Interaction Picture Density Matrix Quantum Monte Carlo

The recently developed density matrix quantum Monte Carlo (DMQMC) algorithm stochastically samples the N -body thermal density matrix and hence provides access to exact properties of many-particle quantum systems at arbitrary temperatures. We demonstrate that moving to the interaction picture provides substantial benefits when applying DMQMC to interacting fermions. In this first study, we focus on a system of much recent interest: the uniform electron gas in the warm dense regime. The basis set incompleteness error at finite temperature is investigated and extrapolated via a simple Monte Carlo sampling procedure. Finally, we provide benchmark calculations for a four-electron system, comparing our results to previous work where possible.Comment: Minor text modifications and added deviation subplot to Fig. 9 following referee's review comments. Include link to supplementary material in reference

Accurate exchange-correlation energies for the warm dense electron gas

Density matrix quantum Monte Carlo (DMQMC) is used to sample exact-on-average $N$-body density matrices for uniform electron gas systems of up to 10$^{124}$ matrix elements via a stochastic solution of the Bloch equation. The results of these calculations resolve a current debate over the accuracy of the data used to parametrize finite-temperature density functionals. Exchange-correlation energies calculated using the real-space restricted path-integral formalism and the $k$-space configuration path-integral formalism disagree by up to $\sim$$10$\% at certain reduced temperatures $T/T_F \le 0.5$ and densities $r_s \le 1$. Our calculations confirm the accuracy of the configuration path-integral Monte Carlo results available at high density and bridge the gap to lower densities, providing trustworthy data in the regime typical of planetary interiors and solids subject to laser irradiation. We demonstrate that DMQMC can calculate free energies directly and present exact free energies for $T/T_F \ge 1$ and $r_s \le 2$.Comment: Accepted version: added free energy data and restructured text. Now includes supplementary materia

VIDA: a virus database system for the organization of animal virus genome open reading frames

VIDA is a new virus database that organizes open reading frames (ORFs) from partial and complete genomic sequences from animal viruses. Currently VIDA includes all sequences from GenBank for Herpesviridae, Coronaviridae and Arteriviridae. The ORFs are organized into homologous protein families, which are identified on the basis of sequence similarity relationships, Conserved sequence regions of potential functional importance are identified and can be retrieved as sequence alignments. We use a controlled taxonomical and functional classification for all the proteins and protein families in the database. When available, protein structures that are related to the families have also been included. The database is available for online search and sequence information retrieval at http://www.biochem.ucl.ac.uk/bsm/virus-database/ VIDA.html

The design-by-adaptation approach to universal access: learning from videogame technology

This paper proposes an alternative approach to the design of universally accessible interfaces to that provided by formal design frameworks applied ab initio to the development of new software. This approach, design-byadaptation, involves the transfer of interface technology and/or design principles from one application domain to another, in situations where the recipient domain is similar to the host domain in terms of modelled systems, tasks and users. Using the example of interaction in 3D virtual environments, the paper explores how principles underlying the design of videogame interfaces may be applied to a broad family of visualization and analysis software which handles geographical data (virtual geographic environments, or VGEs). One of the motivations behind the current study is that VGE technology lags some way behind videogame technology in the modelling of 3D environments, and has a less-developed track record in providing the variety of interaction methods needed to undertake varied tasks in 3D virtual worlds by users with varied levels of experience. The current analysis extracted a set of interaction principles from videogames which were used to devise a set of 3D task interfaces that have been implemented in a prototype VGE for formal evaluation

Determination of the refractive index of organic material from atmospheric aerosol over the visible wavelength range using optical tweezers

Optical trapping combined with Mie spectroscopy is a new technique used to record the refractive index of insoluble organic material extracted from atmospheric aerosol samples over a wide wavelength range. The refractive index of the insoluble organic extracts was shown to follow a Cauchy equation between 460 and 700 nm for organic aerosol extracts collected from urban (London) and remote (Antarctica) locations. Cauchy coefficients for the remote sample were for the Austral summer and gave the Cauchy coefficients of A  =  1.467 and B  =  1000 nm2 with a real refractive index of 1.489 at a wavelength of 589 nm. Cauchy coefficients for the urban samples varied with season, with extracts collected during summer having Cauchy coefficients of A  =  1.465  ±  0.005 and B  =  4625  ±  1200 nm2 with a representative real refractive index of 1.478 at a wavelength of 589 nm, whilst samples extracted during autumn had larger Cauchy coefficients of A  =  1.505 and B  =  600 nm2 with a representative real refractive index of 1.522 at a wavelength of 589 nm. The refractive index of absorbing aerosol was also recorded. The absorption Ångström exponent was determined for woodsmoke and humic acid aerosol extract. Typical values of the Cauchy coefficient for the woodsmoke aerosol extract were A  =  1.541  ±  0.03 and B  =  14 800  ±  2900 nm2, resulting in a real refractive index of 1.584  ±  0.007 at a wavelength of 589 nm and an absorption Ångström exponent of 8.0. The measured values of refractive index compare well with previous monochromatic or very small wavelength range measurements of refractive index. In general, the real component of the refractive index increases from remote to urban to woodsmoke. A one-dimensional radiative-transfer calculation of the top-of-the-atmosphere albedo was applied to model an atmosphere containing a 3 km thick layer of aerosol comprising pure water, pure insoluble organic aerosol, or an aerosol consisting of an aqueous core with an insoluble organic shell. The calculation demonstrated that the top-of-the-atmosphere albedo increases by 0.01 to 0.04 for pure organic particles relative to water particles of the same size and that the top-of-the-atmosphere albedo increases by 0.03 for aqueous core-shell particles as volume fraction of the shell material increases to 25 %

The incidence and risk factors for new onset atrial fibrillation in the PROSPER study

Aims Atrial fibrillation/flutter (AF) is the most common arrhythmia in older people. It associates with reduced exercise capacity, increased risk of stroke, and mortality. We aimed to determine retrospectively whether pravastatin reduces the incidence of AF and whether any electrocardiographic measures or clinical conditions might be risk factors for its development. Methods and results The PROspective Study of Pravastatin in the Elderly at Risk (PROSPER) was a randomized, double-blind controlled trial that recruited 5804 individuals aged 70-82 years with a history of, or risk factors for, vascular disease. A total of 2891 were allocated to pravastatin and 2913 to placebo; mean follow-up was 3.2 years. Electrocardiograms (ECGs), which were recorded at baseline, annually thereafter, and at run-out, were processed by computer and reviewed manually. In all, 264 of 2912 (9.1%) of the placebo group and 283 of 2888 (9.8%) of the pravastatin-treated group developed AF [hazard ratio 1.08 (0.92,1.28), P = 0.35)]. Multivariate analysis showed that PR and QTc intervals, age, left ventricular hypertrophy, and ST-T abnormalities were related to development of AF after adjustment for many variables including alcohol consumption, which itself was univariately predictive of developing AF. Previous myocardial infarction on the ECG was not a risk factor. A history of vascular disease was strongly linked with developing AF but not diabetes and hypertension. Conclusion Pravastatin does not reduce the incidence of AF in older people at risk of vascular disease, at least in the short-medium term. Risk factors for AF include older age, prolongation of PR or QTc intervals, left ventricular hypertrophy, and ST-T abnormalities on the EC

Interferometric Phase Calibration Sources in the Declination Range 0deg to -30deg

We present a catalog of 321 compact radio sources in the declination range 0deg > delta > -30deg. The positions of these sources have been measured with a two-dimensional rms accuracy of 35 milliarcseconds using the NRAO Very Large Array. Each source has a peak flux density >50 mJy at 8.4 GHz. We intend for this catalog to be used mainly for selection of phase calibration sources for radio interferometers, although compact radio sources have other scientific uses.Comment: 9 pages. To appear in ApJS. Catalog (Table 3) is abbreviated in printed version. Complete catalog available at ftp://ftp.aoc.nrao.edu/pub/staff/jwrobel/WPW2003_ApJS.tx

Algebraic varieties with automorphism groups of maximal rank

We confirm, to some extent, the belief that a projective variety X has the largest number (relative to the dimension of X) of independent commuting automorphisms of positive entropy only when X is birational to a complex torus or a quotient of a torus. We also include an addendum to an early paper though it is not used in the present paper.Comment: Mathematische Annalen (to appear

The molecular genetic analysis of the expanding pachyonychia congenita case collection

BACKGROUND: Pachyonychia congenita (PC) is a rare autosomal dominant keratinizing disorder characterized by severe, painful, palmoplantar keratoderma and nail dystrophy, often accompanied by oral leucokeratosis, cysts and follicular keratosis. It is caused by mutations in one of five keratin genes: KRT6A, KRT6B, KRT6C, KRT16 or KRT17. OBJECTIVES: To identify mutations in 84 new families with a clinical diagnosis of PC, recruited by the International Pachyonychia Congenita Research Registry during the last few years. METHODS: Genomic DNA isolated from saliva or peripheral blood leucocytes was amplified using primers specific for the PC-associated keratin genes and polymerase chain reaction products were directly sequenced. RESULTS: Mutations were identified in 84 families in the PC-associated keratin genes, comprising 46 distinct keratin mutations. Fourteen were previously unreported mutations, bringing the total number of different keratin mutations associated with PC to 105. CONCLUSIONS: By identifying mutations in KRT6A, KRT6B, KRT6C, KRT16 or KRT17, this study has confirmed, at the molecular level, the clinical diagnosis of PC in these families

On k-Column Sparse Packing Programs

We consider the class of packing integer programs (PIPs) that are column sparse, i.e. there is a specified upper bound k on the number of constraints that each variable appears in. We give an (ek+o(k))-approximation algorithm for k-column sparse PIPs, improving on recent results of $k^2\cdot 2^k$ and $O(k^2)$. We also show that the integrality gap of our linear programming relaxation is at least 2k-1; it is known that k-column sparse PIPs are $\Omega(k/ \log k)$-hard to approximate. We also extend our result (at the loss of a small constant factor) to the more general case of maximizing a submodular objective over k-column sparse packing constraints.Comment: 19 pages, v3: additional detail