145 research outputs found
Introduction to Configuration Path Integral Monte Carlo
In low-temperature high-density plasmas quantum effects of the electrons are
becoming increasingly important. This requires the development of new
theoretical and computational tools. Quantum Monte Carlo methods are among the
most successful approaches to first-principle simulations of many-body quantum
systems. In this chapter we present a recently developed method---the
configuration path integral Monte Carlo (CPIMC) method for moderately coupled,
highly degenerate fermions at finite temperatures. It is based on the second
quantization representation of the -particle density operator in a basis of
(anti-)symmetrized -particle states (configurations of occupation numbers)
and allows to tread arbitrary pair interactions in a continuous space.
We give a detailed description of the method and discuss the application to
electrons or, more generally, Coulomb-interacting fermions. As a test case we
consider a few quantum particles in a one-dimensional harmonic trap. Depending
on the coupling parameter (ratio of the interaction energy to kinetic energy),
the method strongly reduces the sign problem as compared to direct path
integral Monte Carlo (DPIMC) simulations in the regime of strong degeneracy
which is of particular importance for dense matter in laser plasmas or compact
stars. In order to provide a self-contained introduction, the chapter includes
a short introduction to Metropolis Monte Carlo methods and the second
quantization of quantum mechanics.Comment: chapter in book "Introduction to Complex Plasmas: Scientific
Challenges and Technological Opportunities", Michael Bonitz, K. Becker, J.
Lopez and H. Thomsen (Eds.) Springer Series "Atomic, Optical and Plasma
Physics", vol. 82, Springer 2014, pp. 153-194 ISBN: 978-3-319-05436-0 (Print)
978-3-319-05437-7 (Online
Neural Network Parameterizations of Electromagnetic Nucleon Form Factors
The electromagnetic nucleon form-factors data are studied with artificial
feed forward neural networks. As a result the unbiased model-independent
form-factor parametrizations are evaluated together with uncertainties. The
Bayesian approach for the neural networks is adapted for chi2 error-like
function and applied to the data analysis. The sequence of the feed forward
neural networks with one hidden layer of units is considered. The given neural
network represents a particular form-factor parametrization. The so-called
evidence (the measure of how much the data favor given statistical model) is
computed with the Bayesian framework and it is used to determine the best form
factor parametrization.Comment: The revised version is divided into 4 sections. The discussion of the
prior assumptions is added. The manuscript contains 4 new figures and 2 new
tables (32 pages, 15 figures, 2 tables
Eta Carinae -- Physics of the Inner Ejecta
Eta Carinae's inner ejecta are dominated observationally by the bright
Weigelt blobs and their famously rich spectra of nebular emission and
absorption lines. They are dense (n_e ~ 10^7 to 10^8 cm^-3), warm (T_e ~ 6000
to 7000 K) and slow moving (~40 km/s) condensations of mostly neutral (H^0)
gas. Located within 1000 AU of the central star, they contain heavily
CNO-processed material that was ejected from the star about a century ago.
Outside the blobs, the inner ejecta include absorption-line clouds with similar
conditions, plus emission-line gas that has generally lower densities and a
wider range of speeds (reaching a few hundred km/s) compared to the blobs. The
blobs appear to contain a negligible amount of dust and have a nearly dust-free
view of the central source, but our view across the inner ejecta is severely
affected by uncertain amounts of dust having a patchy distribution in the
foreground. Emission lines from the inner ejecta are powered by photoionization
and fluorescent processes. The variable nature of this emission, occurring in a
5.54 yr event cycle, requires specific changes to the incident flux that hold
important clues to the nature of the central object.Comment: This is Chapter 5 in a book entitled: Eta Carinae and the Supernova
Impostors, Kris Davidson and Roberta M. Humphreys, editors Springe
Cytokinesis in bloodstream stage Trypanosoma brucei requires a family of katanins and spastin
Microtubule severing enzymes regulate microtubule dynamics in a wide range of organisms and are implicated in important cell cycle processes such as mitotic spindle assembly and disassembly, chromosome movement and cytokinesis. Here we explore the function of several microtubule severing enzyme homologues, the katanins (KAT80, KAT60a, KAT60b and KAT60c), spastin (SPA) and fidgetin (FID) in the bloodstream stage of the African trypanosome parasite, Trypanosoma brucei. The trypanosome cytoskeleton is microtubule based and remains assembled throughout the cell cycle, necessitating its remodelling during cytokinesis. Using RNA interference to deplete individual proteins, we show that the trypanosome katanin and spastin homologues are non-redundant and essential for bloodstream form proliferation. Further, cell cycle analysis revealed that these proteins play essential but discrete roles in cytokinesis. The KAT60 proteins each appear to be important during the early stages of cytokinesis, while downregulation of KAT80 specifically inhibited furrow ingression and SPA depletion prevented completion of abscission. In contrast, RNA interference of FID did not result in any discernible effects. We propose that the stable microtubule cytoskeleton of T. brucei necessitates the coordinated action of a family of katanins and spastin to bring about the cytoskeletal remodelling necessary to complete cell divisio
Towards the solution of the many-electron problem in real materials: Equation of state of the hydrogen chain with state-of-the-art many-body methods
We present numerical results for the equation of state of an infinite chain of hydrogen atoms. A variety of modern many-body methods are employed, with exhaustive cross-checks and validation. Approaches for reaching the continuous space limit and the thermodynamic limit are investigated, proposed, and tested. The detailed comparisons provide a benchmark for assessing the current state of the art in many-body computation, and for the development of new methods. The ground-state energy per atom in the linear chain is accurately determined versus bond length, with a confidence bound given on all uncertainties
Utilisation of an operative difficulty grading scale for laparoscopic cholecystectomy
Background
A reliable system for grading operative difficulty of laparoscopic cholecystectomy would standardise description of findings and reporting of outcomes. The aim of this study was to validate a difficulty grading system (Nassar scale), testing its applicability and consistency in two large prospective datasets.
Methods
Patient and disease-related variables and 30-day outcomes were identified in two prospective cholecystectomy databases: the multi-centre prospective cohort of 8820 patients from the recent CholeS Study and the single-surgeon series containing 4089 patients. Operative data and patient outcomes were correlated with Nassar operative difficultly scale, using Kendall’s tau for dichotomous variables, or Jonckheere–Terpstra tests for continuous variables. A ROC curve analysis was performed, to quantify the predictive accuracy of the scale for each outcome, with continuous outcomes dichotomised, prior to analysis.
Results
A higher operative difficulty grade was consistently associated with worse outcomes for the patients in both the reference and CholeS cohorts. The median length of stay increased from 0 to 4 days, and the 30-day complication rate from 7.6 to 24.4% as the difficulty grade increased from 1 to 4/5 (both p < 0.001). In the CholeS cohort, a higher difficulty grade was found to be most strongly associated with conversion to open and 30-day mortality (AUROC = 0.903, 0.822, respectively). On multivariable analysis, the Nassar operative difficultly scale was found to be a significant independent predictor of operative duration, conversion to open surgery, 30-day complications and 30-day reintervention (all p < 0.001).
Conclusion
We have shown that an operative difficulty scale can standardise the description of operative findings by multiple grades of surgeons to facilitate audit, training assessment and research. It provides a tool for reporting operative findings, disease severity and technical difficulty and can be utilised in future research to reliably compare outcomes according to case mix and intra-operative difficulty
Electronic Structure Calculation by First Principles for Strongly Correlated Electron Systems
Recent trends of ab initio studies and progress in methodologies for
electronic structure calculations of strongly correlated electron systems are
discussed. The interest for developing efficient methods is motivated by recent
discoveries and characterizations of strongly correlated electron materials and
by requirements for understanding mechanisms of intriguing phenomena beyond a
single-particle picture. A three-stage scheme is developed as renormalized
multi-scale solvers (RMS) utilizing the hierarchical electronic structure in
the energy space. It provides us with an ab initio downfolding of the global
band structure into low-energy effective models followed by low-energy solvers
for the models. The RMS method is illustrated with examples of several
materials. In particular, we overview cases such as dynamics of semiconductors,
transition metals and its compounds including iron-based superconductors and
perovskite oxides, as well as organic conductors of kappa-ET type.Comment: 44 pages including 38 figures, to appear in J. Phys. Soc. Jpn. as an
invited review pape
JVG9, a benzimidazole derivative, alters the surface and cytoskeleton of Trypanosoma cruzi bloodstream trypomastigotes
The ALPS project release 2.0: Open source software for strongly correlated systems
We present release 2.0 of the ALPS (Algorithms and Libraries for Physics
Simulations) project, an open source software project to develop libraries and
application programs for the simulation of strongly correlated quantum lattice
models such as quantum magnets, lattice bosons, and strongly correlated fermion
systems. The code development is centered on common XML and HDF5 data formats,
libraries to simplify and speed up code development, common evaluation and
plotting tools, and simulation programs. The programs enable non-experts to
start carrying out serial or parallel numerical simulations by providing basic
implementations of the important algorithms for quantum lattice models:
classical and quantum Monte Carlo (QMC) using non-local updates, extended
ensemble simulations, exact and full diagonalization (ED), the density matrix
renormalization group (DMRG) both in a static version and a dynamic
time-evolving block decimation (TEBD) code, and quantum Monte Carlo solvers for
dynamical mean field theory (DMFT). The ALPS libraries provide a powerful
framework for programers to develop their own applications, which, for
instance, greatly simplify the steps of porting a serial code onto a parallel,
distributed memory machine. Major changes in release 2.0 include the use of
HDF5 for binary data, evaluation tools in Python, support for the Windows
operating system, the use of CMake as build system and binary installation
packages for Mac OS X and Windows, and integration with the VisTrails workflow
provenance tool. The software is available from our web server at
http://alps.comp-phys.org/.Comment: 18 pages + 4 appendices, 7 figures, 12 code examples, 2 table
Role of SPI-1 Secreted Effectors in Acute Bovine Response to Salmonella enterica Serovar Typhimurium: A Systems Biology Analysis Approach
Salmonella enterica Serovar Typhimurium (S. Typhimurium) causes enterocolitis with diarrhea and polymorphonuclear cell (PMN) influx into the intestinal mucosa in humans and calves. The Salmonella Type III Secretion System (T3SS) encoded at Pathogenicity Island I translocates Salmonella effector proteins SipA, SopA, SopB, SopD, and SopE2 into epithelial cells and is required for induction of diarrhea. These effector proteins act together to induce intestinal fluid secretion and transcription of C-X-C chemokines, recruiting PMNs to the infection site. While individual molecular interactions of the effectors with cultured host cells have been characterized, their combined role in intestinal fluid secretion and inflammation is less understood. We hypothesized that comparison of the bovine intestinal mucosal response to wild type Salmonella and a SipA, SopABDE2 effector mutant relative to uninfected bovine ileum would reveal heretofore unidentified diarrhea-associated host cellular pathways. To determine the coordinated effects of these virulence factors, a bovine ligated ileal loop model was used to measure responses to wild type S. Typhimurium (WT) and a ΔsipA, sopABDE2 mutant (MUT) across 12 hours of infection using a bovine microarray. Data were analyzed using standard microarray analysis and a dynamic Bayesian network modeling approach (DBN). Both analytical methods confirmed increased expression of immune response genes to Salmonella infection and novel gene expression. Gene expression changes mapped to 219 molecular interaction pathways and 1620 gene ontology groups. Bayesian network modeling identified effects of infection on several interrelated signaling pathways including MAPK, Phosphatidylinositol, mTOR, Calcium, Toll-like Receptor, CCR3, Wnt, TGF-β, and Regulation of Actin Cytoskeleton and Apoptosis that were used to model of host-pathogen interactions. Comparison of WT and MUT demonstrated significantly different patterns of host response at early time points of infection (15 minutes, 30 minutes and one hour) within phosphatidylinositol, CCR3, Wnt, and TGF-β signaling pathways and the regulation of actin cytoskeleton pathway
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