scholarly journals Anomalous Diffusion: A Basic Mechanism for the Evolution of Inhomogeneous Systems

2019 ◽  
Vol 7 ◽  
Author(s):  
Fernando A. Oliveira ◽  
Rogelma M. S. Ferreira ◽  
Luciano C. Lapas ◽  
Mendeli H. Vainstein
Keyword(s):  
Anomalous Diffusion ◽  
Basic Mechanism ◽  
Inhomogeneous Systems

Characterization of Modulated Structure Through Structure Images and their Computer Simulation

1990 ◽  
Vol 48 (1) ◽  
pp. 70-71
Author(s):  
Kiyomichi Nakai ◽  
Yusuke Isobe ◽  
Chiken Kinoshita ◽  
Kazutoshi Shinohara
Keyword(s):  
Computer Simulation ◽  
High Resolution ◽  
Spherical Aberration ◽  
High Resolution Electron Microscopy ◽  
Basic Mechanism ◽  
Objective Lens ◽  
Specimen Thickness ◽  
Transmitted Beam ◽  
Modulated Structure ◽  
Resolution Electron

Induced spinodal decomposition under electron irradiation in a Ni-Au alloy has been investigated with respect to its basic mechanism and confirmed to be caused by the relaxation of coherent strain associated with modulated structure. Modulation of white-dots on structure images of modulated structure due to high-resolution electron microscopy is reduced with irradiation. In this paper the atom arrangement of the modulated structure is confirmed with computer simulation on the structure images, and the relaxation of the coherent strain is concluded to be due to the reduction of phase-modulation.Structure images of three-dimensional modulated structure along <100> were taken with the JEM-4000EX high-resolution electron microscope at the HVEM Laboratory, Kyushu University. The transmitted beam and four 200 reflections with their satellites from the modulated structure in an fee Ni-30.0at%Au alloy under illumination of 400keV electrons were used for the structure images under a condition of the spherical aberration constant of the objective lens, Cs = 1mm, the divergence of the beam, α = 3 × 10-4 rad, underfocus, Δf ≃ -50nm and specimen thickness, t ≃ 15nm. The CIHRTEM code was used for the simulation of the structure image.

Anomalous diffusion in presence of boundary conditions

1990 ◽  
Vol 51 (13) ◽  
pp. 1387-1402 ◽  
Author(s):  
A. Giacometti ◽  
A. Maritan
Keyword(s):  
Boundary Conditions ◽  
Anomalous Diffusion

Solution of inverse coefficient problem for fractional anomalous diffusion equation

2012 ◽  
Vol 9 (2) ◽  
pp. 65-70
Author(s):  
E.V. Karachurina ◽  
S.Yu. Lukashchuk
Keyword(s):  
Anomalous Diffusion ◽  
Fractional Derivatives ◽  
Descent Method ◽  
Extremum Problem ◽  
Steepest Descent Method ◽  
Coefficient Problem ◽  
Caputo Fractional Derivatives ◽  
Inverse Coefficient Problem ◽  
Residual Functional ◽  
Inverse Coefficient

An inverse coefficient problem is considered for time-fractional anomalous diffusion equations with the Riemann-Liouville and Caputo fractional derivatives. A numerical algorithm is proposed for identification of anomalous diffusivity which is considered as a function of concentration. The algorithm is based on transformation of inverse coefficient problem to extremum problem for the residual functional. The steepest descent method is used for numerical solving of this extremum problem. Necessary expressions for calculating gradient of residual functional are presented. The efficiency of the proposed algorithm is illustrated by several test examples.

Statistical mechanics

2017 ◽  
Author(s):  
Michael P. Allen ◽  
Dominic J. Tildesley
Keyword(s):  
Statistical Mechanics ◽  
Potential Model ◽  
Quantum Corrections ◽  
Inhomogeneous Systems ◽  
Hard Constraints ◽  
Complex Liquids ◽  
Fluid Membranes ◽  
Dynamical Properties ◽  
Canonical Ensembles ◽  
Grand Canonical

This chapter contains the essential statistical mechanics required to understand the inner workings of, and interpretation of results from, computer simulations. The microcanonical, canonical, isothermal–isobaric, semigrand and grand canonical ensembles are defined. Thermodynamic, structural, and dynamical properties of simple and complex liquids are related to appropriate functions of molecular positions and velocities. A number of important thermodynamic properties are defined in terms of fluctuations in these ensembles. The effect of the inclusion of hard constraints in the underlying potential model on the calculated properties is considered, and the addition of long-range and quantum corrections to classical simulations is presented. The extension of statistical mechanics to describe inhomogeneous systems such as the planar gas–liquid interface, fluid membranes, and liquid crystals, and its application in the simulation of these systems, are discussed.

scholarly journals Increased peak detection accuracy in over-dispersed ChIP-seq data with supervised segmentation models

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Arnaud Liehrmann ◽  
Guillem Rigaill ◽  
Toby Dylan Hocking
Keyword(s):  
Histone Modifications ◽  
Count Data ◽  
High Throughput Sequencing ◽  
Genetic Regulation ◽  
Regulation Of Gene Expression ◽  
Basic Mechanism ◽  
R Package ◽  
Detection Accuracy ◽  
Full Potential ◽  
Segmentation Models

Abstract Background Histone modification constitutes a basic mechanism for the genetic regulation of gene expression. In early 2000s, a powerful technique has emerged that couples chromatin immunoprecipitation with high-throughput sequencing (ChIP-seq). This technique provides a direct survey of the DNA regions associated to these modifications. In order to realize the full potential of this technique, increasingly sophisticated statistical algorithms have been developed or adapted to analyze the massive amount of data it generates. Many of these algorithms were built around natural assumptions such as the Poisson distribution to model the noise in the count data. In this work we start from these natural assumptions and show that it is possible to improve upon them. Results Our comparisons on seven reference datasets of histone modifications (H3K36me3 & H3K4me3) suggest that natural assumptions are not always realistic under application conditions. We show that the unconstrained multiple changepoint detection model with alternative noise assumptions and supervised learning of the penalty parameter reduces the over-dispersion exhibited by count data. These models, implemented in the R package CROCS (https://github.com/aLiehrmann/CROCS), detect the peaks more accurately than algorithms which rely on natural assumptions. Conclusion The segmentation models we propose can benefit researchers in the field of epigenetics by providing new high-quality peak prediction tracks for H3K36me3 and H3K4me3 histone modifications.

Magnetized wake driven anomalous diffusion in complex plasma

2021 ◽  
Vol 28 (8) ◽  
pp. 083703
Author(s):  
Biswajit Dutta ◽  
Pratikshya Bezbaruah ◽  
Nilakshi Das
Keyword(s):  
Anomalous Diffusion ◽  
Complex Plasma
Sign in / Sign up

Export Citation Format

Share Document