, allow one to show that the molecules undergo hindered rotations about the metal atom. The temperature and frequency dependence of the fluorine longitudinal relaxation times shows that the relaxation is due to the molecular motion. The dynamical parameters of this motion are then deduced from the complete study of the fluorine relaxation in the rotating frame. In the liquid phases, the existence of anisotropies allows an estimation of the different contributions to the relaxation. In particular, the frequency and temperature dependence of the relaxation shows it to be dominated by the spin-rotation interaction. We have shown that the strength of this interaction can be deduced from the chemical shifts, and the angle through which the molecule rotates quasi-freely can be determined. In the hexafluorides, this angle is roughly one radian at 70 C, and with the help of this value, the friction coefficients which describe the intermolecular interactions are discussed. (author) [fr

Mixed quantum-classical simulations of the vibrational relaxation of photolyzed carbon monoxide in a hemoprotein

Energy Technology Data Exchange (ETDEWEB)

Schubert, Alexander, E-mail: schubert@irsamc.ups-tlse.fr; Meier, Christoph [Laboratoire Collisions Agrégats et Réactivité, IRSAMC, UMR CNRS 5589, Université Paul Sabatier, 31062 Toulouse (France); Falvo, Cyril [Institut des Sciences Moléculaires d’Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91405 Orsay (France)

2016-08-07

We present mixed quantum-classical simulations on relaxation and dephasing of vibrationally excited carbon monoxide within a protein environment. The methodology is based on a vibrational surface hopping approach treating the vibrational states of CO quantum mechanically, while all remaining degrees of freedom are described by means of classical molecular dynamics. The CO vibrational states form the “surfaces” for the classical trajectories of protein and solvent atoms. In return, environmentally induced non-adiabatic couplings between these states cause transitions describing the vibrational relaxation from first principles. The molecular dynamics simulation yields a detailed atomistic picture of the energy relaxation pathways, taking the molecular structure and dynamics of the protein and its solvent fully into account. Using the ultrafast photolysis of CO in the hemoprotein FixL as an example, we study the relaxation of vibrationally excited CO and evaluate the role of each of the FixL residues forming the heme pocket.

Molecular relaxation behavior and isothermal crystallization above glass transition temperature of amorphous hesperetin.

Science.gov (United States)

Shete, Ganesh; Khomane, Kailas S; Bansal, Arvind Kumar

2014-01-01

The purpose of this paper was to investigate the relaxation behavior of amorphous hesperetin (HRN), using dielectric spectroscopy, and assessment of its crystallization kinetics above glass transition temperature (Tg ). Amorphous HRN exhibited both local (β-) and global (α-) relaxations. β-Relaxation was observed below Tg , whereas α-relaxation prominently emerged above Tg . β-Relaxation was found to be of Johari-Goldstein type and was correlated with α-process by coupling model. Secondly, isothermal crystallization experiments were performed at 363 K (Tg + 16.5 K), 373 K (Tg + 26.5 K), and 383 K (Tg + 36.5 K). The kinetics of crystallization, obtained from the normalized dielectric strength, was modeled using the Avrami model. Havriliak-Negami (HN) shape parameters, αHN and αHN .βHN , were analyzed during the course of crystallization to understand the dynamics of amorphous phase during the emergence of crystallites. HN shape parameters indicated that long range (α-like) were motions affected to a greater extent than short range (β-like) motions during isothermal crystallization studies at all temperature conditions. The variable behavior of α-like motions at different isothermal crystallization temperatures was attributed to evolving crystallites with time and increase in electrical conductivity with temperature. © 2013 Wiley Periodicals, Inc. and the American Pharmacists Association.

Computer Code for Interpreting 13C NMR Relaxation Measurements with Specific Models of Molecular Motion: The Rigid Isotropic and Symmetric Top Rotor Models and the Flexible Symmetric Top Rotor Model

Science.gov (United States)

2017-01-01

top rotor superimposes an effective correlation time, τe, onto a symmetric top rotor to account for internal motion. 2. THEORY The purpose...specifically describe how simple 13C relaxation theory is used to describe quantitatively simple molecular 3 motions. More-detailed accounts ...of nuclear magnetic relaxation can be found in a number of basic textbooks (i.e., Farrar and Becker, 1971; Fukushima and Roeder, 1981; Harris, 1986

Vibrational relaxation and energy transfer of matrix isolated HCl and DCl

Energy Technology Data Exchange (ETDEWEB)

Wiesenfeld, J.M.

1977-12-01

Vibrational kinetic and spectroscopic studies have been performed on matrix-isolated HCl and DCl between 9 and 20 K. Vibrational relaxation rates for v = 2 and v = 1 were measured by a tunable infrared laser-induced, time-resolved fluorescence technique. In an Ar matrix, vibrational decay times are faster than radiative and it is found that HCl relaxes about 35 times more rapidly than CCl, in spite of the fact that HCl must transfer more energy to the lattice than DCl. This result is explained by postulating that the rate-determining step for vibrational relaxation produces a highly rotationally excited guest in a V yield R step; rotational relaxation into lattice phonons follows rapidly. HCl v = 1, but not v = 2, excitation rapidly diffuses through the sample by a resonant dipole-dipole vibrational energy transfer process. Molecular complexes, and in particular the HCl dimer, relax too rapidly for direct observation, less than or approximately 1 ..mu..s, and act as energy sinks in the energy diffusion process. The temperature dependence for all these processes is weak--less than a factor of two between 9 and 20 K. Vibrational relaxation of HCl in N/sub 2/ and O/sub 2/ matrices is unobservable, presumably due to rapid V yield V transfer to the host. A V yield R binary collision model for relaxation in solids is successful in explaining the HCl(DCl)/Ar results as well as results of other experimenters. The model considers relaxation to be the result of ''collisions'' due to molecular motion in quantized lattice normal modes--gas phase potential parameters can fit the matrix kinetic data.

Vibrational relaxation and energy transfer of matrix isolated HCl and DCl

International Nuclear Information System (INIS)

Wiesenfeld, J.M.

1977-12-01

Vibrational kinetic and spectroscopic studies have been performed on matrix-isolated HCl and DCl between 9 and 20 K. Vibrational relaxation rates for v = 2 and v = 1 were measured by a tunable infrared laser-induced, time-resolved fluorescence technique. In an Ar matrix, vibrational decay times are faster than radiative and it is found that HCl relaxes about 35 times more rapidly than CCl, in spite of the fact that HCl must transfer more energy to the lattice than DCl. This result is explained by postulating that the rate-determining step for vibrational relaxation produces a highly rotationally excited guest in a V yield R step; rotational relaxation into lattice phonons follows rapidly. HCl v = 1, but not v = 2, excitation rapidly diffuses through the sample by a resonant dipole-dipole vibrational energy transfer process. Molecular complexes, and in particular the HCl dimer, relax too rapidly for direct observation, less than or approximately 1 μs, and act as energy sinks in the energy diffusion process. The temperature dependence for all these processes is weak--less than a factor of two between 9 and 20 K. Vibrational relaxation of HCl in N 2 and O 2 matrices is unobservable, presumably due to rapid V yield V transfer to the host. A V yield R binary collision model for relaxation in solids is successful in explaining the HCl(DCl)/Ar results as well as results of other experimenters. The model considers relaxation to be the result of ''collisions'' due to molecular motion in quantized lattice normal modes--gas phase potential parameters can fit the matrix kinetic data

Relaxation of coupled nuclear spin systems

International Nuclear Information System (INIS)

Koenigsberger, E.

1985-05-01

The subject of the present work is the relaxation behaviour of scalarly coupled spin-1/2 systems. In the theoretical part the semiclassical Redfield equations are used. Dipolar (D), Chemical Shift Anisotropy (CSA) and Random Field (RF) interactions are considered as relaxation mechanisms. Cross correlations of dipolar interactions of different nuclei pairs and those between the D and the CSA mechanisms are important. The model of anisotropic molecular rotational relaxation and the extreme narrowing approximation are used to obtain the spectral density functions. The longitudinal relaxation data are analyzed into normal modes following Werbelow and Grant. The time evolution of normal modes is derived for the AX system with D-CSA cross terms. In the experimental part the hypothesis of dimerization in the cinnamic acid and the methyl cinnamate - AMX systems with DD cross terms - is corroborated by T 1 -time measurements and a calculation of the diffusion constants. In pentachlorobenzene - an AX system - taking into account of D-CSA cross terms enables the complete determination of movements anosotropy and the determination of the sign of the indirect coupling constant 1 Jsub(CH). (G.Q.)

Molecular motions in sucrose-PVP and sucrose-sorbitol dispersions-II. Implications of annealing on secondary relaxations.

Science.gov (United States)

Bhattacharya, Sisir; Bhardwaj, Sunny P; Suryanarayanan, Raj

2014-10-01

To determine the effect of annealing on the two secondary relaxations in amorphous sucrose and in sucrose solid dispersions. Sucrose was co-lyophilized with either PVP or sorbitol, annealed for different time periods and analyzed by dielectric spectroscopy. In an earlier investigation, we had documented the effect of PVP and sorbitol on the primary and the two secondary relaxations in amorphous sucrose solid dispersions (1). Here we investigated the effect of annealing on local motions, both in amorphous sucrose and in the dispersions. The average relaxation time of the local motion (irrespective of origin) in sucrose, decreased upon annealing. However, the heterogeneity in relaxation time distribution as well as the dielectric strength decreased only for β1- (the slower relaxation) but not for β2-relaxations. The effect of annealing on β2-relaxation times was neutralized by sorbitol while PVP negated the effect of annealing on both β1- and β2-relaxations. An increase in local mobility of sucrose brought about by annealing could be negated with an additive.

Bayesian energy landscape tilting: towards concordant models of molecular ensembles.

Science.gov (United States)

Beauchamp, Kyle A; Pande, Vijay S; Das, Rhiju

2014-03-18

Predicting biological structure has remained challenging for systems such as disordered proteins that take on myriad conformations. Hybrid simulation/experiment strategies have been undermined by difficulties in evaluating errors from computational model inaccuracies and data uncertainties. Building on recent proposals from maximum entropy theory and nonequilibrium thermodynamics, we address these issues through a Bayesian energy landscape tilting (BELT) scheme for computing Bayesian hyperensembles over conformational ensembles. BELT uses Markov chain Monte Carlo to directly sample maximum-entropy conformational ensembles consistent with a set of input experimental observables. To test this framework, we apply BELT to model trialanine, starting from disagreeing simulations with the force fields ff96, ff99, ff99sbnmr-ildn, CHARMM27, and OPLS-AA. BELT incorporation of limited chemical shift and (3)J measurements gives convergent values of the peptide's α, β, and PPII conformational populations in all cases. As a test of predictive power, all five BELT hyperensembles recover set-aside measurements not used in the fitting and report accurate errors, even when starting from highly inaccurate simulations. BELT's principled framework thus enables practical predictions for complex biomolecular systems from discordant simulations and sparse data. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Reconstructing consensus Bayesian network structures with application to learning molecular interaction networks

NARCIS (Netherlands)

Fröhlich, H.; Klau, G.W.

2013-01-01

Bayesian Networks are an established computational approach for data driven network inference. However, experimental data is limited in its availability and corrupted by noise. This leads to an unavoidable uncertainty about the correct network structure. Thus sampling or bootstrap based strategies

Bayesian biostatistics

CERN Document Server

Lesaffre, Emmanuel

2012-01-01

The growth of biostatistics has been phenomenal in recent years and has been marked by considerable technical innovation in both methodology and computational practicality. One area that has experienced significant growth is Bayesian methods. The growing use of Bayesian methodology has taken place partly due to an increasing number of practitioners valuing the Bayesian paradigm as matching that of scientific discovery. In addition, computational advances have allowed for more complex models to be fitted routinely to realistic data sets. Through examples, exercises and a combination of introd

Electron spin relaxation can enhance the performance of a cryptochrome-based magnetic compass sensor

DEFF Research Database (Denmark)

Kattnig, Daniel R; Sowa, Jakub K; Solov'yov, Ilia A

2016-01-01

thaliana cryptochrome 1 were obtained from molecular dynamics (MD) simulations and used to calculate the spin relaxation caused by modulation of the exchange and dipolar interactions. We find that intermediate spin relaxation rates afford substantial enhancements in the sensitivity of the reaction yields....... Here we argue that certain spin relaxation mechanisms can enhance its performance. We focus on the flavin-tryptophan radical pair in cryptochrome, currently the only candidate magnetoreceptor molecule. Correlation functions for fluctuations in the distance between the two radicals in Arabidopsis...... to an Earth-strength magnetic field. Supported by calculations using toy radical pair models, we argue that these enhancements could be consistent with the molecular dynamics and magnetic interactions in avian cryptochromes....

Bayesian data analysis for newcomers.

Science.gov (United States)

Kruschke, John K; Liddell, Torrin M

2018-02-01

This article explains the foundational concepts of Bayesian data analysis using virtually no mathematical notation. Bayesian ideas already match your intuitions from everyday reasoning and from traditional data analysis. Simple examples of Bayesian data analysis are presented that illustrate how the information delivered by a Bayesian analysis can be directly interpreted. Bayesian approaches to null-value assessment are discussed. The article clarifies misconceptions about Bayesian methods that newcomers might have acquired elsewhere. We discuss prior distributions and explain how they are not a liability but an important asset. We discuss the relation of Bayesian data analysis to Bayesian models of mind, and we briefly discuss what methodological problems Bayesian data analysis is not meant to solve. After you have read this article, you should have a clear sense of how Bayesian data analysis works and the sort of information it delivers, and why that information is so intuitive and useful for drawing conclusions from data.

relaxGUI: a new software for fast and simple NMR relaxation data analysis and calculation of ps-ns and μs motion of proteins

International Nuclear Information System (INIS)

Bieri, Michael; D’Auvergne, Edward J.; Gooley, Paul R.

2011-01-01

Investigation of protein dynamics on the ps-ns and μs-ms timeframes provides detailed insight into the mechanisms of enzymes and the binding properties of proteins. Nuclear magnetic resonance (NMR) is an excellent tool for studying protein dynamics at atomic resolution. Analysis of relaxation data using model-free analysis can be a tedious and time consuming process, which requires good knowledge of scripting procedures. The software relaxGUI was developed for fast and simple model-free analysis and is fully integrated into the software package relax. It is written in Python and uses wxPython to build the graphical user interface (GUI) for maximum performance and multi-platform use. This software allows the analysis of NMR relaxation data with ease and the generation of publication quality graphs as well as color coded images of molecular structures. The interface is designed for simple data analysis and management. The software was tested and validated against the command line version of relax.

relaxGUI: a new software for fast and simple NMR relaxation data analysis and calculation of ps-ns and μs motion of proteins.

Science.gov (United States)

Bieri, Michael; d'Auvergne, Edward J; Gooley, Paul R

2011-06-01

Investigation of protein dynamics on the ps-ns and μs-ms timeframes provides detailed insight into the mechanisms of enzymes and the binding properties of proteins. Nuclear magnetic resonance (NMR) is an excellent tool for studying protein dynamics at atomic resolution. Analysis of relaxation data using model-free analysis can be a tedious and time consuming process, which requires good knowledge of scripting procedures. The software relaxGUI was developed for fast and simple model-free analysis and is fully integrated into the software package relax. It is written in Python and uses wxPython to build the graphical user interface (GUI) for maximum performance and multi-platform use. This software allows the analysis of NMR relaxation data with ease and the generation of publication quality graphs as well as color coded images of molecular structures. The interface is designed for simple data analysis and management. The software was tested and validated against the command line version of relax.

Proton NMR relaxivity of blood samples in the presence of some gadolinium and dysprosium compounds

International Nuclear Information System (INIS)

Coroiu, I.; Darabont, Al.; Bogdan, M.

1999-01-01

The use of some new compounds in MRI tissue and blood characterisation based on nuclear spin relaxation time measurements cannot be sustained until the molecular sources of these variations are understood. Tissues and blood are complex molecular systems with complex NMR properties. A better comprehension of the molecular basis of relaxation offers the possibility to predict the changes expected for a given pathology. The purpose of this contribution is to evidence the different relaxation characteristics of some gadolinium and dysprosium compounds in the presence and absence of the blood and to give a possible explanation about the molecular processes that cause occurrence of changes. Some gadolinium and dysprosium compounds such as: Gd-CIT (gadolinium citrate), Dy-DTPA (DTPA-diethylenetriamine pentaacetic acid), iron oxide - gadolinium oxide (or dysprosium oxide)- dextran complexes were prepared. The longitudinal T 1 -1 and transverse T 2 -1 'relaxation rates' measurements have been carried out as a function of molar concentrations. All measurements have been made at room temperature (about 25 deg.C) and the proton Larmor frequency ν o = 90 MHz. The pulsed NMR spectrometer utilised was a commercial Bruker SXP4/100 spectrometer. Transverse relaxation rate measurements have been made using the Carr-Purcell method, while longitudinal relaxation rate measurements using the inversion recovery pulse sequence, 180 angle-τ-90 angle. The accuracy was about 2-3% for the longitudinal relaxation rates and about 5-7% for the transverse relaxation rates. R 1 and R 2 relaxivities, in mM -1 s -1 were determined from the least square determination of the slopes of plots 1/T 1,2 versus compound molar concentration, using at least five independent measurements at several concentrations between 0 and 2 mM. Increased R 2 relaxivity observed for dysprosium compounds in the blood presence can be explained by PRE effect. The largest gain in R 2 relaxivity seems to imply a noncovalent

Non-exponential dynamic relaxation in strongly nonequilibrium nonideal plasmas

International Nuclear Information System (INIS)

Morozov, I V; Norman, G E

2003-01-01

Relaxation of kinetic energy to the equilibrium state is simulated by the molecular dynamics method for nonideal two-component non-degenerate plasmas. Three limiting examples of initial states of strongly nonequilibrium plasma are considered: zero electron velocities, zero ion velocities and zero velocities of both electrons and ions. The initial non-exponential stage, its duration τ nB and subsequent exponential stages of the relaxation process are studied for a wide range of the nonideality parameter and the ion mass

How to practise Bayesian statistics outside the Bayesian church: What philosophy for Bayesian statistical modelling?

NARCIS (Netherlands)

Borsboom, D.; Haig, B.D.

2013-01-01

Unlike most other statistical frameworks, Bayesian statistical inference is wedded to a particular approach in the philosophy of science (see Howson & Urbach, 2006); this approach is called Bayesianism. Rather than being concerned with model fitting, this position in the philosophy of science

Markov state modeling and dynamical coarse-graining via discrete relaxation path sampling.

Science.gov (United States)

Fačkovec, B; Vanden-Eijnden, E; Wales, D J

2015-07-28

A method is derived to coarse-grain the dynamics of complex molecular systems to a Markov jump process (MJP) describing how the system jumps between cells that fully partition its state space. The main inputs are relaxation times for each pair of cells, which are shown to be robust with respect to positioning of the cell boundaries. These relaxation times can be calculated via molecular dynamics simulations performed in each cell separately and are used in an efficient estimator for the rate matrix of the MJP. The method is illustrated through applications to Sinai billiards and a cluster of Lennard-Jones discs.

A Bayesian approach to meta-analysis of plant pathology studies.

Science.gov (United States)

Mila, A L; Ngugi, H K

2011-01-01

Bayesian statistical methods are used for meta-analysis in many disciplines, including medicine, molecular biology, and engineering, but have not yet been applied for quantitative synthesis of plant pathology studies. In this paper, we illustrate the key concepts of Bayesian statistics and outline the differences between Bayesian and classical (frequentist) methods in the way parameters describing population attributes are considered. We then describe a Bayesian approach to meta-analysis and present a plant pathological example based on studies evaluating the efficacy of plant protection products that induce systemic acquired resistance for the management of fire blight of apple. In a simple random-effects model assuming a normal distribution of effect sizes and no prior information (i.e., a noninformative prior), the results of the Bayesian meta-analysis are similar to those obtained with classical methods. Implementing the same model with a Student's t distribution and a noninformative prior for the effect sizes, instead of a normal distribution, yields similar results for all but acibenzolar-S-methyl (Actigard) which was evaluated only in seven studies in this example. Whereas both the classical (P = 0.28) and the Bayesian analysis with a noninformative prior (95% credibility interval [CRI] for the log response ratio: -0.63 to 0.08) indicate a nonsignificant effect for Actigard, specifying a t distribution resulted in a significant, albeit variable, effect for this product (CRI: -0.73 to -0.10). These results confirm the sensitivity of the analytical outcome (i.e., the posterior distribution) to the choice of prior in Bayesian meta-analyses involving a limited number of studies. We review some pertinent literature on more advanced topics, including modeling of among-study heterogeneity, publication bias, analyses involving a limited number of studies, and methods for dealing with missing data, and show how these issues can be approached in a Bayesian framework

A Bayesian network model for predicting aquatic toxicity mode of action using two dimensional theoretical molecular descriptors

Energy Technology Data Exchange (ETDEWEB)

Carriger, John F. [U.S. Environmental Protection Agency, Office of Research and Development, Gulf Ecology Division, Gulf Breeze, FL, 32561 (United States); Martin, Todd M. [U.S. Environmental Protection Agency, Office of Research and Development, Sustainable Technology Division, Cincinnati, OH, 45220 (United States); Barron, Mace G., E-mail: barron.mace@epa.gov [U.S. Environmental Protection Agency, Office of Research and Development, Gulf Ecology Division, Gulf Breeze, FL, 32561 (United States)

2016-11-15

Highlights: • A Bayesian network was developed to classify chemical mode of action (MoA). • The network was based on the aquatic toxicity MoA for over 1000 chemicals. • A Markov blanket algorithm selected a subset of theoretical molecular descriptors. • Sensitivity analyses found influential descriptors for classifying the MoAs. • Overall precision of the Bayesian MoA classification model was 80%. - Abstract: The mode of toxic action (MoA) has been recognized as a key determinant of chemical toxicity, but development of predictive MoA classification models in aquatic toxicology has been limited. We developed a Bayesian network model to classify aquatic toxicity MoA using a recently published dataset containing over one thousand chemicals with MoA assignments for aquatic animal toxicity. Two dimensional theoretical chemical descriptors were generated for each chemical using the Toxicity Estimation Software Tool. The model was developed through augmented Markov blanket discovery from the dataset of 1098 chemicals with the MoA broad classifications as a target node. From cross validation, the overall precision for the model was 80.2%. The best precision was for the AChEI MoA (93.5%) where 257 chemicals out of 275 were correctly classified. Model precision was poorest for the reactivity MoA (48.5%) where 48 out of 99 reactive chemicals were correctly classified. Narcosis represented the largest class within the MoA dataset and had a precision and reliability of 80.0%, reflecting the global precision across all of the MoAs. False negatives for narcosis most often fell into electron transport inhibition, neurotoxicity or reactivity MoAs. False negatives for all other MoAs were most often narcosis. A probabilistic sensitivity analysis was undertaken for each MoA to examine the sensitivity to individual and multiple descriptor findings. The results show that the Markov blanket of a structurally complex dataset can simplify analysis and interpretation by

Bayesian Probability Theory

Science.gov (United States)

von der Linden, Wolfgang; Dose, Volker; von Toussaint, Udo

2014-06-01

Preface; Part I. Introduction: 1. The meaning of probability; 2. Basic definitions; 3. Bayesian inference; 4. Combinatrics; 5. Random walks; 6. Limit theorems; 7. Continuous distributions; 8. The central limit theorem; 9. Poisson processes and waiting times; Part II. Assigning Probabilities: 10. Transformation invariance; 11. Maximum entropy; 12. Qualified maximum entropy; 13. Global smoothness; Part III. Parameter Estimation: 14. Bayesian parameter estimation; 15. Frequentist parameter estimation; 16. The Cramer-Rao inequality; Part IV. Testing Hypotheses: 17. The Bayesian way; 18. The frequentist way; 19. Sampling distributions; 20. Bayesian vs frequentist hypothesis tests; Part V. Real World Applications: 21. Regression; 22. Inconsistent data; 23. Unrecognized signal contributions; 24. Change point problems; 25. Function estimation; 26. Integral equations; 27. Model selection; 28. Bayesian experimental design; Part VI. Probabilistic Numerical Techniques: 29. Numerical integration; 30. Monte Carlo methods; 31. Nested sampling; Appendixes; References; Index.

Molecular potentials and relaxation dynamics

International Nuclear Information System (INIS)

Karo, A.M.

1981-01-01

The use of empirical pseudopotentials, in evaluating interatomic potentials, provides an inexpensive and convenient method for obtaining highly accurate potential curves and permits the modeling of core-valence correlation, and the inclusion of relativistic effects when these are significant. Recent calculations of the X 1 Σ + and a 3 Σ + states of LiH, NaH, KH, RbH, and CsH and the X 2 Σ + states of their anions are discussed. Pseudopotentials, including core polarization terms, have been used to replace the core electrons, and this has been coupled with the development of compact, higly-optimized basis sets for the corresponding one- and two-electron atoms. Comparisons of the neutral potential curves with experiment and other ab initio calculations show good agreement (within 1000 cm -1 over most of the potential curves) with the difference curves being considerably more accurate. In the method of computer molecular dynamics, the force acting on each particle is the resultant of all interactions with other atoms in the neighborhood and is obtained as the derivative of an effective many-body potential. Exploiting the pseudopotential approach, in obtaining the appropriate potentials may be very fruitful in the future. In the molecular dynamics example considered here, the conventional sum-of-pairwise-interatomic-potentials (SPP) approximation is used with the potentials derived either from experimental spectroscopic data or from Hartree-Fock calculations. The problem is the collisional de-excitation of vibrationally excited molecular hydrogen at an Fe surface. The calculations have been carried out for an initial vibrotational state v = 8, J = 1 and a translational temperature corresponding to a gas temperature of 500 0 K. Different angles of approach and different initial random impact points on the surface have been selected. For any given collision with the wall, the molecule may pick up or lose vibrotatonal and translational energy

Methyl group rotation and nuclear relaxation at low temperatures

International Nuclear Information System (INIS)

Zweers, A.E.

1976-01-01

This thesis deals with the proton spin-lattice relaxation of some methyl group compounds at liquid helium temperatures. In these molecular crystals, an energy difference between the ground and first rotational state of the methyl group occurs, the so-called tunnelling splitting, which is of the order of a few degrees Kelvin. This means that the high temperature approximation is inappropriate for the description of the occupation densities of the two lowest rotational levels. A description of the properties of the methyl group in connection with relaxation

Rotational dynamics in supercooled water from nuclear spin relaxation and molecular simulations.

Science.gov (United States)

Qvist, Johan; Mattea, Carlos; Sunde, Erik P; Halle, Bertil

2012-05-28

Structural dynamics in liquid water slow down dramatically in the supercooled regime. To shed further light on the origin of this super-Arrhenius temperature dependence, we report high-precision (17)O and (2)H NMR relaxation data for H(2)O and D(2)O, respectively, down to 37 K below the equilibrium freezing point. With the aid of molecular dynamics (MD) simulations, we provide a detailed analysis of the rotational motions probed by the NMR experiments. The NMR-derived rotational correlation time τ(R) is the integral of a time correlation function (TCF) that, after a subpicosecond librational decay, can be described as a sum of two exponentials. Using a coarse-graining algorithm to map the MD trajectory on a continuous-time random walk (CTRW) in angular space, we show that the slowest TCF component can be attributed to large-angle molecular jumps. The mean jump angle is ∼48° at all temperatures and the waiting time distribution is non-exponential, implying dynamical heterogeneity. We have previously used an analogous CTRW model to analyze quasielastic neutron scattering data from supercooled water. Although the translational and rotational waiting times are of similar magnitude, most translational jumps are not synchronized with a rotational jump of the same molecule. The rotational waiting time has a stronger temperature dependence than the translation one, consistent with the strong increase of the experimentally derived product τ(R) D(T) at low temperatures. The present CTRW jump model is related to, but differs in essential ways from the extended jump model proposed by Laage and co-workers. Our analysis traces the super-Arrhenius temperature dependence of τ(R) to the rotational waiting time. We present arguments against interpreting this temperature dependence in terms of mode-coupling theory or in terms of mixture models of water structure.

Communication: Relaxation-limited electronic currents in extended reservoir simulations

Science.gov (United States)

Gruss, Daniel; Smolyanitsky, Alex; Zwolak, Michael

2017-10-01

Open-system approaches are gaining traction in the simulation of charge transport in nanoscale and molecular electronic devices. In particular, "extended reservoir" simulations, where explicit reservoir degrees of freedom are present, allow for the computation of both real-time and steady-state properties but require relaxation of the extended reservoirs. The strength of this relaxation, γ, influences the conductance, giving rise to a "turnover" behavior analogous to Kramers turnover in chemical reaction rates. We derive explicit, general expressions for the weak and strong relaxation limits. For weak relaxation, the conductance increases linearly with γ and every electronic state of the total explicit system contributes to the electronic current according to its "reduced" weight in the two extended reservoir regions. Essentially, this represents two conductors in series—one at each interface with the implicit reservoirs that provide the relaxation. For strong relaxation, a "dual" expression-one with the same functional form-results, except now proportional to 1/γ and dependent on the system of interest's electronic states, reflecting that the strong relaxation is localizing electrons in the extended reservoirs. Higher order behavior (e.g., γ2 or 1/γ2) can occur when there is a gap in the frequency spectrum. Moreover, inhomogeneity in the frequency spacing can give rise to a pseudo-plateau regime. These findings yield a physically motivated approach to diagnosing numerical simulations and understanding the influence of relaxation, and we examine their occurrence in both simple models and a realistic, fluctuating graphene nanoribbon.

Bayesian methods for data analysis

CERN Document Server

Carlin, Bradley P.

2009-01-01

Approaches for statistical inference Introduction Motivating Vignettes Defining the Approaches The Bayes-Frequentist Controversy Some Basic Bayesian Models The Bayes approach Introduction Prior Distributions Bayesian Inference Hierarchical Modeling Model Assessment Nonparametric Methods Bayesian computation Introduction Asymptotic Methods Noniterative Monte Carlo Methods Markov Chain Monte Carlo Methods Model criticism and selection Bayesian Modeling Bayesian Robustness Model Assessment Bayes Factors via Marginal Density Estimation Bayes Factors

Molecular phylogenetics and historical biogeography of Rhinolophus bats.

Science.gov (United States)

Stoffberg, Samantha; Jacobs, David S; Mackie, Iain J; Matthee, Conrad A

2010-01-01

The phylogenetic relationships within the horseshoe bats (genus Rhinolophus) are poorly resolved, particularly at deeper levels within the tree. We present a better-resolved phylogenetic hypothesis for 30 rhinolophid species based on parsimony and Bayesian analyses of the mitochondrial cytochrome b gene and three nuclear introns (TG, THY and PRKC1). Strong support was found for the existence of two geographic clades within the monophyletic Rhinolophidae: an African group and an Oriental assemblage. The relaxed Bayesian clock method indicated that the two rhinolophid clades diverged approximately 35 million years ago and results from Dispersal Vicariance (DIVA) analysis suggest that the horseshoe bats arose in Asia and subsequently dispersed into Europe and Africa.

Bayesian phylogeography finds its roots.

Directory of Open Access Journals (Sweden)

Philippe Lemey

2009-09-01

Full Text Available As a key factor in endemic and epidemic dynamics, the geographical distribution of viruses has been frequently interpreted in the light of their genetic histories. Unfortunately, inference of historical dispersal or migration patterns of viruses has mainly been restricted to model-free heuristic approaches that provide little insight into the temporal setting of the spatial dynamics. The introduction of probabilistic models of evolution, however, offers unique opportunities to engage in this statistical endeavor. Here we introduce a Bayesian framework for inference, visualization and hypothesis testing of phylogeographic history. By implementing character mapping in a Bayesian software that samples time-scaled phylogenies, we enable the reconstruction of timed viral dispersal patterns while accommodating phylogenetic uncertainty. Standard Markov model inference is extended with a stochastic search variable selection procedure that identifies the parsimonious descriptions of the diffusion process. In addition, we propose priors that can incorporate geographical sampling distributions or characterize alternative hypotheses about the spatial dynamics. To visualize the spatial and temporal information, we summarize inferences using virtual globe software. We describe how Bayesian phylogeography compares with previous parsimony analysis in the investigation of the influenza A H5N1 origin and H5N1 epidemiological linkage among sampling localities. Analysis of rabies in West African dog populations reveals how virus diffusion may enable endemic maintenance through continuous epidemic cycles. From these analyses, we conclude that our phylogeographic framework will make an important asset in molecular epidemiology that can be easily generalized to infer biogeogeography from genetic data for many organisms.

Rotational and translational dynamics and their relation to hydrogen bond lifetimes in an ionic liquid by means of NMR relaxation time experiments and molecular dynamics simulation

Science.gov (United States)

Strate, Anne; Neumann, Jan; Overbeck, Viviane; Bonsa, Anne-Marie; Michalik, Dirk; Paschek, Dietmar; Ludwig, Ralf

2018-05-01

We report a concerted theoretical and experimental effort to determine the reorientational dynamics as well as hydrogen bond lifetimes for the doubly ionic hydrogen bond +OH⋯O- in the ionic liquid (2-hydroxyethyl)trimethylammonium bis(trifluoromethylsulfonyl)imide [Ch][NTf2] by using a combination of NMR relaxation time experiments, density functional theory (DFT) calculations, and molecular dynamics (MD) simulations. Due to fast proton exchange, the determination of rotational correlation times is challenging. For molecular liquids, 17O-enhanced proton relaxation time experiments have been used to determine the rotational correlation times for the OH vectors in water or alcohols. As an alternative to those expensive isotopic substitution experiments, we employed a recently introduced approach which is providing access to the rotational dynamics from a single NMR deuteron quadrupolar relaxation time experiment. Here, the deuteron quadrupole coupling constants (DQCCs) are obtained from a relation between the DQCC and the δ1H proton chemical shifts determined from a set of DFT calculated clusters in combination with experimentally determined proton chemical shifts. The NMR-obtained rotational correlation times were compared to those obtained from MD simulations and then related to viscosities for testing the applicability of popular hydrodynamic models. In addition, hydrogen bond lifetimes were derived, using hydrogen bond population correlation functions computed from MD simulations. Here, two different time domains were observed: The short-time contributions to the hydrogen lifetimes and the reorientational correlation times have roughly the same size and are located in the picosecond range, whereas the long-time contributions decay with relaxation times in the nanosecond regime and are related to rather slow diffusion processes. The computed average hydrogen bond lifetime is dominated by the long-time process, highlighting the importance and longevity of

Bayesian benefits with JASP

NARCIS (Netherlands)

Marsman, M.; Wagenmakers, E.-J.

2017-01-01

We illustrate the Bayesian approach to data analysis using the newly developed statistical software program JASP. With JASP, researchers are able to take advantage of the benefits that the Bayesian framework has to offer in terms of parameter estimation and hypothesis testing. The Bayesian

Bayesian modeling using WinBUGS

CERN Document Server

Ntzoufras, Ioannis

2009-01-01

A hands-on introduction to the principles of Bayesian modeling using WinBUGS Bayesian Modeling Using WinBUGS provides an easily accessible introduction to the use of WinBUGS programming techniques in a variety of Bayesian modeling settings. The author provides an accessible treatment of the topic, offering readers a smooth introduction to the principles of Bayesian modeling with detailed guidance on the practical implementation of key principles. The book begins with a basic introduction to Bayesian inference and the WinBUGS software and goes on to cover key topics, including: Markov Chain Monte Carlo algorithms in Bayesian inference Generalized linear models Bayesian hierarchical models Predictive distribution and model checking Bayesian model and variable evaluation Computational notes and screen captures illustrate the use of both WinBUGS as well as R software to apply the discussed techniques. Exercises at the end of each chapter allow readers to test their understanding of the presented concepts and all ...

Slow molecular dynamics in the β relaxation of semicrystalline polymers studied by pure exchange 13C solid state NMR

International Nuclear Information System (INIS)

Azevedo, Eduardo R. de; Becker-Guedes, Fabio; Bonagamba, Tito J.; Schmidt-Rohr, Klaus; Iowa State University, Ames, IA

2001-01-01

The dynamics in the amorphous regions of semicrystalline polymers exert important influences on mechanical properties, but have been notoriously difficult to characterize. Two new solid-state NMR techniques, PUREX (pure exchange) and CODEX (center band-only detection of exchange) NMR, make it possible to analyze the molecular motions near the glass transition in the amorphous regions of semicrystalline polymers. This is achieved by selectively suppressing the otherwise dominant signals of the static segments in the crystallites. We have applied both NMR techniques to study the slow motions near the glass transition in semicrystalline polymers (β relaxation) and in fully amorphous samples for reference. The studied polymers were isotactic poly(1-butene) (iPB1) (form I), syndiotactic and atactic polypropylenes (sPP, and aPP, respectively), as well as polyisobutylene (PIB). We have analyzed the geometry and time scale of the slow molecular motion for all samples and determined the apparent activation energies. (author)

Tuning the effective spin-orbit coupling in molecular semiconductors

KAUST Repository

Schott, Sam

2017-05-11

The control of spins and spin to charge conversion in organics requires understanding the molecular spin-orbit coupling (SOC), and a means to tune its strength. However, quantifying SOC strengths indirectly through spin relaxation effects has proven difficult due to competing relaxation mechanisms. Here we present a systematic study of the g-tensor shift in molecular semiconductors and link it directly to the SOC strength in a series of high-mobility molecular semiconductors with strong potential for future devices. The results demonstrate a rich variability of the molecular g-shifts with the effective SOC, depending on subtle aspects of molecular composition and structure. We correlate the above g-shifts to spin-lattice relaxation times over four orders of magnitude, from 200 to 0.15 μs, for isolated molecules in solution and relate our findings for isolated molecules in solution to the spin relaxation mechanisms that are likely to be relevant in solid state systems.

Tuning the effective spin-orbit coupling in molecular semiconductors

KAUST Repository

Schott, Sam; McNellis, Erik R.; Nielsen, Christian B.; Chen, Hung-Yang; Watanabe, Shun; Tanaka, Hisaaki; McCulloch, Iain; Takimiya, Kazuo; Sinova, Jairo; Sirringhaus, Henning

2017-01-01

The control of spins and spin to charge conversion in organics requires understanding the molecular spin-orbit coupling (SOC), and a means to tune its strength. However, quantifying SOC strengths indirectly through spin relaxation effects has proven difficult due to competing relaxation mechanisms. Here we present a systematic study of the g-tensor shift in molecular semiconductors and link it directly to the SOC strength in a series of high-mobility molecular semiconductors with strong potential for future devices. The results demonstrate a rich variability of the molecular g-shifts with the effective SOC, depending on subtle aspects of molecular composition and structure. We correlate the above g-shifts to spin-lattice relaxation times over four orders of magnitude, from 200 to 0.15 μs, for isolated molecules in solution and relate our findings for isolated molecules in solution to the spin relaxation mechanisms that are likely to be relevant in solid state systems.

Bayesian approach to inverse statistical mechanics

Science.gov (United States)

Habeck, Michael

2014-05-01

Inverse statistical mechanics aims to determine particle interactions from ensemble properties. This article looks at this inverse problem from a Bayesian perspective and discusses several statistical estimators to solve it. In addition, a sequential Monte Carlo algorithm is proposed that draws the interaction parameters from their posterior probability distribution. The posterior probability involves an intractable partition function that is estimated along with the interactions. The method is illustrated for inverse problems of varying complexity, including the estimation of a temperature, the inverse Ising problem, maximum entropy fitting, and the reconstruction of molecular interaction potentials.

Bayesian optimization for materials science

CERN Document Server

Packwood, Daniel

2017-01-01

This book provides a short and concise introduction to Bayesian optimization specifically for experimental and computational materials scientists. After explaining the basic idea behind Bayesian optimization and some applications to materials science in Chapter 1, the mathematical theory of Bayesian optimization is outlined in Chapter 2. Finally, Chapter 3 discusses an application of Bayesian optimization to a complicated structure optimization problem in computational surface science. Bayesian optimization is a promising global optimization technique that originates in the field of machine learning and is starting to gain attention in materials science. For the purpose of materials design, Bayesian optimization can be used to predict new materials with novel properties without extensive screening of candidate materials. For the purpose of computational materials science, Bayesian optimization can be incorporated into first-principles calculations to perform efficient, global structure optimizations. While re...

From beta-relaxation to alpha-decay: Atomistic picture from molecular dynamics simulations for glass-forming Ni0.5Zr0.5 melt

Energy Technology Data Exchange (ETDEWEB)

Teichler, Helmar [Inst. Materialphysik, Univ Goettingen (Germany)

2013-07-01

In glass-forming melts the decay of structural fluctuation shows the well known transition from beta-relaxation (von-Schweidler law with exponent b) to alpha-decay (KWW law with exponent beta). Here we present results from molecular dynamics simulations for a metallic glass forming Ni0.5Zr0.5 model aimed at giving an understanding of this transition on the atomistic scale. At the considered temperature below mode coupling Tc, the dynamics of the system can be interpreted by residence of the particles in their neighbour cages and escape from the cages as rare processes. Our analysis yields that the fraction of residing particles is characterized by a hierarchical law in time, with von-Schweidler b explicitly related to the exponent of this law. In the alpha-decay regime the stretching exponent reflects, in addition, floating of the cages due to strain effects of escaped particles. Accordingly, the change from beta-relaxation to alpha-decay indicates the transition from low to large fraction of escaped particles.

Collective dynamic dipole moment and orientation fluctuations, cooperative hydrogen bond relaxations, and their connections to dielectric relaxation in ionic acetamide deep eutectics: Microscopic insight from simulations

Energy Technology Data Exchange (ETDEWEB)

Das, Suman [Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata 700098 (India); Biswas, Ranjit, E-mail: ranjit@bose.res.in, E-mail: biswaroop.mukherjee@gmail.com [Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata 700098 (India); Thematic Unit for Excellence – Computational Materials Science, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata 700098 (India); Mukherjee, Biswaroop, E-mail: ranjit@bose.res.in, E-mail: biswaroop.mukherjee@gmail.com [Thematic Unit for Excellence – Computational Materials Science, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata 700098 (India)

2016-08-28

The paper reports a detailed simulation study on collective reorientational relaxation, cooperative hydrogen bond (H-bond) fluctuations, and their connections to dielectric relaxation (DR) in deep eutectic solvents made of acetamide and three uni-univalent electrolytes, lithium nitrate (LiNO{sub 3}), lithium bromide (LiBr), and lithium perchlorate (LiClO{sub 4}). Because cooperative H-bond fluctuations and ion migration complicate the straightforward interpretation of measured DR timescales in terms of molecular dipolar rotations for these conducting media which support extensive intra- and inter-species H-bonding, one needs to separate out the individual components from the overall relaxation for examining the microscopic origin of various timescales. The present study does so and finds that reorientation of ion-complexed acetamide molecules generates relaxation timescales that are in sub-nanosecond to nanosecond range. This explains in molecular terms the nanosecond timescales reported by recent giga-Hertz DR measurements. Interestingly, the simulated survival timescale for the acetamide-Li{sup +} complex has been found to be a few tens of nanosecond, suggesting such a cation-complexed species may be responsible for a similar timescale reported by mega-Hertz DR measurements of acetamide/potassium thiocyanate deep eutectics near room temperature. The issue of collective versus single particle relaxation is discussed, and jump waiting time distributions are determined. Dependence on anion-identity in each of the cases has been examined. In short, the present study demonstrates that assumption of nano-sized domain formation is not required for explaining the DR detected nanosecond and longer timescales in these media.

Nuclear quadrupole relaxation and viscosity in liquid metals

International Nuclear Information System (INIS)

Schirmacher, W.

1976-01-01

It is shown that the nuclear quadrupole relaxation rate due to the molecular motions in liquid metals is related to the shear and bulk viscosity and hence to the absorption coefficient of ultrasound. Application of the 'extended liquid phonon' model of Ortoleva and Nelkin - which is the third of a series of continued-fraction-approximations for the van Hove neutron scattering function - gives a relation to the self diffusion constant. The predictions of the theory concerning the temperature dependence are compared with quadrupole relaxation measurements of Riegel et al. and Kerlin et al. in liquid gallium. Agreement is found only with the data of Riegel et al. (orig.) [de

Understanding Computational Bayesian Statistics

CERN Document Server

Bolstad, William M

2011-01-01

A hands-on introduction to computational statistics from a Bayesian point of view Providing a solid grounding in statistics while uniquely covering the topics from a Bayesian perspective, Understanding Computational Bayesian Statistics successfully guides readers through this new, cutting-edge approach. With its hands-on treatment of the topic, the book shows how samples can be drawn from the posterior distribution when the formula giving its shape is all that is known, and how Bayesian inferences can be based on these samples from the posterior. These ideas are illustrated on common statistic

Bayesian statistics an introduction

CERN Document Server

Lee, Peter M

2012-01-01

Bayesian Statistics is the school of thought that combines prior beliefs with the likelihood of a hypothesis to arrive at posterior beliefs. The first edition of Peter Lee’s book appeared in 1989, but the subject has moved ever onwards, with increasing emphasis on Monte Carlo based techniques. This new fourth edition looks at recent techniques such as variational methods, Bayesian importance sampling, approximate Bayesian computation and Reversible Jump Markov Chain Monte Carlo (RJMCMC), providing a concise account of the way in which the Bayesian approach to statistics develops as wel

Variational formulation of relaxed and multi-region relaxed magnetohydrodynamics

Science.gov (United States)

Dewar, R. L.; Yoshida, Z.; Bhattacharjee, A.; Hudson, S. R.

2015-12-01

> Ideal magnetohydrodynamics (IMHD) is strongly constrained by an infinite number of microscopic constraints expressing mass, entropy and magnetic flux conservation in each infinitesimal fluid element, the latter preventing magnetic reconnection. By contrast, in the Taylor relaxation model for formation of macroscopically self-organized plasma equilibrium states, all these constraints are relaxed save for the global magnetic fluxes and helicity. A Lagrangian variational principle is presented that leads to a new, fully dynamical, relaxed magnetohydrodynamics (RxMHD), such that all static solutions are Taylor states but also allows state with flow. By postulating that some long-lived macroscopic current sheets can act as barriers to relaxation, separating the plasma into multiple relaxation regions, a further generalization, multi-region relaxed magnetohydrodynamics (MRxMHD) is developed.

Bayesian networks with examples in R

CERN Document Server

Scutari, Marco

2014-01-01

Introduction. The Discrete Case: Multinomial Bayesian Networks. The Continuous Case: Gaussian Bayesian Networks. More Complex Cases. Theory and Algorithms for Bayesian Networks. Real-World Applications of Bayesian Networks. Appendices. Bibliography.

Dielectric and mechanical relaxation in isooctylcyanobiphenyl (8*OCB)

Energy Technology Data Exchange (ETDEWEB)

Pawlus, S; Mierzwa, M; Paluch, M; Rzoska, S J [Institute of Physics, University of Silesia, Uniwersytecka 4, 40-007 Katowice (Poland); Roland, C M, E-mail: michal.mierzwa@us.edu.p [Chemistry Division, Naval Research Laboratory, Code 6120, Washington, DC 20375-5342 (United States)

2010-06-16

The dynamics of isooctylcyanobiphenyl (8*OCB) was characterized using dielectric and mechanical spectroscopies. This isomer of the liquid crystalline octylcyanobiphenyl (8OCB) vitrifies during cooling or on application of pressure, exhibiting the typical features of glass-forming liquids: non-Debye relaxation function, non-Arrhenius temperature dependence of the relaxation times, {tau}{sub {alpha}}, a dynamic crossover at T {approx} 1.6T{sub g}. This crossover is evidenced by changes in the behavior of both the peak shape and the temperature dependence of {tau}{sub {alpha}}. The primary relaxation time at the crossover, 2 ns at ambient pressure, is the smallest value reported to date for any molecular liquid or polymer. Interestingly, at all temperatures below this crossover, {tau}{sub {alpha}}and the dc conductivity remain coupled (i.e., conform to the Debye-Stokes-Einstein relation). Two secondary relaxations are observed in the glassy state, one of which is identified as the Johari-Goldstein process. Unlike the case for 8OCB, no liquid crystalline phase could be attained for 8*OCB, demonstrating that relatively small differences in chemical structure can effect substantial changes in the intermolecular potential.

Acrolein relaxes mouse isolated tracheal smooth muscle via a TRPA1-dependent mechanism.

Science.gov (United States)

Cheah, Esther Y; Burcham, Philip C; Mann, Tracy S; Henry, Peter J

2014-05-01

Airway sensory C-fibres express TRPA1 channels which have recently been identified as a key chemosensory receptor for acrolein, a toxic and highly prevalent component of smoke. TRPA1 likely plays an intermediary role in eliciting a range of effects induced by acrolein including cough and neurogenic inflammation. Currently, it is not known whether acrolein-induced activation of TRPA1 produces other airway effects including relaxation of mouse airway smooth muscle. The aims of this study were to examine the effects of acrolein on airway smooth muscle tone in mouse isolated trachea, and to characterise the cellular and molecular mechanisms underpinning the effects of acrolein. Isometric tension recording studies were conducted on mouse isolated tracheal segments to characterise acrolein-induced relaxation responses. Release of the relaxant PGE₂ was measured by EIA to examine its role in the response. Use of selective antagonists/inhibitors permitted pharmacological characterisation of the molecular and cellular mechanisms underlying this relaxation response. Acrolein induced dose-dependent relaxation responses in mouse isolated tracheal segments. Importantly, these relaxation responses were significantly inhibited by the TRPA1 antagonists AP-18 and HC-030031, an NK₁ receptor antagonist RP-67580, and the EP₂ receptor antagonist PF-04418948, whilst completely abolished by the non-selective COX inhibitor indomethacin. Acrolein also caused rapid PGE₂ release which was suppressed by HC-030031. In summary, acrolein induced a novel bronchodilator response in mouse airways. Pharmacologic studies indicate that acrolein-induced relaxation likely involves interplay between TRPA1-expressing airway sensory C-fibres, NK₁ receptor-expressing epithelial cells, and EP₂-receptor expressing airway smooth muscle cells. Copyright © 2014 Elsevier Inc. All rights reserved.

A Bayesian perspective on Markovian dynamics and the fluctuation theorem

Science.gov (United States)

Virgo, Nathaniel

2013-08-01

One of E. T. Jaynes' most important achievements was to derive statistical mechanics from the maximum entropy (MaxEnt) method. I re-examine a relatively new result in statistical mechanics, the Evans-Searles fluctuation theorem, from a MaxEnt perspective. This is done in the belief that interpreting such results in Bayesian terms will lead to new advances in statistical physics. The version of the fluctuation theorem that I will discuss applies to discrete, stochastic systems that begin in a non-equilibrium state and relax toward equilibrium. I will show that for such systems the fluctuation theorem can be seen as a consequence of the fact that the equilibrium distribution must obey the property of detailed balance. Although the principle of detailed balance applies only to equilibrium ensembles, it puts constraints on the form of non-equilibrium trajectories. This will be made clear by taking a novel kind of Bayesian perspective, in which the equilibrium distribution is seen as a prior over the system's set of possible trajectories. Non-equilibrium ensembles are calculated from this prior using Bayes' theorem, with the initial conditions playing the role of the data. I will also comment on the implications of this perspective for the question of how to derive the second law.

Nuclear magnetic relaxation induced by exchange-mediated orientational randomization: longitudinal relaxation dispersion for spin I = 1.

Science.gov (United States)

Nilsson, Tomas; Halle, Bertil

2012-08-07

The frequency dependence of the longitudinal relaxation rate, known as the magnetic relaxation dispersion (MRD), can provide a frequency-resolved characterization of molecular motions in complex biological and colloidal systems on time scales ranging from 1 ns to 100 μs. The conformational dynamics of immobilized proteins and other biopolymers can thus be probed in vitro or in vivo by exploiting internal water molecules or labile hydrogens that exchange with a dominant bulk water pool. Numerous water (1)H and (2)H MRD studies of such systems have been reported, but the widely different theoretical models currently used to analyze the MRD data have resulted in divergent views of the underlying molecular motions. We have argued that the essential mechanism responsible for the main dispersion is the exchange-mediated orientational randomization (EMOR) of anisotropic nuclear (electric quadrupole or magnetic dipole) couplings when internal water molecules or labile hydrogens escape from orientationally confining macromolecular sites. In the EMOR model, the exchange process is thus not just a means of mixing spin populations but it is also the direct cause of spin relaxation. Although the EMOR theory has been used in several studies to analyze water (2)H MRD data from immobilized biopolymers, the fully developed theory has not been described. Here, we present a comprehensive account of a generalized version of the EMOR theory for spin I = 1 nuclides like (2)H. As compared to a previously described version of the EMOR theory, the present version incorporates three generalizations that are all essential in applications to experimental data: (i) a biaxial (residual) electric field gradient tensor, (ii) direct and indirect effects of internal motions, and (iii) multiple sites with different exchange rates. In addition, we describe and assess different approximations to the exact EMOR theory that are useful in various regimes. In particular, we consider the experimentally

A comparison of methods for calculating NMR cross-relaxation rates (NOESY and ROESY intensities) in small peptides

NARCIS (Netherlands)

Feenstra, K Anton; Peter, Christine; Scheek, Ruud M; van Gunsteren, Wilfred F; Mark, Alan E

Three methods for calculating nuclear magnetic resonance cross-relaxation rates from molecular dynamics simulations of small flexible molecules have been compared in terms of their ability to reproduce relaxation data obtained experimentally and to produce consistent descriptions of the system. The

Mechanisms of relaxation and spin decoherence in nanomagnets

Science.gov (United States)

van Tol, Johan

Relaxation in spin systems is of great interest with respect to various possible applications like quantum information processing and storage, spintronics, and dynamic nuclear polarization (DNP). The implementation of high frequencies and fields is crucial in the study of systems with large zero-field splitting or large interactions, as for example molecular magnets and low dimensional magnetic materials. Here we will focus on the implementation of pulsed Electron Paramagnetic Resonance (ERP) at multiple frequencies of 10, 95, 120, 240, and 336 GHz, and the relaxation and decoherence processes as a function of magnetic field and temperature. Firstly, at higher frequencies the direct single-phonon spin-lattice relaxation (SLR) is considerably enhanced, and will more often than not be the dominant relaxation mechanism at low temperatures, and can be much faster than at lower fields and frequencies. In principle the measurement of the SLR rates as a function of the frequency provides a means to map the phonon density of states. Secondly, the high electron spin polarization at high fields has a strong influence on the spin fluctuations in relatively concentrated spin systems, and the contribution of the electron-electron dipolar interactions to the coherence rate can be partially quenched at low temperatures. This not only allows the study of relatively concentrated spin systems by pulsed EPR (as for example magnetic nanoparticles and molecular magnets), it enables the separation of the contribution of the fluctuations of the electron spin system from other decoherence mechanisms. Besides choice of temperature and field, several strategies in sample design, pulse sequences, or clock transitions can be employed to extend the coherence time in nanomagnets. A review will be given of the decoherence mechanisms with an attempt at a quantitative comparison of experimental rates with theory.

Vibrational relaxation in liquids: Comparisons between gas phase and liquid phase theories

International Nuclear Information System (INIS)

Russell, D.J.

1990-12-01

The vibrational relaxation of iodine in liquid xenon was studied to understand what processes are important in determining the density dependence of the vibrational relaxation. This examination will be accomplished by taking simple models and comparing the results to both experimental outcomes and the predictions of molecular dynamics simulations. The vibration relaxation of iodine is extremely sensitive to the iodine potential. The anharmonicity of iodine causes vibrational relaxation to be much faster at the top of the iodine well compared to the vibrational relaxation at the bottom. A number of models are used in order to test the ability of the Isolated Binary Collision theory's ability to predict the density dependence of the vibrational relaxation of iodine in liquid xenon. The models tested vary from the simplest incorporating only the fact that the solvent occupies volume to models that incorporate the short range structure of the liquid in the radial distribution function. None of the models tested do a good job of predicting the actual relaxation rate for a given density. This may be due to a possible error in the choice of potentials to model the system

An Adaptively Accelerated Bayesian Deblurring Method with Entropy Prior

Directory of Open Access Journals (Sweden)

Yong-Hoon Kim

2008-05-01

Full Text Available The development of an efficient adaptively accelerated iterative deblurring algorithm based on Bayesian statistical concept has been reported. Entropy of an image has been used as a “prior” distribution and instead of additive form, used in conventional acceleration methods an exponent form of relaxation constant has been used for acceleration. Thus the proposed method is called hereafter as adaptively accelerated maximum a posteriori with entropy prior (AAMAPE. Based on empirical observations in different experiments, the exponent is computed adaptively using first-order derivatives of the deblurred image from previous two iterations. This exponent improves speed of the AAMAPE method in early stages and ensures stability at later stages of iteration. In AAMAPE method, we also consider the constraint of the nonnegativity and flux conservation. The paper discusses the fundamental idea of the Bayesian image deblurring with the use of entropy as prior, and the analytical analysis of superresolution and the noise amplification characteristics of the proposed method. The experimental results show that the proposed AAMAPE method gives lower RMSE and higher SNR in 44% lesser iterations as compared to nonaccelerated maximum a posteriori with entropy prior (MAPE method. Moreover, AAMAPE followed by wavelet wiener filtering gives better result than the state-of-the-art methods.

Bayesian Mediation Analysis

Science.gov (United States)

Yuan, Ying; MacKinnon, David P.

2009-01-01

In this article, we propose Bayesian analysis of mediation effects. Compared with conventional frequentist mediation analysis, the Bayesian approach has several advantages. First, it allows researchers to incorporate prior information into the mediation analysis, thus potentially improving the efficiency of estimates. Second, under the Bayesian…

Novel spin dynamics in ferrimagnetic molecular chains from 1H NMR and μSR spin-lattice relaxation measurements

International Nuclear Information System (INIS)

Micotti, E.; Lascialfari, A.; Rigamonti, A.; Aldrovandi, S.; Caneschi, A.; Gatteschi, D.; Bogani, L.

2004-01-01

The spin dynamics in the helical chain Co(hfac) 2 NITPhOMe has been investigated by 1 H NMR and μSR relaxation. In the temperature range 15< T<60 K, the results are consistent with the relaxation of the homogeneous magnetization. For T≤15 K, NMR and μSR evidence a second spin relaxation mechanism, undetected by the magnetization measurements. From the analysis of these data, insights on this novel relaxation process are derived

Novel spin dynamics in ferrimagnetic molecular chains from 1H NMR and μSR spin-lattice relaxation measurements

Science.gov (United States)

Micotti, E.; Lascialfari, A.; Rigamonti, A.; Aldrovandi, S.; Caneschi, A.; Gatteschi, D.; Bogani, L.

2004-05-01

The spin dynamics in the helical chain Co(hfac) 2NITPhOMe has been investigated by 1H NMR and μSR relaxation. In the temperature range 15relaxation of the homogeneous magnetization. For T⩽15 K, NMR and μSR evidence a second spin relaxation mechanism, undetected by the magnetization measurements. From the analysis of these data, insights on this novel relaxation process are derived.

Bayesian Inference on Gravitational Waves

Directory of Open Access Journals (Sweden)

Asad Ali

2015-12-01

Full Text Available The Bayesian approach is increasingly becoming popular among the astrophysics data analysis communities. However, the Pakistan statistics communities are unaware of this fertile interaction between the two disciplines. Bayesian methods have been in use to address astronomical problems since the very birth of the Bayes probability in eighteenth century. Today the Bayesian methods for the detection and parameter estimation of gravitational waves have solid theoretical grounds with a strong promise for the realistic applications. This article aims to introduce the Pakistan statistics communities to the applications of Bayesian Monte Carlo methods in the analysis of gravitational wave data with an  overview of the Bayesian signal detection and estimation methods and demonstration by a couple of simplified examples.

A model for the generic alpha relaxation in viscous liquids

DEFF Research Database (Denmark)

Dyre, Jeppe

2005-01-01

Dielectric measurements on molecular liquids just above the glass transition indicate that alpha relaxation is characterized by a generic high-frequency loss varying as one over square root of frequency, whereas deviations from this come from one or more low-lying beta processes [Olsen et al., Phys...

Paramagnetic relaxation effects in perturbed angular correlations for arbitrary electronic relaxation time

International Nuclear Information System (INIS)

Chopin, C.; Spanjaard, D.; Hartmann-Boutron, F.

1975-01-01

Previous perturbation treatments of paramagnetic relaxation effects in γγ PAC were limited to the case of very short electronic relaxation times. This limitation is circumvented by invoking a new perturbation theory recently elaborated by Hirst and others for handling relaxation effects in Moessbauer spectra. Under the assumption of spherical electronic relaxation the perturbation factors are computed as functions of certain relaxation parameters which are directly related to the microscopic relaxation Hamiltonian. The results are compared to those of the stochastic theory of Scherer and Blume [fr

Atomistic simulation of processes in Ni-base alloys with account for local relaxations

International Nuclear Information System (INIS)

Bursik, Jiri

2007-01-01

Ordering in Ni-base superalloys is the crucial process controlling the development of the characteristic two-phase microstructure and subsequently the mechanical properties. Systems containing up to six alloying elements typical of advanced Ni-based superalloys are modelled in this work using a Monte Carlo approach with phenomenological Lennard-Jones pair potentials and interactions up to the third coordination sphere. Three-dimensional crystal block is used with over 10 5 atoms. Molecular dynamics approach is used to relax local atomic positions in course of ordering processes under applied stress. The importance of taking into account both relaxation of modelled block dimensions and relaxation of local atomic positions is discussed

Self-motion and the α-relaxation in glass-forming polymers. Molecular dynamic simulation and quasielastic neutron scattering results in polyisoprene

International Nuclear Information System (INIS)

Colmenero, Juan; Arbe, Arantxa; Alvarez, Fernando; Monkenbusch, Michael; Richter, Dieter; Farago, Bela; Frick, Bernhard

2003-01-01

The momentum transfer dependence of the self-motion of main chain hydrogens in the α-relaxation regime of a glass forming polymer, polyisoprene, has been thoroughly investigated by a combined effort involving fully atomistic molecular dynamic simulations and quasielastic neutron scattering measurements. In this way, we have established the existence of a crossover from a Gaussian regime of sublinear diffusion to a strongly non-Gaussian regime at short distances. We show that an anomalous jump diffusion model with a distribution of jump lengths gives rise to such a crossover. This model leads to a time-dependent non-Gaussian parameter exhibiting all features revealed so far from various simulations of different glass forming systems

Bayesian Option Pricing Framework with Stochastic Volatility for FX Data

Directory of Open Access Journals (Sweden)

Ying Wang

2016-12-01

Full Text Available The application of stochastic volatility (SV models in the option pricing literature usually assumes that the market has sufficient option data to calibrate the model’s risk-neutral parameters. When option data are insufficient or unavailable, market practitioners must estimate the model from the historical returns of the underlying asset and then transform the resulting model into its risk-neutral equivalent. However, the likelihood function of an SV model can only be expressed in a high-dimensional integration, which makes the estimation a highly challenging task. The Bayesian approach has been the classical way to estimate SV models under the data-generating (physical probability measure, but the transformation from the estimated physical dynamic into its risk-neutral counterpart has not been addressed. Inspired by the generalized autoregressive conditional heteroskedasticity (GARCH option pricing approach by Duan in 1995, we propose an SV model that enables us to simultaneously and conveniently perform Bayesian inference and transformation into risk-neutral dynamics. Our model relaxes the normality assumption on innovations of both return and volatility processes, and our empirical study shows that the estimated option prices generate realistic implied volatility smile shapes. In addition, the volatility premium is almost flat across strike prices, so adding a few option data to the historical time series of the underlying asset can greatly improve the estimation of option prices.

Modern problems of relaxation gas dynamics

International Nuclear Information System (INIS)

Losev, S.A.; Osipov, A.I.

1985-01-01

Some of the dynamical characteristics of relaxation processes are studied. Unfortunately, many dynamical characteristics of relaxation processes, necessary for the solution of important scientific and applied problems, are not known. These problems require further development of experimental methods of the study of nonequilibrium gas. It is known, that gas systems are shifted from the equilibrium by different methods: by acoustic and shock wav es, by means of gas expansion in nozzles and jets, by powerful radiations (laser, first of all), by electric discharges, in burning and combustion devices, etc. Non-equilibrium gas is produced in installations of continuum, impulse and periodic regime. Molecular beams, shock tubes (especially with nozzles), flow and jet installations, aerodynamical tubes, plasmatrons, vessels with a gas, influenced by the strong radiation, burners and combustion devices, where the study of non-euilibrium gas is helpful to solve the problems of the determination of kinetic equations and constants of physico-chemical kinetics

Linear rheology and structure of molecular bottlebrushes with short side chains

International Nuclear Information System (INIS)

López-Barrón, Carlos R.; Brant, Patrick; Crowther, Donna J.; Eberle, Aaron P. R.

2015-01-01

We investigate the microstructure and linear viscoelasticity of model molecular bottlebrushes (BBs) using rheological and small-angle X-ray and neutron scattering measurements. Our polymers have short atactic polypropylene (aPP) side chains of molecular weight ranging from 119 g/mol to 259 g/mol and narrow molecular weight distribution (M w /M n 1.02–1.05). The side chain molecular weights are a small fraction of the entanglement molecular weight of the corresponding linear polymer (M e,aPP = 7.05 kg/mol), and as such, they are unentangled. The morphology of the aPP BBs is characterized as semiflexible thick chains with small side chain interdigitation. Their dynamic master curves, obtained by time-temperature superposition, reveal two sequential relaxation processes corresponding to the segmental relaxation and the relaxation of the BB backbone. Due to the short length of the side chains, their fast relaxation could not be distinguished from the glassy relaxation. The fractional free volume is an increasing function of the side chain length (N SC ). Therefore, the glassy behavior of these polymers as well as their molecular friction and dynamic properties are influenced by their N SC values. The apparent flow activation energies are a decreasing function of N SC , and their values explain the differences in zero-shear viscosity measured at different temperatures

On the Informativeness of Dominant and Co-Dominant Genetic Markers for Bayesian Supervised Clustering

DEFF Research Database (Denmark)

Guillot, Gilles; Carpentier-Skandalis, Alexandra

2011-01-01

We study the accuracy of a Bayesian supervised method used to cluster individuals into genetically homogeneous groups on the basis of dominant or codominant molecular markers. We provide a formula relating an error criterion to the number of loci used and the number of clusters. This formula...

Nuclear magnetic relaxation by the dipolar EMOR mechanism: Multi-spin systems

Science.gov (United States)

Chang, Zhiwei; Halle, Bertil

2017-08-01

In aqueous systems with immobilized macromolecules, including biological tissues, the longitudinal spin relaxation of water protons is primarily induced by exchange-mediated orientational randomization (EMOR) of intra- and intermolecular magnetic dipole-dipole couplings. Starting from the stochastic Liouville equation, we have previously developed a rigorous EMOR relaxation theory for dipole-coupled two-spin and three-spin systems. Here, we extend the stochastic Liouville theory to four-spin systems and use these exact results as a guide for constructing an approximate multi-spin theory, valid for spin systems of arbitrary size. This so-called generalized stochastic Redfield equation (GSRE) theory includes the effects of longitudinal-transverse cross-mode relaxation, which gives rise to an inverted step in the relaxation dispersion profile, and coherent spin mode transfer among solid-like spins, which may be regarded as generalized spin diffusion. The GSRE theory is compared to an existing theory, based on the extended Solomon equations, which does not incorporate these phenomena. Relaxation dispersion profiles are computed from the GSRE theory for systems of up to 16 protons, taken from protein crystal structures. These profiles span the range from the motional narrowing limit, where the coherent mode transfer plays a major role, to the ultra-slow motion limit, where the zero-field rate is closely related to the strong-collision limit of the dipolar relaxation rate. Although a quantitative analysis of experimental data is beyond the scope of this work, it is clear from the magnitude of the predicted relaxation rate and the shape of the relaxation dispersion profile that the dipolar EMOR mechanism is the principal cause of water-1H low-field longitudinal relaxation in aqueous systems of immobilized macromolecules, including soft biological tissues. The relaxation theory developed here therefore provides a basis for molecular-level interpretation of endogenous soft

Anisotropic molecular reorientations of quinuclidine in its plastic solid phase: 1H and 14N NMR relaxation study

International Nuclear Information System (INIS)

Brot, C.; Virlet, J.

1979-01-01

14 N and 1 H NMR relaxation times have been measured in quinuclidine in its plastic phase. These measurements rule out isotropic motion. Correlation times for several anisotropic reorientational models are calculated from these NMR data. The best agreement with the values calculated from neutron scattering experiments (preceding paper) is obtained for a model where the molecules reorient by +-90 0 jumps about the crystallographic C 4 axes with a residence time of (22.2+-2).10 -12 s, and by +-120 0 jumps about the molecular C 3 axes with a residence of (5.25+-2.8).10 -12 s, at room temperature. The activation enthalpy is 15.3 kJ.mol. -1 for the +-90 0 jumps, and higher for the +-120 0 jumps. Translational correlation times have also been measured at high temperature, below the melting point

Basics of Bayesian methods.

Science.gov (United States)

Ghosh, Sujit K

2010-01-01

Bayesian methods are rapidly becoming popular tools for making statistical inference in various fields of science including biology, engineering, finance, and genetics. One of the key aspects of Bayesian inferential method is its logical foundation that provides a coherent framework to utilize not only empirical but also scientific information available to a researcher. Prior knowledge arising from scientific background, expert judgment, or previously collected data is used to build a prior distribution which is then combined with current data via the likelihood function to characterize the current state of knowledge using the so-called posterior distribution. Bayesian methods allow the use of models of complex physical phenomena that were previously too difficult to estimate (e.g., using asymptotic approximations). Bayesian methods offer a means of more fully understanding issues that are central to many practical problems by allowing researchers to build integrated models based on hierarchical conditional distributions that can be estimated even with limited amounts of data. Furthermore, advances in numerical integration methods, particularly those based on Monte Carlo methods, have made it possible to compute the optimal Bayes estimators. However, there is a reasonably wide gap between the background of the empirically trained scientists and the full weight of Bayesian statistical inference. Hence, one of the goals of this chapter is to bridge the gap by offering elementary to advanced concepts that emphasize linkages between standard approaches and full probability modeling via Bayesian methods.

Effect of alkali ion on relaxation properties of binary alkali-borate glasses

International Nuclear Information System (INIS)

Lomovskoj, V.A.; Bartenev, G.M.

1992-01-01

Method of relaxation spectrometry were used to analyze the data on internal friction spectra of lithium, sodium, potassium and rubidium alkali-borate glasses in wide range of temperatures and frequencies. The nature of two relaxation processes was clarified: β m -process, related with mobility of alkaline metal cations, and α-process (vitrification), conditioned by system transformation from viscous-flow to vitreous state. It is shown that atomic-molecular mechanism of vitrification process changes when passing from vitreous B 2 O 3 to alkali-borate glasses

Multiplied effect of heat and radiation in chemical stress relaxation

International Nuclear Information System (INIS)

Ito, Masayuki

1981-01-01

About the deterioration of rubber due to radiation, useful knowledge can be obtained by the measurement of chemical stress relaxation. As an example, the rubber coating of cables in a reactor containment vessel is estimated to be irradiated by weak radiation at the temperature between 60 and 90 deg C for about 40 years. In such case, it is desirable to establish the method of accelerated test of the deterioration. The author showed previously that the law of time-dose rate conversion holds in the case of radiation. In this study, the chemical stress relaxation to rubber was measured by the simultaneous application of heat and radiation, and it was found that there was the multiplied effect of heat and radiation in the stress relaxation speed. Therefore the factor of multiplication of heat and radiation was proposed to describe quantitatively the degree of the multiplied effect. The chloroprene rubber used was offered by Hitachi Cable Co., Ltd. The experimental method and the results are reported. The multiplication of heat and radiation is not caused by the direct cut of molecular chains by radiation, instead, it is based on the temperature dependence of various reaction rates at which the activated species reached the cut of molecular chains through complex reaction mechanism and the temperature dependence of the diffusion rate of oxygen in rubber. (Kako, I.)

Novel spin dynamics in ferrimagnetic molecular chains from {sup 1}H NMR and {mu}SR spin-lattice relaxation measurements

Energy Technology Data Exchange (ETDEWEB)

Micotti, E. E-mail: micotti@fisicavolta.unipv.it; Lascialfari, A.; Rigamonti, A.; Aldrovandi, S.; Caneschi, A.; Gatteschi, D.; Bogani, L

2004-05-01

The spin dynamics in the helical chain Co(hfac){sub 2}NITPhOMe has been investigated by {sup 1}H NMR and {mu}SR relaxation. In the temperature range 15relaxation of the homogeneous magnetization. For T{<=}15 K, NMR and {mu}SR evidence a second spin relaxation mechanism, undetected by the magnetization measurements. From the analysis of these data, insights on this novel relaxation process are derived.

Bayesian computation with R

CERN Document Server

Albert, Jim

2009-01-01

There has been a dramatic growth in the development and application of Bayesian inferential methods. Some of this growth is due to the availability of powerful simulation-based algorithms to summarize posterior distributions. There has been also a growing interest in the use of the system R for statistical analyses. R's open source nature, free availability, and large number of contributor packages have made R the software of choice for many statisticians in education and industry. Bayesian Computation with R introduces Bayesian modeling by the use of computation using the R language. The earl

The Bayesian Score Statistic

NARCIS (Netherlands)

Kleibergen, F.R.; Kleijn, R.; Paap, R.

2000-01-01

We propose a novel Bayesian test under a (noninformative) Jeffreys'priorspecification. We check whether the fixed scalar value of the so-calledBayesian Score Statistic (BSS) under the null hypothesis is aplausiblerealization from its known and standardized distribution under thealternative. Unlike

Bayesian methods for proteomic biomarker development

Directory of Open Access Journals (Sweden)

Belinda Hernández

2015-12-01

In this review we provide an introduction to Bayesian inference and demonstrate some of the advantages of using a Bayesian framework. We summarize how Bayesian methods have been used previously in proteomics and other areas of bioinformatics. Finally, we describe some popular and emerging Bayesian models from the statistical literature and provide a worked tutorial including code snippets to show how these methods may be applied for the evaluation of proteomic biomarkers.

Bayesian inference with ecological applications

CERN Document Server

Link, William A

2009-01-01

This text is written to provide a mathematically sound but accessible and engaging introduction to Bayesian inference specifically for environmental scientists, ecologists and wildlife biologists. It emphasizes the power and usefulness of Bayesian methods in an ecological context. The advent of fast personal computers and easily available software has simplified the use of Bayesian and hierarchical models . One obstacle remains for ecologists and wildlife biologists, namely the near absence of Bayesian texts written specifically for them. The book includes many relevant examples, is supported by software and examples on a companion website and will become an essential grounding in this approach for students and research ecologists. Engagingly written text specifically designed to demystify a complex subject Examples drawn from ecology and wildlife research An essential grounding for graduate and research ecologists in the increasingly prevalent Bayesian approach to inference Companion website with analyt...

Comparison of single-ion molecular dynamics in common solvents

Science.gov (United States)

Muralidharan, A.; Pratt, L. R.; Chaudhari, M. I.; Rempe, S. B.

2018-06-01

Laying a basis for molecularly specific theory for the mobilities of ions in solutions of practical interest, we report a broad survey of velocity autocorrelation functions (VACFs) of Li+ and PF6- ions in water, ethylene carbonate, propylene carbonate, and acetonitrile solutions. We extract the memory function, γ(t), which characterizes the random forces governing the mobilities of ions. We provide comparisons controlling for the effects of electrolyte concentration and ion-pairing, van der Waals attractive interactions, and solvent molecular characteristics. For the heavier ion (PF6-), velocity relaxations are all similar: negative tail relaxations for the VACF and a clear second relaxation for γ (t ), observed previously also for other molecular ions and with n-pentanol as the solvent. For the light Li+ ion, short time-scale oscillatory behavior masks simple, longer time-scale relaxation of γ (t ). But the corresponding analysis of the solventberg Li+(H2O)4 does conform to the standard picture set by all the PF6- results.

The Bayesian count rate probability distribution in measurement of ionizing radiation by use of a ratemeter

Energy Technology Data Exchange (ETDEWEB)

Weise, K.

2004-06-01

Recent metrological developments concerning measurement uncertainty, founded on Bayesian statistics, give rise to a revision of several parts of the DIN 25482 and ISO 11929 standard series. These series stipulate detection limits and decision thresholds for ionizing-radiation measurements. Part 3 and, respectively, part 4 of them deal with measurements by use of linear-scale analogue ratemeters. A normal frequency distribution of the momentary ratemeter indication for a fixed count rate value is assumed. The actual distribution, which is first calculated numerically by solving an integral equation, differs, however, considerably from the normal distribution although this one represents an approximation of it for sufficiently large values of the count rate to be measured. As is shown, this similarly holds true for the Bayesian probability distribution of the count rate for sufficiently large given measured values indicated by the ratemeter. This distribution follows from the first one mentioned by means of the Bayes theorem. Its expectation value and variance are needed for the standards to be revised on the basis of Bayesian statistics. Simple expressions are given by the present standards for estimating these parameters and for calculating the detection limit and the decision threshold. As is also shown, the same expressions can similarly be used as sufficient approximations by the revised standards if, roughly, the present indicated value exceeds the reciprocal ratemeter relaxation time constant. (orig.)

Current trends in Bayesian methodology with applications

CERN Document Server

Upadhyay, Satyanshu K; Dey, Dipak K; Loganathan, Appaia

2015-01-01

Collecting Bayesian material scattered throughout the literature, Current Trends in Bayesian Methodology with Applications examines the latest methodological and applied aspects of Bayesian statistics. The book covers biostatistics, econometrics, reliability and risk analysis, spatial statistics, image analysis, shape analysis, Bayesian computation, clustering, uncertainty assessment, high-energy astrophysics, neural networking, fuzzy information, objective Bayesian methodologies, empirical Bayes methods, small area estimation, and many more topics.Each chapter is self-contained and focuses on

Proton spin-lattice relaxation in a liquid crystal-Aerosil complex above the bulk isotropization temperature

Energy Technology Data Exchange (ETDEWEB)

Anoardo, E.; Grinberg, F.; Vilfan, M.; Kimmich, R

2004-02-16

We present a study of the molecular dynamics in an octylcyanobiphenyl (8CB)-Aerosil complex above the bulk isotropization temperature. Using proton nuclear magnetic relaxation experiments in the laboratory frame (T{sub 1}{sup -1}) and in the rotating-frame (T{sub 1{rho}}{sup -1}), we found a notable increase of the relaxation rates in the kHz frequency range as compared to the bulk 8CB liquid crystal at the same temperature. The field-cycling technique was used for the laboratory frame experiments while a conventional apparatus was used for the rotating frame method. The observed behavior is analyzed with the aid of Monte Carlo simulations on the basis of a two-phase fast-exchange model distinguishing surface-ordered and bulk phases. Two processes affecting the low frequency relaxation could be identified: reorientation mediated by translational displacements, accounting for molecular reorientations, and exchange losses of molecules from the surface to the bulk.

Bayesian Semiparametric Density Deconvolution in the Presence of Conditionally Heteroscedastic Measurement Errors

KAUST Repository

Sarkar, Abhra

2014-10-02

We consider the problem of estimating the density of a random variable when precise measurements on the variable are not available, but replicated proxies contaminated with measurement error are available for sufficiently many subjects. Under the assumption of additive measurement errors this reduces to a problem of deconvolution of densities. Deconvolution methods often make restrictive and unrealistic assumptions about the density of interest and the distribution of measurement errors, e.g., normality and homoscedasticity and thus independence from the variable of interest. This article relaxes these assumptions and introduces novel Bayesian semiparametric methodology based on Dirichlet process mixture models for robust deconvolution of densities in the presence of conditionally heteroscedastic measurement errors. In particular, the models can adapt to asymmetry, heavy tails and multimodality. In simulation experiments, we show that our methods vastly outperform a recent Bayesian approach based on estimating the densities via mixtures of splines. We apply our methods to data from nutritional epidemiology. Even in the special case when the measurement errors are homoscedastic, our methodology is novel and dominates other methods that have been proposed previously. Additional simulation results, instructions on getting access to the data set and R programs implementing our methods are included as part of online supplemental materials.

Bayesian Semiparametric Density Deconvolution in the Presence of Conditionally Heteroscedastic Measurement Errors

KAUST Repository

Sarkar, Abhra; Mallick, Bani K.; Staudenmayer, John; Pati, Debdeep; Carroll, Raymond J.

2014-01-01

We consider the problem of estimating the density of a random variable when precise measurements on the variable are not available, but replicated proxies contaminated with measurement error are available for sufficiently many subjects. Under the assumption of additive measurement errors this reduces to a problem of deconvolution of densities. Deconvolution methods often make restrictive and unrealistic assumptions about the density of interest and the distribution of measurement errors, e.g., normality and homoscedasticity and thus independence from the variable of interest. This article relaxes these assumptions and introduces novel Bayesian semiparametric methodology based on Dirichlet process mixture models for robust deconvolution of densities in the presence of conditionally heteroscedastic measurement errors. In particular, the models can adapt to asymmetry, heavy tails and multimodality. In simulation experiments, we show that our methods vastly outperform a recent Bayesian approach based on estimating the densities via mixtures of splines. We apply our methods to data from nutritional epidemiology. Even in the special case when the measurement errors are homoscedastic, our methodology is novel and dominates other methods that have been proposed previously. Additional simulation results, instructions on getting access to the data set and R programs implementing our methods are included as part of online supplemental materials.

A Bayesian framework for risk perception

NARCIS (Netherlands)

van Erp, H.R.N.

2017-01-01

We present here a Bayesian framework of risk perception. This framework encompasses plausibility judgments, decision making, and question asking. Plausibility judgments are modeled by way of Bayesian probability theory, decision making is modeled by way of a Bayesian decision theory, and relevancy

Bayesian flood forecasting methods: A review

Science.gov (United States)

Han, Shasha; Coulibaly, Paulin

2017-08-01

Over the past few decades, floods have been seen as one of the most common and largely distributed natural disasters in the world. If floods could be accurately forecasted in advance, then their negative impacts could be greatly minimized. It is widely recognized that quantification and reduction of uncertainty associated with the hydrologic forecast is of great importance for flood estimation and rational decision making. Bayesian forecasting system (BFS) offers an ideal theoretic framework for uncertainty quantification that can be developed for probabilistic flood forecasting via any deterministic hydrologic model. It provides suitable theoretical structure, empirically validated models and reasonable analytic-numerical computation method, and can be developed into various Bayesian forecasting approaches. This paper presents a comprehensive review on Bayesian forecasting approaches applied in flood forecasting from 1999 till now. The review starts with an overview of fundamentals of BFS and recent advances in BFS, followed with BFS application in river stage forecasting and real-time flood forecasting, then move to a critical analysis by evaluating advantages and limitations of Bayesian forecasting methods and other predictive uncertainty assessment approaches in flood forecasting, and finally discusses the future research direction in Bayesian flood forecasting. Results show that the Bayesian flood forecasting approach is an effective and advanced way for flood estimation, it considers all sources of uncertainties and produces a predictive distribution of the river stage, river discharge or runoff, thus gives more accurate and reliable flood forecasts. Some emerging Bayesian forecasting methods (e.g. ensemble Bayesian forecasting system, Bayesian multi-model combination) were shown to overcome limitations of single model or fixed model weight and effectively reduce predictive uncertainty. In recent years, various Bayesian flood forecasting approaches have been

Spin-lattice relaxation in phosphorescent triplet state molecules

International Nuclear Information System (INIS)

Verbeek, P.J.F.

1979-01-01

The present thesis contains the results of a study of spin-lattice relaxation (SLR) in the photo-excited triplet state of aromatic molecules, dissolved in a molecular host crystal. It appears that SLR in phosphorescent triplet state molecules often is related to the presence of so-called (pseudo) localized phonons in the molecular mixed crystals. These local phonons can be thought to correspond with vibrations (librations) of the guest molecule in the force field of the surrounding host molecules. Since the intermolecular forces are relatively weak, the frequencies corresponding with these vibrations are relatively low and usually are of the order of 10-30 cm -1 . (Auth.)

Nuclear relaxation and critical fluctuations in membranes containing cholesterol

Science.gov (United States)

McConnell, Harden

2009-04-01

Nuclear resonance frequencies in bilayer membranes depend on lipid composition. Our calculations describe the combined effects of composition fluctuations and diffusion on nuclear relaxation near a miscibility critical point. Both tracer and gradient diffusion are included. The calculations involve correlation functions and a correlation length ξ =ξ0T/(T -Tc), where T -Tc is temperature above the critical temperature and ξ0 is a parameter of molecular length. Several correlation functions are examined, each of which is related in some degree to the Ising model correlation function. These correlation functions are used in the calculation of transverse deuterium relaxation rates in magic angle spinning and quadrupole echo experiments. The calculations are compared with experiments that report maxima in deuterium and proton nuclear relaxation rates at the critical temperature [Veatch et al., Proc. Nat. Acad. Sci. U.S.A. 104, 17650 (2007)]. One Ising-model-related correlation function yields a maximum 1/T2 relaxation rate at the critical temperature for both magic angle spinning and quadrupole echo experiments. The calculated rates at the critical temperature are close to the experimental rates. The rate maxima involve relatively rapid tracer diffusion in a static composition gradient over distances of up to 10-100 nm.

Rouse mode analysis of chain relaxation in polymer nanocomposites.

Science.gov (United States)

Kalathi, Jagannathan T; Kumar, Sanat K; Rubinstein, Michael; Grest, Gary S

2015-05-28

Large-scale molecular dynamics simulations are used to study the internal relaxations of chains in nanoparticle (NP)/polymer composites. We examine the Rouse modes of the chains, a quantity that is closest in spirit to the self-intermediate scattering function, typically determined in an (incoherent) inelastic neutron scattering experiment. Our simulations show that for weakly interacting mixtures of NPs and polymers, the effective monomeric relaxation rates are faster than in a neat melt when the NPs are smaller than the entanglement mesh size. In this case, the NPs serve to reduce both the monomeric friction and the entanglements in the polymer melt, as in the case of a polymer-solvent system. However, for NPs larger than half the entanglement mesh size, the effective monomer relaxation is essentially unaffected for low NP concentrations. Even in this case, we observe a strong reduction in chain entanglements for larger NP loadings. Thus, the role of NPs is to always reduce the number of entanglements, with this effect only becoming pronounced for small NPs or for high concentrations of large NPs. Our studies of the relaxation of single chains resonate with recent neutron spin echo (NSE) experiments, which deduce a similar entanglement dilution effect.

Topics in Bayesian statistics and maximum entropy

International Nuclear Information System (INIS)

Mutihac, R.; Cicuttin, A.; Cerdeira, A.; Stanciulescu, C.

1998-12-01

Notions of Bayesian decision theory and maximum entropy methods are reviewed with particular emphasis on probabilistic inference and Bayesian modeling. The axiomatic approach is considered as the best justification of Bayesian analysis and maximum entropy principle applied in natural sciences. Particular emphasis is put on solving the inverse problem in digital image restoration and Bayesian modeling of neural networks. Further topics addressed briefly include language modeling, neutron scattering, multiuser detection and channel equalization in digital communications, genetic information, and Bayesian court decision-making. (author)

Book review: Bayesian analysis for population ecology

Science.gov (United States)

Link, William A.

2011-01-01

Brian Dennis described the field of ecology as “fertile, uncolonized ground for Bayesian ideas.” He continued: “The Bayesian propagule has arrived at the shore. Ecologists need to think long and hard about the consequences of a Bayesian ecology. The Bayesian outlook is a successful competitor, but is it a weed? I think so.” (Dennis 2004)

Superresolution radar imaging based on fast inverse-free sparse Bayesian learning for multiple measurement vectors

Science.gov (United States)

He, Xingyu; Tong, Ningning; Hu, Xiaowei

2018-01-01

Compressive sensing has been successfully applied to inverse synthetic aperture radar (ISAR) imaging of moving targets. By exploiting the block sparse structure of the target image, sparse solution for multiple measurement vectors (MMV) can be applied in ISAR imaging and a substantial performance improvement can be achieved. As an effective sparse recovery method, sparse Bayesian learning (SBL) for MMV involves a matrix inverse at each iteration. Its associated computational complexity grows significantly with the problem size. To address this problem, we develop a fast inverse-free (IF) SBL method for MMV. A relaxed evidence lower bound (ELBO), which is computationally more amiable than the traditional ELBO used by SBL, is obtained by invoking fundamental property for smooth functions. A variational expectation-maximization scheme is then employed to maximize the relaxed ELBO, and a computationally efficient IF-MSBL algorithm is proposed. Numerical results based on simulated and real data show that the proposed method can reconstruct row sparse signal accurately and obtain clear superresolution ISAR images. Moreover, the running time and computational complexity are reduced to a great extent compared with traditional SBL methods.

Relaxation characteristics of hastelloy X

International Nuclear Information System (INIS)

Suzuki, Kazuhiko

1980-02-01

Relaxation diagrams of Hastelloy X (relaxation curves, relaxation design diagrams, etc.) were generated from the creep constitutive equation of Hastelloy X, using inelastic stress analysis code TEPICC-J. These data are in good agreement with experimental relaxation data of ORNL-5479. Three typical inelastic stress analyses were performed for various relaxation behaviors of the high-temperature structures. An attempt was also made to predict these relaxation behaviors by the relaxation curves. (author)

Curie-type paramagnetic NMR relaxation in the aqueous solution of Ni(II).

Science.gov (United States)

Mareš, Jiří; Hanni, Matti; Lantto, Perttu; Lounila, Juhani; Vaara, Juha

2014-04-21

Ni(2+)(aq) has been used for many decades as a model system for paramagnetic nuclear magnetic resonance (pNMR) relaxation studies. More recently, its magnetic properties and also nuclear magnetic relaxation rates have been studied computationally. We have calculated electron paramagnetic resonance and NMR parameters using quantum-mechanical (QM) computation of molecular dynamics snapshots, obtained using a polarizable empirical force field. Statistical averages of hyperfine coupling, g- and zero-field splitting tensors, as well as the pNMR shielding terms, are compared to the available experimental and computational data. In accordance with our previous work, the isotropic hyperfine coupling as well as nuclear shielding values agree well with experimental measurements for the (17)O nuclei of water molecules in the first solvation shell of the nickel ion, whereas larger deviations are found for (1)H centers. We report, for the first time, the Curie-type contribution to the pNMR relaxation rate using QM calculations together with Redfield relaxation theory. The Curie relaxation mechanism is analogous to chemical shift anisotropy relaxation, well-known in diamagnetic NMR. Due to the predominance of other types of paramagnetic relaxation mechanisms for this system, it is possible to extract the Curie term only computationally. The Curie mechanism alone would result in around 16 and 20 s(-1) of relaxation rates (R1 and R2 respectively) for the (1)H nuclei of water molecules bonded to the Ni(2+) center, in a magnetic field of 11.7 T. The corresponding (17)O relaxation rates are around 33 and 38 s(-1). We also report the Curie contribution to the relaxation rate for molecules beyond the first solvation shell in a 1 M solution of Ni(2+) in water.

On real statistics of relaxation in gases

Science.gov (United States)

Kuzovlev, Yu. E.

2016-02-01

By example of a particle interacting with ideal gas, it is shown that the statistics of collisions in statistical mechanics at any value of the gas rarefaction parameter qualitatively differ from that conjugated with Boltzmann's hypothetical molecular chaos and kinetic equation. In reality, the probability of collisions of the particle in itself is random. Because of that, the relaxation of particle velocity acquires a power-law asymptotic behavior. An estimate of its exponent is suggested on the basis of simple kinematic reasons.

Bayesian Fundamentalism or Enlightenment? On the explanatory status and theoretical contributions of Bayesian models of cognition.

Science.gov (United States)

Jones, Matt; Love, Bradley C

2011-08-01

The prominence of Bayesian modeling of cognition has increased recently largely because of mathematical advances in specifying and deriving predictions from complex probabilistic models. Much of this research aims to demonstrate that cognitive behavior can be explained from rational principles alone, without recourse to psychological or neurological processes and representations. We note commonalities between this rational approach and other movements in psychology - namely, Behaviorism and evolutionary psychology - that set aside mechanistic explanations or make use of optimality assumptions. Through these comparisons, we identify a number of challenges that limit the rational program's potential contribution to psychological theory. Specifically, rational Bayesian models are significantly unconstrained, both because they are uninformed by a wide range of process-level data and because their assumptions about the environment are generally not grounded in empirical measurement. The psychological implications of most Bayesian models are also unclear. Bayesian inference itself is conceptually trivial, but strong assumptions are often embedded in the hypothesis sets and the approximation algorithms used to derive model predictions, without a clear delineation between psychological commitments and implementational details. Comparing multiple Bayesian models of the same task is rare, as is the realization that many Bayesian models recapitulate existing (mechanistic level) theories. Despite the expressive power of current Bayesian models, we argue they must be developed in conjunction with mechanistic considerations to offer substantive explanations of cognition. We lay out several means for such an integration, which take into account the representations on which Bayesian inference operates, as well as the algorithms and heuristics that carry it out. We argue this unification will better facilitate lasting contributions to psychological theory, avoiding the pitfalls

Dielectric studies of molecular motions in glassy and liquid nicotine

Energy Technology Data Exchange (ETDEWEB)

Kaminski, K [Institute of Physics, Silesian University, ulica Uniwersytecka 4, 40-007 Katowice (Poland); Paluch, M [Institute of Physics, Silesian University, ulica Uniwersytecka 4, 40-007 Katowice (Poland); Ziolo, J [Institute of Physics, Silesian University, ulica Uniwersytecka 4, 40-007 Katowice (Poland); Ngai, K L [Naval Research Laboratory, Washington DC 20375-5320 (United States)

2006-06-21

The dielectric permittivity and loss spectra of glassy and liquid states of nicotine have been measured over the frequency range 10{sup -2}-10{sup 9} Hz. The relaxation spectra are similar to common small molecular glass-forming substances, showing the structural {alpha}-relaxation and its precursor, the Johari-Goldstein {beta}-relaxation. The {alpha}-relaxation is well described by the Fourier transform of the Kohlrausch-Williams-Watts stretched exponential function with an approximately constant stretch exponent that is equal to 0.70 as the glass transition temperature is approached. The dielectric {alpha}-relaxation time measured over 11 orders of magnitude cannot be described by a single Vogel-Fulcher-Tamman-Hesse equation. The most probable Johari-Goldstein {beta}-relaxation time determined from the dielectric spectra is in good agreement with the primitive relaxation time of the coupling model calculated from parameters of the structural {alpha}-relaxation. The shape of the dielectric spectra of nicotine is compared with that of other glass-formers having about the same stretch exponent, and they are shown to be nearly isomorphic. The results indicate that the molecular dynamics of nicotine conform to the general pattern found in other glass-formers, and the presence of the universal Johari-Goldstein secondary relaxation, which plays a role in the crystallization of amorphous pharmaceuticals.

Molecular mobility of nematic E7 confined to molecular sieves with a low filling degree.

Science.gov (United States)

Brás, A R; Frunza, S; Guerreiro, L; Fonseca, I M; Corma, A; Frunza, L; Dionísio, M; Schönhals, A

2010-06-14

The nematic liquid crystalline mixture E7 was confined with similar filling degrees to molecular sieves with constant composition but different pore diameters (from 2.8 to 6.8 nm). Fourier transform infrared analysis proved that the E7 molecules interact via the cyanogroup with the pore walls of the molecular sieves. The molecular dynamics of the system was investigated by broadband dielectric spectroscopy (10(-2)-10(9) Hz) covering a wide temperature range of approximately 200 K from temperatures well above the isotropic-nematic transition down to the glass transition of bulk E7. A variety of relaxation processes is observed including two modes that are located close to the bulk behavior in its temperature dependence. For all confined samples, two relaxation processes, at frequencies lower than the processes observed for the bulk, were detected. At lower temperatures, their relaxation rates have different temperature dependencies whereas at higher temperatures, they seem to collapse into one chart. The temperature dependence of the slowest process (S-process) obeys the Vogel-Fulcher-Tammann law indicating a glassy dynamics of the E7 molecules anchored to the pore surface. The pore size dependence of both the Vogel temperature and fragility revealed a steplike transition around 4 nm pore size, which indicates a transition from a strong to a fragile behavior. The process with a relaxation rate in between the bulklike and the S-process (I-process) shows no dependence on the pore size. The agreement of the I-process with the behavior of a 5CB surface layer adsorbed on nonporous silica leads to the assignment of E7 molecules anchored at the outer surface of the microcrystals of the molecular sieves.

3rd Bayesian Young Statisticians Meeting

CERN Document Server

Lanzarone, Ettore; Villalobos, Isadora; Mattei, Alessandra

2017-01-01

This book is a selection of peer-reviewed contributions presented at the third Bayesian Young Statisticians Meeting, BAYSM 2016, Florence, Italy, June 19-21. The meeting provided a unique opportunity for young researchers, M.S. students, Ph.D. students, and postdocs dealing with Bayesian statistics to connect with the Bayesian community at large, to exchange ideas, and to network with others working in the same field. The contributions develop and apply Bayesian methods in a variety of fields, ranging from the traditional (e.g., biostatistics and reliability) to the most innovative ones (e.g., big data and networks).

Robust bayesian analysis of an autoregressive model with ...

African Journals Online (AJOL)

In this work, robust Bayesian analysis of the Bayesian estimation of an autoregressive model with exponential innovations is performed. Using a Bayesian robustness methodology, we show that, using a suitable generalized quadratic loss, we obtain optimal Bayesian estimators of the parameters corresponding to the ...

Plug & Play object oriented Bayesian networks

DEFF Research Database (Denmark)

Bangsø, Olav; Flores, J.; Jensen, Finn Verner

2003-01-01

been shown to be quite suitable for dynamic domains as well. However, processing object oriented Bayesian networks in practice does not take advantage of their modular structure. Normally the object oriented Bayesian network is transformed into a Bayesian network and, inference is performed...... dynamic domains. The communication needed between instances is achieved by means of a fill-in propagation scheme....

The Bayesian New Statistics: Hypothesis testing, estimation, meta-analysis, and power analysis from a Bayesian perspective.

Science.gov (United States)

Kruschke, John K; Liddell, Torrin M

2018-02-01

In the practice of data analysis, there is a conceptual distinction between hypothesis testing, on the one hand, and estimation with quantified uncertainty on the other. Among frequentists in psychology, a shift of emphasis from hypothesis testing to estimation has been dubbed "the New Statistics" (Cumming 2014). A second conceptual distinction is between frequentist methods and Bayesian methods. Our main goal in this article is to explain how Bayesian methods achieve the goals of the New Statistics better than frequentist methods. The article reviews frequentist and Bayesian approaches to hypothesis testing and to estimation with confidence or credible intervals. The article also describes Bayesian approaches to meta-analysis, randomized controlled trials, and power analysis.

F{sup 19} relaxation in non-magnetic hexafluorides; Contribution a l'etude de la relaxation des fluors dans les hexafluorures non magnetiques

Energy Technology Data Exchange (ETDEWEB)

Rigny, P [Commissariat a l' Energie Atomique, Saclay (France). Centre d' Etudes Nucleaires

1967-12-01

The interesting properties of the fluorine magnetic resonance in the hexafluorides of molybdenum, tungsten and uranium, are very much due to large anisotropies of the chemical shift tensors. In the solid phases these anisotropies, the values of which are deduced from line shape studies, allow one to show that the molecules undergo hindered rotations about the metal atom. The temperature and frequency dependence of the fluorine longitudinal relaxation times shows that the relaxation is due to the molecular motion. The dynamical parameters of this motion are then deduced from the complete study of the fluorine relaxation in the rotating frame. In the liquid phases, the existence of anisotropies allows an estimation of the different contributions to the relaxation. In particular, the frequency and temperature dependence of the relaxation shows it to be dominated by the spin-rotation interaction. We have shown that the strength of this interaction can be deduced from the chemical shifts, and the angle through which the molecule rotates quasi-freely can be determined. In the hexafluorides, this angle is roughly one radian at 70 C, and with the help of this value, the friction coefficients which describe the intermolecular interactions are discussed. (author) [French] Les proprietes de la resonance magnetique des fluors dans les hexafluorures de molybdene, tungstene et uranium sont influencees par l'existence de deplacements chimiques tres anisotropes. Dans les phases solides, la valeur de cette anisotropie peut etre determinee par l'analyse des formes de raies et son existence permet de montrer que les molecules sont en rotation empechee autour de leur atome central. L'etude du temps de relaxation longitudinal en fonction de la temperature et de la frequence montre que la relaxation est due aux mouvements moleculaires, aux plus hautes temperatures. Les proprietes dynamiques du mouvement sont obtenues par l'etude complete de la relaxation spin-reseau dans le referentiel

Investigation of oxygen vibrational relaxation by quasi-classical trajectory method

International Nuclear Information System (INIS)

Andrienko, Daniil; Boyd, Iain D.

2015-01-01

Highlights: • Importance of attraction for the O 2 –O energy exchange in hypersonic flows. • O 2 –O vibrational relaxation time cannot be described by the Millikan–White equation. • Weak dependence of exothermic transition rates on translational temperature. • Multiquantum jumps in molecular oxygen occur mostly via the exchange reaction. - Abstract: O 2 –O collisions are studied by the quasi-classical trajectory method. A full set of cross sections for the vibrational ladder is obtained utilizing an accurate O 3 potential energy surface. Vibrational relaxation is investigated at temperatures between 1000 and 10,000 K, that are relevant to hypersonic flows. The relaxation time is derived based on the removal rate for the first excited vibrational level. A significant deviation from the formula by Millikan and White is observed for temperatures beyond those reported in experimental work. Relaxation becomes less efficient at high temperatures, suggesting that the efficiency of the energy randomization is strongly to the attractive component of the O 3 potential energy surface. These results are explained by analyzing the microscopic parameter of collisions that reflects the number of exchanges in the shortest interatomic distance. The rates of exothermic transitions are found to be nearly independent of the translational temperature in the range of interest.

2nd Bayesian Young Statisticians Meeting

CERN Document Server

Bitto, Angela; Kastner, Gregor; Posekany, Alexandra

2015-01-01

The Second Bayesian Young Statisticians Meeting (BAYSM 2014) and the research presented here facilitate connections among researchers using Bayesian Statistics by providing a forum for the development and exchange of ideas. WU Vienna University of Business and Economics hosted BAYSM 2014 from September 18th to 19th. The guidance of renowned plenary lecturers and senior discussants is a critical part of the meeting and this volume, which follows publication of contributions from BAYSM 2013. The meeting's scientific program reflected the variety of fields in which Bayesian methods are currently employed or could be introduced in the future. Three brilliant keynote lectures by Chris Holmes (University of Oxford), Christian Robert (Université Paris-Dauphine), and Mike West (Duke University), were complemented by 24 plenary talks covering the major topics Dynamic Models, Applications, Bayesian Nonparametrics, Biostatistics, Bayesian Methods in Economics, and Models and Methods, as well as a lively poster session ...

Bayesian natural language semantics and pragmatics

CERN Document Server

Zeevat, Henk

2015-01-01

The contributions in this volume focus on the Bayesian interpretation of natural languages, which is widely used in areas of artificial intelligence, cognitive science, and computational linguistics. This is the first volume to take up topics in Bayesian Natural Language Interpretation and make proposals based on information theory, probability theory, and related fields. The methodologies offered here extend to the target semantic and pragmatic analyses of computational natural language interpretation. Bayesian approaches to natural language semantics and pragmatics are based on methods from signal processing and the causal Bayesian models pioneered by especially Pearl. In signal processing, the Bayesian method finds the most probable interpretation by finding the one that maximizes the product of the prior probability and the likelihood of the interpretation. It thus stresses the importance of a production model for interpretation as in Grice's contributions to pragmatics or in interpretation by abduction.

Molecular motions of non-crystalline poly(aryl ether-ether-ketone) PEEK and influence of electron beam irradiation

International Nuclear Information System (INIS)

Sasuga, T.; Hagiwara, M.

1985-01-01

The dynamic mechanical relaxation of non-crystalline poly(aryl ether-ether-ketone) PEEK and the one irradiated with electron beam were studied. The three distinct γ, β, α' relaxation maxima were observed in unirradiated PEEK from low to high temperature. It was revealed from the study on the irradiation effects that three different molecular processes are overlapped in γ relaxation peak, i.e., molecular motion of water bound to main chain, local motion of main chain, and local mode of the aligned and/or oriented moiety. The β relaxation connected with the glass transition occurred at 150 deg C and it shifted to higher temperature by irradiation. The α' relaxation which can be attributed to rearrangement of molecular chain due to crystallization was observed in unirradiated PEEK approx. 180 deg C and its magnitude decreased with the increase in irradiation dose. This effect indicates the formation of structures inhibiting crystallization such as crosslinking and/or short branching during irradiation. A new relaxation, β', appeared in the temperature range of 40 deg to 100 deg C by irradiation and its magnitude increased with dose. This relaxation was attributed to rearrangement of molecular chain from loosened packing around chain ends, which were introduced into the non-crystalline region by chain scission under irradiation, to more rigid molecular packing. (author)

Glass transition and relaxation dynamics of propylene glycol-water solutions confined in clay

Science.gov (United States)

Elamin, Khalid; Björklund, Jimmy; Nyhlén, Fredrik; Yttergren, Madeleine; Mârtensson, Lena; Swenson, Jan

2014-07-01

The molecular dynamics of aqueous solutions of propylene glycol (PG) and propylene glycol methylether (PGME) confined in a two-dimensional layer-structured Na-vermiculite clay has been studied by broadband dielectric spectroscopy and differential scanning calorimetry. As typical for liquids in confined geometries the intensity of the cooperative α-relaxation becomes considerably more suppressed than the more local β-like relaxation processes. In fact, at high water contents the calorimetric glass transition and related structural α-relaxation cannot even be observed, due to the confinement. Thus, the intensity of the viscosity related α-relaxation is dramatically reduced, but its time scale as well as the related glass transition temperature Tg are for both systems only weakly influenced by the confinement. In the case of the PGME-water solutions it is an important finding since in the corresponding bulk system a pronounced non-monotonic concentration dependence of the glass transition related dynamics has been observed due to the growth of hydrogen bonded relaxing entities of water bridging between PGME molecules [J. Sjöström, J. Mattsson, R. Bergman, and J. Swenson, Phys. Chem. B 115, 10013 (2011)]. The present results suggest that the same type of structural entities are formed in the quasi-two-dimensional space between the clay platelets. It is also observed that the main water relaxation cannot be distinguished from the β-relaxation of PG or PGME in the concentration range up to intermediate water contents. This suggests that these two processes are coupled and that the water molecules affect the time scale of the β-relaxation. However, this is most likely true also for the corresponding bulk solutions, which exhibit similar time scales of this combined relaxation process below Tg. Finally, it is found that at higher water contents the water relaxation does not merge with, or follow, the α-relaxation above Tg, but instead crosses the α-relaxation

Uncovering robust patterns of microRNA co-expression across cancers using Bayesian Relevance Networks.

Directory of Open Access Journals (Sweden)

Parameswaran Ramachandran

Full Text Available Co-expression networks have long been used as a tool for investigating the molecular circuitry governing biological systems. However, most algorithms for constructing co-expression networks were developed in the microarray era, before high-throughput sequencing-with its unique statistical properties-became the norm for expression measurement. Here we develop Bayesian Relevance Networks, an algorithm that uses Bayesian reasoning about expression levels to account for the differing levels of uncertainty in expression measurements between highly- and lowly-expressed entities, and between samples with different sequencing depths. It combines data from groups of samples (e.g., replicates to estimate group expression levels and confidence ranges. It then computes uncertainty-moderated estimates of cross-group correlations between entities, and uses permutation testing to assess their statistical significance. Using large scale miRNA data from The Cancer Genome Atlas, we show that our Bayesian update of the classical Relevance Networks algorithm provides improved reproducibility in co-expression estimates and lower false discovery rates in the resulting co-expression networks. Software is available at www.perkinslab.ca.

Bayesian methods in reliability

Science.gov (United States)

Sander, P.; Badoux, R.

1991-11-01

The present proceedings from a course on Bayesian methods in reliability encompasses Bayesian statistical methods and their computational implementation, models for analyzing censored data from nonrepairable systems, the traits of repairable systems and growth models, the use of expert judgment, and a review of the problem of forecasting software reliability. Specific issues addressed include the use of Bayesian methods to estimate the leak rate of a gas pipeline, approximate analyses under great prior uncertainty, reliability estimation techniques, and a nonhomogeneous Poisson process. Also addressed are the calibration sets and seed variables of expert judgment systems for risk assessment, experimental illustrations of the use of expert judgment for reliability testing, and analyses of the predictive quality of software-reliability growth models such as the Weibull order statistics.

Ultrafast Librational Relaxation of H2O in Liquid Water

DEFF Research Database (Denmark)

Petersen, Jakob; Møller, Klaus Braagaard; Rey, Rossend

2013-01-01

The ultrafast librational (hindered rotational) relaxation of a rotationally excited H2O molecule in pure liquid water is investigated by means of classical nonequilibrium molecular dynamics simulations and a power and work analysis. This analysis allows the mechanism of the energy transfer from...... the excited H2O to its water neighbors, which occurs on a sub-100 fs time scale, to be followed in molecular detail, i.e., to determine which water molecules receive the energy and in which degrees of freedom. It is found that the dominant energy flow is to the four hydrogen-bonded water partners in the first...

Bayesian networks and food security - An introduction

NARCIS (Netherlands)

Stein, A.

2004-01-01

This paper gives an introduction to Bayesian networks. Networks are defined and put into a Bayesian context. Directed acyclical graphs play a crucial role here. Two simple examples from food security are addressed. Possible uses of Bayesian networks for implementation and further use in decision

Mozart versus new age music: relaxation states, stress, and ABC relaxation theory.

Science.gov (United States)

Smith, Jonathan C; Joyce, Carol A

2004-01-01

Smith's (2001) Attentional Behavioral Cognitive (ABC) relaxation theory proposes that all approaches to relaxation (including music) have the potential for evoking one or more of 15 factor-analytically derived relaxation states, or "R-States" (Sleepiness, Disengagement, Rested / Refreshed, Energized, Physical Relaxation, At Ease/Peace, Joy, Mental Quiet, Childlike Innocence, Thankfulness and Love, Mystery, Awe and Wonder, Prayerfulness, Timeless/Boundless/Infinite, and Aware). The present study investigated R-States and stress symptom-patterns associated with listening to Mozart versus New Age music. Students (N = 63) were divided into three relaxation groups based on previously determined preferences. Fourteen listened to a 28-minute tape recording of Mozart's Eine Kleine Nachtmusik and 14 listened to a 28-minute tape of Steven Halpern's New Age Serenity Suite. Others (n = 35) did not want music and instead chose a set of popular recreational magazines. Participants engaged in their relaxation activity at home for three consecutive days for 28 minutes a session. Before and after each session, each person completed the Smith Relaxation States Inventory (Smith, 2001), a comprehensive questionnaire tapping 15 R-States as well as the stress states of somatic stress, worry, and negative emotion. Results revealed no differences at Session 1. At Session 2, those who listened to Mozart reported higher levels of At Ease/Peace and lower levels of Negative Emotion. Pronounced differences emerged at Session 3. Mozart listeners uniquely reported substantially higher levels of Mental Quiet, Awe and Wonder, and Mystery. Mozart listeners reported higher levels, and New Age listeners slightly elevated levels, of At Ease/Peace and Rested/Refreshed. Both Mozart and New Age listeners reported higher levels of Thankfulness and Love. In summary, those who listened to Mozart's Eine Kleine Nachtmusik reported more psychological relaxation and less stress than either those who listened to

Mechanical relaxation in glasses

International Nuclear Information System (INIS)

Hiki, Y.

2004-01-01

The basic properties of glasses and the characteristics of mechanical relaxation in glasses were briefly reviewed, and then our studies concerned were presented. Experimental methods adopted were viscosity, internal friction, ultrasonic attenuation, and Brillouin scattering measurements. The specimens used were several kinds of inorganic, organic, and metallic glasses. The measurements were mainly carried out from the room temperature up to the glass transition temperature, and the relaxation time was determined as a function of temperature. The 'double relaxation' composed of two Arrhenius-type relaxations was observed in many materials. In both relaxations, the 'compensation effect' showing a correlation of the pre-exponential factor and the activation energy was observed. These results were explained by considering the 'complex relaxation' due to cooperative motions of atoms or group of atoms. Values of activation energy near the glass transition determined by the various experimental methods were compared with each other

Molecular phylogeny of Pompilinae (Hymenoptera: Pompilidae): Evidence for rapid diversification and host shifts in spider wasps.

Science.gov (United States)

Rodriguez, Juanita; Pitts, James P; Florez, Jaime A; Bond, Jason E; von Dohlen, Carol D

2016-01-01

Pompilinae is one of the largest subfamilies of spider wasps (Pompilidae). Most pompilines are generalist spider predators at the family level, but some taxa exhibit ecological specificity (i.e., to spider-host guild). Here we present the first molecular phylogenetic analysis of Pompilinae, toward the aim of evaluating the monophyly of tribes and genera. We further test whether changes in the rate of diversification are associated with host-guild shifts. Molecular data were collected from five nuclear loci (28S, EF1-F2, LWRh, Wg, Pol2) for 76 taxa in 39 genera. Data were analyzed using maximum likelihood (ML) and Bayesian inference (BI). The phylogenetic results were compared with previous hypotheses of subfamilial and tribal classification, as well as generic relationships in the subfamily. The classification of Pompilus and Agenioideus is also discussed. A Bayesian relaxed molecular clock analysis was used to examine divergence times. Diversification rate-shift tests accounted for taxon-sampling bias using ML and BI approaches. Ancestral host family and host guild were reconstructed using MP and ML methods. Ancestral host guild for all Pompilinae, for the ancestor at the node where a diversification rate-shift was detected, and two more nodes back in time was inferred using BI. In the resulting phylogenies, Aporini was the only previously proposed monophyletic tribe. Several genera (e.g., Pompilus, Microphadnus and Schistonyx) are also not monophyletic. Dating analyses produced a well-supported chronogram consistent with topologies from BI and ML results. The BI ancestral host-use reconstruction inferred the use of spiders belonging to the guild "other hunters" (frequenting the ground and vegetation) as the ancestral state for Pompilinae. This guild had the highest probability for the ML reconstruction and was equivocal for the MP reconstruction; various switching events to other guilds occurred throughout the evolution of the group. The diversification of

12th Brazilian Meeting on Bayesian Statistics

CERN Document Server

Louzada, Francisco; Rifo, Laura; Stern, Julio; Lauretto, Marcelo

2015-01-01

Through refereed papers, this volume focuses on the foundations of the Bayesian paradigm; their comparison to objectivistic or frequentist Statistics counterparts; and the appropriate application of Bayesian foundations. This research in Bayesian Statistics is applicable to data analysis in biostatistics, clinical trials, law, engineering, and the social sciences. EBEB, the Brazilian Meeting on Bayesian Statistics, is held every two years by the ISBrA, the International Society for Bayesian Analysis, one of the most active chapters of the ISBA. The 12th meeting took place March 10-14, 2014 in Atibaia. Interest in foundations of inductive Statistics has grown recently in accordance with the increasing availability of Bayesian methodological alternatives. Scientists need to deal with the ever more difficult choice of the optimal method to apply to their problem. This volume shows how Bayes can be the answer. The examination and discussion on the foundations work towards the goal of proper application of Bayesia...

Kernel Bayesian ART and ARTMAP.

Science.gov (United States)

Masuyama, Naoki; Loo, Chu Kiong; Dawood, Farhan

2018-02-01

Adaptive Resonance Theory (ART) is one of the successful approaches to resolving "the plasticity-stability dilemma" in neural networks, and its supervised learning model called ARTMAP is a powerful tool for classification. Among several improvements, such as Fuzzy or Gaussian based models, the state of art model is Bayesian based one, while solving the drawbacks of others. However, it is known that the Bayesian approach for the high dimensional and a large number of data requires high computational cost, and the covariance matrix in likelihood becomes unstable. This paper introduces Kernel Bayesian ART (KBA) and ARTMAP (KBAM) by integrating Kernel Bayes' Rule (KBR) and Correntropy Induced Metric (CIM) to Bayesian ART (BA) and ARTMAP (BAM), respectively, while maintaining the properties of BA and BAM. The kernel frameworks in KBA and KBAM are able to avoid the curse of dimensionality. In addition, the covariance-free Bayesian computation by KBR provides the efficient and stable computational capability to KBA and KBAM. Furthermore, Correntropy-based similarity measurement allows improving the noise reduction ability even in the high dimensional space. The simulation experiments show that KBA performs an outstanding self-organizing capability than BA, and KBAM provides the superior classification ability than BAM, respectively. Copyright © 2017 Elsevier Ltd. All rights reserved.

Bayesian networks improve causal environmental ...

Science.gov (United States)

Rule-based weight of evidence approaches to ecological risk assessment may not account for uncertainties and generally lack probabilistic integration of lines of evidence. Bayesian networks allow causal inferences to be made from evidence by including causal knowledge about the problem, using this knowledge with probabilistic calculus to combine multiple lines of evidence, and minimizing biases in predicting or diagnosing causal relationships. Too often, sources of uncertainty in conventional weight of evidence approaches are ignored that can be accounted for with Bayesian networks. Specifying and propagating uncertainties improve the ability of models to incorporate strength of the evidence in the risk management phase of an assessment. Probabilistic inference from a Bayesian network allows evaluation of changes in uncertainty for variables from the evidence. The network structure and probabilistic framework of a Bayesian approach provide advantages over qualitative approaches in weight of evidence for capturing the impacts of multiple sources of quantifiable uncertainty on predictions of ecological risk. Bayesian networks can facilitate the development of evidence-based policy under conditions of uncertainty by incorporating analytical inaccuracies or the implications of imperfect information, structuring and communicating causal issues through qualitative directed graph formulations, and quantitatively comparing the causal power of multiple stressors on value

Bayesian Latent Class Analysis Tutorial.

Science.gov (United States)

Li, Yuelin; Lord-Bessen, Jennifer; Shiyko, Mariya; Loeb, Rebecca

2018-01-01

This article is a how-to guide on Bayesian computation using Gibbs sampling, demonstrated in the context of Latent Class Analysis (LCA). It is written for students in quantitative psychology or related fields who have a working knowledge of Bayes Theorem and conditional probability and have experience in writing computer programs in the statistical language R . The overall goals are to provide an accessible and self-contained tutorial, along with a practical computation tool. We begin with how Bayesian computation is typically described in academic articles. Technical difficulties are addressed by a hypothetical, worked-out example. We show how Bayesian computation can be broken down into a series of simpler calculations, which can then be assembled together to complete a computationally more complex model. The details are described much more explicitly than what is typically available in elementary introductions to Bayesian modeling so that readers are not overwhelmed by the mathematics. Moreover, the provided computer program shows how Bayesian LCA can be implemented with relative ease. The computer program is then applied in a large, real-world data set and explained line-by-line. We outline the general steps in how to extend these considerations to other methodological applications. We conclude with suggestions for further readings.

Kinetic details of crystallization in supercooled liquid Pb during the isothermal relaxation

International Nuclear Information System (INIS)

Zhou Lili; Liu Rangsu; Tian Zean; Liu Hairong; Hou Zhaoyang; Peng Ping; Zhu Xuanmin; Liu Quanhui

2012-01-01

The kinetic details of crystallization in supercooled liquid Pb during the isothermal relaxation process have been investigated by molecular dynamics simulations, and the microstructure evolution analyzed by the cluster-type index method (CTIM) and the tracing method. It has been found that, the dynamic features are consistently correlated with the microstructure evolution and the crystallization characteristics in the mean square displacement (MSD) and the non-Gaussian parameter (NGP): the β relaxation regime corresponds to the minor structural rearrangement because of the “cage effect”, and the atoms attempt to escape from the “cages”; the α relaxation regime is related to a more diffusive movement of atoms, and the appearance of the second plateau in MSD and the non-zero plateau in NGP corresponds to the completion of crystallization. In addition, three distinct stages of nucleation, growth of nuclei and coarsening of crystallites in the crystallization process have been clearly revealed.

Bayesian policy reuse

CSIR Research Space (South Africa)

Rosman, Benjamin

2016-02-01

Full Text Available Keywords Policy Reuse · Reinforcement Learning · Online Learning · Online Bandits · Transfer Learning · Bayesian Optimisation · Bayesian Decision Theory. 1 Introduction As robots and software agents are becoming more ubiquitous in many applications.... The agent has access to a library of policies (pi1, pi2 and pi3), and has previously experienced a set of task instances (τ1, τ2, τ3, τ4), as well as samples of the utilities of the library policies on these instances (the black dots indicate the means...

Bulk viscosity of molecular fluids

Science.gov (United States)

Jaeger, Frederike; Matar, Omar K.; Müller, Erich A.

2018-05-01

The bulk viscosity of molecular models of gases and liquids is determined by molecular simulations as a combination of a dilute gas contribution, arising due to the relaxation of internal degrees of freedom, and a configurational contribution, due to the presence of intermolecular interactions. The dilute gas contribution is evaluated using experimental data for the relaxation times of vibrational and rotational degrees of freedom. The configurational part is calculated using Green-Kubo relations for the fluctuations of the pressure tensor obtained from equilibrium microcanonical molecular dynamics simulations. As a benchmark, the Lennard-Jones fluid is studied. Both atomistic and coarse-grained force fields for water, CO2, and n-decane are considered and tested for their accuracy, and where possible, compared to experimental data. The dilute gas contribution to the bulk viscosity is seen to be significant only in the cases when intramolecular relaxation times are in the μs range, and for low vibrational wave numbers (<1000 cm-1); This explains the abnormally high values of bulk viscosity reported for CO2. In all other cases studied, the dilute gas contribution is negligible and the configurational contribution dominates the overall behavior. In particular, the configurational term is responsible for the enhancement of the bulk viscosity near the critical point.

Inverse problems in the Bayesian framework

International Nuclear Information System (INIS)

Calvetti, Daniela; Somersalo, Erkki; Kaipio, Jari P

2014-01-01

The history of Bayesian methods dates back to the original works of Reverend Thomas Bayes and Pierre-Simon Laplace: the former laid down some of the basic principles on inverse probability in his classic article ‘An essay towards solving a problem in the doctrine of chances’ that was read posthumously in the Royal Society in 1763. Laplace, on the other hand, in his ‘Memoirs on inverse probability’ of 1774 developed the idea of updating beliefs and wrote down the celebrated Bayes’ formula in the form we know today. Although not identified yet as a framework for investigating inverse problems, Laplace used the formalism very much in the spirit it is used today in the context of inverse problems, e.g., in his study of the distribution of comets. With the evolution of computational tools, Bayesian methods have become increasingly popular in all fields of human knowledge in which conclusions need to be drawn based on incomplete and noisy data. Needless to say, inverse problems, almost by definition, fall into this category. Systematic work for developing a Bayesian inverse problem framework can arguably be traced back to the 1980s, (the original first edition being published by Elsevier in 1987), although articles on Bayesian methodology applied to inverse problems, in particular in geophysics, had appeared much earlier. Today, as testified by the articles in this special issue, the Bayesian methodology as a framework for considering inverse problems has gained a lot of popularity, and it has integrated very successfully with many traditional inverse problems ideas and techniques, providing novel ways to interpret and implement traditional procedures in numerical analysis, computational statistics, signal analysis and data assimilation. The range of applications where the Bayesian framework has been fundamental goes from geophysics, engineering and imaging to astronomy, life sciences and economy, and continues to grow. There is no question that Bayesian

Relaxation and final-state structure in XPS of atoms, molecules, and metals

International Nuclear Information System (INIS)

Shirley, D.A.; Martin, R.L.; McFeely, F.R.; Kowalczyk, S.P.; Ley, L.

1975-03-01

Photoemission from a many-electron system is a many-electron process, even though the transition operator may affect only one electron directly. Relaxation and ''shake-up'' structure are related by a sum rule. When one is present, the other must be also. Shake-up structure is shown to be accurately predictable in atomic neon and molecular HF if the CI calculations are done carefully. In metals the sum rule also applies but final-state effects usually appear as relaxation energy, which is large even for valence electrons. Finally, in rare-earth metals discrete shake-up structure is observable in the 4p region. (7 figs, 30 refs) (auth)

Bayesian models: A statistical primer for ecologists

Science.gov (United States)

Hobbs, N. Thompson; Hooten, Mevin B.

2015-01-01

Bayesian modeling has become an indispensable tool for ecological research because it is uniquely suited to deal with complexity in a statistically coherent way. This textbook provides a comprehensive and accessible introduction to the latest Bayesian methods—in language ecologists can understand. Unlike other books on the subject, this one emphasizes the principles behind the computations, giving ecologists a big-picture understanding of how to implement this powerful statistical approach.Bayesian Models is an essential primer for non-statisticians. It begins with a definition of probability and develops a step-by-step sequence of connected ideas, including basic distribution theory, network diagrams, hierarchical models, Markov chain Monte Carlo, and inference from single and multiple models. This unique book places less emphasis on computer coding, favoring instead a concise presentation of the mathematical statistics needed to understand how and why Bayesian analysis works. It also explains how to write out properly formulated hierarchical Bayesian models and use them in computing, research papers, and proposals.This primer enables ecologists to understand the statistical principles behind Bayesian modeling and apply them to research, teaching, policy, and management.Presents the mathematical and statistical foundations of Bayesian modeling in language accessible to non-statisticiansCovers basic distribution theory, network diagrams, hierarchical models, Markov chain Monte Carlo, and moreDeemphasizes computer coding in favor of basic principlesExplains how to write out properly factored statistical expressions representing Bayesian models

The current state of Bayesian methods in medical product development: survey results and recommendations from the DIA Bayesian Scientific Working Group.

Science.gov (United States)

Natanegara, Fanni; Neuenschwander, Beat; Seaman, John W; Kinnersley, Nelson; Heilmann, Cory R; Ohlssen, David; Rochester, George

2014-01-01

Bayesian applications in medical product development have recently gained popularity. Despite many advances in Bayesian methodology and computations, increase in application across the various areas of medical product development has been modest. The DIA Bayesian Scientific Working Group (BSWG), which includes representatives from industry, regulatory agencies, and academia, has adopted the vision to ensure Bayesian methods are well understood, accepted more broadly, and appropriately utilized to improve decision making and enhance patient outcomes. As Bayesian applications in medical product development are wide ranging, several sub-teams were formed to focus on various topics such as patient safety, non-inferiority, prior specification, comparative effectiveness, joint modeling, program-wide decision making, analytical tools, and education. The focus of this paper is on the recent effort of the BSWG Education sub-team to administer a Bayesian survey to statisticians across 17 organizations involved in medical product development. We summarize results of this survey, from which we provide recommendations on how to accelerate progress in Bayesian applications throughout medical product development. The survey results support findings from the literature and provide additional insight on regulatory acceptance of Bayesian methods and information on the need for a Bayesian infrastructure within an organization. The survey findings support the claim that only modest progress in areas of education and implementation has been made recently, despite substantial progress in Bayesian statistical research and software availability. Copyright © 2013 John Wiley & Sons, Ltd.

Breathing and Relaxation

Science.gov (United States)

... Find a Doctor Relaxation is the absence of tension in muscle groups and a minimum or absence ... Drill Meditation Progressive Muscle Relaxation Minimizing Shortness of Breath Visualization This information has been approved by Shelby ...

Bayesian Alternation During Tactile Augmentation

Directory of Open Access Journals (Sweden)

Caspar Mathias Goeke

2016-10-01

Full Text Available A large number of studies suggest that the integration of multisensory signals by humans is well described by Bayesian principles. However, there are very few reports about cue combination between a native and an augmented sense. In particular, we asked the question whether adult participants are able to integrate an augmented sensory cue with existing native sensory information. Hence for the purpose of this study we build a tactile augmentation device. Consequently, we compared different hypotheses of how untrained adult participants combine information from a native and an augmented sense. In a two-interval forced choice (2 IFC task, while subjects were blindfolded and seated on a rotating platform, our sensory augmentation device translated information on whole body yaw rotation to tactile stimulation. Three conditions were realized: tactile stimulation only (augmented condition, rotation only (native condition, and both augmented and native information (bimodal condition. Participants had to choose one out of two consecutive rotations with higher angular rotation. For the analysis, we fitted the participants’ responses with a probit model and calculated the just notable difference (JND. Then we compared several models for predicting bimodal from unimodal responses. An objective Bayesian alternation model yielded a better prediction (χred2 = 1.67 than the Bayesian integration model (χred2= 4.34. Slightly higher accuracy showed a non-Bayesian winner takes all model (χred2= 1.64, which either used only native or only augmented values per subject for prediction. However the performance of the Bayesian alternation model could be substantially improved (χred2= 1.09 utilizing subjective weights obtained by a questionnaire. As a result, the subjective Bayesian alternation model predicted bimodal performance most accurately among all tested models. These results suggest that information from augmented and existing sensory modalities in

An introduction to Bayesian statistics in health psychology.

Science.gov (United States)

Depaoli, Sarah; Rus, Holly M; Clifton, James P; van de Schoot, Rens; Tiemensma, Jitske

2017-09-01

The aim of the current article is to provide a brief introduction to Bayesian statistics within the field of health psychology. Bayesian methods are increasing in prevalence in applied fields, and they have been shown in simulation research to improve the estimation accuracy of structural equation models, latent growth curve (and mixture) models, and hierarchical linear models. Likewise, Bayesian methods can be used with small sample sizes since they do not rely on large sample theory. In this article, we discuss several important components of Bayesian statistics as they relate to health-based inquiries. We discuss the incorporation and impact of prior knowledge into the estimation process and the different components of the analysis that should be reported in an article. We present an example implementing Bayesian estimation in the context of blood pressure changes after participants experienced an acute stressor. We conclude with final thoughts on the implementation of Bayesian statistics in health psychology, including suggestions for reviewing Bayesian manuscripts and grant proposals. We have also included an extensive amount of online supplementary material to complement the content presented here, including Bayesian examples using many different software programmes and an extensive sensitivity analysis examining the impact of priors.

Bayesian Network Induction via Local Neighborhoods

National Research Council Canada - National Science Library

Margaritis, Dimitris

1999-01-01

.... We present an efficient algorithm for learning Bayesian networks from data. Our approach constructs Bayesian networks by first identifying each node's Markov blankets, then connecting nodes in a consistent way...

Bayesian inference as a tool for analysis of first-principles calculations of complex materials: an application to the melting point of Ti2GaN

International Nuclear Information System (INIS)

Davis, Sergio; Gutiérrez, Gonzalo

2013-01-01

We present a systematic implementation of the recently developed Z-method for computing melting points of solids, augmented by a Bayesian analysis of the data obtained from molecular dynamics simulations. The use of Bayesian inference allows us to extract valuable information from limited data, reducing the computational cost of drawing the isochoric curve. From this Bayesian Z-method we obtain posterior distributions for the melting temperature T m , the critical superheating temperature T LS and the slopes dT/dE of the liquid and solid phases. The method therefore gives full quantification of the errors in the prediction of the melting point. This procedure is applied to the estimation of the melting point of Ti 2 GaN (one of the so-called MAX phases), a complex, laminar material, by density functional theory molecular dynamics, finding an estimate T m of 2591.61 ± 89.61 K, which is in good agreement with melting points of similar ceramics. (paper)

A Bayesian encourages dropout

OpenAIRE

Maeda, Shin-ichi

2014-01-01

Dropout is one of the key techniques to prevent the learning from overfitting. It is explained that dropout works as a kind of modified L2 regularization. Here, we shed light on the dropout from Bayesian standpoint. Bayesian interpretation enables us to optimize the dropout rate, which is beneficial for learning of weight parameters and prediction after learning. The experiment result also encourages the optimization of the dropout.

Bayesian Data Analysis (lecture 2)

CERN Multimedia

CERN. Geneva

2018-01-01

framework but we will also go into more detail and discuss for example the role of the prior. The second part of the lecture will cover further examples and applications that heavily rely on the bayesian approach, as well as some computational tools needed to perform a bayesian analysis.

Bayesian Data Analysis (lecture 1)

CERN Multimedia

CERN. Geneva

2018-01-01

framework but we will also go into more detail and discuss for example the role of the prior. The second part of the lecture will cover further examples and applications that heavily rely on the bayesian approach, as well as some computational tools needed to perform a bayesian analysis.

Sleep, Stress & Relaxation: Rejuvenate Body & Mind

Science.gov (United States)

Sleep, Stress & Relaxation: Rejuvenate Body & Mind; Relieve Stress; best ways to relieve stress; best way to relieve stress; different ways to relieve stress; does smoking relieve stress; does tobacco relieve stress; how can I relieve stress; how can you relieve stress; how do I relieve stress; reduce stress; does smoking reduce stress; how can I reduce stress; how to reduce stress; reduce stress; reduce stress levels; reducing stress; smoking reduce stress; smoking reduces stress; stress reducing techniques; techniques to reduce stress; stress relief; best stress relief; natural stress relief; need stress relief; relief for stress; relief from stress; relief of stress; smoking and stress relief; smoking for stress relief; smoking stress relief; deal with stress; dealing with stress; dealing with anger; dealing with stress; different ways of dealing with stress; help dealing with stress; how to deal with anger; how to deal with stress; how to deal with stress when quitting smoking; stress management; free stress management; how can you manage stress; how do you manage stress; how to manage stress; manage stress; management of stress; management stress; managing stress; strategies for managing stress; coping with stress; cope with stress; copeing with stress; coping and stress; coping skills for stress; coping strategies for stress; coping strategies with stress; coping strategy for stress; coping with stress; coping with stress and anxiety; emotional health; emotional health; emotional health article; emotional health articles; deep relaxation; deep breathing relaxation techniques; deep muscle relaxation; deep relaxation; deep relaxation meditation; deep relaxation technique; deep relaxation techniques; meditation exercises; mindful exercises; mindful meditation exercises; online relaxation exercises; relaxation breathing exercises; relaxation exercise; relaxation exercises; stress relaxation; methods of relaxation for stress; relax stress; relax techniques stress

Learning Local Components to Understand Large Bayesian Networks

DEFF Research Database (Denmark)

Zeng, Yifeng; Xiang, Yanping; Cordero, Jorge

2009-01-01

(domain experts) to extract accurate information from a large Bayesian network due to dimensional difficulty. We define a formulation of local components and propose a clustering algorithm to learn such local components given complete data. The algorithm groups together most inter-relevant attributes......Bayesian networks are known for providing an intuitive and compact representation of probabilistic information and allowing the creation of models over a large and complex domain. Bayesian learning and reasoning are nontrivial for a large Bayesian network. In parallel, it is a tough job for users...... in a domain. We evaluate its performance on three benchmark Bayesian networks and provide results in support. We further show that the learned components may represent local knowledge more precisely in comparison to the full Bayesian networks when working with a small amount of data....

Philosophy and the practice of Bayesian statistics.

Science.gov (United States)

Gelman, Andrew; Shalizi, Cosma Rohilla

2013-02-01

A substantial school in the philosophy of science identifies Bayesian inference with inductive inference and even rationality as such, and seems to be strengthened by the rise and practical success of Bayesian statistics. We argue that the most successful forms of Bayesian statistics do not actually support that particular philosophy but rather accord much better with sophisticated forms of hypothetico-deductivism. We examine the actual role played by prior distributions in Bayesian models, and the crucial aspects of model checking and model revision, which fall outside the scope of Bayesian confirmation theory. We draw on the literature on the consistency of Bayesian updating and also on our experience of applied work in social science. Clarity about these matters should benefit not just philosophy of science, but also statistical practice. At best, the inductivist view has encouraged researchers to fit and compare models without checking them; at worst, theorists have actively discouraged practitioners from performing model checking because it does not fit into their framework. © 2012 The British Psychological Society.

r1 and r2 Relaxivities of Dendrons Based on a OEG-DTPA Architecture: Effect of Gd3+ Placement and Dendron Functionalization

International Nuclear Information System (INIS)

Fransen, P.; Simon-Gracia, L.; Albericio, F.; Fransen, P.; Pulido, D.; Simon-Gracia, L.; Candiata, A.P.; Arus, C.; Albericio, F.; Royo, M.; Pulido, D.; Royo, M.; Candiata, A.P.; Arus, C.; Candiata, A.P.; Albericio, F.; Candiata, A.P.

2015-01-01

In magnetic resonance imaging, contrast agents are employed to enhance the signal intensity. However, current commercial contrast agents are hindered by a low relaxivity constant. Dendrimers can be employed to create higher molecular weight contrast agents which have an increased relaxivity due to a lower molecular rotation. In this study, dendrimers containing DTPA derivatives as cores and/or branching units were used to chelate gadolinium ions. Locating the gadolinium ions inside the dendrimers results in higher relaxivity constants, possibly because the paramagnetic center is closer to the rotational axis of the macromolecule. The highest gain in relaxivity was produced by decorating the dendron surface with peptide sequences, which could be explained by the presence of more second-sphere water molecules attracted by the peptides. These findings could contribute to the development of more effective contrast agents, either by placing the paramagnetic gadolinium ion in a strategic position or through functionalization of the dendron surface.

r1 and r2 Relaxivities of Dendrons Based on a OEG-DTPA Architecture: Effect of Gd3+ Placement and Dendron Functionalization

Directory of Open Access Journals (Sweden)

Peter Fransen

2015-01-01

Full Text Available In magnetic resonance imaging, contrast agents are employed to enhance the signal intensity. However, current commercial contrast agents are hindered by a low relaxivity constant. Dendrimers can be employed to create higher molecular weight contrast agents which have an increased relaxivity due to a lower molecular rotation. In this study, dendrimers containing DTPA derivatives as cores and/or branching units were used to chelate gadolinium ions. Locating the gadolinium ions inside the dendrimers results in higher relaxivity constants, possibly because the paramagnetic center is closer to the rotational axis of the macromolecule. The highest gain in relaxivity was produced by decorating the dendron surface with peptide sequences, which could be explained by the presence of more second-sphere water molecules attracted by the peptides. These findings could contribute to the development of more effective contrast agents, either by placing the paramagnetic gadolinium ion in a strategic position or through functionalization of the dendron surface.

Memory effects in the relaxation of a confined granular gas

Science.gov (United States)

Brey, J. Javier; de Soria, M. I. García; Maynar, P.; Buzón, V.

2014-09-01

The accuracy of a model to describe the horizontal dynamics of a confined quasi-two-dimensional system of inelastic hard spheres is discussed by comparing its predictions for the relaxation of the temperature in a homogenous system with molecular dynamics simulation results for the original system. A reasonably good agreement is found. Next the model is used to investigate the peculiarities of the nonlinear evolution of the temperature when the parameter controlling the energy injection is instantaneously changed while the system was relaxing. This can be considered as a nonequilibrium generalization of the Kovacs effect. It is shown that, in the low-density limit, the effect can be accurately described by using a simple kinetic theory based on the first Sonine approximation for the one-particle distribution function. Some possible experimental implications are indicated.

Hydration water dynamics in biopolymers from NMR relaxation in the rotating frame.

Science.gov (United States)

Blicharska, Barbara; Peemoeller, Hartwig; Witek, Magdalena

2010-12-01

Assuming dipole-dipole interaction as the dominant relaxation mechanism of protons of water molecules adsorbed onto macromolecule (biopolymer) surfaces we have been able to model the dependences of relaxation rates on temperature and frequency. For adsorbed water molecules the correlation times are of the order of 10(-5)s, for which the dispersion region of spin-lattice relaxation rates in the rotating frame R(1)(ρ)=1/T(1)(ρ) appears over a range of easily accessible B(1) values. Measurements of T(1)(ρ) at constant temperature and different B(1) values then give the "dispersion profiles" for biopolymers. Fitting a theoretical relaxation model to these profiles allows for the estimation of correlation times. This way of obtaining the correlation time is easier and faster than approaches involving measurements of the temperature dependence of R(1)=1/T(1). The T(1)(ρ) dispersion approach, as a tool for molecular dynamics study, has been demonstrated for several hydrated biopolymer systems including crystalline cellulose, starch of different origins (potato, corn, oat, wheat), paper (modern, old) and lyophilized proteins (albumin, lysozyme). Copyright © 2010 Elsevier Inc. All rights reserved.

DUST SPECTRAL ENERGY DISTRIBUTIONS IN THE ERA OF HERSCHEL AND PLANCK: A HIERARCHICAL BAYESIAN-FITTING TECHNIQUE

International Nuclear Information System (INIS)

Kelly, Brandon C.; Goodman, Alyssa A.; Shetty, Rahul; Stutz, Amelia M.; Launhardt, Ralf; Kauffmann, Jens

2012-01-01

We present a hierarchical Bayesian method for fitting infrared spectral energy distributions (SEDs) of dust emission to observed fluxes. Under the standard assumption of optically thin single temperature (T) sources, the dust SED as represented by a power-law-modified blackbody is subject to a strong degeneracy between T and the spectral index β. The traditional non-hierarchical approaches, typically based on χ 2 minimization, are severely limited by this degeneracy, as it produces an artificial anti-correlation between T and β even with modest levels of observational noise. The hierarchical Bayesian method rigorously and self-consistently treats measurement uncertainties, including calibration and noise, resulting in more precise SED fits. As a result, the Bayesian fits do not produce any spurious anti-correlations between the SED parameters due to measurement uncertainty. We demonstrate that the Bayesian method is substantially more accurate than the χ 2 fit in recovering the SED parameters, as well as the correlations between them. As an illustration, we apply our method to Herschel and submillimeter ground-based observations of the star-forming Bok globule CB244. This source is a small, nearby molecular cloud containing a single low-mass protostar and a starless core. We find that T and β are weakly positively correlated—in contradiction with the χ 2 fits, which indicate a T-β anti-correlation from the same data set. Additionally, in comparison to the χ 2 fits the Bayesian SED parameter estimates exhibit a reduced range in values.

The effects of progressive muscle relaxation and autogenic relaxation on young soccer players' mood states.

Science.gov (United States)

Hashim, Hairul Anuar; Hanafi Ahmad Yusof, Hazwani

2011-06-01

This study was designed to compare the effects of two different relaxation techniques, namely progressive muscle relaxation (PMR) and autogenic relaxation (AGR) on moods of young soccer players. sixteen adolescent athletes (mean age: 14.1 ± 1.3) received either PMR or AGR training. Using Profile of Mood States- Adolescents, their mood states were measured one week before relaxation training, before the first relaxation session, and after the twelfth relaxation session. Mixed ANOVA revealed no significant interaction effects and no significant main effects in any of the subscales. However, significant main effects for testing sessions were found for confusion, depression, fatigue, and tension subscales. Post hoc tests revealed post-intervention reductions in the confusion, depression, fatigue, and tension subscale scores. These two relaxation techniques induce equivalent mood responses and may be used to regulate young soccer players' mood states.

Bayesian Utilitarianism

OpenAIRE

ZHOU, Lin

1996-01-01

In this paper I consider social choices under uncertainty. I prove that any social choice rule that satisfies independence of irrelevant alternatives, translation invariance, and weak anonymity is consistent with ex post Bayesian utilitarianism

Learning Bayesian networks for discrete data

KAUST Repository

Liang, Faming; Zhang, Jian

2009-01-01

Bayesian networks have received much attention in the recent literature. In this article, we propose an approach to learn Bayesian networks using the stochastic approximation Monte Carlo (SAMC) algorithm. Our approach has two nice features. Firstly

Searching Algorithm Using Bayesian Updates

Science.gov (United States)

Caudle, Kyle

2010-01-01

In late October 1967, the USS Scorpion was lost at sea, somewhere between the Azores and Norfolk Virginia. Dr. Craven of the U.S. Navy's Special Projects Division is credited with using Bayesian Search Theory to locate the submarine. Bayesian Search Theory is a straightforward and interesting application of Bayes' theorem which involves searching…

The Effects of Progressive Muscle Relaxation and Autogenic Relaxation on Young Soccer Players’ Mood States

Science.gov (United States)

Hashim, Hairul Anuar; Hanafi@Ahmad Yusof, Hazwani

2011-01-01

Purpose This study was designed to compare the effects of two different relaxation techniques, namely progressive muscle relaxation (PMR) and autogenic relaxation (AGR) on moods of young soccer players. Methods Sixteen adolescent athletes (mean age: 14.1 ± 1.3) received either PMR or AGR training. Using Profile of Mood States- Adolescents, their mood states were measured one week before relaxation training, before the first relaxation session, and after the twelfth relaxation session. Results Mixed ANOVA revealed no significant interaction effects and no significant main effects in any of the subscales. However, significant main effects for testing sessions were found for confusion, depression, fatigue, and tension subscales. Post hoc tests revealed post-intervention reductions in the confusion, depression, fatigue, and tension subscale scores. Conclusion These two relaxation techniques induce equivalent mood responses and may be used to regulate young soccer players’ mood states. PMID:22375225

The effect of the Magnus force on skyrmion relaxation dynamics

OpenAIRE

Brown, Barton L.; Täuber, Uwe C.; Pleimling, Michel

2018-01-01

We perform systematic Langevin molecular dynamics simulations of interacting skyrmions in thin films. The interplay between Magnus force, repulsive skyrmion-skyrmion interaction and thermal noise yields different regimes during non-equilibrium relaxation. In the noise-dominated regime the Magnus force enhances the disordering effects of the thermal noise. In the Magnus-force-dominated regime, the Magnus force cooperates with the skyrmion-skyrmion interaction to yield a dynamic regime with slo...

Bayesian estimates of linkage disequilibrium

Directory of Open Access Journals (Sweden)

Abad-Grau María M

2007-06-01

Full Text Available Abstract Background The maximum likelihood estimator of D' – a standard measure of linkage disequilibrium – is biased toward disequilibrium, and the bias is particularly evident in small samples and rare haplotypes. Results This paper proposes a Bayesian estimation of D' to address this problem. The reduction of the bias is achieved by using a prior distribution on the pair-wise associations between single nucleotide polymorphisms (SNPs that increases the likelihood of equilibrium with increasing physical distances between pairs of SNPs. We show how to compute the Bayesian estimate using a stochastic estimation based on MCMC methods, and also propose a numerical approximation to the Bayesian estimates that can be used to estimate patterns of LD in large datasets of SNPs. Conclusion Our Bayesian estimator of D' corrects the bias toward disequilibrium that affects the maximum likelihood estimator. A consequence of this feature is a more objective view about the extent of linkage disequilibrium in the human genome, and a more realistic number of tagging SNPs to fully exploit the power of genome wide association studies.

Viscoelastic characterization of compacted pharmaceutical excipient materials by analysis of frequency-dependent mechanical relaxation processes

Science.gov (United States)

Welch, K.; Mousavi, S.; Lundberg, B.; Strømme, M.

2005-09-01

A newly developed method for determining the frequency-dependent complex Young's modulus was employed to analyze the mechanical response of compacted microcrystalline cellulose, sorbitol, ethyl cellulose and starch for frequencies up to 20 kHz. A Debye-like relaxation was observed in all the studied pharmaceutical excipient materials and a comparison with corresponding dielectric spectroscopy data was made. The location in frequency of the relaxation peak was shown to correlate to the measured tensile strength of the tablets, and the relaxation was interpreted as the vibrational response of the interparticle hydrogen and van der Waals bindings in the tablets. Further, the measured relaxation strength, holding information about the energy loss involved in the relaxation processes, showed that the weakest material in terms of tensile strength, starch, is the material among the four tested ones that is able to absorb the most energy within its structure when exposed to external perturbations inducing vibrations in the studied frequency range. The results indicate that mechanical relaxation analysis performed over relatively broad frequency ranges should be useful for predicting material properties of importance for the functionality of a material in applications such as, e.g., drug delivery, drug storage and handling, and also for clarifying the origin of hitherto unexplained molecular processes.

Learning Bayesian networks for discrete data

KAUST Repository

Liang, Faming

2009-02-01

Bayesian networks have received much attention in the recent literature. In this article, we propose an approach to learn Bayesian networks using the stochastic approximation Monte Carlo (SAMC) algorithm. Our approach has two nice features. Firstly, it possesses the self-adjusting mechanism and thus avoids essentially the local-trap problem suffered by conventional MCMC simulation-based approaches in learning Bayesian networks. Secondly, it falls into the class of dynamic importance sampling algorithms; the network features can be inferred by dynamically weighted averaging the samples generated in the learning process, and the resulting estimates can have much lower variation than the single model-based estimates. The numerical results indicate that our approach can mix much faster over the space of Bayesian networks than the conventional MCMC simulation-based approaches. © 2008 Elsevier B.V. All rights reserved.

Sedative and muscle relaxant activities of diterpenoids from Phlomidoschema parviflorum

Directory of Open Access Journals (Sweden)

Abdur Rauf

Full Text Available Abstract Phlomidoschema parviflorum (Benth. Vved. (Basionym: Stachys parviflora Benth. Lamiaceae, have significance medicinal importance as it is used in number of health disorders including diarrhea, fever, sore mouth and throat, internal bleeding, weaknesses of the liver and heart genital tumors, sclerosis of the spleen, inflammatory tumors and cancerous ulcers. The present contribution deals with the sedative and muscle relaxant like effects of diterpenoids trivially named stachysrosane and stachysrosane, isolated from the ethyl acetate soluble fraction of P. parviflorum. Both compounds (at 5, 10 and 15 mg/kg, i.p were assessed for their in vivo sedative and muscle relaxant activity in open field and inclined plane test, respectively. The geometries of both compounds were optimized with density functional theory. The molecular docking of both compounds were performed with receptor gamma aminobutyric acid. Both compounds showed marked activity in a dose dependent manner. The docking studies showed that both compounds interact strongly with important residues in receptor gamma aminobutyric acid. The reported data demonstrate that both compounds exhibited significant sedative and muscle relaxant-like effects in animal models, which opens a door for novel therapeutic applications.

Molecular theory for nuclear magnetic relaxation in protein solutions and tissue; Surface diffusion and free-volume analogy

Energy Technology Data Exchange (ETDEWEB)

Kimmich, R; Nusser, W; Gneiting, T [Ulm Universitaet (Federal Republic of Germany). Sektion Kernresonanzspektroskopie

1990-04-01

A model theory is presented explaining a series of striking phenomena observed with nuclear magnetic relaxation in protein systems such as solutions or tissue. The frequency, concentration and temperature dependences of proton or deuteron relaxation times of protein solutions and tissue are explained. It is concluded that the translational diffusion of water molecules along the rugged surfaces of proteins and, to a minor degree, protein backbone fluctuations are crucial processes. The rate limiting factor of macromolecular tumbling is assumed to be given by the free water content in a certain analogy to the free-volume model of Cohen ad Turnbull. There are two characteristic water mass fractions indicating the saturation of the hydration shells and the onset of protein tumbling. A closed and relatively simple set of relaxation formulas is presented. The potentially fractal nature of the diffusion of water molecules on the protein surface is discussed. (author). 43 refs.; 4 figs.

Thermodynamically consistent Bayesian analysis of closed biochemical reaction systems

Directory of Open Access Journals (Sweden)

Goutsias John

2010-11-01

Full Text Available Abstract Background Estimating the rate constants of a biochemical reaction system with known stoichiometry from noisy time series measurements of molecular concentrations is an important step for building predictive models of cellular function. Inference techniques currently available in the literature may produce rate constant values that defy necessary constraints imposed by the fundamental laws of thermodynamics. As a result, these techniques may lead to biochemical reaction systems whose concentration dynamics could not possibly occur in nature. Therefore, development of a thermodynamically consistent approach for estimating the rate constants of a biochemical reaction system is highly desirable. Results We introduce a Bayesian analysis approach for computing thermodynamically consistent estimates of the rate constants of a closed biochemical reaction system with known stoichiometry given experimental data. Our method employs an appropriately designed prior probability density function that effectively integrates fundamental biophysical and thermodynamic knowledge into the inference problem. Moreover, it takes into account experimental strategies for collecting informative observations of molecular concentrations through perturbations. The proposed method employs a maximization-expectation-maximization algorithm that provides thermodynamically feasible estimates of the rate constant values and computes appropriate measures of estimation accuracy. We demonstrate various aspects of the proposed method on synthetic data obtained by simulating a subset of a well-known model of the EGF/ERK signaling pathway, and examine its robustness under conditions that violate key assumptions. Software, coded in MATLAB®, which implements all Bayesian analysis techniques discussed in this paper, is available free of charge at http://www.cis.jhu.edu/~goutsias/CSS%20lab/software.html. Conclusions Our approach provides an attractive statistical methodology for

A default Bayesian hypothesis test for ANOVA designs

NARCIS (Netherlands)

Wetzels, R.; Grasman, R.P.P.P.; Wagenmakers, E.J.

2012-01-01

This article presents a Bayesian hypothesis test for analysis of variance (ANOVA) designs. The test is an application of standard Bayesian methods for variable selection in regression models. We illustrate the effect of various g-priors on the ANOVA hypothesis test. The Bayesian test for ANOVA

Bayesian Networks An Introduction

CERN Document Server

Koski, Timo

2009-01-01

Bayesian Networks: An Introduction provides a self-contained introduction to the theory and applications of Bayesian networks, a topic of interest and importance for statisticians, computer scientists and those involved in modelling complex data sets. The material has been extensively tested in classroom teaching and assumes a basic knowledge of probability, statistics and mathematics. All notions are carefully explained and feature exercises throughout. Features include:.: An introduction to Dirichlet Distribution, Exponential Families and their applications.; A detailed description of learni

Nonmaxwell relaxation in disordered media: Physical mechanisms and fractional relaxation equations

International Nuclear Information System (INIS)

Arkhincheev, V.E.

2004-12-01

The problem of charge relaxation in disordered systems has been solved. It is shown, that due to the inhomogeneity of the medium the charge relaxation has a non-Maxwell character. The two physical mechanisms of a such behavior have been founded. The first one is connected with the 'fractality' of conducting ways. The second mechanism of nonexponential non-Maxwell behavior is connected with the frequency dispersion of effective conductivity of heterogeneous medium, initially consisting of conducting phases without dispersion. The new generalized relaxation equations in the form of fractional temporal integro-differential equations are deduced. (author)

A default Bayesian hypothesis test for mediation.

Science.gov (United States)

Nuijten, Michèle B; Wetzels, Ruud; Matzke, Dora; Dolan, Conor V; Wagenmakers, Eric-Jan

2015-03-01

In order to quantify the relationship between multiple variables, researchers often carry out a mediation analysis. In such an analysis, a mediator (e.g., knowledge of a healthy diet) transmits the effect from an independent variable (e.g., classroom instruction on a healthy diet) to a dependent variable (e.g., consumption of fruits and vegetables). Almost all mediation analyses in psychology use frequentist estimation and hypothesis-testing techniques. A recent exception is Yuan and MacKinnon (Psychological Methods, 14, 301-322, 2009), who outlined a Bayesian parameter estimation procedure for mediation analysis. Here we complete the Bayesian alternative to frequentist mediation analysis by specifying a default Bayesian hypothesis test based on the Jeffreys-Zellner-Siow approach. We further extend this default Bayesian test by allowing a comparison to directional or one-sided alternatives, using Markov chain Monte Carlo techniques implemented in JAGS. All Bayesian tests are implemented in the R package BayesMed (Nuijten, Wetzels, Matzke, Dolan, & Wagenmakers, 2014).

Critical thickness for strain relaxation of Ge{sub 1−x}Sn{sub x} (x ≤ 0.17) grown by molecular beam epitaxy on Ge(001)

Energy Technology Data Exchange (ETDEWEB)

Wang, Wei; Zhou, Qian; Dong, Yuan; Yeo, Yee-Chia, E-mail: yeo@ieee.org [Department of Electrical and Computer Engineering, National University of Singapore, Singapore 117576 (Singapore); Tok, Eng Soon [Department of Physics, National University of Singapore, Singapore 117551 (Singapore)

2015-06-08

We investigated the critical thickness (h{sub c}) for plastic relaxation of Ge{sub 1−x}Sn{sub x} grown by molecular beam epitaxy. Ge{sub 1−x}Sn{sub x} films with various Sn mole fraction x (x ≤ 0.17) and different thicknesses were grown on Ge(001). The strain relaxation of Ge{sub 1−x}Sn{sub x} films and the h{sub c} were investigated by high-resolution x-ray diffraction and reciprocal space mapping. It demonstrates that the measured h{sub c} values of Ge{sub 1−x}Sn{sub x} layers are as much as an order of magnitude larger than that predicted by the Matthews and Blakeslee (M-B) model. The People and Bean (P-B) model was also used to predict the h{sub c} values in Ge{sub 1−x}Sn{sub x}/Ge system. The measured h{sub c} values for various Sn content follow the trend, but slightly larger than that predicted by the P-B model.

A Bayesian model for binary Markov chains

Directory of Open Access Journals (Sweden)

Belkheir Essebbar

2004-02-01

Full Text Available This note is concerned with Bayesian estimation of the transition probabilities of a binary Markov chain observed from heterogeneous individuals. The model is founded on the Jeffreys' prior which allows for transition probabilities to be correlated. The Bayesian estimator is approximated by means of Monte Carlo Markov chain (MCMC techniques. The performance of the Bayesian estimates is illustrated by analyzing a small simulated data set.

NMR structural refinement of an extrahelical adenosine tridecamer d(CGCAGAATTCGCG)2 via a hybrid relaxation matrix procedure

International Nuclear Information System (INIS)

Nikonowicz, E.P.; Meadows, R.P.; Gorenstein, D.G.

1990-01-01

Until very recently interproton distances from NOESY experiments have been derived solely from the two-spin approximation method. Unfortunately, even at short mixing times, there is a significant error in many of these distances. A complete relaxation matrix approach employing a matrix eigenvalue/eigenvector solution to the Bloch equations avoids the approximation of the two-spin method. The authors calculated the structure of an extrahelical adenosine tridecamer oligodeoxyribonucleotide duplex, d-(CGCAGAATTCGCG) 2 , by an iterative refinement approach using a hybrid relaxation matrix method combined with restrained molecular dynamics calculations. Distances from the 2D NOESY spectra have been calculated from the relaxation rate matrix which has been evaluated from a hybrid NOESY volume matrix comprising elements from the experiment and those calculated from an initial structure. The hybrid matrix derived distances have then been used in a restrained molecular dynamics procedure to obtain a new structure that better approximates the NOESY spectra. The resulting partially refined structure is then used to calculate an improved theoretical NOESY volume matrix which is once again merged with the experimental matrix until refinement is complete. Although the crystal structure of the tridecamer clearly shows the extrahelical adenosine looped out way from the duplex, the NOESY distance restrained hybrid matrix/molecular dynamics structural refinement establishes that the extrahelical adenosine stacks into the duplex

Inference in hybrid Bayesian networks

DEFF Research Database (Denmark)

Lanseth, Helge; Nielsen, Thomas Dyhre; Rumí, Rafael

2009-01-01

Since the 1980s, Bayesian Networks (BNs) have become increasingly popular for building statistical models of complex systems. This is particularly true for boolean systems, where BNs often prove to be a more efficient modelling framework than traditional reliability-techniques (like fault trees...... decade's research on inference in hybrid Bayesian networks. The discussions are linked to an example model for estimating human reliability....

Relaxed geometries and dipole moments of positron complexes with diatomic molecules

Energy Technology Data Exchange (ETDEWEB)

Assafrao, Denise; Mohallem, Jose R, E-mail: rachid@fisica.ufmg.b [Laboratorio de Atomos e Moleculas Especiais, Departamento de Fisica, ICEx, Universidade Federal de Minas Gerais, CP 702, 30123-970, Belo Horizonte, MG (Brazil)

2010-01-01

Relaxed geometries and dipole moments of diatomic molecules interacting with a slow positron are reported as functions of the positron distance to the more electronegative atom. A molecular model for the complex that allows applications to large systems is used. The electron population on the positron is proposed as a weighting function to calculate the average quantities. Results show Self-Consistent-Field quality or better.

Theory of relaxation phenomena in a spin-3/2 Ising system near the second-order phase transition temperature

International Nuclear Information System (INIS)

Keskin, Mustafa; Canko, Osman

2005-01-01

The relaxation behavior of the spin-3/2 Ising model Hamiltonian with bilinear and biquadratic interactions near the second-order phase transition temperature or critical temperature is studied by means of the Onsager's theory of irreversible thermodynamics or the Onsager reciprocity theorem (ORT). First, we give the equilibrium case briefly within the molecular-field approximation in order to study the relaxation behavior by using the ORT. Then, the ORT is applied to the model and the kinetic equations are obtained. By solving these equations, three relaxation times are calculated and examined for temperatures near the second-order phase transition temperature. It is found that one of the relaxation times goes to infinity near the critical temperature on either side, the second relaxation time makes a cusp at the critical temperature and third one behaves very differently in which it terminates at the critical temperature while approaching it, then showing a 'flatness' property and then decreases. We also study the influences of the Onsager rate coefficients on the relaxation times. The behavior of these relaxation times is discussed and compared with the spin-1/2 and spin-1 Ising systems

Time, stress, and temperature-dependent deformation in nanostructured copper: Stress relaxation tests and simulations

International Nuclear Information System (INIS)

Yang, Xu-Sheng; Wang, Yun-Jiang; Wang, Guo-Yong; Zhai, Hui-Ru; Dai, L.H.; Zhang, Tong-Yi

2016-01-01

In the present work, stress relaxation tests, high-resolution transmission electron microscopy (HRTEM), and molecular dynamics (MD) simulations were conducted on coarse-grained (cg), nanograined (ng), and nanotwinned (nt) copper at temperatures of 22 °C (RT), 30 °C, 40 °C, 50 °C, and 75 °C. The comprehensive investigations provide sufficient information for the building-up of a formula to describe the time, stress, and temperature-dependent deformation and clarify the relationship among the strain rate sensitivity parameter, stress exponent, and activation volume. The typically experimental curves of logarithmic plastic strain rate versus stress exhibited a three staged relaxation process from a linear high stress relaxation region to a subsequent nonlinear stress relaxation region and finally to a linear low stress relaxation region, which only showed-up at the test temperatures higher than 22 °C, 22 °C, and 30 °C, respectively, in the tested cg-, ng-, and nt-Cu specimens. The values of stress exponent, stress-independent activation energy, and activation volume were determined from the experimental data in the two linear regions. The determined activation parameters, HRTEM images, and MD simulations consistently suggest that dislocation-mediated plastic deformation is predominant in all tested cg-, ng-, and nt-Cu specimens in the initial linear high stress relaxation region at the five relaxation temperatures, whereas in the linear low stress relaxation region, the grain boundary (GB) diffusion-associated deformation is dominant in the ng- and cg-Cu specimens, while twin boundary (TB) migration, i.e., twinning and detwinning with parallel partial dislocations, governs the time, stress, and temperature-dependent deformation in the nt-Cu specimens.

Multiple-decker phthalocyaninato dinuclear lanthanoid(III) single-molecule magnets with dual-magnetic relaxation processes.

Science.gov (United States)

Katoh, Keiichi; Horii, Yoji; Yasuda, Nobuhiro; Wernsdorfer, Wolfgang; Toriumi, Koshiro; Breedlove, Brian K; Yamashita, Masahiro

2012-11-28

The SMM behaviour of dinuclear Ln(III)-Pc multiple-decker complexes (Ln = Tb(3+) and Dy(3+)) with energy barriers and slow-relaxation behaviour were explained by using X-ray crystallography and static and dynamic susceptibility measurements. In particular, interactions among the 4f electrons of several dinuclear Ln(III)-Pc type SMMs have never been discussed on the basis of the crystal structure. For dinuclear Tb(III)-Pc complexes, a dual magnetic relaxation process was observed. The relaxation processes are due to the anisotropic centres. Our results clearly show that the two Tb(3+) ion sites are equivalent and are consistent with the crystal structure. On the other hand, the mononuclear Tb(III)-Pc complex exhibited only a single magnetic relaxation process. This is clear evidence that the magnetic relaxation mechanism depends heavily on the dipole-dipole (f-f) interactions between the Tb(3+) ions in the dinuclear systems. Furthermore, the SMM behaviour of dinuclear Dy(III)-Pc type SMMs with smaller energy barriers compared with that of Tb(III)-Pc and slow-relaxation behaviour was explained. Dinuclear Dy(III)-Pc SMMs exhibited single-component magnetic relaxation behaviour. The results indicate that the magnetic relaxation properties of dinuclear Ln(III)-Pc multiple-decker complexes are affected by the local molecular symmetry and are extremely sensitive to tiny distortions in the coordination geometry. In other words, the spatial arrangement of the Ln(3+) ions (f-f interactions) in the crystal is important. Our work shows that the SMM properties can be fine-tuned by introducing weak intermolecular magnetic interactions in a controlled SMM spatial arrangement.

Bayesian theory and applications

CERN Document Server

Dellaportas, Petros; Polson, Nicholas G; Stephens, David A

2013-01-01

The development of hierarchical models and Markov chain Monte Carlo (MCMC) techniques forms one of the most profound advances in Bayesian analysis since the 1970s and provides the basis for advances in virtually all areas of applied and theoretical Bayesian statistics. This volume guides the reader along a statistical journey that begins with the basic structure of Bayesian theory, and then provides details on most of the past and present advances in this field. The book has a unique format. There is an explanatory chapter devoted to each conceptual advance followed by journal-style chapters that provide applications or further advances on the concept. Thus, the volume is both a textbook and a compendium of papers covering a vast range of topics. It is appropriate for a well-informed novice interested in understanding the basic approach, methods and recent applications. Because of its advanced chapters and recent work, it is also appropriate for a more mature reader interested in recent applications and devel...

NMR and molecular dynamics of small solutes in liquid crystals

International Nuclear Information System (INIS)

Luyten, P.R.

1984-01-01

NMR relaxation measurements, using a wide variety of modern pulse techniques, can yield valuable information about molecular motions. In this thesis the applicability of theories developed to describe spin relaxation phenomena in partially ordered media is studied for small solutes in liquid crystals. 1 H, 2 H, 13 C and 14 N relaxation measurements are interpreted by means of a model, in which fast anisotropic re-orientational motion in an orienting potential combined with contributions from cooperative fluctuations in the surrounding liquid crystal molecules, induce the observed frequency dependent relaxation behavior. (orig.)

Bayesian quantification of thermodynamic uncertainties in dense gas flows

International Nuclear Information System (INIS)

Merle, X.; Cinnella, P.

2015-01-01

A Bayesian inference methodology is developed for calibrating complex equations of state used in numerical fluid flow solvers. Precisely, the input parameters of three equations of state commonly used for modeling the thermodynamic behavior of the so-called dense gas flows, – i.e. flows of gases characterized by high molecular weights and complex molecules, working in thermodynamic conditions close to the liquid–vapor saturation curve – are calibrated by means of Bayesian inference from reference aerodynamic data for a dense gas flow over a wing section. Flow thermodynamic conditions are such that the gas thermodynamic behavior strongly deviates from that of a perfect gas. In the aim of assessing the proposed methodology, synthetic calibration data – specifically, wall pressure data – are generated by running the numerical solver with a more complex and accurate thermodynamic model. The statistical model used to build the likelihood function includes a model-form inadequacy term, accounting for the gap between the model output associated to the best-fit parameters and the true phenomenon. Results show that, for all of the relatively simple models under investigation, calibrations lead to informative posterior probability density distributions of the input parameters and improve the predictive distribution significantly. Nevertheless, calibrated parameters strongly differ from their expected physical values. The relationship between this behavior and model-form inadequacy is discussed. - Highlights: • Development of a Bayesian inference procedure for calibrating dense-gas flow solvers. • Complex thermodynamic models calibrated by using aerodynamic data for the flow. • Preliminary Sobol analysis used to reduce parameter space. • Piecewise polynomial surrogate model constructed to reduce computational cost. • Calibration results show the crucial role played by model-form inadequacies

Universal Darwinism As a Process of Bayesian Inference.

Science.gov (United States)

Campbell, John O

2016-01-01

Many of the mathematical frameworks describing natural selection are equivalent to Bayes' Theorem, also known as Bayesian updating. By definition, a process of Bayesian Inference is one which involves a Bayesian update, so we may conclude that these frameworks describe natural selection as a process of Bayesian inference. Thus, natural selection serves as a counter example to a widely-held interpretation that restricts Bayesian Inference to human mental processes (including the endeavors of statisticians). As Bayesian inference can always be cast in terms of (variational) free energy minimization, natural selection can be viewed as comprising two components: a generative model of an "experiment" in the external world environment, and the results of that "experiment" or the "surprise" entailed by predicted and actual outcomes of the "experiment." Minimization of free energy implies that the implicit measure of "surprise" experienced serves to update the generative model in a Bayesian manner. This description closely accords with the mechanisms of generalized Darwinian process proposed both by Dawkins, in terms of replicators and vehicles, and Campbell, in terms of inferential systems. Bayesian inference is an algorithm for the accumulation of evidence-based knowledge. This algorithm is now seen to operate over a wide range of evolutionary processes, including natural selection, the evolution of mental models and cultural evolutionary processes, notably including science itself. The variational principle of free energy minimization may thus serve as a unifying mathematical framework for universal Darwinism, the study of evolutionary processes operating throughout nature.

Effect of extender oils on the stress relaxation behavior of thermoplastic vulcanizates

Directory of Open Access Journals (Sweden)

2008-11-01

Full Text Available The long term mechanical behavior of oil extended thermoplastic vulcanizates (TPV based on polypropylene (PP and acrylonitrile-butadiene rubber (NBR has been characterized by means of stress relaxation experiments. The morphology of TPV and the phase specific oil distribution which depend on the content and type of oil as well as on the mixing regime have been characterized by means of Atomic Force Microscopy (AFM, Dynamic Mechanical Thermal Analysis (DMTA and Differential Scanning Calorimetrie (DSC. The discussion of the stress relaxation behavior was carried out using the two-component model, which allows splitting the initial stress into two components: a thermal activated stress component and an athermal one. A master curve was created by shifting the relaxation curves vertically and horizontally towards the reference curve. The vertical shift factor bT is a function of the temperature dependence of the athermal stress components. It was found that the oil distribution strongly affects the athermal stress component which is related to the contribution of the structural changes, e.g. crystallinity of the PP phase and the average molecular weight between the crosslinks of the NBR phase. From the temperature dependence of the horizontal shift factor aT the main viscoelastic relaxation process was determined as the α-relaxation process of the crystalline PP phase. It is not dependent on the polarity and content of the oil as well as the mixing regime.

Vibrational relaxation dynamics of SD molecules in As2S3: Observation of an anomalous isotope effect

International Nuclear Information System (INIS)

Engholm, J.R.; Happek, U.; Rella, C.W.

1995-01-01

It is generally assumed that the vibrational relaxation of molecular impurities in crystals and glasses mainly depends on the order of the decay process, with lower order processes leading to more rapid relaxation (a behavior that is known under the term open-quotes gap-lawclose quotes). Here we present measurements that contradict this assumption. Using high intensity psec pulses of the Stanford FEL we measured the relaxation rate of the SD vibrational stretch mode (at a frequency of 1800 cm) by applying a pump-probe technique. We find relaxation rates on the order of 2x10 9 sec -1 , which are a factor of 2 lower than those found for the isotope molecule SH (at a frequency of about 2500 cm - 1 ) in the same host 1 . We recall that the relaxation of the SD vibrational stretch mode is controlled by a lower order process as compared to the SH molecule, which is due to the smaller number of host vibrational quanta to match the energy of the stretch mode; a fact we have confirmed experimentally by temperature dependent relaxation measurements. Thus our remits are in marked contrast to the so-called open-quotes Gap-Lawclose quotes and emphasize the importance of the molecule - host coupling in the relaxation dynamics

Exploring the dynamics about the glass transition by muon spin relaxation and muon spin rotation

International Nuclear Information System (INIS)

Bermejo, F J; Bustinduy, I; Cox, S F J; Lord, J S; Cabrillo, C; Gonzalez, M A

2006-01-01

The capability of muon spin rotation and muon spin relaxation to explore dynamics in the vicinity of the glass transition is illustrated by results pertaining to three materials exhibiting two different glass-forming abilities. Measurements under transverse magnetic fields enable us to monitor the dynamics of muonium-labelled closed-shell molecules within the microsecond range. The results display the onset of stochastic molecular motions taking place upon crossing from below the glass-transition temperature. In turn, the molecular dynamics of radicals formed by addition of atomic muonium to unsaturated organic molecules can also be explored up to far shorter times by means of relaxation measurements under longitudinal fields. The technique is then shown to be capable of singling out stochastic reorientational motions from others, which usually are strongly coupled to them and usually dominate the material response when measured using higher-frequency probes such as neutron and light scattering

TEACHING NEUROMUSCULAR RELAXATION.

Science.gov (United States)

NORRIS, JEANNE E.; STEINHAUS, ARTHUR H.

THIS STUDY ATTEMPTED TO FIND OUT WHETHER (1) THE METHODS FOR ATTAINING NEUROMUSCULAR RELAXATION THAT HAVE PROVED FRUITFUL IN THE ONE-TO-ONE RELATIONSHIP OF THE CLINIC CAN BE SUCCESSFULLY ADAPTED TO THE TEACHER-CLASS RELATIONSHIP OF THE CLASSROOM AND GYMNASIUM, AND (2) NEUROMUSCULAR RELAXATION CAN BE TAUGHT SUCCESSFULLY BY AN APPROPRIATELY TRAINED…

Daniel Goodman’s empirical approach to Bayesian statistics

Science.gov (United States)

Gerrodette, Tim; Ward, Eric; Taylor, Rebecca L.; Schwarz, Lisa K.; Eguchi, Tomoharu; Wade, Paul; Himes Boor, Gina

2016-01-01

Bayesian statistics, in contrast to classical statistics, uses probability to represent uncertainty about the state of knowledge. Bayesian statistics has often been associated with the idea that knowledge is subjective and that a probability distribution represents a personal degree of belief. Dr. Daniel Goodman considered this viewpoint problematic for issues of public policy. He sought to ground his Bayesian approach in data, and advocated the construction of a prior as an empirical histogram of “similar” cases. In this way, the posterior distribution that results from a Bayesian analysis combined comparable previous data with case-specific current data, using Bayes’ formula. Goodman championed such a data-based approach, but he acknowledged that it was difficult in practice. If based on a true representation of our knowledge and uncertainty, Goodman argued that risk assessment and decision-making could be an exact science, despite the uncertainties. In his view, Bayesian statistics is a critical component of this science because a Bayesian analysis produces the probabilities of future outcomes. Indeed, Goodman maintained that the Bayesian machinery, following the rules of conditional probability, offered the best legitimate inference from available data. We give an example of an informative prior in a recent study of Steller sea lion spatial use patterns in Alaska.

Signal-BNF: A Bayesian Network Fusing Approach to Predict Signal Peptides

Directory of Open Access Journals (Sweden)

Zhi Zheng

2012-01-01

Full Text Available A signal peptide is a short peptide chain that directs the transport of a protein and has become the crucial vehicle in finding new drugs or reprogramming cells for gene therapy. As the avalanche of new protein sequences generated in the postgenomic era, the challenge of identifying new signal sequences has become even more urgent and critical in biomedical engineering. In this paper, we propose a novel predictor called Signal-BNF to predict the N-terminal signal peptide as well as its cleavage site based on Bayesian reasoning network. Signal-BNF is formed by fusing the results of different Bayesian classifiers which used different feature datasets as its input through weighted voting system. Experiment results show that Signal-BNF is superior to the popular online predictors such as Signal-3L and PrediSi. Signal-BNF is featured by high prediction accuracy that may serve as a useful tool for further investigating many unclear details regarding the molecular mechanism of the zip code protein-sorting system in cells.

The Effects of Progressive Relaxation and Music on Attention, Relaxation, and Stress Responses: An Investigation of the Cognitive-Behavioral Model of Relaxation

National Research Council Canada - National Science Library

Scheufele, Peter

1999-01-01

...) suggested that stress management techniques have specific effects A compromise position suggests that the specific effects of relaxation techniques are superimposed upon a general relaxation response...

Approximation methods for efficient learning of Bayesian networks

CERN Document Server

Riggelsen, C

2008-01-01

This publication offers and investigates efficient Monte Carlo simulation methods in order to realize a Bayesian approach to approximate learning of Bayesian networks from both complete and incomplete data. For large amounts of incomplete data when Monte Carlo methods are inefficient, approximations are implemented, such that learning remains feasible, albeit non-Bayesian. The topics discussed are: basic concepts about probabilities, graph theory and conditional independence; Bayesian network learning from data; Monte Carlo simulation techniques; and, the concept of incomplete data. In order to provide a coherent treatment of matters, thereby helping the reader to gain a thorough understanding of the whole concept of learning Bayesian networks from (in)complete data, this publication combines in a clarifying way all the issues presented in the papers with previously unpublished work.

Bayesian community detection

DEFF Research Database (Denmark)

Mørup, Morten; Schmidt, Mikkel N

2012-01-01

Many networks of scientific interest naturally decompose into clusters or communities with comparatively fewer external than internal links; however, current Bayesian models of network communities do not exert this intuitive notion of communities. We formulate a nonparametric Bayesian model...... for community detection consistent with an intuitive definition of communities and present a Markov chain Monte Carlo procedure for inferring the community structure. A Matlab toolbox with the proposed inference procedure is available for download. On synthetic and real networks, our model detects communities...... consistent with ground truth, and on real networks, it outperforms existing approaches in predicting missing links. This suggests that community structure is an important structural property of networks that should be explicitly modeled....

Inverse Problems in a Bayesian Setting

KAUST Repository

Matthies, Hermann G.

2016-02-13

In a Bayesian setting, inverse problems and uncertainty quantification (UQ)—the propagation of uncertainty through a computational (forward) model—are strongly connected. In the form of conditional expectation the Bayesian update becomes computationally attractive. We give a detailed account of this approach via conditional approximation, various approximations, and the construction of filters. Together with a functional or spectral approach for the forward UQ there is no need for time-consuming and slowly convergent Monte Carlo sampling. The developed sampling-free non-linear Bayesian update in form of a filter is derived from the variational problem associated with conditional expectation. This formulation in general calls for further discretisation to make the computation possible, and we choose a polynomial approximation. After giving details on the actual computation in the framework of functional or spectral approximations, we demonstrate the workings of the algorithm on a number of examples of increasing complexity. At last, we compare the linear and nonlinear Bayesian update in form of a filter on some examples.

Inverse Problems in a Bayesian Setting

KAUST Repository

Matthies, Hermann G.; Zander, Elmar; Rosić, Bojana V.; Litvinenko, Alexander; Pajonk, Oliver

2016-01-01

In a Bayesian setting, inverse problems and uncertainty quantification (UQ)—the propagation of uncertainty through a computational (forward) model—are strongly connected. In the form of conditional expectation the Bayesian update becomes computationally attractive. We give a detailed account of this approach via conditional approximation, various approximations, and the construction of filters. Together with a functional or spectral approach for the forward UQ there is no need for time-consuming and slowly convergent Monte Carlo sampling. The developed sampling-free non-linear Bayesian update in form of a filter is derived from the variational problem associated with conditional expectation. This formulation in general calls for further discretisation to make the computation possible, and we choose a polynomial approximation. After giving details on the actual computation in the framework of functional or spectral approximations, we demonstrate the workings of the algorithm on a number of examples of increasing complexity. At last, we compare the linear and nonlinear Bayesian update in form of a filter on some examples.

Implementing the Bayesian paradigm in risk analysis

International Nuclear Information System (INIS)

Aven, T.; Kvaloey, J.T.

2002-01-01

The Bayesian paradigm comprises a unified and consistent framework for analyzing and expressing risk. Yet, we see rather few examples of applications where the full Bayesian setting has been adopted with specifications of priors of unknown parameters. In this paper, we discuss some of the practical challenges of implementing Bayesian thinking and methods in risk analysis, emphasizing the introduction of probability models and parameters and associated uncertainty assessments. We conclude that there is a need for a pragmatic view in order to 'successfully' apply the Bayesian approach, such that we can do the assignments of some of the probabilities without adopting the somewhat sophisticated procedure of specifying prior distributions of parameters. A simple risk analysis example is presented to illustrate ideas

Dielectric relaxation studies in super-cooled liquid and glassy phases of anti-cancerous alkaloid: Brucine

Science.gov (United States)

Afzal, Aboothahir; Shahin Thayyil, M.; Sulaiman, M. K.; Kulkarni, A. R.

2018-05-01

Brucine has good anti-tumor effects, on both liver cancer and breast cancer. It has bioavailability of 40.83%. Since the bioavailability of the drug is low, an alternative method to increase its bioavailability and solubility is by changing the drug into glassy form. We used Differential Scanning Calorimetry (DSC) for studying the glass forming ability of the drug. Brucine was found to be a very good glass former glass transition temperature 365 K. Based on the DSC analysis we have used broadband dielectric spectroscopy (BDS) for studying the drug in the super cooled and glassy state. BDS is an effective tool to probe the molecular dynamics in the super cooled and glassy state. Molecular mobility is found to be present even in the glassy state of this active pharmaceutical ingredient (API) which is responsible for the instability. Our aim is to study the factors responsible for instability of this API in amorphous form. Cooling curves for dielectric permittivity and dielectric loss revealed the presence of structural (α) and secondary relaxations (β and γ). Temperature dependence of relaxation time is fitted by Vogel-Fulcher-Tammann equation and found the values of activation energy of the α relaxation, fragility and glass transition temperature. Paluch's anti correlation is also verified, that the width of the α-loss peak at or near the glass transition temperature Tg is strongly anticorrelated with the polarity of the molecule. The larger the dielectric relaxation strength Δɛ (Tg) of the system, the narrower is the α-loss peak (higher value of βKWW).

Interactive Instruction in Bayesian Inference

DEFF Research Database (Denmark)

Khan, Azam; Breslav, Simon; Hornbæk, Kasper

2018-01-01

An instructional approach is presented to improve human performance in solving Bayesian inference problems. Starting from the original text of the classic Mammography Problem, the textual expression is modified and visualizations are added according to Mayer’s principles of instruction. These pri......An instructional approach is presented to improve human performance in solving Bayesian inference problems. Starting from the original text of the classic Mammography Problem, the textual expression is modified and visualizations are added according to Mayer’s principles of instruction....... These principles concern coherence, personalization, signaling, segmenting, multimedia, spatial contiguity, and pretraining. Principles of self-explanation and interactivity are also applied. Four experiments on the Mammography Problem showed that these principles help participants answer the questions...... that an instructional approach to improving human performance in Bayesian inference is a promising direction....

On the microscopic fluctuations driving the NMR relaxation of quadrupolar ions in water

Energy Technology Data Exchange (ETDEWEB)

Carof, Antoine; Salanne, Mathieu; Rotenberg, Benjamin, E-mail: benjamin.rotenberg@upmc.fr [Sorbonne Universités, UPMC Univ. Paris 06, CNRS, Laboratoire PHENIX, Case 51, 4 Place Jussieu, F-75005 Paris (France); Charpentier, Thibault [CEA, IRAMIS, NIMBE, LSDRM, UMR CEA-CNRS 3685, F-91191 Gif-sur-Yvette Cedex (France)

2015-11-21

Nuclear Magnetic Resonance (NMR) relaxation is sensitive to the local structure and dynamics around the probed nuclei. The Electric Field Gradient (EFG) is the key microscopic quantity to understand the NMR relaxation of quadrupolar ions, such as {sup 7}Li{sup +}, {sup 23}Na{sup +}, {sup 25}Mg{sup 2+}, {sup 35}Cl{sup −}, {sup 39}K{sup +}, or {sup 133}Cs{sup +}. Using molecular dynamics simulations, we investigate the statistical and dynamical properties of the EFG experienced by alkaline, alkaline Earth, and chloride ions at infinite dilution in water. Specifically, we analyze the effect of the ionic charge and size on the distribution of the EFG tensor and on the multi-step decay of its auto-correlation function. The main contribution to the NMR relaxation time arises from the slowest mode, with a characteristic time on the picosecond time scale. The first solvation shell of the ion plays a dominant role in the fluctuations of the EFG, all the more that the ion radius is small and its charge is large. We propose an analysis based on a simplified charge distribution around the ion, which demonstrates that the auto-correlation of the EFG, hence the NMR relaxation time, reflects primarily the collective translational motion of water molecules in the first solvation shell of the cations. Our findings provide a microscopic route to the quantitative interpretation of NMR relaxation measurements and open the way to the design of improved analytical theories for NMR relaxation for small ionic solutes, which should focus on water density fluctuations around the ion.

Universal Darwinism as a process of Bayesian inference

Directory of Open Access Journals (Sweden)

John Oberon Campbell

2016-06-01

Full Text Available Many of the mathematical frameworks describing natural selection are equivalent to Bayes’ Theorem, also known as Bayesian updating. By definition, a process of Bayesian Inference is one which involves a Bayesian update, so we may conclude that these frameworks describe natural selection as a process of Bayesian inference. Thus natural selection serves as a counter example to a widely-held interpretation that restricts Bayesian Inference to human mental processes (including the endeavors of statisticians. As Bayesian inference can always be cast in terms of (variational free energy minimization, natural selection can be viewed as comprising two components: a generative model of an ‘experiment’ in the external world environment, and the results of that 'experiment' or the 'surprise' entailed by predicted and actual outcomes of the ‘experiment’. Minimization of free energy implies that the implicit measure of 'surprise' experienced serves to update the generative model in a Bayesian manner. This description closely accords with the mechanisms of generalized Darwinian process proposed both by Dawkins, in terms of replicators and vehicles, and Campbell, in terms of inferential systems. Bayesian inference is an algorithm for the accumulation of evidence-based knowledge. This algorithm is now seen to operate over a wide range of evolutionary processes, including natural selection, the evolution of mental models and cultural evolutionary processes, notably including science itself. The variational principle of free energy minimization may thus serve as a unifying mathematical framework for universal Darwinism, the study of evolutionary processes operating throughout nature.

Bayesian analysis of magnetic island dynamics

International Nuclear Information System (INIS)

Preuss, R.; Maraschek, M.; Zohm, H.; Dose, V.

2003-01-01

We examine a first order differential equation with respect to time used to describe magnetic islands in magnetically confined plasmas. The free parameters of this equation are obtained by employing Bayesian probability theory. Additionally, a typical Bayesian change point is solved in the process of obtaining the data

Strain relaxation and ambipolar electrical transport in GaAs/InSb core-shell nanowires.

Science.gov (United States)

Rieger, Torsten; Zellekens, Patrick; Demarina, Natalia; Hassan, Ali Al; Hackemüller, Franz Josef; Lüth, Hans; Pietsch, Ullrich; Schäpers, Thomas; Grützmacher, Detlev; Lepsa, Mihail Ion

2017-11-30

The growth, crystal structure, strain relaxation and room temperature transport characteristics of GaAs/InSb core-shell nanowires grown using molecular beam epitaxy are investigated. Due to the large lattice mismatch between GaAs and InSb of 14%, a transition from island-based to layer-like growth occurs during the formation of the shell. High resolution transmission electron microscopy in combination with geometric phase analyses as well as X-ray diffraction with synchrotron radiation are used to investigate the strain relaxation and prove the existence of different dislocations relaxing the strain on zinc blende and wurtzite core-shell nanowire segments. While on the wurtzite phase only Frank partial dislocations are found, the strain on the zinc blende phase is relaxed by dislocations with perfect, Shockley partial and Frank partial dislocations. Even for ultrathin shells of about 2 nm thickness, the strain caused by the high lattice mismatch between GaAs and InSb is relaxed almost completely. Transfer characteristics of the core-shell nanowires show an ambipolar conductance behavior whose strength strongly depends on the dimensions of the nanowires. The interpretation is given based on an electronic band profile which is calculated for completely relaxed core/shell structures. The peculiarities of the band alignment in this situation implies simultaneously occupied electron and hole channels in the InSb shell. The ambipolar behavior is then explained by the change of carrier concentration in both channels by the gate voltage.

Crystallization Behavior and Relaxation Dynamics of Supercooled S‑Ketoprofen and the Racemic Mixture along an Isochrone

DEFF Research Database (Denmark)

Adrjanowicz, Karolina; Kaminski, Kamil; Paluch, Marian

2015-01-01

In this paper, we study crystallization behavior and molecular dynamics in the supercooled liquid state of the pharmaceutically important compound ketoprofen at various thermodynamic conditions. Dielectric relaxation for a racemic mixture was investigated in a wide range of temperatures and press...

Automated NMR relaxation dispersion data analysis using NESSY

Directory of Open Access Journals (Sweden)

Gooley Paul R

2011-10-01

Full Text Available Abstract Background Proteins are dynamic molecules with motions ranging from picoseconds to longer than seconds. Many protein functions, however, appear to occur on the micro to millisecond timescale and therefore there has been intense research of the importance of these motions in catalysis and molecular interactions. Nuclear Magnetic Resonance (NMR relaxation dispersion experiments are used to measure motion of discrete nuclei within the micro to millisecond timescale. Information about conformational/chemical exchange, populations of exchanging states and chemical shift differences are extracted from these experiments. To ensure these parameters are correctly extracted, accurate and careful analysis of these experiments is necessary. Results The software introduced in this article is designed for the automatic analysis of relaxation dispersion data and the extraction of the parameters mentioned above. It is written in Python for multi platform use and highest performance. Experimental data can be fitted to different models using the Levenberg-Marquardt minimization algorithm and different statistical tests can be used to select the best model. To demonstrate the functionality of this program, synthetic data as well as NMR data were analyzed. Analysis of these data including the generation of plots and color coded structures can be performed with minimal user intervention and using standard procedures that are included in the program. Conclusions NESSY is easy to use open source software to analyze NMR relaxation data. The robustness and standard procedures are demonstrated in this article.

Brownian relaxation of an inelastic sphere in air

Energy Technology Data Exchange (ETDEWEB)

Bird, G. A., E-mail: gab@gab.com.au [University of Sydney, Sydney, NSW 2006 (Australia)

2016-06-15

The procedures that are used to calculate the forces and moments on an aerodynamic body in the rarefied gas of the upper atmosphere are applied to a small sphere of the size of an aerosol particle at sea level. While the gas-surface interaction model that provides accurate results for macroscopic bodies may not be appropriate for bodies that are comprised of only about a thousand atoms, it provides a limiting case that is more realistic than the elastic model. The paper concentrates on the transfer of energy from the air to an initially stationary sphere as it acquires Brownian motion. Individual particle trajectories vary wildly, but a clear relaxation process emerges from an ensemble average over tens of thousands of trajectories. The translational and rotational energies in equilibrium Brownian motion are determined. Empirical relationships are obtained for the mean translational and rotational relaxation times, the mean initial power input to the particle, the mean rates of energy transfer between the particle and air, and the diffusivity. These relationships are functions of the ratio of the particle mass to an average air molecule mass and the Knudsen number, which is the ratio of the mean free path in the air to the particle diameter. The ratio of the molecular radius to the particle radius also enters as a correction factor. The implications of Brownian relaxation for the second law of thermodynamics are discussed.

Ion peening and stress relaxation induced by low-energy atom bombardment of covalent solids

International Nuclear Information System (INIS)

Koster, Monika; Urbassek, Herbert M.

2001-01-01

Using molecular-dynamics simulation, we study the buildup and relaxation of stress induced by low-energy (≤150 eV) atom bombardment of a target material. The effect is brought out most clearly by using an initially compressed specimen. As target material, we employ Si, based on the Tersoff potential. By varying the bond strength in the potential, we can specifically study its effect on damage production and stress changes. We find that in general, stress is relaxed by the atom bombardment; only for low bombarding energies and strong bonds, atom bombardment increases stress. We rationalize this behavior by considering the role of energized atoms and of recoil-implanted target atoms

Dielectric relaxation and hydrogen bonding interaction in xylitol-water mixtures using time domain reflectometry

Science.gov (United States)

Rander, D. N.; Joshi, Y. S.; Kanse, K. S.; Kumbharkhane, A. C.

2016-01-01

The measurements of complex dielectric permittivity of xylitol-water mixtures have been carried out in the frequency range of 10 MHz-30 GHz using a time domain reflectometry technique. Measurements have been done at six temperatures from 0 to 25 °C and at different weight fractions of xylitol (0 xylitol-water can be well described by Cole-Davidson model having an asymmetric distribution of relaxation times. The dielectric parameters such as static dielectric constant and relaxation time for the mixtures have been evaluated. The molecular interaction between xylitol and water molecules is discussed using the Kirkwood correlation factor ( g eff ) and thermodynamic parameter.

Relaxation dynamics and thermophysical properties of vegetable oils using time-domain reflectometry.

Science.gov (United States)

Sonkamble, Anil A; Sonsale, Rahul P; Kanshette, Mahesh S; Kabara, Komal B; Wananje, Kunal H; Kumbharkhane, Ashok C; Sarode, Arvind V

2017-04-01

Dielectric relaxation studies of vegetable oils are important for insights into their hydrogen bonding and intermolecular dynamics. The dielectric relaxation and thermo physical properties of triglycerides present in some vegetable oils have been measured over the frequency range of 10 MHz to 7 GHz in the temperature region 25 to 10 °C using a time-domain reflectometry approach. The frequency and temperature dependence of dielectric constants and dielectric loss factors were determined for coconut, peanut, soya bean, sunflower, palm, and olive oils. The dielectric permittivity spectra for each of the studied vegetable oils are explained using the Debye model with their complex dielectric permittivity analyzed using the Havriliak-Negami equation. The dielectric parameters static permittivity (ε 0 ), high-frequency limiting static permittivity (ε ∞ ), average relaxation time (τ 0 ), and thermodynamic parameters such as free energy (∆F τ ), enthalpy (∆H τ ), and entropy of activation (∆S τ ) were also measured. Calculation and analysis of these thermodynamic parameters agrees with the determined dielectric parameters, giving insights into the temperature dependence of the molecular dynamics of these systems.

Two-dimensional 1H and 31P NMR spectra and restrained molecular dynamics structure of an oligodeoxyribonucleotide duplex refined via a hybrid relaxation matrix procedure

International Nuclear Information System (INIS)

Powers, R.; Jones, C.R.; Gorenstein, D.G.

1990-01-01

Assignment of the 1H and 31P resonances of a decamer DNA duplex, d(CGCTTAAGCG)2 was determined by two-dimensional COSY, NOESY and 1H-31P Pure Absorption phase Constant time (PAC) heteronuclear correlation spectroscopy. The solution structure of the decamer was calculated by an iterative hybrid relaxation matrix method combined with NOESY-distance restrained molecular dynamics. The distances from the 2D NOESY spectra were calculated from the relaxation rate matrix which were evaluated from a hybrid NOESY volume matrix comprising elements from the experiment and those calculated from an initial structure. The hybrid matrix-derived distances were then used in a restrained molecular dynamics procedure to obtain a new structure that better approximates the NOESY spectra. The resulting partially refined structure was then used to calculate an improved theoretical NOESY volume matrix which is once again merged with the experimental matrix until refinement is complete. JH3'-P coupling constants for each of the phosphates of the decamer were obtained from 1H-31P J-resolved selective proton flip 2D spectra. By using a modified Karplus relationship the C4'-C3'-O3'-P torsional angles were obtained. Comparison of the 31P chemical shifts and JH3'-P coupling constants of this sequence has allowed a greater insight into the various factors responsible for 31P chemical shift variations in oligonucleotides. It also provides an important probe of the sequence-dependent structural variation of the deoxyribose phosphate backbone of DNA in solution. These correlations are consistent with the hypothesis that changes in local helical structure perturb the deoxyribose phosphate backbone. The variation of the 31P chemical shift, and the degree of this variation from one base step to the next is proposed as a potential probe of local helical conformation within the DNA double helix

Rapid simultaneous high-resolution mapping of myelin water fraction and relaxation times in human brain using BMC-mcDESPOT.

Science.gov (United States)

Bouhrara, Mustapha; Spencer, Richard G

2017-02-15

A number of central nervous system (CNS) diseases exhibit changes in myelin content and magnetic resonance longitudinal, T 1 , and transverse, T 2 , relaxation times, which therefore represent important biomarkers of CNS pathology. Among the methods applied for measurement of myelin water fraction (MWF) and relaxation times, the multicomponent driven equilibrium single pulse observation of T 1 and T 2 (mcDESPOT) approach is of particular interest. mcDESPOT permits whole brain mapping of multicomponent T 1 and T 2 , with data acquisition accomplished within a clinically realistic acquisition time. Unfortunately, previous studies have indicated the limited performance of mcDESPOT in the setting of the modest signal-to-noise range of high-resolution mapping, required for the depiction of small structures and to reduce partial volume effects. Recently, we showed that a new Bayesian Monte Carlo (BMC) analysis substantially improved determination of MWF from mcDESPOT imaging data. However, our previous study was limited in that it did not discuss determination of relaxation times. Here, we extend the BMC analysis to the simultaneous determination of whole-brain MWF and relaxation times using the two-component mcDESPOT signal model. Simulation analyses and in-vivo human brain studies indicate the overall greater performance of this approach compared to the stochastic region contraction (SRC) algorithm, conventionally used to derive parameter estimates from mcDESPOT data. SRC estimates of the transverse relaxation time of the long T 2 fraction, T 2,l , and the longitudinal relaxation time of the short T 1 fraction, T 1,s , clustered towards the lower and upper parameter search space limits, respectively, indicating failure of the fitting procedure. We demonstrate that this effect is absent in the BMC analysis. Our results also showed improved parameter estimation for BMC as compared to SRC for high-resolution mapping. Overall we find that the combination of BMC analysis

Bayesian Decision Theoretical Framework for Clustering

Science.gov (United States)

Chen, Mo

2011-01-01

In this thesis, we establish a novel probabilistic framework for the data clustering problem from the perspective of Bayesian decision theory. The Bayesian decision theory view justifies the important questions: what is a cluster and what a clustering algorithm should optimize. We prove that the spectral clustering (to be specific, the…

Superradiance from crystals of molecular nanomagnets.

Science.gov (United States)

Chudnovsky, E M; Garanin, D A

2002-10-07

We show that crystals of molecular nanomagnets can exhibit giant magnetic relaxation due to the Dicke superradiance of electromagnetic waves. Rigorous theory is presented that combines superradiance with the Landau-Zener effect.

Relaxation dynamics in quantum dissipative systems: The microscopic effect of intramolecular vibrational energy redistribution

Energy Technology Data Exchange (ETDEWEB)

Uranga-Piña, L. [Facultad de Física, Universidad de la Habana, San Lázaro y L, Vedado, 10400 Havana (Cuba); Institute for Chemistry and Biochemistry, Freie Universität Berlin, Takustr. 3, D-14195 Berlin (Germany); Tremblay, J. C., E-mail: jean.c.tremblay@gmail.com [Institute for Chemistry and Biochemistry, Freie Universität Berlin, Takustr. 3, D-14195 Berlin (Germany)

2014-08-21

We investigate the effect of inter-mode coupling on the vibrational relaxation dynamics of molecules in weak dissipative environments. The simulations are performed within the reduced density matrix formalism in the Markovian regime, assuming a Lindblad form for the system-bath interaction. The prototypical two-dimensional model system representing two CO molecules approaching a Cu(100) surface is adapted from an ab initio potential, while the diatom-diatom vibrational coupling strength is systematically varied. In the weak system-bath coupling limit and at low temperatures, only first order non-adiabatic uni-modal coupling terms contribute to surface-mediated vibrational relaxation. Since dissipative dynamics is non-unitary, the choice of representation will affect the evolution of the reduced density matrix. Two alternative representations for computing the relaxation rates and the associated operators are thus compared: the fully coupled spectral basis, and a factorizable ansatz. The former is well-established and serves as a benchmark for the solution of Liouville-von Neumann equation. In the latter, a contracted grid basis of potential-optimized discrete variable representation is tailored to incorporate most of the inter-mode coupling, while the Lindblad operators are represented as tensor products of one-dimensional operators, for consistency. This procedure results in a marked reduction of the grid size and in a much more advantageous scaling of the computational cost with respect to the increase of the dimensionality of the system. The factorizable method is found to provide an accurate description of the dissipative quantum dynamics of the model system, specifically of the time evolution of the state populations and of the probability density distribution of the molecular wave packet. The influence of intra-molecular vibrational energy redistribution appears to be properly taken into account by the new model on the whole range of coupling strengths. It

Magnetic relaxation in anisotropic magnets

DEFF Research Database (Denmark)

Lindgård, Per-Anker

1971-01-01

The line shape and the kinematic and thermodynamic slowing down of the critical and paramagnetic relaxation in axially anisotropic materials are discussed. Kinematic slowing down occurs only in the longitudinal relaxation function. The thermodynamic slowing down occurs in either the transverse...... or longitudinal relaxation function depending on the sign of the axial anisotropy....

Convergence among cave catfishes: long-branch attraction and a Bayesian relative rates test.

Science.gov (United States)

Wilcox, T P; García de León, F J; Hendrickson, D A; Hillis, D M

2004-06-01

Convergence has long been of interest to evolutionary biologists. Cave organisms appear to be ideal candidates for studying convergence in morphological, physiological, and developmental traits. Here we report apparent convergence in two cave-catfishes that were described on morphological grounds as congeners: Prietella phreatophila and Prietella lundbergi. We collected mitochondrial DNA sequence data from 10 species of catfishes, representing five of the seven genera in Ictaluridae, as well as seven species from a broad range of siluriform outgroups. Analysis of the sequence data under parsimony supports a monophyletic Prietella. However, both maximum-likelihood and Bayesian analyses support polyphyly of the genus, with P. lundbergi sister to Ictalurus and P. phreatophila sister to Ameiurus. The topological difference between parsimony and the other methods appears to result from long-branch attraction between the Prietella species. Similarly, the sequence data do not support several other relationships within Ictaluridae supported by morphology. We develop a new Bayesian method for examining variation in molecular rates of evolution across a phylogeny.

Quantum-Like Representation of Non-Bayesian Inference

Science.gov (United States)

Asano, M.; Basieva, I.; Khrennikov, A.; Ohya, M.; Tanaka, Y.

2013-01-01

This research is related to the problem of "irrational decision making or inference" that have been discussed in cognitive psychology. There are some experimental studies, and these statistical data cannot be described by classical probability theory. The process of decision making generating these data cannot be reduced to the classical Bayesian inference. For this problem, a number of quantum-like coginitive models of decision making was proposed. Our previous work represented in a natural way the classical Bayesian inference in the frame work of quantum mechanics. By using this representation, in this paper, we try to discuss the non-Bayesian (irrational) inference that is biased by effects like the quantum interference. Further, we describe "psychological factor" disturbing "rationality" as an "environment" correlating with the "main system" of usual Bayesian inference.

Correct Bayesian and frequentist intervals are similar

International Nuclear Information System (INIS)

Atwood, C.L.

1986-01-01

This paper argues that Bayesians and frequentists will normally reach numerically similar conclusions, when dealing with vague data or sparse data. It is shown that both statistical methodologies can deal reasonably with vague data. With sparse data, in many important practical cases Bayesian interval estimates and frequentist confidence intervals are approximately equal, although with discrete data the frequentist intervals are somewhat longer. This is not to say that the two methodologies are equally easy to use: The construction of a frequentist confidence interval may require new theoretical development. Bayesians methods typically require numerical integration, perhaps over many variables. Also, Bayesian can easily fall into the trap of over-optimism about their amount of prior knowledge. But in cases where both intervals are found correctly, the two intervals are usually not very different. (orig.)

Relaxation and physical aging in network glasses: a review.

Science.gov (United States)

Micoulaut, Matthieu

2016-06-01

Recent progress in the description of glassy relaxation and aging are reviewed for the wide class of network-forming materials such as GeO2, Ge x Se1-x , silicates (SiO2-Na2O) or borates (B2O3-Li2O), all of which have an important usefulness in domestic, geological or optoelectronic applications. A brief introduction of the glass transition phenomenology is given, together with the salient features that are revealed both from theory and experiments. Standard experimental methods used for the characterization of the slowing down of the dynamics are reviewed. We then discuss the important role played by aspects of network topology and rigidity for the understanding of the relaxation of the glass transition, while also permitting analytical predictions of glass properties from simple and insightful models based on the network structure. We also emphasize the great utility of computer simulations which probe the dynamics at the molecular level, and permit the calculation of various structure-related functions in connection with glassy relaxation and the physics of aging which reveal the non-equilibrium nature of glasses. We discuss the notion of spatial variations of structure which leads to the concept of 'dynamic heterogeneities', and recent results in relation to this important topic for network glasses are also reviewed.

Excitation relaxation and structure of TPPS4 J-aggregates

International Nuclear Information System (INIS)

Kelbauskas, L.; Bagdonas, S.; Dietel, W.; Rotomskis, R.

2003-01-01

The energy relaxation kinetics and the structure of the J-aggregates of water-soluble porphyrin 5,10,15,20-tetrasulphonatophenyl porphine (TPPS 4 ) were investigated in aqueous medium by means of time-resolved fluorescence spectroscopy and confocal laser-scanning fluorescence microscopy. The excitation of the J-aggregates, at excitation intensities higher than ∼10 15 photons/cm 2 per pulse, results in a remarkable decrease of the fluorescence quantum yield and in the appearance of an additional, non-exponential energy relaxation channel with a decay constant that depends on the excitation intensity. This relaxation mechanism was attributed to the exciton single-singlet annihilation. The exciton lifetime in the absence of the annihilation was calculated to be ∼150 ps. Using exciton annihilation theory, the exciton migration within the J-aggregates could be characterized by determining the exciton diffusion constant (1.8±0.9) 10 -3 cm 2 /s and the hopping time (1.2±0.6) ps. Using the experimental data, the size of the J-aggregate could be evaluated and was seen to yield at least 20 TPPS 4 molecules per aggregate. It was shown by means of confocal fluorescence laser scanning microscopy that TPPS 4 does self-associate in polyvinyl alcohol (PVA) at acidic pH forming molecular macro-assemblies on a scale of ∼1 μm in PVA matrices

Using consensus bayesian network to model the reactive oxygen species regulatory pathway.

Directory of Open Access Journals (Sweden)

Liangdong Hu

Full Text Available Bayesian network is one of the most successful graph models for representing the reactive oxygen species regulatory pathway. With the increasing number of microarray measurements, it is possible to construct the bayesian network from microarray data directly. Although large numbers of bayesian network learning algorithms have been developed, when applying them to learn bayesian networks from microarray data, the accuracies are low due to that the databases they used to learn bayesian networks contain too few microarray data. In this paper, we propose a consensus bayesian network which is constructed by combining bayesian networks from relevant literatures and bayesian networks learned from microarray data. It would have a higher accuracy than the bayesian networks learned from one database. In the experiment, we validated the bayesian network combination algorithm on several classic machine learning databases and used the consensus bayesian network to model the Escherichia coli's ROS pathway.

Bayesian analysis of rare events

Energy Technology Data Exchange (ETDEWEB)

Straub, Daniel, E-mail: straub@tum.de; Papaioannou, Iason; Betz, Wolfgang

2016-06-01

In many areas of engineering and science there is an interest in predicting the probability of rare events, in particular in applications related to safety and security. Increasingly, such predictions are made through computer models of physical systems in an uncertainty quantification framework. Additionally, with advances in IT, monitoring and sensor technology, an increasing amount of data on the performance of the systems is collected. This data can be used to reduce uncertainty, improve the probability estimates and consequently enhance the management of rare events and associated risks. Bayesian analysis is the ideal method to include the data into the probabilistic model. It ensures a consistent probabilistic treatment of uncertainty, which is central in the prediction of rare events, where extrapolation from the domain of observation is common. We present a framework for performing Bayesian updating of rare event probabilities, termed BUS. It is based on a reinterpretation of the classical rejection-sampling approach to Bayesian analysis, which enables the use of established methods for estimating probabilities of rare events. By drawing upon these methods, the framework makes use of their computational efficiency. These methods include the First-Order Reliability Method (FORM), tailored importance sampling (IS) methods and Subset Simulation (SuS). In this contribution, we briefly review these methods in the context of the BUS framework and investigate their applicability to Bayesian analysis of rare events in different settings. We find that, for some applications, FORM can be highly efficient and is surprisingly accurate, enabling Bayesian analysis of rare events with just a few model evaluations. In a general setting, BUS implemented through IS and SuS is more robust and flexible.

Dielectric Relaxation Studies of 2-Butoxyethanol with Aniline and Substituted Anilines Using Time Domain Reflectometry

Directory of Open Access Journals (Sweden)

P. Jeevanandham

2014-01-01

Full Text Available The complex dielectric spectra of 2-butoxyethanol with aniline and substituted anilines like aniline, o-chloroaniline, m-chloroaniline, o-anisidine and m-anisidine binary mixtures in the composition of different volumes of percent (0%, 25%, 50%, 75%, and 100% have been measured as a function of frequency between 10 MHz and 30 GHz at 298.15 K. The dielectric parameters like static dielectric constant ε0 and relaxation time τ have been obtained by using least square fit method. By using these parameters ε0,τ, effective Kirkwood correlation factor geff, corrective Kirkwood correlation factor gf, Bruggeman factor fB, excess dielectric constant εE, and excess inverse relaxation time 1/τE values are calculated and discussed to yield information on the dipolar alignment and molecular rotation of the binary liquid mixtures. From all the derived dielectric parameters, molecular interactions are interpreted through hydrogen bonding.

Nuclear magnetic relaxation by the dipolar EMOR mechanism: General theory with applications to two-spin systems.

Science.gov (United States)

Chang, Zhiwei; Halle, Bertil

2016-02-28

In aqueous systems with immobilized macromolecules, including biological tissue, the longitudinal spin relaxation of water protons is primarily induced by exchange-mediated orientational randomization (EMOR) of intra- and intermolecular magnetic dipole-dipole couplings. We have embarked on a systematic program to develop, from the stochastic Liouville equation, a general and rigorous theory that can describe relaxation by the dipolar EMOR mechanism over the full range of exchange rates, dipole coupling strengths, and Larmor frequencies. Here, we present a general theoretical framework applicable to spin systems of arbitrary size with symmetric or asymmetric exchange. So far, the dipolar EMOR theory is only available for a two-spin system with symmetric exchange. Asymmetric exchange, when the spin system is fragmented by the exchange, introduces new and unexpected phenomena. Notably, the anisotropic dipole couplings of non-exchanging spins break the axial symmetry in spin Liouville space, thereby opening up new relaxation channels in the locally anisotropic sites, including longitudinal-transverse cross relaxation. Such cross-mode relaxation operates only at low fields; at higher fields it becomes nonsecular, leading to an unusual inverted relaxation dispersion that splits the extreme-narrowing regime into two sub-regimes. The general dipolar EMOR theory is illustrated here by a detailed analysis of the asymmetric two-spin case, for which we present relaxation dispersion profiles over a wide range of conditions as well as analytical results for integral relaxation rates and time-dependent spin modes in the zero-field and motional-narrowing regimes. The general theoretical framework presented here will enable a quantitative analysis of frequency-dependent water-proton longitudinal relaxation in model systems with immobilized macromolecules and, ultimately, will provide a rigorous link between relaxation-based magnetic resonance image contrast and molecular parameters.

WISDOM Project - II. Molecular gas measurement of the supermassive black hole mass in NGC 4697

Science.gov (United States)

Davis, Timothy A.; Bureau, Martin; Onishi, Kyoko; Cappellari, Michele; Iguchi, Satoru; Sarzi, Marc

2017-07-01

As part of the mm-Wave Interferometric Survey of Dark Object Masses (WISDOM) project, we present an estimate of the mass of the supermassive black hole (SMBH) in the nearby fast-rotating early-type galaxy NGC 4697. This estimate is based on Atacama Large Millimeter/submillimeter Array (ALMA) cycle-3 observations of the 12CO(2-1) emission line with a linear resolution of 29 pc (0.53 arcsec). We find that NGC 4697 hosts a small relaxed central molecular gas disc with a mass of 1.6 × 107 M⊙, co-spatial with the obscuring dust disc visible in optical Hubble Space Telescope imaging. We also resolve thermal 1 mm continuum emission from the dust in this disc. NGC 4697 is found to have a very low molecular gas velocity dispersion, σgas = 1.65^{+0.68}_{-0.65} km s-1. This seems to be partially because the giant molecular cloud mass function is not fully sampled, but other mechanisms such as chemical differentiation in a hard radiation field or morphological quenching also seem to be required. We detect a Keplerian increase of the rotation of the molecular gas in the very centre of NGC 4697, and use forward modelling of the ALMA data cube in a Bayesian framework with the KINematic Molecular Simulation (kinms) code to estimate an SMBH mass of (1.3_{-0.17}^{+0.18}) × 108 M⊙ and an I-band mass-to-light ratio of 2.14_{-0.05}^{+0.04} M⊙/L⊙ (at the 99 per cent confidence level). Our estimate of the SMBH mass is entirely consistent with previous measurements from stellar kinematics. This increases confidence in the growing number of SMBH mass estimates being obtained in the ALMA era.

Bayesian models a statistical primer for ecologists

CERN Document Server

Hobbs, N Thompson

2015-01-01

Bayesian modeling has become an indispensable tool for ecological research because it is uniquely suited to deal with complexity in a statistically coherent way. This textbook provides a comprehensive and accessible introduction to the latest Bayesian methods-in language ecologists can understand. Unlike other books on the subject, this one emphasizes the principles behind the computations, giving ecologists a big-picture understanding of how to implement this powerful statistical approach. Bayesian Models is an essential primer for non-statisticians. It begins with a definition of probabili

Communication: Slow relaxation, spatial mobility gradients, and vitrification in confined films

International Nuclear Information System (INIS)

Mirigian, Stephen; Schweizer, Kenneth S.

2014-01-01

Two decades of experimental research indicate that spatial confinement of glass-forming molecular and polymeric liquids results in major changes of their slow dynamics beginning at large confinement distances. A fundamental understanding remains elusive given the generic complexity of activated relaxation in supercooled liquids and the major complications of geometric confinement, interfacial effects, and spatial inhomogeneity. We construct a predictive, quantitative, force-level theory of relaxation in free-standing films for the central question of the nature of the spatial mobility gradient. The key new idea is that vapor interfaces speed up barrier hopping in two distinct, but coupled, ways by reducing near surface local caging constraints and spatially long range collective elastic distortion. Effective vitrification temperatures, dynamic length scales, and mobile layer thicknesses naturally follow. Our results provide a unified basis for central observations of dynamic and pseudo-thermodynamic measurements

Communication: Slow relaxation, spatial mobility gradients, and vitrification in confined films

Energy Technology Data Exchange (ETDEWEB)

Mirigian, Stephen [Department of Materials Science, University of Illinois, Urbana, Illinois 61801 (United States); Frederick Seitz Materials Research Laboratory, University of Illinois, Urbana, Illinois 61801 (United States); Schweizer, Kenneth S., E-mail: kschweiz@illinois.edu [Department of Materials Science, University of Illinois, Urbana, Illinois 61801 (United States); Frederick Seitz Materials Research Laboratory, University of Illinois, Urbana, Illinois 61801 (United States); Department of Chemistry, University of Illinois, Urbana, Illinois 61801 (United States); Department of Chemical and Biomolecular Engineering, University of Illinois, Urbana, Illinois 61801 (United States)

2014-10-28

Two decades of experimental research indicate that spatial confinement of glass-forming molecular and polymeric liquids results in major changes of their slow dynamics beginning at large confinement distances. A fundamental understanding remains elusive given the generic complexity of activated relaxation in supercooled liquids and the major complications of geometric confinement, interfacial effects, and spatial inhomogeneity. We construct a predictive, quantitative, force-level theory of relaxation in free-standing films for the central question of the nature of the spatial mobility gradient. The key new idea is that vapor interfaces speed up barrier hopping in two distinct, but coupled, ways by reducing near surface local caging constraints and spatially long range collective elastic distortion. Effective vitrification temperatures, dynamic length scales, and mobile layer thicknesses naturally follow. Our results provide a unified basis for central observations of dynamic and pseudo-thermodynamic measurements.

Cross relaxation in nitroxide spin labels

DEFF Research Database (Denmark)

Marsh, Derek

2016-01-01

Cross relaxation, and mI-dependence of the intrinsic electron spin-lattice relaxation rate We, are incorporated explicitly into the rate equations for the electron-spin population differences that govern the saturation behaviour of 14N- and 15N-nitroxide spin labels. Both prove important in spin......-label EPR and ELDOR, particularly for saturation recovery studies. Neither for saturation recovery, nor for CW-saturation EPR and CW-ELDOR, can cross relaxation be described simply by increasing the value of We, the intrinsic spin-lattice relaxation rate. Independence of the saturation recovery rates from...... the hyperfine line pumped or observed follows directly from solution of the rate equations including cross relaxation, even when the intrinsic spin-lattice relaxation rate We is mI-dependent....

Study of the Molecular Dynamics of Multiarm Star Polymers with a Poly(ethyleneimine) Core and Poly(lactide) Multiarms.

Science.gov (United States)

Román, Frida; Colomer, Pere; Calventus, Yolanda; Hutchinson, John M

2017-02-04

Multiarm star polymers, denoted PEI x -PLA y and containing a hyperbranched poly(ethyleneimine) (PEI) core of different molecular weights x and poly(lactide) (PLA) arms with y ratio of lactide repeat units to N links were used in this work. Samples were preconditioned to remove the moisture content and then characterized by thermogravimetric analysis (TGA), differential scanning calorimetry (DSC) and dielectric relaxation spectroscopy (DRS). The glass transition temperature, T g , is between 48 and 50 °C for all the PEI x -PLA y samples. The dielectric curves show four dipolar relaxations: γ, β, α, and α' in order of increasing temperature. The temperatures at which these relaxations appear, together with their dependence on the frequency, allows relaxation maps to be drawn, from which the activation energies of the sub- T g γ- and β-relaxations and the Vogel-Fulcher-Tammann parameters of the α-relaxation glass transition are obtained. The dependence of the characteristic features of these relaxations on the molecular weight of the PEI core and on the ratio of lactide repeat units to N links permits the assignation of molecular motions to each relaxation. The γ-relaxation is associated with local motions of the -OH groups of the poly(lactide) chains, the β-relaxation with motions of the main chain of poly(lactide), the α-relaxation with global motions of the complete assembly of PEI core and PLA arms, and the α'-relaxation is related to the normal mode relaxation due to fluctuations of the end-to-end vector in the PLA arms, without excluding the possibility that it could be a Maxwell-Wagner-Sillars type ionic peak because the material may have nano-regions of different conductivity.

Study of the Molecular Dynamics of Multiarm Star Polymers with a Poly(ethyleneimine Core and Poly(lactide Multiarms

Directory of Open Access Journals (Sweden)

Frida Román

2017-02-01

Full Text Available Multiarm star polymers, denoted PEIx-PLAy and containing a hyperbranched poly(ethyleneimine (PEI core of different molecular weights x and poly(lactide (PLA arms with y ratio of lactide repeat units to N links were used in this work. Samples were preconditioned to remove the moisture content and then characterized by thermogravimetric analysis (TGA, differential scanning calorimetry (DSC and dielectric relaxation spectroscopy (DRS. The glass transition temperature, Tg, is between 48 and 50 °C for all the PEIx-PLAy samples. The dielectric curves show four dipolar relaxations: γ, β, α, and α′ in order of increasing temperature. The temperatures at which these relaxations appear, together with their dependence on the frequency, allows relaxation maps to be drawn, from which the activation energies of the sub-Tg γ- and β-relaxations and the Vogel–Fulcher–Tammann parameters of the α-relaxation glass transition are obtained. The dependence of the characteristic features of these relaxations on the molecular weight of the PEI core and on the ratio of lactide repeat units to N links permits the assignation of molecular motions to each relaxation. The γ-relaxation is associated with local motions of the –OH groups of the poly(lactide chains, the β-relaxation with motions of the main chain of poly(lactide, the α-relaxation with global motions of the complete assembly of PEI core and PLA arms, and the α′-relaxation is related to the normal mode relaxation due to fluctuations of the end-to-end vector in the PLA arms, without excluding the possibility that it could be a Maxwell–Wagner–Sillars type ionic peak because the material may have nano-regions of different conductivity.

Robust Bayesian detection of unmodelled bursts

International Nuclear Information System (INIS)

Searle, Antony C; Sutton, Patrick J; Tinto, Massimo; Woan, Graham

2008-01-01

We develop a Bayesian treatment of the problem of detecting unmodelled gravitational wave bursts using the new global network of interferometric detectors. We also compare this Bayesian treatment with existing coherent methods, and demonstrate that the existing methods make implicit assumptions on the distribution of signals that make them sub-optimal for realistic signal populations

BAYESIAN ESTIMATION OF THERMONUCLEAR REACTION RATES

Energy Technology Data Exchange (ETDEWEB)

Iliadis, C.; Anderson, K. S. [Department of Physics and Astronomy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3255 (United States); Coc, A. [Centre de Sciences Nucléaires et de Sciences de la Matière (CSNSM), CNRS/IN2P3, Univ. Paris-Sud, Université Paris–Saclay, Bâtiment 104, F-91405 Orsay Campus (France); Timmes, F. X.; Starrfield, S., E-mail: iliadis@unc.edu [School of Earth and Space Exploration, Arizona State University, Tempe, AZ 85287-1504 (United States)

2016-11-01

The problem of estimating non-resonant astrophysical S -factors and thermonuclear reaction rates, based on measured nuclear cross sections, is of major interest for nuclear energy generation, neutrino physics, and element synthesis. Many different methods have been applied to this problem in the past, almost all of them based on traditional statistics. Bayesian methods, on the other hand, are now in widespread use in the physical sciences. In astronomy, for example, Bayesian statistics is applied to the observation of extrasolar planets, gravitational waves, and Type Ia supernovae. However, nuclear physics, in particular, has been slow to adopt Bayesian methods. We present astrophysical S -factors and reaction rates based on Bayesian statistics. We develop a framework that incorporates robust parameter estimation, systematic effects, and non-Gaussian uncertainties in a consistent manner. The method is applied to the reactions d(p, γ ){sup 3}He, {sup 3}He({sup 3}He,2p){sup 4}He, and {sup 3}He( α , γ ){sup 7}Be, important for deuterium burning, solar neutrinos, and Big Bang nucleosynthesis.

Prior approval: the growth of Bayesian methods in psychology.

Science.gov (United States)

Andrews, Mark; Baguley, Thom

2013-02-01

Within the last few years, Bayesian methods of data analysis in psychology have proliferated. In this paper, we briefly review the history or the Bayesian approach to statistics, and consider the implications that Bayesian methods have for the theory and practice of data analysis in psychology.

Can a significance test be genuinely Bayesian?

OpenAIRE

Pereira, Carlos A. de B.; Stern, Julio Michael; Wechsler, Sergio

2008-01-01

The Full Bayesian Significance Test, FBST, is extensively reviewed. Its test statistic, a genuine Bayesian measure of evidence, is discussed in detail. Its behavior in some problems of statistical inference like testing for independence in contingency tables is discussed.

Bayesian estimation of realized stochastic volatility model by Hybrid Monte Carlo algorithm

International Nuclear Information System (INIS)

Takaishi, Tetsuya

2014-01-01

The hybrid Monte Carlo algorithm (HMCA) is applied for Bayesian parameter estimation of the realized stochastic volatility (RSV) model. Using the 2nd order minimum norm integrator (2MNI) for the molecular dynamics (MD) simulation in the HMCA, we find that the 2MNI is more efficient than the conventional leapfrog integrator. We also find that the autocorrelation time of the volatility variables sampled by the HMCA is very short. Thus it is concluded that the HMCA with the 2MNI is an efficient algorithm for parameter estimations of the RSV model

Bayesian image restoration, using configurations

OpenAIRE

Thorarinsdottir, Thordis

2006-01-01

In this paper, we develop a Bayesian procedure for removing noise from images that can be viewed as noisy realisations of random sets in the plane. The procedure utilises recent advances in configuration theory for noise free random sets, where the probabilities of observing the different boundary configurations are expressed in terms of the mean normal measure of the random set. These probabilities are used as prior probabilities in a Bayesian image restoration approach. Estimation of the re...

Bayesian Networks and Influence Diagrams

DEFF Research Database (Denmark)

Kjærulff, Uffe Bro; Madsen, Anders Læsø

 Probabilistic networks, also known as Bayesian networks and influence diagrams, have become one of the most promising technologies in the area of applied artificial intelligence, offering intuitive, efficient, and reliable methods for diagnosis, prediction, decision making, classification......, troubleshooting, and data mining under uncertainty. Bayesian Networks and Influence Diagrams: A Guide to Construction and Analysis provides a comprehensive guide for practitioners who wish to understand, construct, and analyze intelligent systems for decision support based on probabilistic networks. Intended...

Compiling Relational Bayesian Networks for Exact Inference

DEFF Research Database (Denmark)

Jaeger, Manfred; Chavira, Mark; Darwiche, Adnan

2004-01-01

We describe a system for exact inference with relational Bayesian networks as defined in the publicly available \\primula\\ tool. The system is based on compiling propositional instances of relational Bayesian networks into arithmetic circuits and then performing online inference by evaluating...

Vibrational energy relaxation: proposed pathway of fast local chromatin denaturation

International Nuclear Information System (INIS)

Harder, D.; Greinert, R.

2002-01-01

The molecular mechanism responsible for the a component of exchange-type chromosome aberrations, of chromosome fragmentation and of reproductive cell death is one of the unsolved issues of radiation biology. Under review is whether vibrational energy relaxation in the constitutive biopolymers of chromatin, induced by inelastic energy deposition events and mediated via highly excited vibrational states, may provide a pathway of fast local chromatin denaturation, thereby producing the severe DNA lesion able to interact chemically with other, non-damaged chromatin. (author)

Identification of structural relaxation in the dielectric response of water

DEFF Research Database (Denmark)

Hansen, Jesper Schmidt; Kisliuk, Alexander; Solokov, Alexei P.

2016-01-01

One century ago pioneering dielectric results obtained for water and n-alcohols triggered the advent of molecular rotation diffusion theory considered by Debye to describe the primary dielectric absorption in these liquids. Comparing dielectric, viscoelastic, and light scattering results, we...... unambiguously demonstrate that the structural relaxation appears only as a high-frequency shoulder in the dielectric spectra of water. In contrast, the main dielectric peak is related to a supramolecular structure, analogous to the Debye-like peak observed in monoalcohols....

Bayesian analysis of CCDM models

Science.gov (United States)

Jesus, J. F.; Valentim, R.; Andrade-Oliveira, F.

2017-09-01

Creation of Cold Dark Matter (CCDM), in the context of Einstein Field Equations, produces a negative pressure term which can be used to explain the accelerated expansion of the Universe. In this work we tested six different spatially flat models for matter creation using statistical criteria, in light of SNe Ia data: Akaike Information Criterion (AIC), Bayesian Information Criterion (BIC) and Bayesian Evidence (BE). These criteria allow to compare models considering goodness of fit and number of free parameters, penalizing excess of complexity. We find that JO model is slightly favoured over LJO/ΛCDM model, however, neither of these, nor Γ = 3αH0 model can be discarded from the current analysis. Three other scenarios are discarded either because poor fitting or because of the excess of free parameters. A method of increasing Bayesian evidence through reparameterization in order to reducing parameter degeneracy is also developed.

Bayesian analysis of CCDM models

Energy Technology Data Exchange (ETDEWEB)

Jesus, J.F. [Universidade Estadual Paulista (Unesp), Câmpus Experimental de Itapeva, Rua Geraldo Alckmin 519, Vila N. Sra. de Fátima, Itapeva, SP, 18409-010 Brazil (Brazil); Valentim, R. [Departamento de Física, Instituto de Ciências Ambientais, Químicas e Farmacêuticas—ICAQF, Universidade Federal de São Paulo (UNIFESP), Unidade José Alencar, Rua São Nicolau No. 210, Diadema, SP, 09913-030 Brazil (Brazil); Andrade-Oliveira, F., E-mail: jfjesus@itapeva.unesp.br, E-mail: valentim.rodolfo@unifesp.br, E-mail: felipe.oliveira@port.ac.uk [Institute of Cosmology and Gravitation—University of Portsmouth, Burnaby Road, Portsmouth, PO1 3FX United Kingdom (United Kingdom)

2017-09-01

Creation of Cold Dark Matter (CCDM), in the context of Einstein Field Equations, produces a negative pressure term which can be used to explain the accelerated expansion of the Universe. In this work we tested six different spatially flat models for matter creation using statistical criteria, in light of SNe Ia data: Akaike Information Criterion (AIC), Bayesian Information Criterion (BIC) and Bayesian Evidence (BE). These criteria allow to compare models considering goodness of fit and number of free parameters, penalizing excess of complexity. We find that JO model is slightly favoured over LJO/ΛCDM model, however, neither of these, nor Γ = 3α H {sub 0} model can be discarded from the current analysis. Three other scenarios are discarded either because poor fitting or because of the excess of free parameters. A method of increasing Bayesian evidence through reparameterization in order to reducing parameter degeneracy is also developed.

Sparse Event Modeling with Hierarchical Bayesian Kernel Methods

Science.gov (United States)

2016-01-05

SECURITY CLASSIFICATION OF: The research objective of this proposal was to develop a predictive Bayesian kernel approach to model count data based on...several predictive variables. Such an approach, which we refer to as the Poisson Bayesian kernel model, is able to model the rate of occurrence of... kernel methods made use of: (i) the Bayesian property of improving predictive accuracy as data are dynamically obtained, and (ii) the kernel function

Relaxation System

Science.gov (United States)

1987-01-01

Environ Corporation's relaxation system is built around a body lounge, a kind of super easy chair that incorporates sensory devices. Computer controlled enclosure provides filtered ionized air to create a feeling of invigoration, enhanced by mood changing aromas. Occupant is also surrounded by multidimensional audio and the lighting is programmed to change colors, patterns, and intensity periodically. These and other sensory stimulators are designed to provide an environment in which the learning process is stimulated, because research has proven that while an individual is in a deep state of relaxation, the mind is more receptive to new information.

Bayesian Inference for Functional Dynamics Exploring in fMRI Data

Directory of Open Access Journals (Sweden)

Xuan Guo

2016-01-01

Full Text Available This paper aims to review state-of-the-art Bayesian-inference-based methods applied to functional magnetic resonance imaging (fMRI data. Particularly, we focus on one specific long-standing challenge in the computational modeling of fMRI datasets: how to effectively explore typical functional interactions from fMRI time series and the corresponding boundaries of temporal segments. Bayesian inference is a method of statistical inference which has been shown to be a powerful tool to encode dependence relationships among the variables with uncertainty. Here we provide an introduction to a group of Bayesian-inference-based methods for fMRI data analysis, which were designed to detect magnitude or functional connectivity change points and to infer their functional interaction patterns based on corresponding temporal boundaries. We also provide a comparison of three popular Bayesian models, that is, Bayesian Magnitude Change Point Model (BMCPM, Bayesian Connectivity Change Point Model (BCCPM, and Dynamic Bayesian Variable Partition Model (DBVPM, and give a summary of their applications. We envision that more delicate Bayesian inference models will be emerging and play increasingly important roles in modeling brain functions in the years to come.

Cross-relaxation solid state lasers

International Nuclear Information System (INIS)

Antipenko, B.M.

1989-01-01

Cross-relaxation functional diagrams provide a high quantum efficiency for pumping bands of solid state laser media and a low waste heat. A large number of the cross-relaxation mechanisms for decay rare earth excited states in crystals have been investigated. These investigations have been a starting-point for development of the cross-relaxation solid state lasers. For example, the cross-relaxation interactions, have been used for the laser action development of LiYF 4 :Gd-Tb. These interactions are important elements of the functional diagrams of the 2 μm Ho-doped media sensitized with Er and Tm and the 3 μm Er-doped media. Recently, new efficient 2 μm laser media with cross-relaxation pumping diagrams have been developed. Physical aspects of these media are the subject of this paper. A new concept of the Er-doped medium, sensitized with Yb, is illustrated

Investigation of transitions and relaxation processes in polystyrene by using positron annihilation

International Nuclear Information System (INIS)

Ban, M.; Kyoto, M.

1996-01-01

The glass transition and relaxation processes in polystyrene resins with the number average molecular weight ranging from 7.0 x 10 2 to 9.8 x 10 4 were studied with the positron annihilation technique. The pick-off annihilation lifetime of ortho-positronium (τ 3 ) and its intensity (Ι 3 ) were measured in the temperature range from 20 to 430 K. The glass transition temperature (Τ g ) was determined as an onset temperature coefficient of τ 3 x Τ g shows the molecular weight dependence in these samples. Below Τ g , local motions were detected by measurements of Ι 3 . The local motions could be observed above 100 K in this experiment. Ι 3 show the minimum at around 250 K and it does not show molecular weight dependence. (author)

Particle identification in ALICE: a Bayesian approach

NARCIS (Netherlands)

Adam, J.; Adamova, D.; Aggarwal, M. M.; Rinella, G. Aglieri; Agnello, M.; Agrawal, N.; Ahammed, Z.; Ahn, S. U.; Aiola, S.; Akindinov, A.; Alam, S. N.; Albuquerque, D. S. D.; Aleksandrov, D.; Alessandro, B.; Alexandre, D.; Alfaro Molina, R.; Alici, A.; Alkin, A.; Almaraz, J. R. M.; Alme, J.; Alt, T.; Altinpinar, S.; Altsybeev, I.; Alves Garcia Prado, C.; Andrei, C.; Andronic, A.; Anguelov, V.; Anticic, T.; Antinori, F.; Antonioli, P.; Aphecetche, L.; Appelshaeuser, H.; Arcelli, S.; Arnaldi, R.; Arnold, O. W.; Arsene, I. C.; Arslandok, M.; Audurier, B.; Augustinus, A.; Averbeck, R.; Azmi, M. D.; Badala, A.; Baek, Y. W.; Bagnasco, S.; Bailhache, R.; Bala, R.; Balasubramanian, S.; Baldisseri, A.; Baral, R. C.; Barbano, A. M.; Barbera, R.; Barile, F.; Barnafoeldi, G. G.; Barnby, L. S.; Barret, V.; Bartalini, P.; Barth, K.; Bartke, J.; Bartsch, E.; Basile, M.; Bastid, N.; Bathen, B.; Batigne, G.; Camejo, A. Batista; Batyunya, B.; Batzing, P. C.; Bearden, I. G.; Beck, H.; Bedda, C.; Behera, N. K.; Belikov, I.; Bellini, F.; Bello Martinez, H.; Bellwied, R.; Belmont, R.; Belmont-Moreno, E.; Belyaev, V.; Benacek, P.; Bencedi, G.; Beole, S.; Berceanu, I.; Bercuci, A.; Berdnikov, Y.; Berenyi, D.; Bertens, R. A.; Berzano, D.; Betev, L.; Bhasin, A.; Bhat, I. R.; Bhati, A. K.; Bhattacharjee, B.; Bhom, J.; Bianchi, L.; Bianchi, N.; Bianchin, C.; Bielcik, J.; Bielcikova, J.; Bilandzic, A.; Biro, G.; Biswas, R.; Biswas, S.; Bjelogrlic, S.; Blair, J. T.; Blau, D.; Blume, C.; Bock, F.; Bogdanov, A.; Boggild, H.; Boldizsar, L.; Bombara, M.; Book, J.; Borel, H.; Borissov, A.; Borri, M.; Bossu, F.; Botta, E.; Bourjau, C.; Braun-Munzinger, P.; Bregant, M.; Breitner, T.; Broker, T. A.; Browning, T. A.; Broz, M.; Brucken, E. J.; Bruna, E.; Bruno, G. E.; Budnikov, D.; Buesching, H.; Bufalino, S.; Buncic, P.; Busch, O.; Buthelezi, Z.; Butt, J. B.; Buxton, J. T.; Cabala, J.; Caffarri, D.; Cai, X.; Caines, H.; Diaz, L. Calero; Caliva, A.; Calvo Villar, E.; Camerini, P.; Carena, F.; Carena, W.; Carnesecchi, F.; Castellanos, J. Castillo; Castro, A. J.; Casula, E. A. R.; Sanchez, C. Ceballos; Cepila, J.; Cerello, P.; Cerkala, J.; Chang, B.; Chapeland, S.; Chartier, M.; Charvet, J. L.; Chattopadhyay, S.; Chattopadhyay, S.; Chauvin, A.; Chelnokov, V.; Cherney, M.; Cheshkov, C.; Cheynis, B.; Barroso, V. Chibante; Chinellato, D. D.; Cho, S.; Chochula, P.; Choi, K.; Chojnacki, M.; Choudhury, S.; Christakoglou, P.; Christensen, C. H.; Christiansen, P.; Chujo, T.; Cicalo, C.; Cifarelli, L.; Cindolo, F.; Cleymans, J.; Colamaria, F.; Colella, D.; Collu, A.; Colocci, M.; Balbastre, G. Conesa; del Valle, Z. Conesa; Connors, M. E.; Contreras, J. G.; Cormier, T. M.; Morales, Y. Corrales; Cortes Maldonado, I.; Cortese, P.; Cosentino, M. R.; Costa, F.; Crochet, P.; Cruz Albino, R.; Cuautle, E.; Cunqueiro, L.; Dahms, T.; Dainese, A.; Danisch, M. C.; Danu, A.; Das, I.; Das, S.; Dash, A.; Dash, S.; De, S.; De Caro, A.; de Cataldo, G.; de Conti, C.; de Cuveland, J.; De Falco, A.; De Gruttola, D.; De Marco, N.; De Pasquale, S.; Deisting, A.; Deloff, A.; Denes, E.; Deplano, C.; Dhankher, P.; Di Bari, D.; Di Mauro, A.; Di Nezza, P.; Corchero, M. A. Diaz; Dietel, T.; Dillenseger, P.; Divia, R.; Djuvsland, O.; Dobrin, A.; Gimenez, D. Domenicis; Doenigus, B.; Dordic, O.; Drozhzhova, T.; Dubey, A. K.; Dubla, A.; Ducroux, L.; Dupieux, P.; Ehlers, R. J.; Elia, D.; Endress, E.; Engel, H.; Epple, E.; Erazmus, B.; Erdemir, I.; Erhardt, F.; Espagnon, B.; Estienne, M.; Esumi, S.; Eum, J.; Evans, D.; Evdokimov, S.; Eyyubova, G.; Fabbietti, L.; Fabris, D.; Faivre, J.; Fantoni, A.; Fasel, M.; Feldkamp, L.; Feliciello, A.; Feofilov, G.; Ferencei, J.; Fernandez Tellez, A.; Ferreiro, E. G.; Ferretti, A.; Festanti, A.; Feuillard, V. J. G.; Figiel, J.; Figueredo, M. A. S.; Filchagin, S.; Finogeev, D.; Fionda, F. M.; Fiore, E. M.; Fleck, M. G.; Floris, M.; Foertsch, S.; Foka, P.; Fokin, S.; Fragiacomo, E.; Francescon, A.; Frankenfeld, U.; Fronze, G. G.; Fuchs, U.; Furget, C.; Furs, A.; Girard, M. Fusco; Gaardhoje, J. J.; Gagliardi, M.; Gago, A. M.; Gallio, M.; Gangadharan, D. R.; Ganoti, P.; Gao, C.; Garabatos, C.; Garcia-Solis, E.; Gargiulo, C.; Gasik, P.; Gauger, E. F.; Germain, M.; Gheata, A.; Gheata, M.; Gianotti, P.; Giubellino, P.; Giubilato, P.; Gladysz-Dziadus, E.; Glaessel, P.; Gomez Coral, D. M.; Ramirez, A. Gomez; Gonzalez, A. S.; Gonzalez, V.; Gonzalez-Zamora, P.; Gorbunov, S.; Goerlich, L.; Gotovac, S.; Grabski, V.; Grachov, O. A.; Graczykowski, L. K.; Graham, K. L.; Grelli, A.; Grigoras, A.; Grigoras, C.; Grigoriev, V.; Grigoryan, A.; Grigoryan, S.; Grinyov, B.; Grion, N.; Gronefeld, J. M.; Grosse-Oetringhaus, J. F.; Grosso, R.; Guber, F.; Guernane, R.; Guerzoni, B.; Gulbrandsen, K.; Gunji, T.; Gupta, A.; Haake, R.; Haaland, O.; Hadjidakis, C.; Haiduc, M.; Hamagaki, H.; Hamar, G.; Hamon, J. C.; Harris, J. W.; Harton, A.; Hatzifotiadou, D.; Hayashi, S.; Heckel, S. T.; Hellbaer, E.; Helstrup, H.; Herghelegiu, A.; Herrera Corral, G.; Hess, B. A.; Hetland, K. F.; Hillemanns, H.; Hippolyte, B.; Horak, D.; Hosokawa, R.; Hristov, P.; Humanic, T. J.; Hussain, N.; Hussain, T.; Hutter, D.; Hwang, D. S.; Ilkaev, R.; Inaba, M.; Incani, E.; Ippolitov, M.; Irfan, M.; Ivanov, M.; Ivanov, V.; Izucheev, V.; Jacazio, N.; Jadhav, M. B.; Jadlovska, S.; Jadlovsky, J.; Jahnke, C.; Jakubowska, M. J.; Jang, H. J.; Janik, M. A.; Jayarathna, P. H. S. Y.; Jena, C.; Jena, S.; Bustamante, R. T. Jimenez; Jones, P. G.; Jusko, A.; Kalinak, P.; Kalweit, A.; Kamin, J.; Kaplin, V.; Kar, S.; Uysal, A. Karasu; Karavichev, O.; Karavicheva, T.; Karayan, L.; Karpechev, E.; Kebschull, U.; Keidel, R.; Keijdener, D. L. D.; Keil, M.; Khan, M. Mohisin; Khan, P.; Khan, S. A.; Khanzadeev, A.; Kharlov, Y.; Kileng, B.; Kim, D. W.; Kim, D. J.; Kim, D.; Kim, J. S.; Kim, M.; Kim, T.; Kirsch, S.; Kisel, I.; Kiselev, S.; Kisiel, A.; Kiss, G.; Klay, J. L.; Klein, C.; Klein-Boesing, C.; Klewin, S.; Kluge, A.; Knichel, M. L.; Knospe, A. G.; Kobdaj, C.; Kofarago, M.; Kollegger, T.; Kolojvari, A.; Kondratiev, V.; Kondratyeva, N.; Kondratyuk, E.; Konevskikh, A.; Kopcik, M.; Kostarakis, P.; Kour, M.; Kouzinopoulos, C.; Kovalenko, O.; Kovalenko, V.; Kowalski, M.; Meethaleveedu, G. Koyithatta; Kralik, I.; Kravcakova, A.; Krivda, M.; Krizek, F.; Kryshen, E.; Krzewicki, M.; Kubera, A. M.; Kucera, V.; Kuijer, P. G.; Kumar, J.; Kumar, L.; Kumar, S.; Kurashvili, P.; Kurepin, A.; Kurepin, A. B.; Kuryakin, A.; Kweon, M. J.; Kwon, Y.; La Pointe, S. L.; La Rocca, P.; Ladron de Guevara, P.; Lagana Fernandes, C.; Lakomov, I.; Langoy, R.; Lara, C.; Lardeux, A.; Lattuca, A.; Laudi, E.; Lea, R.; Leardini, L.; Lee, G. R.; Lee, S.; Lehas, F.; Lemmon, R. C.; Lenti, V.; Leogrande, E.; Monzon, I. Leon; Leon Vargas, H.; Leoncino, M.; Levai, P.; Lien, J.; Lietava, R.; Lindal, S.; Lindenstruth, V.; Lippmann, C.; Lisa, M. A.; Ljunggren, H. M.; Lodato, D. F.; Loenne, P. I.; Loginov, V.; Loizides, C.; Lopez, X.; Torres, E. Lopez; Lowe, A.; Luettig, P.; Lunardon, M.; Luparello, G.; Lutz, T. H.; Maevskaya, A.; Mager, M.; Mahajan, S.; Mahmood, S. M.; Maire, A.; Majka, R. D.; Malaev, M.; Maldonado Cervantes, I.; Malinina, L.; Mal'Kevich, D.; Malzacher, P.; Mamonov, A.; Manko, V.; Manso, F.; Manzari, V.; Marchisone, M.; Mares, J.; Margagliotti, G. V.; Margotti, A.; Margutti, J.; Marin, A.; Markert, C.; Marquard, M.; Martin, N. A.; Blanco, J. Martin; Martinengo, P.; Martinez, M. I.; Garcia, G. Martinez; Pedreira, M. Martinez; Mas, A.; Masciocchi, S.; Masera, M.; Masoni, A.; Mastroserio, A.; Matyja, A.; Mayer, C.; Mazer, J.; Mazzoni, M. A.; Mcdonald, D.; Meddi, F.; Melikyan, Y.; Menchaca-Rocha, A.; Meninno, E.; Perez, J. Mercado; Meres, M.; Miake, Y.; Mieskolainen, M. M.; Mikhaylov, K.; Milano, L.; Milosevic, J.; Mischke, A.; Mishra, A. N.; Miskowiec, D.; Mitra, J.; Mitu, C. M.; Mohammadi, N.; Mohanty, B.; Molnar, L.; Montano Zetina, L.; Montes, E.; De Godoy, D. A. Moreira; Moreno, L. A. P.; Moretto, S.; Morreale, A.; Morsch, A.; Muccifora, V.; Mudnic, E.; Muehlheim, D.; Muhuri, S.; Mukherjee, M.; Mulligan, J. D.; Munhoz, M. G.; Munzer, R. H.; Murakami, H.; Murray, S.; Musa, L.; Musinsky, J.; Naik, B.; Nair, R.; Nandi, B. K.; Nania, R.; Nappi, E.; Naru, M. U.; Natal da Luz, H.; Nattrass, C.; Navarro, S. R.; Nayak, K.; Nayak, R.; Nayak, T. K.; Nazarenko, S.; Nedosekin, A.; Nellen, L.; Ng, F.; Nicassio, M.; Niculescu, M.; Niedziela, J.; Nielsen, B. S.; Nikolaev, S.; Nikulin, S.; Nikulin, V.; Noferini, F.; Nomokonov, P.; Nooren, G.; Noris, J. C. C.; Norman, J.; Nyanin, A.; Nystrand, J.; Oeschler, H.; Oh, S.; Oh, S. K.; Ohlson, A.; Okatan, A.; Okubo, T.; Olah, L.; Oleniacz, J.; Oliveira Da Silva, A. C.; Oliver, M. H.; Onderwaater, J.; Oppedisano, C.; Orava, R.; Oravec, M.; Ortiz Velasquez, A.; Oskarsson, A.; Otwinowski, J.; Oyama, K.; Ozdemir, M.; Pachmayer, Y.; Pagano, D.; Pagano, P.; Paic, G.; Pal, S. K.; Pan, J.; Papikyan, V.; Pappalardo, G. S.; Pareek, P.; Park, W. J.; Parmar, S.; Passfeld, A.; Paticchio, V.; Patra, R. N.; Paul, B.; Pei, H.; Peitzmann, T.; Da Costa, H. Pereira; Peresunko, D.; Lara, C. E. Perez; Lezama, E. Perez; Peskov, V.; Pestov, Y.; Petracek, V.; Petrov, V.; Petrovici, M.; Petta, C.; Piano, S.; Pikna, M.; Pillot, P.; Pimentel, L. O. D. L.; Pinazza, O.; Pinsky, L.; Piyarathna, D. B.; Ploskon, M.; Planinic, M.; Pluta, J.; Pochybova, S.; Podesta-Lerma, P. L. M.; Poghosyan, M. G.; Polichtchouk, B.; Poljak, N.; Poonsawat, W.; Pop, A.; Porteboeuf-Houssais, S.; Porter, J.; Pospisil, J.; Prasad, S. K.; Preghenella, R.; Prino, F.; Pruneau, C. A.; Pshenichnov, I.; Puccio, M.; Puddu, G.; Pujahari, P.; Punin, V.; Putschke, J.; Qvigstad, H.; Rachevski, A.; Raha, S.; Rajput, S.; Rak, J.; Rakotozafindrabe, A.; Ramello, L.; Rami, F.; Raniwala, R.; Raniwala, S.; Raesaenen, S. S.; Rascanu, B. T.; Rathee, D.; Read, K. F.; Redlich, K.; Reed, R. J.; Reichelt, P.; Reidt, F.; Ren, X.; Renfordt, R.; Reolon, A. R.; Reshetin, A.; Reygers, K.; Riabov, V.; Ricci, R. A.; Richert, T.; Richter, M.; Riedler, P.; Riegler, W.; Riggi, F.; Ristea, C.; Rocco, E.; Rodriguez Cahuantzi, M.; Manso, A. Rodriguez; Roed, K.; Rogochaya, E.; Rohr, D.; Roehrich, D.; Ronchetti, F.; Ronflette, L.; Rosnet, P.; Rossi, A.; Roukoutakis, F.; Roy, A.; Roy, C.; Roy, P.; Montero, A. J. Rubio; Rui, R.; Russo, R.; Ryabinkin, E.; Ryabov, Y.; Rybicki, A.; Saarinen, S.; Sadhu, S.; Sadovsky, S.; Safarik, K.; Sahlmuller, B.; Sahoo, P.; Sahoo, R.; Sahoo, S.; Sahu, P. K.; Saini, J.; Sakai, S.; Saleh, M. A.; Salzwedel, J.; Sambyal, S.; Samsonov, V.; Sandor, L.; Sandoval, A.; Sano, M.; Sarkar, D.; Sarkar, N.; Sarma, P.; Scapparone, E.; Scarlassara, F.; Schiaua, C.; Schicker, R.; Schmidt, C.; Schmidt, H. R.; Schuchmann, S.; Schukraft, J.; Schulc, M.; Schutz, Y.; Schwarz, K.; Schweda, K.; Scioli, G.; Scomparin, E.; Scott, R.; Sefcik, M.; Seger, J. E.; Sekiguchi, Y.; Sekihata, D.; Selyuzhenkov, I.; Senosi, K.; Senyukov, S.; Serradilla, E.; Sevcenco, A.; Shabanov, A.; Shabetai, A.; Shadura, O.; Shahoyan, R.; Shahzad, M. I.; Shangaraev, A.; Sharma, M.; Sharma, M.; Sharma, N.; Sheikh, A. I.; Shigaki, K.; Shou, Q.; Shtejer, K.; Sibiriak, Y.; Siddhanta, S.; Sielewicz, K. M.; Siemiarczuk, T.; Silvermyr, D.; Silvestre, C.; Simatovic, G.; Simonetti, G.; Singaraju, R.; Singh, R.; Singha, S.; Singhal, V.; Sinha, B. C.; Sinha, T.; Sitar, B.; Sitta, M.; Skaali, T. B.; Slupecki, M.; Smirnov, N.; Snellings, R. J. M.; Snellman, T. W.; Song, J.; Song, M.; Song, Z.; Soramel, F.; Sorensen, S.; de Souza, R. D.; Sozzi, F.; Spacek, M.; Spiriti, E.; Sputowska, I.; Spyropoulou-Stassinaki, M.; Stachel, J.; Stan, I.; Stankus, P.; Stenlund, E.; Steyn, G.; Stiller, J. H.; Stocco, D.; Strmen, P.; Suaide, A. A. P.; Sugitate, T.; Suire, C.; Suleymanov, M.; Suljic, M.; Sultanov, R.; Sumbera, M.; Sumowidagdo, S.; Szabo, A.; Szanto de Toledo, A.; Szarka, I.; Szczepankiewicz, A.; Szymanski, M.; Tabassam, U.; Takahashi, J.; Tambave, G. J.; Tanaka, N.; Tarhini, M.; Tariq, M.; Tarzila, M. G.; Tauro, A.; Tejeda Munoz, G.; Telesca, A.; Terasaki, K.; Terrevoli, C.; Teyssier, B.; Thaeder, J.; Thakur, D.; Thomas, D.; Tieulent, R.; Timmins, A. R.; Toia, A.; Trogolo, S.; Trombetta, G.; Trubnikov, V.; Trzaska, W. H.; Tsuji, T.; Tumkin, A.; Turrisi, R.; Tveter, T. S.; Ullaland, K.; Uras, A.; Usai, G. L.; Utrobicic, A.; Vala, M.; Palomo, L. Valencia; Vallero, S.; Van Der Maarel, J.; Van Hoorne, J. W.; van Leeuwen, M.; Vanat, T.; Vyvre, P. Vande; Varga, D.; Vargas, A.; Vargyas, M.; Varma, R.; Vasileiou, M.; Vasiliev, A.; Vauthier, A.; Vechernin, V.; Veen, A. M.; Veldhoen, M.; Velure, A.; Vercellin, E.; Vergara Limon, S.; Vernet, R.; Verweij, M.; Vickovic, L.; Viesti, G.; Viinikainen, J.; Vilakazi, Z.; Baillie, O. Villalobos; Villatoro Tello, A.; Vinogradov, A.; Vinogradov, L.; Vinogradov, Y.; Virgili, T.; Vislavicius, V.; Viyogi, Y. P.; Vodopyanov, A.; Voelkl, M. A.; Voloshin, K.; Voloshin, S. A.; Volpe, G.; von Haller, B.; Vorobyev, I.; Vranic, D.; Vrlakova, J.; Vulpescu, B.; Wagner, B.; Wagner, J.; Wang, H.; Watanabe, D.; Watanabe, Y.; Weiser, D. F.; Westerhoff, U.; Whitehead, A. M.; Wiechula, J.; Wikne, J.; Wilk, G.; Wilkinson, J.; Williams, M. C. S.; Windelband, B.; Winn, M.; Yang, H.; Yano, S.; Yasin, Z.; Yokoyama, H.; Yoo, I. -K.; Yoon, J. H.; Yurchenko, V.; Yushmanov, I.; Zaborowska, A.; Zaccolo, V.; Zaman, A.; Zampolli, C.; Zanoli, H. J. C.; Zaporozhets, S.; Zardoshti, N.; Zarochentsev, A.; Zavada, P.; Zaviyalov, N.; Zbroszczyk, H.; Zgura, I. S.; Zhalov, M.; Zhang, C.; Zhao, C.; Zhigareva, N.; Zhou, Y.; Zhou, Z.; Zhu, H.; Zichichi, A.; Zimmermann, A.; Zimmermann, M. B.; Zinovjev, G.; Zyzak, M.

2016-01-01

We present a Bayesian approach to particle identification (PID) within the ALICE experiment. The aim is to more effectively combine the particle identification capabilities of its various detectors. After a brief explanation of the adopted methodology and formalism, the performance of the Bayesian

Compiling Relational Bayesian Networks for Exact Inference

DEFF Research Database (Denmark)

Jaeger, Manfred; Darwiche, Adnan; Chavira, Mark

2006-01-01

We describe in this paper a system for exact inference with relational Bayesian networks as defined in the publicly available PRIMULA tool. The system is based on compiling propositional instances of relational Bayesian networks into arithmetic circuits and then performing online inference...

A Bayesian Justification for Random Sampling in Sample Survey

Directory of Open Access Journals (Sweden)

Glen Meeden

2012-07-01

Full Text Available In the usual Bayesian approach to survey sampling the sampling design, plays a minimal role, at best. Although a close relationship between exchangeable prior distributions and simple random sampling has been noted; how to formally integrate simple random sampling into the Bayesian paradigm is not clear. Recently it has been argued that the sampling design can be thought of as part of a Bayesian's prior distribution. We will show here that under this scenario simple random sample can be given a Bayesian justification in survey sampling.

Hierarchical Bayesian Modeling of Fluid-Induced Seismicity

Science.gov (United States)

Broccardo, M.; Mignan, A.; Wiemer, S.; Stojadinovic, B.; Giardini, D.

2017-11-01

In this study, we present a Bayesian hierarchical framework to model fluid-induced seismicity. The framework is based on a nonhomogeneous Poisson process with a fluid-induced seismicity rate proportional to the rate of injected fluid. The fluid-induced seismicity rate model depends upon a set of physically meaningful parameters and has been validated for six fluid-induced case studies. In line with the vision of hierarchical Bayesian modeling, the rate parameters are considered as random variables. We develop both the Bayesian inference and updating rules, which are used to develop a probabilistic forecasting model. We tested the Basel 2006 fluid-induced seismic case study to prove that the hierarchical Bayesian model offers a suitable framework to coherently encode both epistemic uncertainty and aleatory variability. Moreover, it provides a robust and consistent short-term seismic forecasting model suitable for online risk quantification and mitigation.

The relaxation time approximation

International Nuclear Information System (INIS)

Gairola, R.P.; Indu, B.D.

1991-01-01

A plausible approximation has been made to estimate the relaxation time from a knowledge of the transition probability of phonons from one state (r vector, q vector) to other state (r' vector, q' vector), as a result of collision. The relaxation time, thus obtained, shows a strong dependence on temperature and weak dependence on the wave vector. In view of this dependence, relaxation time has been expressed in terms of a temperature Taylor's series in the first Brillouin zone. Consequently, a simple model for estimating the thermal conductivity is suggested. the calculations become much easier than the Callaway model. (author). 14 refs

The Development of Bayesian Theory and Its Applications in Business and Bioinformatics

Science.gov (United States)

Zhang, Yifei

2018-03-01

Bayesian Theory originated from an Essay of a British mathematician named Thomas Bayes in 1763, and after its development in 20th century, Bayesian Statistics has been taking a significant part in statistical study of all fields. Due to the recent breakthrough of high-dimensional integral, Bayesian Statistics has been improved and perfected, and now it can be used to solve problems that Classical Statistics failed to solve. This paper summarizes Bayesian Statistics’ history, concepts and applications, which are illustrated in five parts: the history of Bayesian Statistics, the weakness of Classical Statistics, Bayesian Theory and its development and applications. The first two parts make a comparison between Bayesian Statistics and Classical Statistics in a macroscopic aspect. And the last three parts focus on Bayesian Theory in specific -- from introducing some particular Bayesian Statistics’ concepts to listing their development and finally their applications.

Empirical Bayesian inference and model uncertainty

International Nuclear Information System (INIS)

Poern, K.

1994-01-01

This paper presents a hierarchical or multistage empirical Bayesian approach for the estimation of uncertainty concerning the intensity of a homogeneous Poisson process. A class of contaminated gamma distributions is considered to describe the uncertainty concerning the intensity. These distributions in turn are defined through a set of secondary parameters, the knowledge of which is also described and updated via Bayes formula. This two-stage Bayesian approach is an example where the modeling uncertainty is treated in a comprehensive way. Each contaminated gamma distributions, represented by a point in the 3D space of secondary parameters, can be considered as a specific model of the uncertainty about the Poisson intensity. Then, by the empirical Bayesian method each individual model is assigned a posterior probability

Strain relaxation of CdTe on Ge studied by medium energy ion scattering

Energy Technology Data Exchange (ETDEWEB)

Pillet, J.C., E-mail: jean-christophe.pillet@cea.fr [Univ. Grenoble Alpes, CEA, LETI, MINATEC campus, F38000 Grenoble (France); CEA, LETI, Département Optique et Photonique, F38054 Grenoble (France); Pierre, F. [Univ. Grenoble Alpes, CEA, LETI, MINATEC campus, F38000 Grenoble (France); CEA, LETI, Service de Caractérisation des Matériaux et Composants, F38054 Grenoble (France); Jalabert, D. [Univ. Grenoble Alpes, CEA, LETI, MINATEC campus, F38000 Grenoble (France); CEA-INAC/UJF-Grenoble 1 UMR-E, SP2M, LEMMA, Minatec Grenoble F-38054 (France)

2016-10-01

We have used the medium energy ion scattering (MEIS) technique to assess the strain relaxation in molecular-beam epitaxial (MBE) grown CdTe (2 1 1)/Ge (2 1 1) system. A previous X-ray diffraction study, on 10 samples of the same heterostructure having thicknesses ranging from 25 nm to 10 μm has allowed the measurement of the strain relaxation on a large scale. However, the X-ray diffraction measurements cannot achieve a stress measurement in close proximity to the CdTe/Ge interface at the nanometer scale. Due to the huge lattice misfit between the CdTe and Ge, a high degree of disorder is expected at the interface. The MEIS in channeling mode is a good alternative in order to profile defects with a high depth resolution. For a 21 nm thick CdTe layer, we observed, at the interface, a high density of Cd and/or Te atoms moved from their expected crystallographic positions followed by a rapid recombination of defects. Strain relaxation mechanisms in the vicinity of the interface are discussed.

Nuclear relaxation induced by diffusion in confined media; the case of inverted micelles

International Nuclear Information System (INIS)

Llor, Antoine

1983-01-01

This work emphasizes the specificities of molecular motions in restricted media observed by NMR. The observation of proton nuclear relaxation of small water pools in AOT reversed micelles has led to separation of dipolar contributions using substitution by deuterium. The water-water contributions to relaxation are easily explained by well-known models and show that water rotational movements are, at most, five times slower than in pure water. The other contributions display a strong frequency dependence with spectrometer frequency and, in order to explain them, a specific dipolar relaxation model was developed between two particles whose movements are restricted to the surface of a sphere and in a concentric sphere respectively. This model was generalized to all cases of diffusion movements of particles in a spherical symmetry environment. In the case of AOT micelles, this model can not explain the experimental results. An elementary discussion taking into account the polar heads specificities and their interactions with water lead to a qualitative interpretation of the experimental data. (author) [fr

Advances in Bayesian Modeling in Educational Research

Science.gov (United States)

Levy, Roy

2016-01-01

In this article, I provide a conceptually oriented overview of Bayesian approaches to statistical inference and contrast them with frequentist approaches that currently dominate conventional practice in educational research. The features and advantages of Bayesian approaches are illustrated with examples spanning several statistical modeling…

Objective Bayesianism and the Maximum Entropy Principle

Directory of Open Access Journals (Sweden)

Jon Williamson

2013-09-01

Full Text Available Objective Bayesian epistemology invokes three norms: the strengths of our beliefs should be probabilities; they should be calibrated to our evidence of physical probabilities; and they should otherwise equivocate sufficiently between the basic propositions that we can express. The three norms are sometimes explicated by appealing to the maximum entropy principle, which says that a belief function should be a probability function, from all those that are calibrated to evidence, that has maximum entropy. However, the three norms of objective Bayesianism are usually justified in different ways. In this paper, we show that the three norms can all be subsumed under a single justification in terms of minimising worst-case expected loss. This, in turn, is equivalent to maximising a generalised notion of entropy. We suggest that requiring language invariance, in addition to minimising worst-case expected loss, motivates maximisation of standard entropy as opposed to maximisation of other instances of generalised entropy. Our argument also provides a qualified justification for updating degrees of belief by Bayesian conditionalisation. However, conditional probabilities play a less central part in the objective Bayesian account than they do under the subjective view of Bayesianism, leading to a reduced role for Bayes’ Theorem.

Classifying emotion in Twitter using Bayesian network

Science.gov (United States)

Surya Asriadie, Muhammad; Syahrul Mubarok, Mohamad; Adiwijaya

2018-03-01

Language is used to express not only facts, but also emotions. Emotions are noticeable from behavior up to the social media statuses written by a person. Analysis of emotions in a text is done in a variety of media such as Twitter. This paper studies classification of emotions on twitter using Bayesian network because of its ability to model uncertainty and relationships between features. The result is two models based on Bayesian network which are Full Bayesian Network (FBN) and Bayesian Network with Mood Indicator (BNM). FBN is a massive Bayesian network where each word is treated as a node. The study shows the method used to train FBN is not very effective to create the best model and performs worse compared to Naive Bayes. F1-score for FBN is 53.71%, while for Naive Bayes is 54.07%. BNM is proposed as an alternative method which is based on the improvement of Multinomial Naive Bayes and has much lower computational complexity compared to FBN. Even though it’s not better compared to FBN, the resulting model successfully improves the performance of Multinomial Naive Bayes. F1-Score for Multinomial Naive Bayes model is 51.49%, while for BNM is 52.14%.

Probability biases as Bayesian inference

Directory of Open Access Journals (Sweden)

Andre; C. R. Martins

2006-11-01

Full Text Available In this article, I will show how several observed biases in human probabilistic reasoning can be partially explained as good heuristics for making inferences in an environment where probabilities have uncertainties associated to them. Previous results show that the weight functions and the observed violations of coalescing and stochastic dominance can be understood from a Bayesian point of view. We will review those results and see that Bayesian methods should also be used as part of the explanation behind other known biases. That means that, although the observed errors are still errors under the be understood as adaptations to the solution of real life problems. Heuristics that allow fast evaluations and mimic a Bayesian inference would be an evolutionary advantage, since they would give us an efficient way of making decisions. %XX In that sense, it should be no surprise that humans reason with % probability as it has been observed.

Bayesian data analysis in population ecology: motivations, methods, and benefits

Science.gov (United States)

Dorazio, Robert

2016-01-01

During the 20th century ecologists largely relied on the frequentist system of inference for the analysis of their data. However, in the past few decades ecologists have become increasingly interested in the use of Bayesian methods of data analysis. In this article I provide guidance to ecologists who would like to decide whether Bayesian methods can be used to improve their conclusions and predictions. I begin by providing a concise summary of Bayesian methods of analysis, including a comparison of differences between Bayesian and frequentist approaches to inference when using hierarchical models. Next I provide a list of problems where Bayesian methods of analysis may arguably be preferred over frequentist methods. These problems are usually encountered in analyses based on hierarchical models of data. I describe the essentials required for applying modern methods of Bayesian computation, and I use real-world examples to illustrate these methods. I conclude by summarizing what I perceive to be the main strengths and weaknesses of using Bayesian methods to solve ecological inference problems.

Plasmon-mediated energy relaxation in graphene

Energy Technology Data Exchange (ETDEWEB)

Ferry, D. K. [School of Electrical, Computer, and Energy Engineering, Arizona State University, Tempe, Arizona 85287-5706 (United States); Somphonsane, R. [Department of Physics, King Mongkut' s Institute of Technology, Ladkrabang, Bangkok 10520 (Thailand); Ramamoorthy, H.; Bird, J. P. [Department of Electrical Engineering, University at Buffalo, the State University of New York, Buffalo, New York 14260-1500 (United States)

2015-12-28

Energy relaxation of hot carriers in graphene is studied at low temperatures, where the loss rate may differ significantly from that predicted for electron-phonon interactions. We show here that plasmons, important in the relaxation of energetic carriers in bulk semiconductors, can also provide a pathway for energy relaxation in transport experiments in graphene. We obtain a total loss rate to plasmons that results in energy relaxation times whose dependence on temperature and density closely matches that found experimentally.

Bayesian psychometric scaling

NARCIS (Netherlands)

Fox, Gerardus J.A.; van den Berg, Stéphanie Martine; Veldkamp, Bernard P.; Irwing, P.; Booth, T.; Hughes, D.

2015-01-01

In educational and psychological studies, psychometric methods are involved in the measurement of constructs, and in constructing and validating measurement instruments. Assessment results are typically used to measure student proficiency levels and test characteristics. Recently, Bayesian item

Learning Bayesian Networks with Incomplete Data by Augmentation

OpenAIRE

Adel, Tameem; de Campos, Cassio P.

2016-01-01

We present new algorithms for learning Bayesian networks from data with missing values using a data augmentation approach. An exact Bayesian network learning algorithm is obtained by recasting the problem into a standard Bayesian network learning problem without missing data. To the best of our knowledge, this is the first exact algorithm for this problem. As expected, the exact algorithm does not scale to large domains. We build on the exact method to create an approximate algorithm using a ...

Idiosyncratic reality claims, relaxation dispositions, and ABC relaxation theory: happiness, literal christianity, miraculous powers, metaphysics, and the paranormal.

Science.gov (United States)

Smith, Jonathan C; Karmin, Aaron D

2002-12-01

This study examined idiosyncratic reality claims, that is, irrational or paranormal beliefs often claimed to enhance relaxation and happiness and reduce stress. The Smith Idiosyncratic Reality Claims Inventory and the Smith Relaxation Dispositions Inventory (which measures relaxation and stress dispositions, or enduring states of mind frequently associated with relaxation or stress) were given to 310 junior college student volunteers. Principal components factor analysis with varimax rotation identified five idiosyncratic reality claim factors: belief in Literal Christianity; Magic; Space Aliens: After Death experiences; and Miraculous Powers of Meditation, Prayer, and Belief. No factor correlated with increased relaxation dispositions Peace, Energy, or Joy, or reduced dispositional somatic stress, worry, or negative emotion on the Smith Relaxation Dispositions Inventory. It was concluded that idiosyncratic reality claims may not be associated with reported relaxation, happiness, or stress. In contrast, previous research strongly supported self-affirming beliefs with few paranormal assumptions display such an association.

Anomalous enthalpy relaxation in vitreous silica

DEFF Research Database (Denmark)

Yue, Yuanzheng

2015-01-01

scans. It is known that the liquid fragility (i.e., the speed of the viscous slow-down of a supercooled liquid at its Tg during cooling) has impact on enthalpy relaxation in glass. Here, we find that vitreous silica (as a strong system) exhibits striking anomalies in both glass transition and enthalpy...... relaxation compared to fragile oxide systems. The anomalous enthalpy relaxation of vitreous silica is discovered by performing the hyperquenching-annealing-calorimetry experiments. We argue that the strong systems like vitreous silica and vitreous Germania relax in a structurally cooperative manner, whereas...... the fragile ones do in a structurally independent fashion. We discuss the origin of the anomalous enthalpy relaxation in the HQ vitreous silica....

Bayesian optimization for computationally extensive probability distributions.

Science.gov (United States)

Tamura, Ryo; Hukushima, Koji

2018-01-01

An efficient method for finding a better maximizer of computationally extensive probability distributions is proposed on the basis of a Bayesian optimization technique. A key idea of the proposed method is to use extreme values of acquisition functions by Gaussian processes for the next training phase, which should be located near a local maximum or a global maximum of the probability distribution. Our Bayesian optimization technique is applied to the posterior distribution in the effective physical model estimation, which is a computationally extensive probability distribution. Even when the number of sampling points on the posterior distributions is fixed to be small, the Bayesian optimization provides a better maximizer of the posterior distributions in comparison to those by the random search method, the steepest descent method, or the Monte Carlo method. Furthermore, the Bayesian optimization improves the results efficiently by combining the steepest descent method and thus it is a powerful tool to search for a better maximizer of computationally extensive probability distributions.

An Intuitive Dashboard for Bayesian Network Inference

International Nuclear Information System (INIS)

Reddy, Vikas; Farr, Anna Charisse; Wu, Paul; Mengersen, Kerrie; Yarlagadda, Prasad K D V

2014-01-01

Current Bayesian network software packages provide good graphical interface for users who design and develop Bayesian networks for various applications. However, the intended end-users of these networks may not necessarily find such an interface appealing and at times it could be overwhelming, particularly when the number of nodes in the network is large. To circumvent this problem, this paper presents an intuitive dashboard, which provides an additional layer of abstraction, enabling the end-users to easily perform inferences over the Bayesian networks. Unlike most software packages, which display the nodes and arcs of the network, the developed tool organises the nodes based on the cause-and-effect relationship, making the user-interaction more intuitive and friendly. In addition to performing various types of inferences, the users can conveniently use the tool to verify the behaviour of the developed Bayesian network. The tool has been developed using QT and SMILE libraries in C++

An Intuitive Dashboard for Bayesian Network Inference

Science.gov (United States)

Reddy, Vikas; Charisse Farr, Anna; Wu, Paul; Mengersen, Kerrie; Yarlagadda, Prasad K. D. V.

2014-03-01

Current Bayesian network software packages provide good graphical interface for users who design and develop Bayesian networks for various applications. However, the intended end-users of these networks may not necessarily find such an interface appealing and at times it could be overwhelming, particularly when the number of nodes in the network is large. To circumvent this problem, this paper presents an intuitive dashboard, which provides an additional layer of abstraction, enabling the end-users to easily perform inferences over the Bayesian networks. Unlike most software packages, which display the nodes and arcs of the network, the developed tool organises the nodes based on the cause-and-effect relationship, making the user-interaction more intuitive and friendly. In addition to performing various types of inferences, the users can conveniently use the tool to verify the behaviour of the developed Bayesian network. The tool has been developed using QT and SMILE libraries in C++.

Dynamics of the α-relaxation in glass-forming polymers. Study by neutron scattering and relaxation techniques

Science.gov (United States)

Colmenero, J.

1993-12-01

The dynamics of the α-relaxation in three different polymeric systems, poly(vinyl methyl ether) (PVME), poly(vinyl chloride) (PVC) and poly(bisphenol A, 2-hydroxypropylether) (PH) has been studied by means of relaxation techniques and quasielastic neutron scattering (backscattering spectrometers IN10 and IN13 at the ILL-Grenoble). By using these techniques we have covered a wide time scale ranging from mesoscopic to macroscopic times (10 -10 -10 1 s). For analyzing the experimental data we have developed a phenomenological procedure in the frequency domain based on the Havriliak-Negami relaxation function, which in fact implies a Kohlrausch-Williams-Watts relaxation function in the time domain. The results obtained indicate that the dynamics of the α-relaxation in a wide time scale shows a clear non-Debye behaviour. The shape of the relaxation functions is found to be similar for the different techniques used and independent of temperature and momentum transfer ( Q). Moreover, the characteristic relaxation times deduced from the fitting of the experimental data can also be described using only one Vogel-Fulcher functional form. Besides we found that the Q-dependence of the relaxation times obtained by QENS is given by a power law, τ( Q) ∞ Q- n ( n>2), n being dependent on the system, and that the Q-behaviour and the non-Debye behaviour are directly correlated. In the case of PVC, time of flight (TOF) neutron scattering experiments confirm these results in a shorter time scale (2×10 -11 -2× 10 -12 s). Moreover, TOF results also suggest the possibility of interpreting the “fast process” usually detected in glass-forming systems as a Debye-like short regime of the α-relaxation.

The relationships between suggestibility, influenceability, and relaxability.

Science.gov (United States)

Polczyk, Romuald; Frey, Olga; Szpitalak, Malwina

2013-01-01

This research explores the relationships between relaxability and various aspects of suggestibility and influenceability. The Jacobson Progressive Muscle Relaxation procedure was used to induce relaxation. Tests of direct suggestibility, relating to the susceptibility of overt suggestions, and indirect suggestibility, referring to indirect hidden influence, as well as self-description questionnaires on suggestibility and the tendency to comply were used. Thayer's Activation-Deactivation Adjective Check List, measuring various kinds of activation and used as a pre- and posttest, determined the efficacy of the relaxation procedure. Indirect, direct, and self-measured suggestibility proved to be positively related to the ability to relax, measured by Thayer's subscales relating to emotions. Compliance was not related to relaxability. The results are discussed in terms of the aspects of relaxation training connected with suggestibility.

Bayesian disease mapping: hierarchical modeling in spatial epidemiology

National Research Council Canada - National Science Library

Lawson, Andrew

2013-01-01

.... Exploring these new developments, Bayesian Disease Mapping: Hierarchical Modeling in Spatial Epidemiology, Second Edition provides an up-to-date, cohesive account of the full range of Bayesian disease mapping methods and applications...

NMR relaxation induced by iron oxide particles: testing theoretical models.

Science.gov (United States)

Gossuin, Y; Orlando, T; Basini, M; Henrard, D; Lascialfari, A; Mattea, C; Stapf, S; Vuong, Q L

2016-04-15

Superparamagnetic iron oxide particles find their main application as contrast agents for cellular and molecular magnetic resonance imaging. The contrast they bring is due to the shortening of the transverse relaxation time T 2 of water protons. In order to understand their influence on proton relaxation, different theoretical relaxation models have been developed, each of them presenting a certain validity domain, which depends on the particle characteristics and proton dynamics. The validation of these models is crucial since they allow for predicting the ideal particle characteristics for obtaining the best contrast but also because the fitting of T 1 experimental data by the theory constitutes an interesting tool for the characterization of the nanoparticles. In this work, T 2 of suspensions of iron oxide particles in different solvents and at different temperatures, corresponding to different proton diffusion properties, were measured and were compared to the three main theoretical models (the motional averaging regime, the static dephasing regime, and the partial refocusing model) with good qualitative agreement. However, a real quantitative agreement was not observed, probably because of the complexity of these nanoparticulate systems. The Roch theory, developed in the motional averaging regime (MAR), was also successfully used to fit T 1 nuclear magnetic relaxation dispersion (NMRD) profiles, even outside the MAR validity range, and provided a good estimate of the particle size. On the other hand, the simultaneous fitting of T 1 and T 2 NMRD profiles by the theory was impossible, and this occurrence constitutes a clear limitation of the Roch model. Finally, the theory was shown to satisfactorily fit the deuterium T 1 NMRD profile of superparamagnetic particle suspensions in heavy water.

Statistical foundation of the Kubo-Tomita theory of magnetic relaxation

International Nuclear Information System (INIS)

Yul'met'ev, R.M.

1974-01-01

With the aim to give the statistical foundation of the Kubo-Tomita theory the theoretical-functional method of the projection operators is applied to the phenomenon of magnetic relaxation. The exact nonmarkov nonlinear kinetic equations are found for the time correlation functions (TCF) of the longitudinal and transversal components of the spin magnetization of a system including the spin-lattice interaction lambda H' in a general form. The markov kinetic equations of the well-known Bloch-type are derived in the weak coupling Van Hove limits t → infinity, lambda → 0, lambda 2 t=const., and the rate of the spin-lattice (T 1 -1 ) and spin-spin (T 2 -1 ) relaxation is obtained from the relaxation coefficients. It is found that the formulas of the Kubo-Tomita for T 1 -1 and T 2 -1 are correct only in the case of rapid thermal motions when ω 0 tau 0 0 is the resonance frequency and tau 0 is the typical correlation time of the molecular thermal motions). In the other limiting case (ω 0 tau 0 >>1) of slow motion, the effective spectral densities which enter T 1 and T 2 are determined by a set of relaxation times Tsub(β)sup(n) of the spin irreducible operators Vsub(β)sup(n) from the spin-lattice interaction lambda H'. It is found that the time dependence of the transversal component of magnetization had been left out in the collision integral of Kubo-Tomita's theory. Precisely considering this circumstance the frequency dependence of T 2 -1 on the resonance frequency must be changed. (author)

Relaxation of Anisotropic Glasses

DEFF Research Database (Denmark)

Deubener, Joachim; Martin, Birgit; Wondraczek, Lothar

2004-01-01

. When the load was removed at room temperature a permanent optical anisotropy (birefringence) was observed only perpendicular to cylinder axis and the pressure direction indicating complete elimination of thermal stresses. Relaxation of structural anisotropy was studied from reheating experiments using...... the energy release, thermo-mechanical and optical relaxation behaviour are drawn....

MAP estimators and their consistency in Bayesian nonparametric inverse problems

KAUST Repository

Dashti, M.

2013-09-01

We consider the inverse problem of estimating an unknown function u from noisy measurements y of a known, possibly nonlinear, map applied to u. We adopt a Bayesian approach to the problem and work in a setting where the prior measure is specified as a Gaussian random field μ0. We work under a natural set of conditions on the likelihood which implies the existence of a well-posed posterior measure, μy. Under these conditions, we show that the maximum a posteriori (MAP) estimator is well defined as the minimizer of an Onsager-Machlup functional defined on the Cameron-Martin space of the prior; thus, we link a problem in probability with a problem in the calculus of variations. We then consider the case where the observational noise vanishes and establish a form of Bayesian posterior consistency for the MAP estimator. We also prove a similar result for the case where the observation of can be repeated as many times as desired with independent identically distributed noise. The theory is illustrated with examples from an inverse problem for the Navier-Stokes equation, motivated by problems arising in weather forecasting, and from the theory of conditioned diffusions, motivated by problems arising in molecular dynamics. © 2013 IOP Publishing Ltd.

MAP estimators and their consistency in Bayesian nonparametric inverse problems

International Nuclear Information System (INIS)

Dashti, M; Law, K J H; Stuart, A M; Voss, J

2013-01-01

We consider the inverse problem of estimating an unknown function u from noisy measurements y of a known, possibly nonlinear, map G applied to u. We adopt a Bayesian approach to the problem and work in a setting where the prior measure is specified as a Gaussian random field μ 0 . We work under a natural set of conditions on the likelihood which implies the existence of a well-posed posterior measure, μ y . Under these conditions, we show that the maximum a posteriori (MAP) estimator is well defined as the minimizer of an Onsager–Machlup functional defined on the Cameron–Martin space of the prior; thus, we link a problem in probability with a problem in the calculus of variations. We then consider the case where the observational noise vanishes and establish a form of Bayesian posterior consistency for the MAP estimator. We also prove a similar result for the case where the observation of G(u) can be repeated as many times as desired with independent identically distributed noise. The theory is illustrated with examples from an inverse problem for the Navier–Stokes equation, motivated by problems arising in weather forecasting, and from the theory of conditioned diffusions, motivated by problems arising in molecular dynamics. (paper)

Using Bayesian Networks to Improve Knowledge Assessment

Science.gov (United States)

Millan, Eva; Descalco, Luis; Castillo, Gladys; Oliveira, Paula; Diogo, Sandra

2013-01-01

In this paper, we describe the integration and evaluation of an existing generic Bayesian student model (GBSM) into an existing computerized testing system within the Mathematics Education Project (PmatE--Projecto Matematica Ensino) of the University of Aveiro. This generic Bayesian student model had been previously evaluated with simulated…

Learning dynamic Bayesian networks with mixed variables

DEFF Research Database (Denmark)

Bøttcher, Susanne Gammelgaard

This paper considers dynamic Bayesian networks for discrete and continuous variables. We only treat the case, where the distribution of the variables is conditional Gaussian. We show how to learn the parameters and structure of a dynamic Bayesian network and also how the Markov order can be learned...

Bayesian Statistics: Concepts and Applications in Animal Breeding – A Review

Directory of Open Access Journals (Sweden)

Lsxmikant-Sambhaji Kokate

2011-07-01

Full Text Available Statistics uses two major approaches- conventional (or frequentist and Bayesian approach. Bayesian approach provides a complete paradigm for both statistical inference and decision making under uncertainty. Bayesian methods solve many of the difficulties faced by conventional statistical methods, and extend the applicability of statistical methods. It exploits the use of probabilistic models to formulate scientific problems. To use Bayesian statistics, there is computational difficulty and secondly, Bayesian methods require specifying prior probability distributions. Markov Chain Monte-Carlo (MCMC methods were applied to overcome the computational difficulty, and interest in Bayesian methods was renewed. In Bayesian statistics, Bayesian structural equation model (SEM is used. It provides a powerful and flexible approach for studying quantitative traits for wide spectrum problems and thus it has no operational difficulties, with the exception of some complex cases. In this method, the problems are solved at ease, and the statisticians feel it comfortable with the particular way of expressing the results and employing the software available to analyze a large variety of problems.

Relaxation Estimation of RMSD in Molecular Dynamics Immunosimulations

Directory of Open Access Journals (Sweden)

Wolfgang Schreiner

2012-01-01

Full Text Available Molecular dynamics simulations have to be sufficiently long to draw reliable conclusions. However, no method exists to prove that a simulation has converged. We suggest the method of “lagged RMSD-analysis” as a tool to judge if an MD simulation has not yet run long enough. The analysis is based on RMSD values between pairs of configurations separated by variable time intervals Δt. Unless RMSD(Δt has reached a stationary shape, the simulation has not yet converged.

Relaxation techniques for stress

Science.gov (United States)

... raise your heart rate. This is called the stress response. Relaxation techniques can help your body relax and lower your blood pressure ... also many other types of breathing techniques you can learn. In many cases, you do not need much ... including those that cause stress. Meditation has been practiced for thousands of years, ...

Adiabatic fast passage application in solid state NMR study of cross relaxation and molecular dynamics in heteronuclear systems.

Science.gov (United States)

Baranowski, M; Woźniak-Braszak, A; Jurga, K

2016-01-01

The paper presents the benefits of using fast adiabatic passage for the study of molecular dynamics in the solid state heteronuclear systems in the laboratory frame. A homemade pulse spectrometer operating at the frequency of 30.2MHz and 28.411MHz for protons and fluorines, respectively, has been enhanced with microcontroller direct digital synthesizer DDS controller [1-4]. This work briefly describes how to construct a low-cost and easy-to-assemble adiabatic extension set for homemade and commercial spectrometers based on recently very popular Arduino shields. The described set was designed for fast adiabatic generation. Timing and synchronization problems are discussed. The cross-relaxation experiments with different initial states of the two spin systems have been performed. Contrary to our previous work [5] where the steady-state NOE experiments were conducted now proton spins (1)H are polarized in the magnetic field B0 while fluorine spins (19)F are perturbed by selective saturation for a short time and then the system is allowed to evolve for a period in the absence of a saturating field. The adiabatic passage application leads to a reversal of magnetization of fluorine spins and increases the amplitude of the signal. Copyright © 2015 Elsevier Inc. All rights reserved.

The Effects of Suggestibility on Relaxation.

Science.gov (United States)

Rickard, Henry C.; And Others

1985-01-01

Selected undergraduates (N=32) on the basis of Creative Imagination Scale scores and randomly assigned high and low suggestibility subjects to progressive relaxation (PR) and suggestions of relaxation (SR) training modes. Results revealed a significant pre-post relaxation effect, and main efffects for both suggestibility and training mode. (NRB)

Magneto-dependent stress relaxation of magnetorheological gels

KAUST Repository

Xu, Yangguang; Liu, Taixiang; Liao, G J; Lubineau, Gilles

2017-01-01

The stress relaxation behaviors of magnetorheological (MR) gels under stepwise shear loading are systematically investigated. The particle-enhanced effect, the magneto-induced effect, and the temperature-enhanced effect on the stress relaxation of MR gels are discussed. For further analysis of the magneto-induced stress relaxation mechanism in MR gels, a phenomenological model is established to describe the stress relaxation behavior of the matrix and the magnetic particle chains. All characteristic parameters introduced in the model, i.e. relaxation time, instantaneous modulus, and stable modulus, have well-defined physical meanings and are fitted based on the experimental results. The influence of each parameter on the macroscopic response is discussed and it is found that the relaxation stress induced by the magneto-mechanical coupling effect plays an important role in the stress relaxation process of MR gels.

Magneto-dependent stress relaxation of magnetorheological gels

KAUST Repository

Xu, Yangguang

2017-09-01

The stress relaxation behaviors of magnetorheological (MR) gels under stepwise shear loading are systematically investigated. The particle-enhanced effect, the magneto-induced effect, and the temperature-enhanced effect on the stress relaxation of MR gels are discussed. For further analysis of the magneto-induced stress relaxation mechanism in MR gels, a phenomenological model is established to describe the stress relaxation behavior of the matrix and the magnetic particle chains. All characteristic parameters introduced in the model, i.e. relaxation time, instantaneous modulus, and stable modulus, have well-defined physical meanings and are fitted based on the experimental results. The influence of each parameter on the macroscopic response is discussed and it is found that the relaxation stress induced by the magneto-mechanical coupling effect plays an important role in the stress relaxation process of MR gels.

Evolutionary Analysis of Dengue Serotype 2 Viruses Using Phylogenetic and Bayesian Methods from New Delhi, India.

Directory of Open Access Journals (Sweden)

Nazia Afreen

2016-03-01

Full Text Available Dengue fever is the most important arboviral disease in the tropical and sub-tropical countries of the world. Delhi, the metropolitan capital state of India, has reported many dengue outbreaks, with the last outbreak occurring in 2013. We have recently reported predominance of dengue virus serotype 2 during 2011-2014 in Delhi. In the present study, we report molecular characterization and evolutionary analysis of dengue serotype 2 viruses which were detected in 2011-2014 in Delhi. Envelope genes of 42 DENV-2 strains were sequenced in the study. All DENV-2 strains grouped within the Cosmopolitan genotype and further clustered into three lineages; Lineage I, II and III. Lineage III replaced lineage I during dengue fever outbreak of 2013. Further, a novel mutation Thr404Ile was detected in the stem region of the envelope protein of a single DENV-2 strain in 2014. Nucleotide substitution rate and time to the most recent common ancestor were determined by molecular clock analysis using Bayesian methods. A change in effective population size of Indian DENV-2 viruses was investigated through Bayesian skyline plot. The study will be a vital road map for investigation of epidemiology and evolutionary pattern of dengue viruses in India.

Non-linear Bayesian update of PCE coefficients

KAUST Repository

Litvinenko, Alexander

2014-01-06

Given: a physical system modeled by a PDE or ODE with uncertain coefficient q(?), a measurement operator Y (u(q), q), where u(q, ?) uncertain solution. Aim: to identify q(?). The mapping from parameters to observations is usually not invertible, hence this inverse identification problem is generally ill-posed. To identify q(!) we derived non-linear Bayesian update from the variational problem associated with conditional expectation. To reduce cost of the Bayesian update we offer a unctional approximation, e.g. polynomial chaos expansion (PCE). New: We apply Bayesian update to the PCE coefficients of the random coefficient q(?) (not to the probability density function of q).

Non-linear Bayesian update of PCE coefficients

KAUST Repository

Litvinenko, Alexander; Matthies, Hermann G.; Pojonk, Oliver; Rosic, Bojana V.; Zander, Elmar

2014-01-01

Given: a physical system modeled by a PDE or ODE with uncertain coefficient q(?), a measurement operator Y (u(q), q), where u(q, ?) uncertain solution. Aim: to identify q(?). The mapping from parameters to observations is usually not invertible, hence this inverse identification problem is generally ill-posed. To identify q(!) we derived non-linear Bayesian update from the variational problem associated with conditional expectation. To reduce cost of the Bayesian update we offer a unctional approximation, e.g. polynomial chaos expansion (PCE). New: We apply Bayesian update to the PCE coefficients of the random coefficient q(?) (not to the probability density function of q).

A Fast Iterative Bayesian Inference Algorithm for Sparse Channel Estimation

DEFF Research Database (Denmark)

Pedersen, Niels Lovmand; Manchón, Carles Navarro; Fleury, Bernard Henri

2013-01-01

representation of the Bessel K probability density function; a highly efficient, fast iterative Bayesian inference method is then applied to the proposed model. The resulting estimator outperforms other state-of-the-art Bayesian and non-Bayesian estimators, either by yielding lower mean squared estimation error...

A Gentle Introduction to Bayesian Analysis : Applications to Developmental Research

NARCIS (Netherlands)

Van de Schoot, Rens; Kaplan, David; Denissen, Jaap; Asendorpf, Jens B.; Neyer, Franz J.; van Aken, Marcel A G

2014-01-01

Bayesian statistical methods are becoming ever more popular in applied and fundamental research. In this study a gentle introduction to Bayesian analysis is provided. It is shown under what circumstances it is attractive to use Bayesian estimation, and how to interpret properly the results. First,

A gentle introduction to Bayesian analysis : Applications to developmental research

NARCIS (Netherlands)

van de Schoot, R.; Kaplan, D.; Denissen, J.J.A.; Asendorpf, J.B.; Neyer, F.J.; van Aken, M.A.G.

2014-01-01

Bayesian statistical methods are becoming ever more popular in applied and fundamental research. In this study a gentle introduction to Bayesian analysis is provided. It is shown under what circumstances it is attractive to use Bayesian estimation, and how to interpret properly the results. First,

A nonparametric Bayesian approach for genetic evaluation in ...

African Journals Online (AJOL)

South African Journal of Animal Science ... the Bayesian and Classical models, a Bayesian procedure is provided which allows these random ... data from the Elsenburg Dormer sheep stud and data from a simulation experiment are utilized. >

3D Bayesian contextual classifiers

DEFF Research Database (Denmark)

Larsen, Rasmus

2000-01-01

We extend a series of multivariate Bayesian 2-D contextual classifiers to 3-D by specifying a simultaneous Gaussian distribution for the feature vectors as well as a prior distribution of the class variables of a pixel and its 6 nearest 3-D neighbours.......We extend a series of multivariate Bayesian 2-D contextual classifiers to 3-D by specifying a simultaneous Gaussian distribution for the feature vectors as well as a prior distribution of the class variables of a pixel and its 6 nearest 3-D neighbours....

Bayesian probability theory and inverse problems

International Nuclear Information System (INIS)

Kopec, S.

1994-01-01

Bayesian probability theory is applied to approximate solving of the inverse problems. In order to solve the moment problem with the noisy data, the entropic prior is used. The expressions for the solution and its error bounds are presented. When the noise level tends to zero, the Bayesian solution tends to the classic maximum entropy solution in the L 2 norm. The way of using spline prior is also shown. (author)

Variations on Bayesian Prediction and Inference

Science.gov (United States)

2016-05-09

inference 2.2.1 Background There are a number of statistical inference problems that are not generally formulated via a full probability model...problem of inference about an unknown parameter, the Bayesian approach requires a full probability 1. REPORT DATE (DD-MM-YYYY) 4. TITLE AND...the problem of inference about an unknown parameter, the Bayesian approach requires a full probability model/likelihood which can be an obstacle

Bayesian inference for psychology. Part II: Example applications with JASP.

Science.gov (United States)

Wagenmakers, Eric-Jan; Love, Jonathon; Marsman, Maarten; Jamil, Tahira; Ly, Alexander; Verhagen, Josine; Selker, Ravi; Gronau, Quentin F; Dropmann, Damian; Boutin, Bruno; Meerhoff, Frans; Knight, Patrick; Raj, Akash; van Kesteren, Erik-Jan; van Doorn, Johnny; Šmíra, Martin; Epskamp, Sacha; Etz, Alexander; Matzke, Dora; de Jong, Tim; van den Bergh, Don; Sarafoglou, Alexandra; Steingroever, Helen; Derks, Koen; Rouder, Jeffrey N; Morey, Richard D

2018-02-01

Bayesian hypothesis testing presents an attractive alternative to p value hypothesis testing. Part I of this series outlined several advantages of Bayesian hypothesis testing, including the ability to quantify evidence and the ability to monitor and update this evidence as data come in, without the need to know the intention with which the data were collected. Despite these and other practical advantages, Bayesian hypothesis tests are still reported relatively rarely. An important impediment to the widespread adoption of Bayesian tests is arguably the lack of user-friendly software for the run-of-the-mill statistical problems that confront psychologists for the analysis of almost every experiment: the t-test, ANOVA, correlation, regression, and contingency tables. In Part II of this series we introduce JASP ( http://www.jasp-stats.org ), an open-source, cross-platform, user-friendly graphical software package that allows users to carry out Bayesian hypothesis tests for standard statistical problems. JASP is based in part on the Bayesian analyses implemented in Morey and Rouder's BayesFactor package for R. Armed with JASP, the practical advantages of Bayesian hypothesis testing are only a mouse click away.

Role of Thickness Confinement on Relaxations of the Fast Component in a Miscible A/B Blend

Energy Technology Data Exchange (ETDEWEB)

Green, Peter [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Sharma, Ravi P. [University of Michigan; Dong, Ban Xuan [University of Michigan

2018-01-18

Spatial compositional heterogeneity strongly influences the dynamics of the A and B components of bulk miscible blends. Its effects are especially apparent in mixtures, such as poly(vinyl methyl ether) (PVME)/polystyrene (PS), where there exist significant disparities between the component glass transition temperatures (Tgs) and relaxation times. The relaxation processes characterized by distinct temperature dependencies and relaxation rates manifest different local compositional environments for temperatures above and below the glass transition temperature of the miscible blend. This same behavior is shown to exist in miscible PS/PVME films as thin as 100 nm. Moreover, in thin films, the characteristic segmental relaxation times t of the PVME component of miscible PVME/PS blends confined between aluminum (Al) substrates decrease with increasing molecular weight M of the PS component. These relaxation rates are film thickness dependent, in films up to a few hundred nanometers in thickness. This is in remarkable contrast to homopolymer films, where thickness confinement effects are apparent only on length scales on the order of nanometers. These surprisingly large length scales and M dependence are associated with the preferential interfacial enrichment - wetting layer formation - of the PVME component at the external Al interfaces, which alters the local spatial blend composition within the interior of the film. The implications are that the dynamics of miscible thin film blends are dictated in part by component Tg differences, disparities in component relaxation rates, component-substrate interactions, and chain lengths (entropy of mixing).

Effect of the Magnus force on skyrmion relaxation dynamics

Science.gov (United States)

Brown, Barton L.; Täuber, Uwe C.; Pleimling, Michel

2018-01-01

We perform systematic Langevin molecular dynamics simulations of interacting skyrmions in thin films. The interplay between the Magnus force, the repulsive skyrmion-skyrmion interaction, and the thermal noise yields different regimes during nonequilibrium relaxation. In the noise-dominated regime, the Magnus force enhances the disordering effects of the thermal noise. In the Magnus-force-dominated regime, the Magnus force cooperates with the skyrmion-skyrmion interaction to yield a dynamic regime with slow decaying correlations. These two regimes are characterized by different values of the aging exponent. In general, the Magnus force accelerates the approach to the steady state.

Improving Transparency and Replication in Bayesian Statistics : The WAMBS-Checklist

NARCIS (Netherlands)

Depaoli, Sarah; van de Schoot, Rens

2017-01-01

Bayesian statistical methods are slowly creeping into all fields of science and are becoming ever more popular in applied research. Although it is very attractive to use Bayesian statistics, our personal experience has led us to believe that naively applying Bayesian methods can be dangerous for at

An introduction to using Bayesian linear regression with clinical data.

Science.gov (United States)

Baldwin, Scott A; Larson, Michael J

2017-11-01

Statistical training psychology focuses on frequentist methods. Bayesian methods are an alternative to standard frequentist methods. This article provides researchers with an introduction to fundamental ideas in Bayesian modeling. We use data from an electroencephalogram (EEG) and anxiety study to illustrate Bayesian models. Specifically, the models examine the relationship between error-related negativity (ERN), a particular event-related potential, and trait anxiety. Methodological topics covered include: how to set up a regression model in a Bayesian framework, specifying priors, examining convergence of the model, visualizing and interpreting posterior distributions, interval estimates, expected and predicted values, and model comparison tools. We also discuss situations where Bayesian methods can outperform frequentist methods as well has how to specify more complicated regression models. Finally, we conclude with recommendations about reporting guidelines for those using Bayesian methods in their own research. We provide data and R code for replicating our analyses. Copyright © 2017 Elsevier Ltd. All rights reserved.

Bayesian ARTMAP for regression.

Science.gov (United States)

Sasu, L M; Andonie, R

2013-10-01

Bayesian ARTMAP (BA) is a recently introduced neural architecture which uses a combination of Fuzzy ARTMAP competitive learning and Bayesian learning. Training is generally performed online, in a single-epoch. During training, BA creates input data clusters as Gaussian categories, and also infers the conditional probabilities between input patterns and categories, and between categories and classes. During prediction, BA uses Bayesian posterior probability estimation. So far, BA was used only for classification. The goal of this paper is to analyze the efficiency of BA for regression problems. Our contributions are: (i) we generalize the BA algorithm using the clustering functionality of both ART modules, and name it BA for Regression (BAR); (ii) we prove that BAR is a universal approximator with the best approximation property. In other words, BAR approximates arbitrarily well any continuous function (universal approximation) and, for every given continuous function, there is one in the set of BAR approximators situated at minimum distance (best approximation); (iii) we experimentally compare the online trained BAR with several neural models, on the following standard regression benchmarks: CPU Computer Hardware, Boston Housing, Wisconsin Breast Cancer, and Communities and Crime. Our results show that BAR is an appropriate tool for regression tasks, both for theoretical and practical reasons. Copyright © 2013 Elsevier Ltd. All rights reserved.

Using Bayesian belief networks in adaptive management.

Science.gov (United States)

J.B. Nyberg; B.G. Marcot; R. Sulyma

2006-01-01

Bayesian belief and decision networks are relatively new modeling methods that are especially well suited to adaptive-management applications, but they appear not to have been widely used in adaptive management to date. Bayesian belief networks (BBNs) can serve many purposes for practioners of adaptive management, from illustrating system relations conceptually to...

Rovibrational coupling in molecular nitrogen at high temperature: An atomic-level study

Energy Technology Data Exchange (ETDEWEB)

Valentini, Paolo, E-mail: vale0142@umn.edu; Norman, Paul, E-mail: norma198@umn.edu; Zhang, Chonglin, E-mail: zhang993@umn.edu; Schwartzentruber, Thomas E., E-mail: schwart@aem.umn.edu [Department of Aerospace Engineering and Mechanics, College of Science and Engineering, University of Minnesota, Minneapolis, Minnesota 55455 (United States)

2014-05-15

This article contains an atomic-level numerical investigation of rovibrational relaxation in molecular nitrogen at high temperature (>4000 K), neglecting dissociation. We conduct our study with the use of pure Molecular Dynamics (MD) and Classical Trajectory Calculations (CTC) Direct Simulation Monte Carlo (DSMC), verified to produce statistically identical results at the conditions of interest here. MD and CTC DSMC solely rely on the specification of a potential energy surface: in this work, the site-site Ling-Rigby potential. Additionally, dissociation is prevented by modeling the N–N bond either as a harmonic or an anharmonic spring. The selected molecular model was shown to (i) recover the shear viscosity (obtained from equilibrium pure MD Green-Kubo calculations) of molecular nitrogen over a wide range of temperatures, up to dissociation; (ii) predict well the near-equilibrium rotational relaxation behavior of N{sub 2}; (iii) reproduce vibrational relaxation times in excellent accordance with the Millikan-White correlation and previous semi-classical trajectory calculations in the low temperature range, i.e., between 4000 K and 10 000 K. By simulating isothermal relaxations in a periodic box, we found that the traditional two-temperature model assumptions become invalid at high temperatures (>10 000 K), due to a significant coupling between rotational and vibrational modes for bound states. This led us to add a modification to both the Jeans and the Landau-Teller equations to include a coupling term, essentially described by an additional relaxation time for internal energy equilibration. The degree of anharmonicity of the N{sub 2} bond determines the strength of the rovibrational coupling. Although neglecting N{sub 2} dissociation only provides a partial description of a nitrogen system at very high temperatures, high-energy trends for bound-bound transitions are essential to understand nonequilibrium gas flows, with possible implications on rovibration

Rovibrational coupling in molecular nitrogen at high temperature: An atomic-level study

International Nuclear Information System (INIS)

Valentini, Paolo; Norman, Paul; Zhang, Chonglin; Schwartzentruber, Thomas E.

2014-01-01

This article contains an atomic-level numerical investigation of rovibrational relaxation in molecular nitrogen at high temperature (>4000 K), neglecting dissociation. We conduct our study with the use of pure Molecular Dynamics (MD) and Classical Trajectory Calculations (CTC) Direct Simulation Monte Carlo (DSMC), verified to produce statistically identical results at the conditions of interest here. MD and CTC DSMC solely rely on the specification of a potential energy surface: in this work, the site-site Ling-Rigby potential. Additionally, dissociation is prevented by modeling the N–N bond either as a harmonic or an anharmonic spring. The selected molecular model was shown to (i) recover the shear viscosity (obtained from equilibrium pure MD Green-Kubo calculations) of molecular nitrogen over a wide range of temperatures, up to dissociation; (ii) predict well the near-equilibrium rotational relaxation behavior of N 2 ; (iii) reproduce vibrational relaxation times in excellent accordance with the Millikan-White correlation and previous semi-classical trajectory calculations in the low temperature range, i.e., between 4000 K and 10 000 K. By simulating isothermal relaxations in a periodic box, we found that the traditional two-temperature model assumptions become invalid at high temperatures (>10 000 K), due to a significant coupling between rotational and vibrational modes for bound states. This led us to add a modification to both the Jeans and the Landau-Teller equations to include a coupling term, essentially described by an additional relaxation time for internal energy equilibration. The degree of anharmonicity of the N 2 bond determines the strength of the rovibrational coupling. Although neglecting N 2 dissociation only provides a partial description of a nitrogen system at very high temperatures, high-energy trends for bound-bound transitions are essential to understand nonequilibrium gas flows, with possible implications on rovibration

Sandpile model for relaxation in complex systems

International Nuclear Information System (INIS)

Vazquez, A.; Sotolongo-Costa, O.; Brouers, F.

1997-10-01

The relaxation in complex systems is, in general, nonexponential. After an initial rapid decay the system relaxes slowly following a long time tail. In the present paper a sandpile moderation of the relaxation in complex systems is analysed. Complexity is introduced by a process of avalanches in the Bethe lattice and a feedback mechanism which leads to slower decay with increasing time. In this way, some features of relaxation in complex systems: long time tails relaxation, aging, and fractal distribution of characteristic times, are obtained by simple computer simulations. (author)

Doing bayesian data analysis a tutorial with R and BUGS

CERN Document Server

Kruschke, John K

2011-01-01

There is an explosion of interest in Bayesian statistics, primarily because recently created computational methods have finally made Bayesian analysis obtainable to a wide audience. Doing Bayesian Data Analysis, A Tutorial Introduction with R and BUGS provides an accessible approach to Bayesian data analysis, as material is explained clearly with concrete examples. The book begins with the basics, including essential concepts of probability and random sampling, and gradually progresses to advanced hierarchical modeling methods for realistic data. The text delivers comprehensive coverage of all

Bayesian estimation of dose rate effectiveness

International Nuclear Information System (INIS)

Arnish, J.J.; Groer, P.G.

2000-01-01

A Bayesian statistical method was used to quantify the effectiveness of high dose rate 137 Cs gamma radiation at inducing fatal mammary tumours and increasing the overall mortality rate in BALB/c female mice. The Bayesian approach considers both the temporal and dose dependence of radiation carcinogenesis and total mortality. This paper provides the first direct estimation of dose rate effectiveness using Bayesian statistics. This statistical approach provides a quantitative description of the uncertainty of the factor characterising the dose rate in terms of a probability density function. The results show that a fixed dose from 137 Cs gamma radiation delivered at a high dose rate is more effective at inducing fatal mammary tumours and increasing the overall mortality rate in BALB/c female mice than the same dose delivered at a low dose rate. (author)

BATSE gamma-ray burst line search. 2: Bayesian consistency methodology

Science.gov (United States)

Band, D. L.; Ford, L. A.; Matteson, J. L.; Briggs, M.; Paciesas, W.; Pendleton, G.; Preece, R.; Palmer, D.; Teegarden, B.; Schaefer, B.

1994-01-01

We describe a Bayesian methodology to evaluate the consistency between the reported Ginga and Burst and Transient Source Experiment (BATSE) detections of absorption features in gamma-ray burst spectra. Currently no features have been detected by BATSE, but this methodology will still be applicable if and when such features are discovered. The Bayesian methodology permits the comparison of hypotheses regarding the two detectors' observations and makes explicit the subjective aspects of our analysis (e.g., the quantification of our confidence in detector performance). We also present non-Bayesian consistency statistics. Based on preliminary calculations of line detectability, we find that both the Bayesian and non-Bayesian techniques show that the BATSE and Ginga observations are consistent given our understanding of these detectors.

Bayesian phylogenetic estimation of fossil ages.

Science.gov (United States)

Drummond, Alexei J; Stadler, Tanja

2016-07-19

Recent advances have allowed for both morphological fossil evidence and molecular sequences to be integrated into a single combined inference of divergence dates under the rule of Bayesian probability. In particular, the fossilized birth-death tree prior and the Lewis-Mk model of discrete morphological evolution allow for the estimation of both divergence times and phylogenetic relationships between fossil and extant taxa. We exploit this statistical framework to investigate the internal consistency of these models by producing phylogenetic estimates of the age of each fossil in turn, within two rich and well-characterized datasets of fossil and extant species (penguins and canids). We find that the estimation accuracy of fossil ages is generally high with credible intervals seldom excluding the true age and median relative error in the two datasets of 5.7% and 13.2%, respectively. The median relative standard error (RSD) was 9.2% and 7.2%, respectively, suggesting good precision, although with some outliers. In fact, in the two datasets we analyse, the phylogenetic estimate of fossil age is on average less than 2 Myr from the mid-point age of the geological strata from which it was excavated. The high level of internal consistency found in our analyses suggests that the Bayesian statistical model employed is an adequate fit for both the geological and morphological data, and provides evidence from real data that the framework used can accurately model the evolution of discrete morphological traits coded from fossil and extant taxa. We anticipate that this approach will have diverse applications beyond divergence time dating, including dating fossils that are temporally unconstrained, testing of the 'morphological clock', and for uncovering potential model misspecification and/or data errors when controversial phylogenetic hypotheses are obtained based on combined divergence dating analyses.This article is part of the themed issue 'Dating species divergences using

Molecular phylogenetic analysis supports a Gondwanan origin of the Hyriidae (Mollusca: Bivalvia: Unionida) and the paraphyly of Australasian taxa.

Science.gov (United States)

Graf, Daniel L; Jones, Hugh; Geneva, Anthony J; Pfeiffer, John M; Klunzinger, Michael W

2015-04-01

The freshwater mussel family Hyriidae (Mollusca: Bivalvia: Unionida) has a disjunct trans-Pacific distribution in Australasia and South America. Previous phylogenetic analyses have estimated the evolutionary relationships of the family and the major infra-familial taxa (Velesunioninae and Hyriinae: Hyridellini in Australia; Hyriinae: Hyriini, Castaliini, and Rhipidodontini in South America), but taxon and character sampling have been too incomplete to support a predictive classification or allow testing of biogeographical hypotheses. We sampled 30 freshwater mussel individuals representing the aforementioned hyriid taxa, as well as outgroup species representing the five other freshwater mussel families and their marine sister group (order Trigoniida). Our ingroup included representatives of all Australian genera. Phylogenetic relationships were estimated from three gene fragments (nuclear 28S, COI and 16S mtDNA) using maximum parsimony, maximum likelihood, and Bayesian inference, and we applied a Bayesian relaxed clock model calibrated with fossil dates to estimate node ages. Our analyses found good support for monophyly of the Hyriidae and the subfamilies and tribes, as well as the paraphyly of the Australasian taxa (Velesunioninae, (Hyridellini, (Rhipidodontini, (Castaliini, Hyriini)))). The Hyriidae was recovered as sister to a clade comprised of all other Recent freshwater mussel families. Our molecular date estimation supported Cretaceous origins of the major hyriid clades, pre-dating the Tertiary isolation of South America from Antarctica/Australia. We hypothesize that early diversification of the Hyriidae was driven by terrestrial barriers on Gondwana rather than marine barriers following disintegration of the super-continent. Copyright © 2015 Elsevier Inc. All rights reserved.

Relaxation Time of High-Density Amorphous Ice

Science.gov (United States)

Handle, Philip H.; Seidl, Markus; Loerting, Thomas

2012-06-01

Amorphous water plays a fundamental role in astrophysics, cryoelectron microscopy, hydration of matter, and our understanding of anomalous liquid water properties. Yet, the characteristics of the relaxation processes taking place in high-density amorphous ice (HDA) are unknown. We here reveal that the relaxation processes in HDA at 110-135 K at 0.1-0.2 GPa are of collective and global nature, resembling the alpha relaxation in glassy material. Measured relaxation times suggest liquid-like relaxation characteristics in the vicinity of the crystallization temperature at 145 K. By carefully relaxing pressurized HDA for several hours at 135 K, we produce a state that is closer to the ideal glass state than all HDA states discussed so far in literature.

Bayesian signal processing classical, modern, and particle filtering methods

CERN Document Server

Candy, James V

2016-01-01

This book aims to give readers a unified Bayesian treatment starting from the basics (Baye's rule) to the more advanced (Monte Carlo sampling), evolving to the next-generation model-based techniques (sequential Monte Carlo sampling). This next edition incorporates a new chapter on "Sequential Bayesian Detection," a new section on "Ensemble Kalman Filters" as well as an expansion of Case Studies that detail Bayesian solutions for a variety of applications. These studies illustrate Bayesian approaches to real-world problems incorporating detailed particle filter designs, adaptive particle filters and sequential Bayesian detectors. In addition to these major developments a variety of sections are expanded to "fill-in-the gaps" of the first edition. Here metrics for particle filter (PF) designs with emphasis on classical "sanity testing" lead to ensemble techniques as a basic requirement for performance analysis. The expansion of information theory metrics and their application to PF designs is fully developed an...

Bayesian Networks for Modeling Dredging Decisions

Science.gov (United States)

2011-10-01

years, that algorithms have been developed to solve these problems efficiently. Most modern Bayesian network software uses junction tree (a.k.a. join... software was used to develop the network . This is by no means an exhaustive list of Bayesian network applications, but it is representative of recent...characteristic node (SCN), state- defining node ( SDN ), effect node (EFN), or value node. The five types of nodes can be described as follows: ERDC/EL TR-11

A Bayesian classifier for symbol recognition

OpenAIRE

Barrat , Sabine; Tabbone , Salvatore; Nourrissier , Patrick

2007-01-01

URL : http://www.buyans.com/POL/UploadedFile/134_9977.pdf; International audience; We present in this paper an original adaptation of Bayesian networks to symbol recognition problem. More precisely, a descriptor combination method, which enables to improve significantly the recognition rate compared to the recognition rates obtained by each descriptor, is presented. In this perspective, we use a simple Bayesian classifier, called naive Bayes. In fact, probabilistic graphical models, more spec...

Sparse reconstruction using distribution agnostic bayesian matching pursuit

KAUST Repository

Masood, Mudassir; Al-Naffouri, Tareq Y.

2013-01-01

A fast matching pursuit method using a Bayesian approach is introduced for sparse signal recovery. This method performs Bayesian estimates of sparse signals even when the signal prior is non-Gaussian or unknown. It is agnostic on signal statistics

Π4U: A high performance computing framework for Bayesian uncertainty quantification of complex models

Science.gov (United States)

Hadjidoukas, P. E.; Angelikopoulos, P.; Papadimitriou, C.; Koumoutsakos, P.

2015-03-01

We present Π4U, an extensible framework, for non-intrusive Bayesian Uncertainty Quantification and Propagation (UQ+P) of complex and computationally demanding physical models, that can exploit massively parallel computer architectures. The framework incorporates Laplace asymptotic approximations as well as stochastic algorithms, along with distributed numerical differentiation and task-based parallelism for heterogeneous clusters. Sampling is based on the Transitional Markov Chain Monte Carlo (TMCMC) algorithm and its variants. The optimization tasks associated with the asymptotic approximations are treated via the Covariance Matrix Adaptation Evolution Strategy (CMA-ES). A modified subset simulation method is used for posterior reliability measurements of rare events. The framework accommodates scheduling of multiple physical model evaluations based on an adaptive load balancing library and shows excellent scalability. In addition to the software framework, we also provide guidelines as to the applicability and efficiency of Bayesian tools when applied to computationally demanding physical models. Theoretical and computational developments are demonstrated with applications drawn from molecular dynamics, structural dynamics and granular flow.

Π4U: A high performance computing framework for Bayesian uncertainty quantification of complex models

International Nuclear Information System (INIS)

Hadjidoukas, P.E.; Angelikopoulos, P.; Papadimitriou, C.; Koumoutsakos, P.

2015-01-01

We present Π4U, 1 an extensible framework, for non-intrusive Bayesian Uncertainty Quantification and Propagation (UQ+P) of complex and computationally demanding physical models, that can exploit massively parallel computer architectures. The framework incorporates Laplace asymptotic approximations as well as stochastic algorithms, along with distributed numerical differentiation and task-based parallelism for heterogeneous clusters. Sampling is based on the Transitional Markov Chain Monte Carlo (TMCMC) algorithm and its variants. The optimization tasks associated with the asymptotic approximations are treated via the Covariance Matrix Adaptation Evolution Strategy (CMA-ES). A modified subset simulation method is used for posterior reliability measurements of rare events. The framework accommodates scheduling of multiple physical model evaluations based on an adaptive load balancing library and shows excellent scalability. In addition to the software framework, we also provide guidelines as to the applicability and efficiency of Bayesian tools when applied to computationally demanding physical models. Theoretical and computational developments are demonstrated with applications drawn from molecular dynamics, structural dynamics and granular flow

Bayesian emulation for optimization in multi-step portfolio decisions

OpenAIRE

Irie, Kaoru; West, Mike

2016-01-01

We discuss the Bayesian emulation approach to computational solution of multi-step portfolio studies in financial time series. "Bayesian emulation for decisions" involves mapping the technical structure of a decision analysis problem to that of Bayesian inference in a purely synthetic "emulating" statistical model. This provides access to standard posterior analytic, simulation and optimization methods that yield indirect solutions of the decision problem. We develop this in time series portf...

Accelerated evolution of innate immunity proteins in social insects: adaptive evolution or relaxed constraint?

Science.gov (United States)

Harpur, Brock A; Zayed, Amro

2013-07-01

The genomes of eusocial insects have a reduced complement of immune genes-an unusual finding considering that sociality provides ideal conditions for disease transmission. The following three hypotheses have been invoked to explain this finding: 1) social insects are attacked by fewer pathogens, 2) social insects have effective behavioral or 3) novel molecular mechanisms for combating pathogens. At the molecular level, these hypotheses predict that canonical innate immune pathways experience a relaxation of selective constraint. A recent study of several innate immune genes in ants and bees showed a pattern of accelerated amino acid evolution, which is consistent with either positive selection or a relaxation of constraint. We studied the population genetics of innate immune genes in the honey bee Apis mellifera by partially sequencing 13 genes from the bee's Toll pathway (∼10.5 kb) and 20 randomly chosen genes (∼16.5 kb) sequenced in 43 diploid workers. Relative to the random gene set, Toll pathway genes had significantly higher levels of amino acid replacement mutations segregating within A. mellifera and fixed between A. mellifera and A. cerana. However, levels of diversity and divergence at synonymous sites did not differ between the two gene sets. Although we detect strong signs of balancing selection on the pathogen recognition gene pgrp-sa, many of the genes in the Toll pathway show signatures of relaxed selective constraint. These results are consistent with the reduced complement of innate immune genes found in social insects and support the hypothesis that some aspect of eusociality renders canonical innate immunity superfluous.

Relaxation in x-space magnetic particle imaging.

Science.gov (United States)

Croft, Laura R; Goodwill, Patrick W; Conolly, Steven M

2012-12-01

Magnetic particle imaging (MPI) is a new imaging modality that noninvasively images the spatial distribution of superparamagnetic iron oxide nanoparticles (SPIOs). MPI has demonstrated high contrast and zero attenuation with depth, and MPI promises superior safety compared to current angiography methods, X-ray, computed tomography, and magnetic resonance imaging angiography. Nanoparticle relaxation can delay the SPIO magnetization, and in this work we investigate the open problem of the role relaxation plays in MPI scanning and its effect on the image. We begin by amending the x-space theory of MPI to include nanoparticle relaxation effects. We then validate the amended theory with experiments from a Berkeley x-space relaxometer and a Berkeley x-space projection MPI scanner. Our theory and experimental data indicate that relaxation reduces SNR and asymmetrically blurs the image in the scanning direction. While relaxation effects can have deleterious effects on the MPI scan, we show theoretically and experimentally that x-space reconstruction remains robust in the presence of relaxation. Furthermore, the role of relaxation in x-space theory provides guidance as we develop methods to minimize relaxation-induced blurring. This will be an important future area of research for the MPI community.

Estimating side-chain order in methyl-protonated, perdeuterated proteins via multiple-quantum relaxation violated coherence transfer NMR spectroscopy

International Nuclear Information System (INIS)

Sun Hechao; Godoy-Ruiz, Raquel; Tugarinov, Vitali

2012-01-01

Relaxation violated coherence transfer NMR spectroscopy (Tugarinov et al. in J Am Chem Soc 129:1743–1750, 2007) is an established experimental tool for quantitative estimation of the amplitudes of side-chain motions in methyl-protonated, highly deuterated proteins. Relaxation violated coherence transfer experiments monitor the build-up of methyl proton multiple-quantum coherences that can be created in magnetically equivalent spin-systems as long as their transverse magnetization components relax with substantially different rates. The rate of this build-up is a reporter of the methyl-bearing side-chain mobility. Although the build-up of multiple-quantum 1 H coherences is monitored in these experiments, the decay of the methyl signal during relaxation delays occurs when methyl proton magnetization is in a single-quantum state. We describe a relaxation violated coherence transfer approach where the relaxation of multiple-quantum 1 H– 13 C methyl coherences during the relaxation delay period is quantified. The NMR experiment and the associated fitting procedure that models the time-dependence of the signal build-up, are applicable to the characterization of side-chain order in [ 13 CH 3 ]-methyl-labeled, highly deuterated protein systems up to ∼100 kDa in molecular weight. The feasibility of extracting reliable measures of side-chain order is experimentally verified on methyl-protonated, perdeuterated samples of an 8.5-kDa ubiquitin at 10°C and an 82-kDa Malate Synthase G at 37°C.

Hair Dye and Hair Relaxers

Science.gov (United States)

... For Consumers Consumer Information by Audience For Women Hair Dye and Hair Relaxers Share Tweet Linkedin Pin it More sharing ... products. If you have a bad reaction to hair dyes and relaxers, you should: Stop using the ...

Bayesian Analysis for Penalized Spline Regression Using WinBUGS

Directory of Open Access Journals (Sweden)

Ciprian M. Crainiceanu

2005-09-01

Full Text Available Penalized splines can be viewed as BLUPs in a mixed model framework, which allows the use of mixed model software for smoothing. Thus, software originally developed for Bayesian analysis of mixed models can be used for penalized spline regression. Bayesian inference for nonparametric models enjoys the flexibility of nonparametric models and the exact inference provided by the Bayesian inferential machinery. This paper provides a simple, yet comprehensive, set of programs for the implementation of nonparametric Bayesian analysis in WinBUGS. Good mixing properties of the MCMC chains are obtained by using low-rank thin-plate splines, while simulation times per iteration are reduced employing WinBUGS specific computational tricks.

Comparative Study of Inference Methods for Bayesian Nonnegative Matrix Factorisation

DEFF Research Database (Denmark)

Brouwer, Thomas; Frellsen, Jes; Liò, Pietro

2017-01-01

In this paper, we study the trade-offs of different inference approaches for Bayesian matrix factorisation methods, which are commonly used for predicting missing values, and for finding patterns in the data. In particular, we consider Bayesian nonnegative variants of matrix factorisation and tri......-factorisation, and compare non-probabilistic inference, Gibbs sampling, variational Bayesian inference, and a maximum-a-posteriori approach. The variational approach is new for the Bayesian nonnegative models. We compare their convergence, and robustness to noise and sparsity of the data, on both synthetic and real...

Simulations of the flipping images and microparameters of molecular orientations in liquids according to the molecule string model

International Nuclear Information System (INIS)

Wang Li-Na; Zhao Xing-Yu; Zhang Li-Li; Huang Yi-Neng

2012-01-01

The relaxation dynamics of liquids is one of the fundamental problems in liquid physics, and it is also one of the key issues to understand the glass transition mechanism. It will undoubtedly provide enlightenment on understanding and calculating the relaxation dynamics if the molecular orientation flipping images and relevant microparameters of liquids are studied. In this paper, we first give five microparameters to describe the individual molecular string (MS) relaxation based on the dynamical Hamiltonian of the MS model, and then simulate the images of individual MS ensemble, and at the same time calculate the parameters of the equilibrium state. The results show that the main molecular orientation flipping image in liquids (including supercooled liquid) is similar to the random walk. In addition, two pairs of the parameters are equal, and one can be ignored compared with the other. This conclusion will effectively reduce the difficulties in calculating the individual MS relaxation based on the single-molecule orientation flipping rate of the general Glauber type, and the computer simulation time of interaction MS relaxation. Moreover, the conclusion is of reference significance for solving and simulating the multi-state MS model. (condensed matter: structural, mechanical, and thermal properties)

Pulsed NMR studies of crosslinking and entanglements in high molecular weight linear polydimethylsiloxanes

International Nuclear Information System (INIS)

Folland, R.; Charlesby, A.

1977-01-01

Pulsed NMR studies of proton spin relaxation are used to investigate both radiation-induced cross linking and entanglements in three high molecular weight linear polydimethylsiloxanes (Msub(w) = 26,000, 63,000 and 110,000). Particular emphasis is placed on the spin-spin relaxation since this is determined by the slower relative translational motions of the polymer chains and hence profoundly affected by the presence of intermolecular couplings such as crosslinks or entanglements. The spin-lattice relaxation times, T 1 , are determined by the fast anisotropic chain rotations and are rather insensitive to such intermolecular couplings. The spin-spin relaxation in these materials is represented by a double exponential decay involving two time constants, Tsub(2S) and Tsub(2L). The shorter component, Tsub(2S), is attributed to network material, which may be either of a dynamic form arising from temporary entanglements or of a permanent nature due to crosslinks. The concentration of entanglements depends on the initial molecular weight of the sample whereas the concentration of crosslinks is a function of the radiation dose. The longer component, Tsub(2L), is attributed to the non-network molecules. On the time scale of the NMR measurements the entanglements are shown to act in the same way as crosslinks. The variation of the relative proportions of network and non-network material with dose is shown to be accounted for by using standard gelation theory when allowance is made for the initial effective crosslink density due to entanglements. The analysis provides a value for the average molecular weight per entanglement point of 27,000 +- 1000 which is consistent with the critical molecular weight for entanglements of 29,000. The dependences of Tsub(2S) and Tsub(2L) on dose and molecular weight are also discussed in terms of the molecular motion. (author)

Relaxation of a steep density gradient in a simple fluid: Comparison between atomistic and continuum modeling

International Nuclear Information System (INIS)

Pourali, Meisam; Maghari, Ali; Meloni, Simone; Magaletti, Francesco; Casciola, Carlo Massimo; Ciccotti, Giovanni

2014-01-01

We compare dynamical nonequilibrium molecular dynamics and continuum simulations of the dynamics of relaxation of a fluid system characterized by a non-uniform density profile. Results match quite well as long as the lengthscale of density nonuniformities are greater than the molecular scale (∼10 times the molecular size). In presence of molecular scale features some of the continuum fields (e.g., density and momentum) are in good agreement with atomistic counterparts, but are smoother. On the contrary, other fields, such as the temperature field, present very large difference with respect to reference (atomistic) ones. This is due to the limited accuracy of some of the empirical relations used in continuum models, the equation of state of the fluid in the present example

Optimizing Prediction Using Bayesian Model Averaging: Examples Using Large-Scale Educational Assessments.

Science.gov (United States)

Kaplan, David; Lee, Chansoon

2018-01-01

This article provides a review of Bayesian model averaging as a means of optimizing the predictive performance of common statistical models applied to large-scale educational assessments. The Bayesian framework recognizes that in addition to parameter uncertainty, there is uncertainty in the choice of models themselves. A Bayesian approach to addressing the problem of model uncertainty is the method of Bayesian model averaging. Bayesian model averaging searches the space of possible models for a set of submodels that satisfy certain scientific principles and then averages the coefficients across these submodels weighted by each model's posterior model probability (PMP). Using the weighted coefficients for prediction has been shown to yield optimal predictive performance according to certain scoring rules. We demonstrate the utility of Bayesian model averaging for prediction in education research with three examples: Bayesian regression analysis, Bayesian logistic regression, and a recently developed approach for Bayesian structural equation modeling. In each case, the model-averaged estimates are shown to yield better prediction of the outcome of interest than any submodel based on predictive coverage and the log-score rule. Implications for the design of large-scale assessments when the goal is optimal prediction in a policy context are discussed.

Inelastic neutron scattering investigation of the α-β crossover in glass-formers as a function of molecular architecture

International Nuclear Information System (INIS)

Levelut, C.; Faivre, A.; Pelous, J.; Durand, D.

1999-01-01

Complete text of publication follows. An experimental investigation of the relaxational processes related to the glass transition in several glass formers with more or less complex molecular architecture is presented. This inelastic neutron scattering study concentrates on the region around 1.1 to 1.5 T g where the two relaxation processes usually identified in most glass formers, the α and the β relaxations, are expected to merge or cross. A recent study comparing the dynamics of Sorbitol and Maltitol (two low molecular and complementary glasses) seems to show that the way on which the α and β processes merge depends on the differences in the chemical architecture of these polyols [1]. In the present work, linear diols, three-arm-star triols and crosslinked polyurethanes, synthesized from the latter are studied. This work is an extension of a previous study of the relaxational processes in cross-linked polyurethanes [2]. For such series of samples of similar chemical composition but with increasing complexity in the architecture, the influence of the molecular complexity on the type of merging between α and β processes is tested. This allows to discuss the α-β cross-over on molecular level. (author)

Molecular Mobility of an Amorphous Chiral Pharmaceutical Compound: Impact of Chirality and Chemical Purity.

Science.gov (United States)

Viel, Quentin; Delbreilh, Laurent; Coquerel, Gérard; Petit, Samuel; Dargent, Eric

2017-08-17

A dielectric relaxation spectroscopy (DRS) study was performed to investigate the molecular mobility of amorphous chiral diprophylline (DPL). For this purpose, both racemic DPL and a single enantiomer of DPL were considered. After fast cooling from the melt at very low temperature (-140 °C), progressive heating below and above the glass transition (T g ≈ 37 °C) induces two secondary relaxations (γ- and δ-) and primary relaxations (α-) for both enantiomeric compositions. After chemical purification of our samples by means of cooling recrystallization, no γ-process could be detected by DRS. Hence, it was highlighted that the molecular mobility in the glassy state is influenced by the presence of theophylline (TPH), the main impurity in DPL samples. We also proved that the dynamic behavior of a single enantiomer and the racemic mixture of the same purified compound are quasi-identical. This study demonstrates that the relative stability and the molecular mobility of chiral amorphous drugs are strongly sensitive to chemical purity.

Can natural selection encode Bayesian priors?

Science.gov (United States)

Ramírez, Juan Camilo; Marshall, James A R

2017-08-07

The evolutionary success of many organisms depends on their ability to make decisions based on estimates of the state of their environment (e.g., predation risk) from uncertain information. These decision problems have optimal solutions and individuals in nature are expected to evolve the behavioural mechanisms to make decisions as if using the optimal solutions. Bayesian inference is the optimal method to produce estimates from uncertain data, thus natural selection is expected to favour individuals with the behavioural mechanisms to make decisions as if they were computing Bayesian estimates in typically-experienced environments, although this does not necessarily imply that favoured decision-makers do perform Bayesian computations exactly. Each individual should evolve to behave as if updating a prior estimate of the unknown environment variable to a posterior estimate as it collects evidence. The prior estimate represents the decision-maker's default belief regarding the environment variable, i.e., the individual's default 'worldview' of the environment. This default belief has been hypothesised to be shaped by natural selection and represent the environment experienced by the individual's ancestors. We present an evolutionary model to explore how accurately Bayesian prior estimates can be encoded genetically and shaped by natural selection when decision-makers learn from uncertain information. The model simulates the evolution of a population of individuals that are required to estimate the probability of an event. Every individual has a prior estimate of this probability and collects noisy cues from the environment in order to update its prior belief to a Bayesian posterior estimate with the evidence gained. The prior is inherited and passed on to offspring. Fitness increases with the accuracy of the posterior estimates produced. Simulations show that prior estimates become accurate over evolutionary time. In addition to these 'Bayesian' individuals, we also

Molecular Viscosity Sensors with Two Rotators for Optimizing the Fluorescence Intensity-Contrast Trade-Off.

Science.gov (United States)

Lee, Seung-Chul; Lee, Chang-Lyoul; Heo, Jeongyun; Jeong, Chan-Uk; Lee, Gyeong-Hui; Kim, Sehoon; Yoon, Woojin; Yun, Hoseop; Park, Sung O; Kwak, Sang Kyu; Park, Sung-Ha; Kwon, O-Pil

2018-02-26

A series of fluorescent molecular rotors obtained by introducing two rotational groups ("rotators"), which exhibit different rotational and electron-donating abilities, are discussed. Whereas the control molecular rotor, PH, includes a single rotator (the widely used phenyl group), the PO molecular rotors consist of two rotators (a phenyl group and an alkoxy group), which exhibit simultaneous strongly electron-donating and easy rotational abilities. Compared with the control rotor PH, PO molecular rotors exhibited one order of magnitude higher quantum yield (fluorescence intensity) and simultaneously exhibited significantly higher fluorescence contrast. These properties are directly related to the strong electron-donating ability and low energy barrier of rotation of the alkoxy group, as confirmed by dynamic fluorescence experiments and quantum chemical calculations. The PO molecular rotors exhibited two fluorescence relaxation pathways, whereas the PH molecular rotor exhibited a single fluorescence relaxation pathway. Cellular fluorescence imaging with PO molecular rotors for mapping cellular viscosity was successfully demonstrated. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Mechanistic curiosity will not kill the Bayesian cat

NARCIS (Netherlands)

Borsboom, D.; Wagenmakers, E.-J.; Romeijn, J.-W.

2011-01-01

Jones & Love (J&L) suggest that Bayesian approaches to the explanation of human behavior should be constrained by mechanistic theories. We argue that their proposal misconstrues the relation between process models, such as the Bayesian model, and mechanisms. While mechanistic theories can answer

Mechanistic curiosity will not kill the Bayesian cat

NARCIS (Netherlands)

Borsboom, Denny; Wagenmakers, Eric-Jan; Romeijn, Jan-Willem

Jones & Love (J&L) suggest that Bayesian approaches to the explanation of human behavior should be constrained by mechanistic theories. We argue that their proposal misconstrues the relation between process models, such as the Bayesian model, and mechanisms. While mechanistic theories can answer

A Robust Bayesian Approach to an Optimal Replacement Policy for Gas Pipelines

Directory of Open Access Journals (Sweden)

José Pablo Arias-Nicolás

2015-06-01

Full Text Available In the paper, we address Bayesian sensitivity issues when integrating experts’ judgments with available historical data in a case study about strategies for the preventive maintenance of low-pressure cast iron pipelines in an urban gas distribution network. We are interested in replacement priorities, as determined by the failure rates of pipelines deployed under different conditions. We relax the assumptions, made in previous papers, about the prior distributions on the failure rates and study changes in replacement priorities under different choices of generalized moment-constrained classes of priors. We focus on the set of non-dominated actions, and among them, we propose the least sensitive action as the optimal choice to rank different classes of pipelines, providing a sound approach to the sensitivity problem. Moreover, we are also interested in determining which classes have a failure rate exceeding a given acceptable value, considered as the threshold determining no need for replacement. Graphical tools are introduced to help decisionmakers to determine if pipelines are to be replaced and the corresponding priorities.

Statistics: a Bayesian perspective

National Research Council Canada - National Science Library

Berry, Donald A

1996-01-01

...: it is the only introductory textbook based on Bayesian ideas, it combines concepts and methods, it presents statistics as a means of integrating data into the significant process, it develops ideas...

Gd-DTPA-Dopamine-Bisphytanyl Amphiphile: Synthesis, Characterisation and Relaxation Parameters of the Nanoassemblies and Their Potential as MRI Contrast Agents.

Science.gov (United States)

Gupta, Abhishek; Willis, Scott A; Waddington, Lynne J; Stait-Gardner, Tim; de Campo, Liliana; Hwang, Dennis W; Kirby, Nigel; Price, William S; Moghaddam, Minoo J

2015-09-28

Here, a new amphiphilic magnetic resonance imaging (MRI) contrast agent, a Gd(III)-chelated diethylenetriaminepentaacetic acid conjugated to two branched alkyl chains via a dopamine spacer, Gd-DTPA-dopamine-bisphytanyl (Gd-DTPA-Dop-Phy), which is readily capable of self-assembling into liposomal nanoassemblies upon dispersion in an aqueous solution, is reported. In vitro relaxivities of the dispersions were found to be much higher than Magnevist, a commercially available contrast agent, at 0.47 T but comparable at 9.40 T. Analysis of variable temperature (17)O NMR transverse relaxation measurements revealed the water exchange of the nanoassemblies to be faster than that previously reported for paramagnetic liposomes. Molecular reorientation dynamics were probed by (1)H NMRD profiles using a classical inner and outer sphere relaxation model and a Lipari-Szabo "model-free" approach. High payloads of Gd(III) ions in the liposomal nanoassemblies made solely from the Gd-DTPA-Dop-Phy amphiphiles, in combination with slow molecular reorientation and fast water exchange makes this novel amphiphile a suitable candidate to be investigated as an advanced MRI contrast agent. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Embedding the results of focussed Bayesian fusion into a global context

Science.gov (United States)

Sander, Jennifer; Heizmann, Michael

2014-05-01

Bayesian statistics offers a well-founded and powerful fusion methodology also for the fusion of heterogeneous information sources. However, except in special cases, the needed posterior distribution is not analytically derivable. As consequence, Bayesian fusion may cause unacceptably high computational and storage costs in practice. Local Bayesian fusion approaches aim at reducing the complexity of the Bayesian fusion methodology significantly. This is done by concentrating the actual Bayesian fusion on the potentially most task relevant parts of the domain of the Properties of Interest. Our research on these approaches is motivated by an analogy to criminal investigations where criminalists pursue clues also only locally. This publication follows previous publications on a special local Bayesian fusion technique called focussed Bayesian fusion. Here, the actual calculation of the posterior distribution gets completely restricted to a suitably chosen local context. By this, the global posterior distribution is not completely determined. Strategies for using the results of a focussed Bayesian analysis appropriately are needed. In this publication, we primarily contrast different ways of embedding the results of focussed Bayesian fusion explicitly into a global context. To obtain a unique global posterior distribution, we analyze the application of the Maximum Entropy Principle that has been shown to be successfully applicable in metrology and in different other areas. To address the special need for making further decisions subsequently to the actual fusion task, we further analyze criteria for decision making under partial information.

A Bayesian Optimal Design for Sequential Accelerated Degradation Testing

Directory of Open Access Journals (Sweden)

Xiaoyang Li

2017-07-01

Full Text Available When optimizing an accelerated degradation testing (ADT plan, the initial values of unknown model parameters must be pre-specified. However, it is usually difficult to obtain the exact values, since many uncertainties are embedded in these parameters. Bayesian ADT optimal design was presented to address this problem by using prior distributions to capture these uncertainties. Nevertheless, when the difference between a prior distribution and actual situation is large, the existing Bayesian optimal design might cause some over-testing or under-testing issues. For example, the implemented ADT following the optimal ADT plan consumes too much testing resources or few accelerated degradation data are obtained during the ADT. To overcome these obstacles, a Bayesian sequential step-down-stress ADT design is proposed in this article. During the sequential ADT, the test under the highest stress level is firstly conducted based on the initial prior information to quickly generate degradation data. Then, the data collected under higher stress levels are employed to construct the prior distributions for the test design under lower stress levels by using the Bayesian inference. In the process of optimization, the inverse Gaussian (IG process is assumed to describe the degradation paths, and the Bayesian D-optimality is selected as the optimal objective. A case study on an electrical connector’s ADT plan is provided to illustrate the application of the proposed Bayesian sequential ADT design method. Compared with the results from a typical static Bayesian ADT plan, the proposed design could guarantee more stable and precise estimations of different reliability measures.

Continuous monitoring of the zinc-phosphate acid-base cement setting reaction by proton nuclear magnetic relaxation

International Nuclear Information System (INIS)

Apih, T.; Lebar, A.; Pawlig, O.; Trettin, R.

2001-01-01

Proton nuclear magnetic relaxation is a well-established technique for continuous and non destructive monitoring of hydration of conventional Portland building cements. Here, we demonstrate the feasibility of nuclear magnetic resonance (NMR) monitoring of the setting reaction of zinc-phosphate acid-base dental cements, which harden in minutes as compared to days, as in the case of Portland cements. We compare the setting of cement powder (mainly, zinc oxide) prepared with clinically used aluminum-modified orthophosphoric acid solution with the setting of a model system where cement powder is mixed with pure orthophosphoric acid solution. In contrast to previously published NMR studies of setting Portland cements, where a decrease of spin-lattice relaxation time is attributed to enhanced relaxation at the growing internal surface, spin-lattice relaxation time T 1 increases during the set of clinically used zinc-phosphate cement. Comparison of these results with a detailed study of diffusion, viscosity, and magnetic-field dispersion of T 1 in pure and aluminum-modified orthophosphoric acid demonstrates that the increase of T 1 in the setting cement is connected with the increase of molecular mobility in the residual phosphoric acid solution. Although not taken into account so far, such effects may also significantly influence the relaxation times in setting Portland cements, particularly when admixtures with an effect on water viscosity are used. [copyright] 2001 American Institute of Physics

A Bayesian Method for Weighted Sampling

OpenAIRE

Lo, Albert Y.

1993-01-01

Bayesian statistical inference for sampling from weighted distribution models is studied. Small-sample Bayesian bootstrap clone (BBC) approximations to the posterior distribution are discussed. A second-order property for the BBC in unweighted i.i.d. sampling is given. A consequence is that BBC approximations to a posterior distribution of the mean and to the sampling distribution of the sample average, can be made asymptotically accurate by a proper choice of the random variables that genera...

Bayesian Geostatistical Design

DEFF Research Database (Denmark)

Diggle, Peter; Lophaven, Søren Nymand

2006-01-01

locations to, or deletion of locations from, an existing design, and prospective design, which consists of choosing positions for a new set of sampling locations. We propose a Bayesian design criterion which focuses on the goal of efficient spatial prediction whilst allowing for the fact that model...

Lineshape theory of pigment-protein complexes: How the finite relaxation time of nuclei influences the exciton relaxation-induced lifetime broadening

Energy Technology Data Exchange (ETDEWEB)

Dinh, Thanh-Chung; Renger, Thomas, E-mail: thomas.renger@jku.at [Institut für Theoretische Physik, Johannes Kepler University Linz, Altenberger Str. 69, 4040 Linz (Austria)

2016-07-21

In pigment-protein complexes, often the excited states are partially delocalized and the exciton-vibrational coupling in the basis of delocalized states contains large diagonal and small off-diagonal elements. This inequality may be used to introduce potential energy surfaces (PESs) of exciton states and to treat the inter-PES coupling in Markov and secular approximations. The resulting lineshape function consists of a Lorentzian peak that is broadened by the finite lifetime of the exciton states caused by the inter-PES coupling and a vibrational sideband that results from the mutual displacement of the excitonic PESs with respect to that of the ground state. So far analytical expressions have been derived that relate the exciton relaxation-induced lifetime broadening to the Redfield [T. Renger and R. A. Marcus, J. Chem. Phys. 116, 9997 (2002)] or modified Redfield [M. Schröder, U. Kleinekathöfer, and M. Schreiber, J. Chem. Phys. 124, 084903 (2006)] rate constants of exciton relaxation, assuming that intra-PES nuclear relaxation is fast compared to inter-PES transfer. Here, we go beyond this approximation and provide an analytical expression, termed Non-equilibrium Modified Redfield (NeMoR) theory, for the lifetime broadening that takes into account the finite nuclear relaxation time. In an application of the theory to molecular dimers, we find that, for a widely used experimental spectral density of the exciton-vibrational coupling of pigment-protein complexes, the NeMoR spectrum at low-temperatures (T < 150 K) is better approximated by Redfield than by modified Redfield theory. At room temperature, the lifetime broadening obtained with Redfield theory underestimates the NeMoR broadening, whereas modified Redfield theory overestimates it by a similar amount. A fortuitous error compensation in Redfield theory is found to explain the good performance of this theory at low temperatures. Since steady state spectra of PPCs are often measured at low temperatures

Relaxation of synchronization on complex networks.

Science.gov (United States)

Son, Seung-Woo; Jeong, Hawoong; Hong, Hyunsuk

2008-07-01

We study collective synchronization in a large number of coupled oscillators on various complex networks. In particular, we focus on the relaxation dynamics of the synchronization, which is important from the viewpoint of information transfer or the dynamics of system recovery from a perturbation. We measure the relaxation time tau that is required to establish global synchronization by varying the structural properties of the networks. It is found that the relaxation time in a strong-coupling regime (K>Kc) logarithmically increases with network size N , which is attributed to the initial random phase fluctuation given by O(N-1/2) . After elimination of the initial-phase fluctuation, the relaxation time is found to be independent of the system size; this implies that the local interaction that depends on the structural connectivity is irrelevant in the relaxation dynamics of the synchronization in the strong-coupling regime. The relaxation dynamics is analytically derived in a form independent of the system size, and it exhibits good consistency with numerical simulations. As an application, we also explore the recovery dynamics of the oscillators when perturbations enter the system.

Evolving fuzzy rules for relaxed-criteria negotiation.

Science.gov (United States)

Sim, Kwang Mong

2008-12-01

In the literature on automated negotiation, very few negotiation agents are designed with the flexibility to slightly relax their negotiation criteria to reach a consensus more rapidly and with more certainty. Furthermore, these relaxed-criteria negotiation agents were not equipped with the ability to enhance their performance by learning and evolving their relaxed-criteria negotiation rules. The impetus of this work is designing market-driven negotiation agents (MDAs) that not only have the flexibility of relaxing bargaining criteria using fuzzy rules, but can also evolve their structures by learning new relaxed-criteria fuzzy rules to improve their negotiation outcomes as they participate in negotiations in more e-markets. To this end, an evolutionary algorithm for adapting and evolving relaxed-criteria fuzzy rules was developed. Implementing the idea in a testbed, two kinds of experiments for evaluating and comparing EvEMDAs (MDAs with relaxed-criteria rules that are evolved using the evolutionary algorithm) and EMDAs (MDAs with relaxed-criteria rules that are manually constructed) were carried out through stochastic simulations. Empirical results show that: 1) EvEMDAs generally outperformed EMDAs in different types of e-markets and 2) the negotiation outcomes of EvEMDAs generally improved as they negotiated in more e-markets.

Stress relaxation under cyclic electron irradiation

International Nuclear Information System (INIS)

Bystrov, L.N.; Reznitskij, M.E.

1990-01-01

The kinetics of deformation process in a relaxating sample under 2 MeV electron cyclic irradiation was studied experimentally. The Al-Mg alloys with controllable and different (in dislocation density precipitate presence and their character) structure were used in experiments. It was established that after the beam was switched on the deformation rate increased sharply and then, during prolonged irradiation, in a gradual manner. After the switching-off the relaxation rate decreases by jumps up to values close to extrapolated rates of pre-radiation relaxation. The exhibition of these effects with radiation switching-off and switchin-on is dependent on the initial rate of thermal relaxation, the test temperature, the preliminary cold deformation and the dominating deformation dislocation mechanism. The preliminary cold deformation and test temperature elevation slightly decrease the effect of instantaneous relaxation acceleration with the irradiation switch-on. 17 refs., 5 figs

Structure, interface abruptness and strain relaxation in self-assisted grown InAs/GaAs nanowires

Energy Technology Data Exchange (ETDEWEB)

Frigeri, Cesare, E-mail: frigeri@imem.cnr.it [CNR-IMEM Institute, Parma (Italy); Scarpellini, David [L–NESS and Dept. Materials Science, University of Milano Bicocca, Milano (Italy); Department of Industrial Engineering University of Rome Tor Vergata, Rome (Italy); Fedorov, Alexey [LNESS and CNR-IFN, Como (Italy); Bietti, Sergio; Somaschini, Claudio [L–NESS and Dept. Materials Science, University of Milano Bicocca, Milano (Italy); Grillo, Vincenzo [CNR-IMEM Institute, Parma (Italy); CNR-S3-NANO Center, Modena (Italy); Esposito, Luca; Salvalaglio, Marco; Marzegalli, Anna; Montalenti, Francesco [L–NESS and Dept. Materials Science, University of Milano Bicocca, Milano (Italy); Sanguinetti, Stefano [L–NESS and Dept. Materials Science, University of Milano Bicocca, Milano (Italy); LNESS and CNR-IFN, Como (Italy)

2017-02-15

Highlights: • We study 2 critical issues (interface abruptness and strain release) in InAs/GaAs NWs. • Structural and chemical interface sharpness ≤1.5 nm, better than in previous reports. • Simultaneous elastic and plastic relaxation is shown that agrees with FEM simulations. • Structural, chemical and strain release investigations were performed by STEM. • New MBE self-seeded method whereby InAs is grown by splitting In and As depositions. - Abstract: The structure, interface abruptness and strain relaxation in InAs/GaAs nanowires grown by molecular beam epitaxy in the Ga self-catalysed mode on (111) Si have been investigated by transmission electron microscopy. The nanowires had the zincblende phase. The InAs/GaAs interface was atomically and chemically sharp with a width around 1.5 nm, i.e. significantly smaller than previously reported values. This was achieved by the consumption of the Ga droplet and formation of a flat top facet of the GaAs followed by the growth of InAs by splitting the depositions of In and As. Both elastic and plastic strain relaxation took place simultaneously. Experimental TEM results about strain relaxation very well agree with linear elasticity theory calculations by the finite element methods.

Structure, interface abruptness and strain relaxation in self-assisted grown InAs/GaAs nanowires

International Nuclear Information System (INIS)

Frigeri, Cesare; Scarpellini, David; Fedorov, Alexey; Bietti, Sergio; Somaschini, Claudio; Grillo, Vincenzo; Esposito, Luca; Salvalaglio, Marco; Marzegalli, Anna; Montalenti, Francesco; Sanguinetti, Stefano

2017-01-01

Highlights: • We study 2 critical issues (interface abruptness and strain release) in InAs/GaAs NWs. • Structural and chemical interface sharpness ≤1.5 nm, better than in previous reports. • Simultaneous elastic and plastic relaxation is shown that agrees with FEM simulations. • Structural, chemical and strain release investigations were performed by STEM. • New MBE self-seeded method whereby InAs is grown by splitting In and As depositions. - Abstract: The structure, interface abruptness and strain relaxation in InAs/GaAs nanowires grown by molecular beam epitaxy in the Ga self-catalysed mode on (111) Si have been investigated by transmission electron microscopy. The nanowires had the zincblende phase. The InAs/GaAs interface was atomically and chemically sharp with a width around 1.5 nm, i.e. significantly smaller than previously reported values. This was achieved by the consumption of the Ga droplet and formation of a flat top facet of the GaAs followed by the growth of InAs by splitting the depositions of In and As. Both elastic and plastic strain relaxation took place simultaneously. Experimental TEM results about strain relaxation very well agree with linear elasticity theory calculations by the finite element methods.

Bayesian inference for psychology. Part I : Theoretical advantages and practical ramifications

NARCIS (Netherlands)

Wagenmakers, E.-J.; Marsman, M.; Jamil, T.; Ly, A.; Verhagen, J.; Love, J.; Selker, R.; Gronau, Q.F.; Šmíra, M.; Epskamp, S.; Matzke, D.; Rouder, J.N.; Morey, R.D.

2018-01-01

Bayesian parameter estimation and Bayesian hypothesis testing present attractive alternatives to classical inference using confidence intervals and p values. In part I of this series we outline ten prominent advantages of the Bayesian approach. Many of these advantages translate to concrete

A tutorial introduction to Bayesian models of cognitive development.

Science.gov (United States)

Perfors, Amy; Tenenbaum, Joshua B; Griffiths, Thomas L; Xu, Fei

2011-09-01

We present an introduction to Bayesian inference as it is used in probabilistic models of cognitive development. Our goal is to provide an intuitive and accessible guide to the what, the how, and the why of the Bayesian approach: what sorts of problems and data the framework is most relevant for, and how and why it may be useful for developmentalists. We emphasize a qualitative understanding of Bayesian inference, but also include information about additional resources for those interested in the cognitive science applications, mathematical foundations, or machine learning details in more depth. In addition, we discuss some important interpretation issues that often arise when evaluating Bayesian models in cognitive science. Copyright © 2010 Elsevier B.V. All rights reserved.

Approximate Bayesian evaluations of measurement uncertainty

Science.gov (United States)

Possolo, Antonio; Bodnar, Olha

2018-04-01

The Guide to the Expression of Uncertainty in Measurement (GUM) includes formulas that produce an estimate of a scalar output quantity that is a function of several input quantities, and an approximate evaluation of the associated standard uncertainty. This contribution presents approximate, Bayesian counterparts of those formulas for the case where the output quantity is a parameter of the joint probability distribution of the input quantities, also taking into account any information about the value of the output quantity available prior to measurement expressed in the form of a probability distribution on the set of possible values for the measurand. The approximate Bayesian estimates and uncertainty evaluations that we present have a long history and illustrious pedigree, and provide sufficiently accurate approximations in many applications, yet are very easy to implement in practice. Differently from exact Bayesian estimates, which involve either (analytical or numerical) integrations, or Markov Chain Monte Carlo sampling, the approximations that we describe involve only numerical optimization and simple algebra. Therefore, they make Bayesian methods widely accessible to metrologists. We illustrate the application of the proposed techniques in several instances of measurement: isotopic ratio of silver in a commercial silver nitrate; odds of cryptosporidiosis in AIDS patients; height of a manometer column; mass fraction of chromium in a reference material; and potential-difference in a Zener voltage standard.

Relaxation along a fictitious field (RAFF and Z-spectroscopy using alternating-phase irradiation (ZAPI in permanent focal cerebral ischemia in rat.

Directory of Open Access Journals (Sweden)

Kimmo T Jokivarsi

Full Text Available Cerebral ischemia alters the molecular dynamics and content of water in brain tissue, which is reflected in NMR relaxation, diffusion and magnetization transfer (MT parameters. In this study, the behavior of two new MRI contrasts, Relaxation Along a Fictitious Field (RAFF and Z-spectroscopy using Alternating-Phase Irradiation (ZAPI, were quantified together with conventional relaxation parameters (T1, T2 and T1ρ and MT ratios in acute cerebral ischemia in rat. The right middle cerebral artery was permanently occluded and quantitative MRI data was acquired sequentially for the above parameters for up to 6 hours. The following conclusions were drawn: 1 Time-dependent changes in RAFF and T1ρ relaxation are not coupled to those in MT. 2 RAFF relaxation evolves more like transverse, rather than longitudinal relaxation. 3 MT measured with ZAPI is less sensitive to ischemia than conventional MT. 4 ZAPI data suggest alterations in the T2 distribution of macromolecules in acute cerebral ischemia. It was shown that both RAFF and ZAPI provide complementary MRI information from acute ischemic brain tissue. The presented multiparametric MRI data may aid in the assessment of brain tissue status early in ischemic stroke.

Study on shielded pump system failure analysis method based on Bayesian network

International Nuclear Information System (INIS)

Bao Yilan; Huang Gaofeng; Tong Lili; Cao Xuewu

2012-01-01

This paper applies Bayesian network to the system failure analysis, with an aim to improve knowledge representation of the uncertainty logic and multi-fault states in system failure analysis. A Bayesian network for shielded pump failure analysis is presented, conducting fault parameter learning, updating Bayesian network parameter based on new samples. Finally, through the Bayesian network inference, vulnerability in this system, the largest possible failure modes, and the fault probability are obtained. The powerful ability of Bayesian network to analyze system fault is illustrated by examples. (authors)

Momentum constraint relaxation

International Nuclear Information System (INIS)

Marronetti, Pedro

2006-01-01

Full relativistic simulations in three dimensions invariably develop runaway modes that grow exponentially and are accompanied by violations of the Hamiltonian and momentum constraints. Recently, we introduced a numerical method (Hamiltonian relaxation) that greatly reduces the Hamiltonian constraint violation and helps improve the quality of the numerical model. We present here a method that controls the violation of the momentum constraint. The method is based on the addition of a longitudinal component to the traceless extrinsic curvature A ij -tilde, generated by a vector potential w i , as outlined by York. The components of w i are relaxed to solve approximately the momentum constraint equations, slowly pushing the evolution towards the space of solutions of the constraint equations. We test this method with simulations of binary neutron stars in circular orbits and show that it effectively controls the growth of the aforementioned violations. We also show that a full numerical enforcement of the constraints, as opposed to the gentle correction of the momentum relaxation scheme, results in the development of instabilities that stop the runs shortly

Bayesian Dark Knowledge

NARCIS (Netherlands)

Korattikara, A.; Rathod, V.; Murphy, K.; Welling, M.; Cortes, C.; Lawrence, N.D.; Lee, D.D.; Sugiyama, M.; Garnett, R.

2015-01-01

We consider the problem of Bayesian parameter estimation for deep neural networks, which is important in problem settings where we may have little data, and/ or where we need accurate posterior predictive densities p(y|x, D), e.g., for applications involving bandits or active learning. One simple

Bayesian grid matching

DEFF Research Database (Denmark)

Hartelius, Karsten; Carstensen, Jens Michael

2003-01-01

A method for locating distorted grid structures in images is presented. The method is based on the theories of template matching and Bayesian image restoration. The grid is modeled as a deformable template. Prior knowledge of the grid is described through a Markov random field (MRF) model which r...

Photoelectron photoion molecular beam spectroscopy

International Nuclear Information System (INIS)

Trevor, D.J.

1980-12-01

The use of supersonic molecular beams in photoionization mass spectroscopy and photoelectron spectroscopy to assist in the understanding of photoexcitation in the vacuum ultraviolet is described. Rotational relaxation and condensation due to supersonic expansion were shown to offer new possibilities for molecular photoionization studies. Molecular beam photoionization mass spectroscopy has been extended above 21 eV photon energy by the use of Stanford Synchrotron Radiation Laboratory (SSRL) facilities. Design considerations are discussed that have advanced the state-of-the-art in high resolution vuv photoelectron spectroscopy. To extend gas-phase studies to 160 eV photon energy, a windowless vuv-xuv beam line design is proposed

An introduction to Bayesian statistics in health psychology

NARCIS (Netherlands)

Depaoli, Sarah; Rus, Holly; Clifton, James; van de Schoot, A.G.J.; Tiemensma, Jitske

2017-01-01

The aim of the current article is to provide a brief introduction to Bayesian statistics within the field of Health Psychology. Bayesian methods are increasing in prevalence in applied fields, and they have been shown in simulation research to improve the estimation accuracy of structural equation

Bayesian estimation of the discrete coefficient of determination.

Science.gov (United States)

Chen, Ting; Braga-Neto, Ulisses M

2016-12-01

The discrete coefficient of determination (CoD) measures the nonlinear interaction between discrete predictor and target variables and has had far-reaching applications in Genomic Signal Processing. Previous work has addressed the inference of the discrete CoD using classical parametric and nonparametric approaches. In this paper, we introduce a Bayesian framework for the inference of the discrete CoD. We derive analytically the optimal minimum mean-square error (MMSE) CoD estimator, as well as a CoD estimator based on the Optimal Bayesian Predictor (OBP). For the latter estimator, exact expressions for its bias, variance, and root-mean-square (RMS) are given. The accuracy of both Bayesian CoD estimators with non-informative and informative priors, under fixed or random parameters, is studied via analytical and numerical approaches. We also demonstrate the application of the proposed Bayesian approach in the inference of gene regulatory networks, using gene-expression data from a previously published study on metastatic melanoma.

A Bayesian approach to particle identification in ALICE

CERN Multimedia

CERN. Geneva

2016-01-01

Among the LHC experiments, ALICE has unique particle identification (PID) capabilities exploiting different types of detectors. During Run 1, a Bayesian approach to PID was developed and intensively tested. It facilitates the combination of information from different sub-systems. The adopted methodology and formalism as well as the performance of the Bayesian PID approach for charged pions, kaons and protons in the central barrel of ALICE will be reviewed. Results are presented with PID performed via measurements of specific energy loss (dE/dx) and time-of-flight using information from the TPC and TOF detectors, respectively. Methods to extract priors from data and to compare PID efficiencies and misidentification probabilities in data and Monte Carlo using high-purity samples of identified particles will be presented. Bayesian PID results were found consistent with previous measurements published by ALICE. The Bayesian PID approach gives a higher signal-to-background ratio and a similar or larger statist...

Hydrogen Bond Dynamics in Aqueous Solutions: Ab initio Molecular ...

Indian Academy of Sciences (India)

Rate equation for the decay of CHB(t) · Definition of Hydrogen Bonds · Results of Molecular Dynamics · Dynamics of anion-water and water-water hydrogen bonds · Structural relaxation of anion-water & water-water H-bonds · Ab initio Molecular Dynamics : · Slide 14 · Dynamics of hydrogen bonds : CPMD results · Slide 16.

Optimal Detection under the Restricted Bayesian Criterion

Directory of Open Access Journals (Sweden)

Shujun Liu

2017-07-01

Full Text Available This paper aims to find a suitable decision rule for a binary composite hypothesis-testing problem with a partial or coarse prior distribution. To alleviate the negative impact of the information uncertainty, a constraint is considered that the maximum conditional risk cannot be greater than a predefined value. Therefore, the objective of this paper becomes to find the optimal decision rule to minimize the Bayes risk under the constraint. By applying the Lagrange duality, the constrained optimization problem is transformed to an unconstrained optimization problem. In doing so, the restricted Bayesian decision rule is obtained as a classical Bayesian decision rule corresponding to a modified prior distribution. Based on this transformation, the optimal restricted Bayesian decision rule is analyzed and the corresponding algorithm is developed. Furthermore, the relation between the Bayes risk and the predefined value of the constraint is also discussed. The Bayes risk obtained via the restricted Bayesian decision rule is a strictly decreasing and convex function of the constraint on the maximum conditional risk. Finally, the numerical results including a detection example are presented and agree with the theoretical results.

Bayesian approach and application to operation safety

International Nuclear Information System (INIS)

Procaccia, H.; Suhner, M.Ch.

2003-01-01

The management of industrial risks requires the development of statistical and probabilistic analyses which use all the available convenient information in order to compensate the insufficient experience feedback in a domain where accidents and incidents remain too scarce to perform a classical statistical frequency analysis. The Bayesian decision approach is well adapted to this problem because it integrates both the expertise and the experience feedback. The domain of knowledge is widen, the forecasting study becomes possible and the decisions-remedial actions are strengthen thanks to risk-cost-benefit optimization analyzes. This book presents the bases of the Bayesian approach and its concrete applications in various industrial domains. After a mathematical presentation of the industrial operation safety concepts and of the Bayesian approach principles, this book treats of some of the problems that can be solved thanks to this approach: softwares reliability, controls linked with the equipments warranty, dynamical updating of databases, expertise modeling and weighting, Bayesian optimization in the domains of maintenance, quality control, tests and design of new equipments. A synthesis of the mathematical formulae used in this approach is given in conclusion. (J.S.)

Relaxed states with plasma flow

International Nuclear Information System (INIS)

Avinash, K.; Taylor, J.B.

1991-01-01

In the theory of relaxation, a turbulent plasma reaches a state of minimum energy subject to constant magnetic helicity. In this state the plasma velocity is zero. Attempts have been made by introducing a number of different constraints, to obtain relaxed states with plasma flow. It is shown that these alternative constraints depend on two self-helicities, one for ions, and one for electrons. However, whereas there are strong arguments for the effective invariance of the original magnetic-helicity, these arguments do not apply to the self-helicities. Consequently the existence of relaxed states with flow remains in doubt. (author)

Dielectric dispersion, relaxation dynamics and thermodynamic studies of Beta-Alanine in aqueous solutions using picoseconds time domain reflectometry

Science.gov (United States)

Vinoth, K.; Ganesh, T.; Senthilkumar, P.; Sylvester, M. Maria; Karunakaran, D. J. S. Anand; Hudge, Praveen; Kumbharkhane, A. C.

2017-09-01

The aqueous solution of beta-alanine characterised and studied by their dispersive dielectric properties and relaxation process in the frequency domain of 10×106 Hz to 30×109 Hz with varying concentration in mole fractions and temperatures. The molecular interaction and dielectric parameters are discussed in terms of counter-ion concentration theory. The static permittivity (ε0), high frequency dielectric permittivity (ε∞) and excess dielectric parameters are accomplished by frequency depended physical properties and relaxation time (τ). Molecular orientation, ordering and correlation factors are reported as confirmation of intermolecular interactions. Ionic conductivity and thermo dynamical properties are concluded with the behaviour of the mixture constituents. Solute-solvent, solute-solute interaction, structure making and breaking abilities of the solute in aqueous medium are interpreted. Fourier Transform Infrared (FTIR) spectra of beta- alanine single crystal and liquid state have been studied. The 13C Nuclear Magnetic Resonance (NMR) spectral studies give the signature for resonating frequencies and chemical shifts of beta-alanine.

Towards Bayesian Inference of the Fast-Ion Distribution Function

DEFF Research Database (Denmark)

Stagner, L.; Heidbrink, W.W.; Salewski, Mirko

2012-01-01

sensitivity of the measurements are incorporated into Bayesian likelihood probabilities, while prior probabilities enforce physical constraints. As an initial step, this poster uses Bayesian statistics to infer the DIII-D electron density profile from multiple diagnostic measurements. Likelihood functions....... However, when theory and experiment disagree (for one or more diagnostics), it is unclear how to proceed. Bayesian statistics provides a framework to infer the DF, quantify errors, and reconcile discrepant diagnostic measurements. Diagnostic errors and ``weight functions" that describe the phase space...

Bayesian Correlation Analysis for Sequence Count Data.

Directory of Open Access Journals (Sweden)

Daniel Sánchez-Taltavull

Full Text Available Evaluating the similarity of different measured variables is a fundamental task of statistics, and a key part of many bioinformatics algorithms. Here we propose a Bayesian scheme for estimating the correlation between different entities' measurements based on high-throughput sequencing data. These entities could be different genes or miRNAs whose expression is measured by RNA-seq, different transcription factors or histone marks whose expression is measured by ChIP-seq, or even combinations of different types of entities. Our Bayesian formulation accounts for both measured signal levels and uncertainty in those levels, due to varying sequencing depth in different experiments and to varying absolute levels of individual entities, both of which affect the precision of the measurements. In comparison with a traditional Pearson correlation analysis, we show that our Bayesian correlation analysis retains high correlations when measurement confidence is high, but suppresses correlations when measurement confidence is low-especially for entities with low signal levels. In addition, we consider the influence of priors on the Bayesian correlation estimate. Perhaps surprisingly, we show that naive, uniform priors on entities' signal levels can lead to highly biased correlation estimates, particularly when different experiments have widely varying sequencing depths. However, we propose two alternative priors that provably mitigate this problem. We also prove that, like traditional Pearson correlation, our Bayesian correlation calculation constitutes a kernel in the machine learning sense, and thus can be used as a similarity measure in any kernel-based machine learning algorithm. We demonstrate our approach on two RNA-seq datasets and one miRNA-seq dataset.

Inference in hybrid Bayesian networks

International Nuclear Information System (INIS)

Langseth, Helge; Nielsen, Thomas D.; Rumi, Rafael; Salmeron, Antonio

2009-01-01

Since the 1980s, Bayesian networks (BNs) have become increasingly popular for building statistical models of complex systems. This is particularly true for boolean systems, where BNs often prove to be a more efficient modelling framework than traditional reliability techniques (like fault trees and reliability block diagrams). However, limitations in the BNs' calculation engine have prevented BNs from becoming equally popular for domains containing mixtures of both discrete and continuous variables (the so-called hybrid domains). In this paper we focus on these difficulties, and summarize some of the last decade's research on inference in hybrid Bayesian networks. The discussions are linked to an example model for estimating human reliability.

The image recognition based on neural network and Bayesian decision

Science.gov (United States)

Wang, Chugege

2018-04-01

The artificial neural network began in 1940, which is an important part of artificial intelligence. At present, it has become a hot topic in the fields of neuroscience, computer science, brain science, mathematics, and psychology. Thomas Bayes firstly reported the Bayesian theory in 1763. After the development in the twentieth century, it has been widespread in all areas of statistics. In recent years, due to the solution of the problem of high-dimensional integral calculation, Bayesian Statistics has been improved theoretically, which solved many problems that cannot be solved by classical statistics and is also applied to the interdisciplinary fields. In this paper, the related concepts and principles of the artificial neural network are introduced. It also summarizes the basic content and principle of Bayesian Statistics, and combines the artificial neural network technology and Bayesian decision theory and implement them in all aspects of image recognition, such as enhanced face detection method based on neural network and Bayesian decision, as well as the image classification based on the Bayesian decision. It can be seen that the combination of artificial intelligence and statistical algorithms has always been the hot research topic.

Editorial: Bayesian benefits for child psychology and psychiatry researchers.

Science.gov (United States)

Oldehinkel, Albertine J

2016-09-01

For many scientists, performing statistical tests has become an almost automated routine. However, p-values are frequently used and interpreted incorrectly; and even when used appropriately, p-values tend to provide answers that do not match researchers' questions and hypotheses well. Bayesian statistics present an elegant and often more suitable alternative. The Bayesian approach has rarely been applied in child psychology and psychiatry research so far, but the development of user-friendly software packages and tutorials has placed it well within reach now. Because Bayesian analyses require a more refined definition of hypothesized probabilities of possible outcomes than the classical approach, going Bayesian may offer the additional benefit of sparkling the development and refinement of theoretical models in our field. © 2016 Association for Child and Adolescent Mental Health.

On aggregation of relaxed T-indistinguishability operators

Energy Technology Data Exchange (ETDEWEB)

Fuster-Parra, P.

2017-07-01

The notion of T -indistinguishability operator was introduced by E. Trillas in [7] with the aim of fuzzifying the classical (crisp) notion of equivalence relation. Relaxed metrics and indistinguishability operators are closely related. Indeed, in [1] it has been stated that the logical counterpart for relaxed metrics is, in some sense, a generalized indistinguishability operator (relaxed T -indistinguishability operator). Notice that the notion of T -indistinguishability operator is retrieved as a particular case of relaxed T -indistinguishability operator whenever the relaxed T - indistinguishability operator satisfies also the reflexivity. In fact, a relaxed indistinguishability operator is a indistinguishability operator if and only if it holds the reflexivity. The same occurs when we consider T -indistinguishability operator that separates points. Several authors have studied the aggregation of some classes of fuzzy relations (see [3, 4, 5, 6]), where it is stated that transitivity is one of the most important properties of a fuzzy relation. In [5] a study of aggregation of T-indistinguishability operators is presented, motivated by this work the aim of this study is to analyze the case of aggregating relaxed T-indistinguishability operators. (Author)

Relaxation of an unsteady turbulent boundary layer on a flat plate in an expansion tube

Science.gov (United States)

Gurta, R. N.; Trimpi, R. L.

1974-01-01

An analysis is presented for the relaxation of a turbulent boundary layer on a semi-infinite flat plate after passage of a shock wave and a trailing driver gas-driven gas interface. The problem has special application to expansion-tube flows. The flow-governing equations have been transformed into the Crocco variables, and a time-similar solution is presented in terms of the dimensionless distance-time variable alpha and the dimensionless velocity variable beta. An eddy-viscosity model, similar to that of time-steady boundary layers, is applied to the inner and outer regions of the boundary layer. A turbulent Prandtl number equal to the molecular Prandtl number is used to relate the turbulent heat flux to the eddy viscosity. The numerical results, obtained by using the Gauss-Seidel line-relaxation method, indicate that a fully turbulent boundary layer relaxes faster to the final steady-state values of heat transfer and skin friction than a laminar boundary layer. The results also give a fairly good estimate of the local skin friction and heat transfer for near steady-flow conditions.

Molecular Mobility of n-Ethylene Glycol Dimethacrylate Glass Formers Upon Free Radical Polymerization

Science.gov (United States)

Plaza, Maria Teresa Viciosa

When a liquid upon cooling avoids crystallization, it enters the supercooled state. If the temperature continues to decrease, the consequent increase of viscosity is reflected in the molecular mobility in such a way that the characteristic relaxation times of cooperative motions become of the same order of the experimentally accessible timescales. Further cooling finally transforms the highly viscous liquid into a glass, in which only local motions are allowed. The monomers n-ethylene glycol dimethacrylate (n-EGDMA) for n =1 to 4, that constitutes the object of this study, easily circumvent crystallization, being good candidates to study the molecular mobility in both supercooled and glassy states. Dielectric Relaxation Spectroscopy (DRS) was the technique chosen to obtain detailed information about their molecular mobility (Chapters 1 and 2). The first part of this work consisted in the dielectric characterization of the relaxation processes present above and below the glass transition temperature (Tg), which shifts to higher values with the molecular weight ( Mw), result confirmed by Differential Scanning Calorimetry (DSC). While the cooperative alpha-process associated to the glass transition, and the secondary beta process, depend on Mw, the other found secondary process, gamma, seems to be independent from this factor (Chapter 3). In the next Chapters different strategies were carried out in order to clarify the mechanisms in the origin of these two secondary relaxations (beta and gamma), and to learn about its respective relation with the main a relaxation. Monitoring the real time isothermal free radical polymerization of TrEGDMA by Temperature Modulated Differential Scanning Calorimetry (TMDSC), carried out at temperatures below the gamma T of the final polymer network, we shown among others two important features: i) the vitrification of the polymer in formation leads to relatively low degrees of conversion, and ii) the unreacted monomer is expelled from

Bayesian Inference Methods for Sparse Channel Estimation

DEFF Research Database (Denmark)

Pedersen, Niels Lovmand

2013-01-01

This thesis deals with sparse Bayesian learning (SBL) with application to radio channel estimation. As opposed to the classical approach for sparse signal representation, we focus on the problem of inferring complex signals. Our investigations within SBL constitute the basis for the development...... of Bayesian inference algorithms for sparse channel estimation. Sparse inference methods aim at finding the sparse representation of a signal given in some overcomplete dictionary of basis vectors. Within this context, one of our main contributions to the field of SBL is a hierarchical representation...... analysis of the complex prior representation, where we show that the ability to induce sparse estimates of a given prior heavily depends on the inference method used and, interestingly, whether real or complex variables are inferred. We also show that the Bayesian estimators derived from the proposed...

Bayesian-based localization in inhomogeneous transmission media

DEFF Research Database (Denmark)

Nadimi, E. S.; Blanes-Vidal, V.; Johansen, P. M.

2013-01-01

In this paper, we propose a novel robust probabilistic approach based on the Bayesian inference using received-signal-strength (RSS) measurements with varying path-loss exponent. We derived the probability density function (pdf) of the distance between any two sensors in the network with heteroge......In this paper, we propose a novel robust probabilistic approach based on the Bayesian inference using received-signal-strength (RSS) measurements with varying path-loss exponent. We derived the probability density function (pdf) of the distance between any two sensors in the network...... with heterogeneous transmission medium as a function of the given RSS measurements and the characteristics of the heterogeneous medium. The results of this study show that the localization mean square error (MSE) of the Bayesian-based method outperformed all other existing localization approaches. © 2013 ACM....

Impact of noise on molecular network inference.

Directory of Open Access Journals (Sweden)

Radhakrishnan Nagarajan

Full Text Available Molecular entities work in concert as a system and mediate phenotypic outcomes and disease states. There has been recent interest in modelling the associations between molecular entities from their observed expression profiles as networks using a battery of algorithms. These networks have proven to be useful abstractions of the underlying pathways and signalling mechanisms. Noise is ubiquitous in molecular data and can have a pronounced effect on the inferred network. Noise can be an outcome of several factors including: inherent stochastic mechanisms at the molecular level, variation in the abundance of molecules, heterogeneity, sensitivity of the biological assay or measurement artefacts prevalent especially in high-throughput settings. The present study investigates the impact of discrepancies in noise variance on pair-wise dependencies, conditional dependencies and constraint-based Bayesian network structure learning algorithms that incorporate conditional independence tests as a part of the learning process. Popular network motifs and fundamental connections, namely: (a common-effect, (b three-chain, and (c coherent type-I feed-forward loop (FFL are investigated. The choice of these elementary networks can be attributed to their prevalence across more complex networks. Analytical expressions elucidating the impact of discrepancies in noise variance on pairwise dependencies and conditional dependencies for special cases of these motifs are presented. Subsequently, the impact of noise on two popular constraint-based Bayesian network structure learning algorithms such as Grow-Shrink (GS and Incremental Association Markov Blanket (IAMB that implicitly incorporate tests for conditional independence is investigated. Finally, the impact of noise on networks inferred from publicly available single cell molecular expression profiles is investigated. While discrepancies in noise variance are overlooked in routine molecular network inference, the