Classifying program changes during software development

Call number: LD2668 .T4 CMSC 1988 H78Master of ScienceComputing and Information Science

A review of Monte Carlo simulations of polymers with PERM

In this review, we describe applications of the pruned-enriched Rosenbluth method (PERM), a sequential Monte Carlo algorithm with resampling, to various problems in polymer physics. PERM produces samples according to any given prescribed weight distribution, by growing configurations step by step with controlled bias, and correcting "bad" configurations by "population control". The latter is implemented, in contrast to other population based algorithms like e.g. genetic algorithms, by depth-first recursion which avoids storing all members of the population at the same time in computer memory. The problems we discuss all concern single polymers (with one exception), but under various conditions: Homopolymers in good solvents and at the $\Theta$ point, semi-stiff polymers, polymers in confining geometries, stretched polymers undergoing a forced globule-linear transition, star polymers, bottle brushes, lattice animals as a model for randomly branched polymers, DNA melting, and finally -- as the only system at low temperatures, lattice heteropolymers as simple models for protein folding. PERM is for some of these problems the method of choice, but it can also fail. We discuss how to recognize when a result is reliable, and we discuss also some types of bias that can be crucial in guiding the growth into the right directions.Comment: 29 pages, 26 figures, to be published in J. Stat. Phys. (2011

Three-dimensional flux states as a model for the pseudogap phase of transition metal oxides

We propose that the pseudogap state observed in the transition metal oxides can be explained by a three-dimensional flux state, which exhibits spontaneously generated currents in its ground state due to electron-electron correlations. We compare the energy of the flux state to other classes of mean field states, and find that it is stabilized over a wide range of $t$ and $\delta$. The signature of the state will be peaks in the neutron diffraction spectra, the location and intensity of which are presented. The dependence of the pseudogap in the optical conductivity is calculated based on the parameters in the model.Comment: submitted to Phys. Rev. B on January 8, 200

Black holes from high-energy beam--beam collisions

Using a recent technique, proposed by Eardley and Giddings, we extend their results to the high-energy collision of two beams of massless particles, i.e. of two finite-front shock waves. Closed (marginally) trapped surfaces can be determined analytically in several cases even for collisions at non-vanishing impact parameter in D\ge 4 space-time dimensions. We are able to confirm and extend earlier conjectures by Yurtsever, and to deal with arbitrary axisymmetric profiles, including an amusing case of ``fractal'' beams. We finally discuss some implications of our results in high-energy experiments and in cosmology.Comment: 17 pages Revtex, 1 figure, references adde

Violation of the Wiedemann-Franz Law in a Large-N Solution of the t-J Model

We show that the Wiedemann-Franz law, which holds for Landau Fermi liquids, breaks down in a large-n treatment of the t-J model. The calculated ratio of the in-plane thermal and electrical conductivities agrees quantitatively with experiments on the normal state of the electron-doped Pr_{2-x}Ce_xCuO_4 (x = 0.15) cuprate superconductor. The violation of the Wiedemann-Franz law in the uniform phase contrasts with other properties of the phase that are Fermi liquid like.Comment: 4 pages, 2 figures. Typos corrected, one added reference, revised discussion of experiment on 214 cuprate material (x = 0.06

Added Value of Computed Tomography Virtual Intravascular Endoscopy in the Evaluation of Coronary Arteries with Stents or Plaques

Coronary computed tomography angiography (CCTA) is a widely used imaging modality for diagnosing coronary artery disease (CAD) but is limited by a high false positive rate when evaluating coronary arteries with stents and heavy calcifications. Virtual intravascular endoscopy (VIE) images generated from CCTA can be used to qualitatively assess the vascular lumen and might be helpful for overcoming this challenge. In this study, one hundred subjects with coronary stents underwent both CCTA and invasive coronary angiography (ICA). A total of 902 vessel segments were analyzed using CCTA and VIE. The vessel segments were first analyzed on CCTA alone. Then, using VIE, the segments were classified qualitatively as either negative or positive for in-stent restenosis (ISR) or CAD. These results were compared, using ICA as the reference, to determine the added diagnostic value of VIE. Of the 902 analyzed vessel segments, CCTA/VIE had sensitivity, specificity, accuracy, positive predictive value, and negative predictive value (shown in %) of 93.9/90.2, 96.2/98.2, 96.0/97.7, 70.0/83.1, and 99.4/99.0, respectively, in diagnosing ISR or CAD, with significantly improved specificity (p = 0.025), accuracy (p = 0.046), and positive predictive value (p = 0.047). VIE can be a helpful addition to CCTA when evaluating coronary arterie

Multiplex Amplification Refractory Mutation System Polymerase Chain Reaction (ARMS-PCR) for diagnosis of natural infection with canine distemper virus

<p>Abstract</p> <p>Background</p> <p>Canine distemper virus (CDV) is present worldwide and produces a lethal systemic infection of wild and domestic <it>Canidae</it>. Pre-existing antibodies acquired from vaccination or previous CDV infection might interfere the interpretation of a serologic diagnosis method. In addition, due to the high similarity of nucleic acid sequences between wild-type CDV and the new vaccine strain, current PCR derived methods cannot be applied for the definite confirmation of CD infection. Hence, it is worthy of developing a simple and rapid nucleotide-based assay for differentiation of wild-type CDV which is a cause of disease from attenuated CDVs after vaccination. High frequency variations have been found in the region spanning from the 3'-untranslated region (UTR) of the matrix (M) gene to the fusion (F) gene (designated M-F UTR) in a few CDV strains. To establish a differential diagnosis assay, an amplification refractory mutation analysis was established based on the highly variable region on M-F UTR and F regions.</p> <p>Results</p> <p>Sequences of frequent polymorphisms were found scattered throughout the M-F UTR region; the identity of nucleic acid between local strains and vaccine strains ranged from 82.5% to 93.8%. A track of AAA residue located 35 nucleotides downstream from F gene start codon highly conserved in three vaccine strains were replaced with TGC in the local strains; that severed as target sequences for deign of discrimination primers. The method established in the present study successfully differentiated seven Taiwanese CDV field isolates, all belonging to the Asia-1 lineage, from vaccine strains.</p> <p>Conclusions</p> <p>The method described herein would be useful for several clinical applications, such as confirmation of nature CDV infection, evaluation of vaccination status and verification of the circulating viral genotypes.</p

Model for a Universe described by a non-minimally coupled scalar field and interacting dark matter

In this work it is investigated the evolution of a Universe where a scalar field, non-minimally coupled to space-time curvature, plays the role of quintessence and drives the Universe to a present accelerated expansion. A non-relativistic dark matter constituent that interacts directly with dark energy is also considered, where the dark matter particle mass is assumed to be proportional to the value of the scalar field. Two models for dark matter pressure are considered: the usual one, pressureless, and another that comes from a thermodynamic theory and relates the pressure with the coupling between the scalar field and the curvature scalar. Although the model has a strong dependence on the initial conditions, it is shown that the mixture consisted of dark components plus baryonic matter and radiation can reproduce the expected red-shift behavior of the deceleration parameter, density parameters and luminosity distance.Comment: 11 pages and 6 figures. To appear in GR

Partial Deconfinement in Color Superconductivity

We analyze the fate of the unbroken SU(2) color gauge interactions for 2 light flavors color superconductivity at non zero temperature. Using a simple model we compute the deconfining/confining critical temperature and show that is smaller than the critical temperature for the onset of the superconductive state itself. The breaking of Lorentz invariance, induced already at zero temperature by the quark chemical potential, is shown to heavily affect the value of the critical temperature and all of the relevant features related to the deconfining transition. Modifying the Polyakov loop model to describe the SU(2) immersed in the diquark medium we argue that the deconfinement transition is second order. Having constructed part of the equation of state for the 2 color superconducting phase at low temperatures our results are relevant for the physics of compact objects featuring a two flavor color superconductive state.Comment: 9 pp, 4 eps-figs, version to appear in PR