148 research outputs found
Hydrogen Dynamics in Superprotonic CsHSO4
We present a detailed study of proton dynamics in the hydrogen-bonded
superprotonic conductor CsHSO4 from first-principles molecular dynamics
simulations, isolating the subtle interplay between the dynamics of the O--H
chemical bonds, the O...H hydrogen bonds, and the SO4 tetrahedra in promoting
proton diffusion. We find that the Grotthus mechanism of proton transport is
primarily responsible for the dynamics of the chemical bonds, whereas the
reorganization of the hydrogen-bond network is dominated by rapid angular hops
in concert with small reorientations of the SO4 tetrahedra. Frequent proton
jumping across the O--H...O complex is countered by a high rate of jump
reversal, which we show is connected to the dynamics of the SO4 tetrahedra,
resulting in a diminished CsHSO4/CsDSO4 isotope effect. We also find evidence
of multiple timescales for SO4 reorientation events, leading to distinct
diffusion mechanisms along the different crystal lattice directions. Finally,
we employ graph-theoretic techniques to characterize the topology of the
hydrogen-bond network and demonstrate a clear relationship between certain
connectivity configurations and the likelihood for diffusive jump events.Comment: 12 pages, 10 figure
An interacting spin flip model for one-dimensional proton conduction
A discrete asymmetric exclusion process (ASEP) is developed to model proton
conduction along one-dimensional water wires. Each lattice site represents a
water molecule that can be in only one of three states; protonated,
left-pointing, and right-pointing. Only a right(left)-pointing water can accept
a proton from its left(right). Results of asymptotic mean field analysis and
Monte-Carlo simulations for the three-species, open boundary exclusion model
are presented and compared. The mean field results for the steady-state proton
current suggest a number of regimes analogous to the low and maximal current
phases found in the single species ASEP [B. Derrida, Physics Reports, {\bf
301}, 65-83, (1998)]. We find that the mean field results are accurate
(compared with lattice Monte-Carlo simulations) only in the certain regimes.
Refinements and extensions including more elaborate forces and pore defects are
also discussed.Comment: 13pp, 6 fig
CHAMPION: Chalmers Hierarchical Atomic, Molecular, Polymeric & Ionic Analysis Toolkit
We present CHAMPION: a software developed to automatically detect
time-dependent bonds between atoms based on their dynamics, classify the local
graph topology around them, and analyze the physicochemical properties of these
topologies by statistical physics. In stark contrast to methodologies where
bonds are detected based on static conditions such as cut-off distances,
CHAMPION considers pairs of atoms to be bound only if they move together and
act as a bound pair over time. Furthermore, the time-dependent global bond
graph is possible to split into dynamically shifting connected components or
subgraphs around a certain chemical motif and thereby allow the physicochemical
properties of each such topology to be analyzed by statistical physics.
Applicable to condensed matter and liquids in general, and electrolytes in
particular, this allows both quantitative and qualitative descriptions of local
structure, as well as dynamical processes such as speciation and diffusion. We
present here a detailed overview of CHAMPION, including its underlying
methodology, implementation and capabilities.Comment: 11 pages, 8 figure
Non-equilibrium statistical mechanics: From a paradigmatic model to biological transport
Unlike equilibrium statistical mechanics, with its well-established
foundations, a similar widely-accepted framework for non-equilibrium
statistical mechanics (NESM) remains elusive. Here, we review some of the many
recent activities on NESM, focusing on some of the fundamental issues and
general aspects. Using the language of stochastic Markov processes, we
emphasize general properties of the evolution of configurational probabilities,
as described by master equations. Of particular interest are systems in which
the dynamics violate detailed balance, since such systems serve to model a wide
variety of phenomena in nature. We next review two distinct approaches for
investigating such problems. One approach focuses on models sufficiently simple
to allow us to find exact, analytic, non-trivial results. We provide detailed
mathematical analyses of a one-dimensional continuous-time lattice gas, the
totally asymmetric exclusion process (TASEP). It is regarded as a paradigmatic
model for NESM, much like the role the Ising model played for equilibrium
statistical mechanics. It is also the starting point for the second approach,
which attempts to include more realistic ingredients in order to be more
applicable to systems in nature. Restricting ourselves to the area of
biophysics and cellular biology, we review a number of models that are relevant
for transport phenomena. Successes and limitations of these simple models are
also highlighted.Comment: 72 pages, 18 figures, Accepted to: Reports on Progress in Physic
The Type 2 Diabetes Knowledge Portal: an open access genetic resource dedicated to type 2 diabetes and related traits
Associations between human genetic variation and clinical phenotypes have become a foundation of biomedical research. Most repositories of these data seek to be disease-agnostic and therefore lack disease-focused views. The Type 2 Diabetes Knowledge Portal (T2DKP) is a public resource of genetic datasets and genomic annotations dedicated to type 2 diabetes (T2D) and related traits. Here, we seek to make the T2DKP more accessible to prospective users and more useful to existing users. First, we evaluate the T2DKP's comprehensiveness by comparing its datasets with those of other repositories. Second, we describe how researchers unfamiliar with human genetic data can begin using and correctly interpreting them via the T2DKP. Third, we describe how existing users can extend their current workflows to use the full suite of tools offered by the T2DKP. We finally discuss the lessons offered by the T2DKP toward the goal of democratizing access to complex disease genetic results
Application of 3D Zernike descriptors to shape-based ligand similarity searching
Background: The identification of promising drug leads from a large database of compounds is an important step in the preliminary stages of drug design. Although shape is known to play a key role in the molecular recognition process, its application to virtual screening poses significant hurdles both in terms of the encoding scheme and speed. Results: In this study, we have examined the efficacy of the alignment independent three-dimensional Zernike descriptor (3DZD) for fast shape based similarity searching. Performance of this approach was compared with several other methods including the statistical moments based ultrafast shape recognition scheme (USR) and SIMCOMP, a graph matching algorithm that compares atom environments. Three benchmark datasets are used to thoroughly test the methods in terms of their ability for molecular classification, retrieval rate, and performance under the situation that simulates actual virtual screening tasks over a large pharmaceutical database. The 3DZD performed better than or comparable to the other methods examined, depending on the datasets and evaluation metrics used. Reasons for the success and the failure of the shape based methods for specific cases are investigated. Based on the results for the three datasets, general conclusions are drawn with regard to their efficiency and applicability
Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel
A major use of the 1000 Genomes Project (1000GP) data is genotype imputation in genome-wide association studies (GWAS). Here we develop a method to estimate haplotypes from low-coverage sequencing data that can take advantage of single-nucleotide polymorphism (SNP) microarray genotypes on the same samples. First the SNP array data are phased to build a backbone (or 'scaffold') of haplotypes across each chromosome. We then phase the sequence data 'onto' this haplotype scaffold. This approach can take advantage of relatedness between sequenced and non-sequenced samples to improve accuracy. We use this method to create a new 1000GP haplotype reference set for use by the human genetic community. Using a set of validation genotypes at SNP and bi-allelic indels we show that these haplotypes have lower genotype discordance and improved imputation performance into downstream GWAS samples, especially at low-frequency variants. © 2014 Macmillan Publishers Limited. All rights reserved
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