1,720,966 research outputs found
Nonequilibrium dynamical transition in the asymmetric exclusion process
Full text linkOver the last few decades the interests of statistical physicists have broadened to include
the detailed quantitative study of many systems - chemical, biological and even social
- that were not traditionally part of the discipline. These systems can feature rich
and complex spatiotemporal behaviour, often due to continued interaction with the
environment and characterised by the dissipation of flows of energy and/or mass. This
has led to vigorous research aimed at extending the established theoretical framework and
adapting analytical methods that originate in the study of systems at thermodynamic
equilibrium to deal with out-of-equilibrium situations, which are much more prevalent in
nature.
This thesis focuses on a microscopic model known as the asymmetric exclusion process,
or ASEP, which describes the stochastic motion of particles on a one-dimensional lattice.
Though in the first instance a model of a lattice gas, it is sufficiently general to have
served as the basis to model a wide variety of phenomena. That, as well as substantial
progress made in analysing its stationary behaviour, including the locations and nature
of phase transitions, have led to it becoming a paradigmatic model of an exactly solvable
nonequilibrium system. Recently an exact solution for the dynamics found a somewhat
enigmatic transition, which has not been well understood. This thesis is an attempt
to verify and better understand the nature of that dynamical transition, including its
relation, if any, to the static phase transitions.
I begin in Chapter 2 by reviewing known results for the ASEP, in particular the
totally asymmetric variant (TASEP), driven at the boundaries. I present the exact
dynamical transition as it was first derived, and a reduced description of the dynamics
known as domain wall theory (DWT), which locates the transition at a different place.
In Chapter 3, I investigate solutions of a nonlinear PDE that constitutes a mean-field,
continuum approximation of the ASEP, namely the Burgers equation, and find that a
similar dynamical transition occurs there at the same place as predicted by DWT but in
disagreement with the exact result. Next, in Chapter 4 I report on efforts to observe and
measure the dynamical transition through Monte Carlo simulation. No directly obvious
physical manifestation of the transition was observed. The relaxation of three different
observables was measured and found to agree well with each other but only slightly
better with the exact transition than with DWT. In Chapter 5 I apply a numerical
renormalisation scheme known as the Density Matrix Renormalisation Group (DMRG)
method and find that it confirms the exact dynamical transition, ruling out the behaviour
predicted by DWT. Finally in Chapter 6 I demonstrate that a perturbative calculation,
involving the crossing of eigenvalues, allows us to rederive the location of the dynamical
transition found exactly, thereby offering some insight into the nature of the transition
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Report on CP2K biomolecular QM/MM performance profiling
No full textThis report, which forms part of BioExcel-2 project deliverable D1.6, summarises the analysis and visualisation of the absolute performance, parallel scaling, and subroutine-level profiling of CP2K (versions 8.1 and 8.2) when executing benchmarks taken from the BioExcel biomolecular QM/MM benchmark suite (https://doi.org/10.5281/zenodo.6591692) on different common HPC architectures. This analysis was used to help identify and prioritise CP2K optimisation work during the BioExcel-2 project.
The raw CP2K output logs used to generate the figures in this report are available from:
https://doi.org/10.5281/zenodo.6676034
Our analysis script used to generate the figures from the raw results is available from:
https://doi.org/10.5281/zenodo.667041
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Software to analyse and visualise CP2K parallel MD performance
No full textPython script to analyse standard-format CP2K output log files, compute multi-run-averages and generate visualisations of parallel scaling of runtime (walltime) per MD step, speedup, and subroutine-level profiles (scaling of top n most costly subroutines and their load imbalances across MPI ranks). Uses gnuplot. This is a snapshot of the repository at https://github.com/bioexcel/qmmm_benchmark_script and is provided as part of BioExcel-2 project deliverable D1.6
CP2K biomolecular QM/MM benchmarking data
No full textDataset containing raw CP2K output logs produced by running benchmarks from the BioExcel QM/MM benchmark suite (https://doi.org/10.5281/zenodo.6591692), provided as part of BioExcel-2 project deliverable D1.6.
An analysis of (a subset of) these benchmark results can be found in https://doi.org/10.5281/zenodo.6591574
Machines used for benchmarking:
Cirrus@EPCC (HPE SGI ICE XA):
https://www.cirrus.ac.uk
Infiniband interconnect
CPU compute nodes:
2 x 18-core Intel Xeon (Broadwell) E5-2695, 2.1 GHz
256GB RAM
GPU compute nodes:
2 x NVIDIA Tesla V100 (Volta) SXM2-16GB
2 x 20-core Intel Xeon (Cascade Lake) Gold 6248, 2.4 GHz
384GB RAM
ARCHER2@EPCC (HPE CRAY EX):
https://www.archer2.ac.uk/
Interconnect: HPE Cray Slingshot
Compute nodes:
2 x 64-core AMD EPYC (Zen2 Rome) 7742, 2.25GHz
256GB RAM
Benchmarking protocol
Repeated runs to rule out machine noise variability were performed for each benchmark on each machine for both 1 MD step and 6 MD steps. Subsequent analysis and visualisation of parallel scaling of average runtime per MD step and subroutine-level profiling was performed using our analysis script available from:
https://doi.org/10.5281/zenodo.6591681
Results on Cirrus CPU nodes are for CP2K release version 8.1, whilst results on Cirrus GPU nodes and ARCHER2 are with CP2K version 8.2
D1.6 release of BioExcel QM/MM Benchmark Suite
No full textAn update to the previous D1.4 release of the BioExcel QM/MM benchmark suite (see https://doi.org/10.5281/zenodo.3885124), provided as part of deliverable D1.6.
This is a snapshot of the repository available at https://github.com/bioexcel/qmmm_benchmark_suite
Compared to the previous (D1.4) release, a number of additional benchmarks were included in order to facilitate systematic performance profiling, namely:
Versions of the MQAE (solute-solvent), ClC (ion channel), and CBD_PHY (phytochrome) benchmarks that use the hybrid DFT functionals PBE0 and B3LYP to incorporate Hartree-Fock exchange energy (the initial release of the benchmark suite included only the GGA functionals PBE and BLYP).
Versions of the MQAE and ClC benchmarks that make use of the Auxiliary Density Matrix Method (ADMM) to markedly reduce the high computational cost of the molecular environment optimized MOLOPT basis set when used in combination with hybrid functionals such as B3LYP and PBE0.
Versions of the MQAE and ClC benchmarks that use the EMSL basis set in combination with the B3LYP hybrid functional.
A version of the ClC-19 benchmark that uses the HFX basis set in combination with the B3LYP hybrid functional.
A version of the MQAE benchmark in which the linear size of the cell defining the quantum region is increased by a factor 2, i.e. where the volume of the quantum region is enlarged by a factor
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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