Extended bound states and resonances of two fermions on a periodic lattice

The high-$T_c$ cuprates are possible candidates for d-wave superconductivity, with the Cooper pair wave function belonging to a non-trivial irreducible representation of the lattice point group. We argue that this d-wave symmetry is related to a special form of the fermionic kinetic energy and does not require any novel pairing mechanism. In this context, we present a detailed study of the bound states and resonances formed by two lattice fermions interacting via a non-retarded potential that is attractive for nearest neighbors but repulsive for other relative positions. In the case of strong binding, a pair formed by fermions on adjacent lattice sites can have a small effective mass, thereby implying a high condensation temperature. For a weakly bound state, a pair with non-trivial symmetry tends to be smaller in size than an s-wave pair. These and other findings are discussed in connection with the properties of high-$T_c$ cuprate superconductors.Comment: 21 pages, RevTeX, 4 Postscript figures, arithmetic errors corrected. An abbreviated version (no appendix) appeared in PRB on March 1, 199

The Importance of DNA Repair in Tumor Suppression

The transition from a normal to cancerous cell requires a number of highly specific mutations that affect cell cycle regulation, apoptosis, differentiation, and many other cell functions. One hallmark of cancerous genomes is genomic instability, with mutation rates far greater than those of normal cells. In microsatellite instability (MIN tumors), these are often caused by damage to mismatch repair genes, allowing further mutation of the genome and tumor progression. These mutation rates may lie near the error catastrophe found in the quasispecies model of adaptive RNA genomes, suggesting that further increasing mutation rates will destroy cancerous genomes. However, recent results have demonstrated that DNA genomes exhibit an error threshold at mutation rates far lower than their conservative counterparts. Furthermore, while the maximum viable mutation rate in conservative systems increases indefinitely with increasing master sequence fitness, the semiconservative threshold plateaus at a relatively low value. This implies a paradox, wherein inaccessible mutation rates are found in viable tumor cells. In this paper, we address this paradox, demonstrating an isomorphism between the conservatively replicating (RNA) quasispecies model and the semiconservative (DNA) model with post-methylation DNA repair mechanisms impaired. Thus, as DNA repair becomes inactivated, the maximum viable mutation rate increases smoothly to that of a conservatively replicating system on a transformed landscape, with an upper bound that is dependent on replication rates. We postulate that inactivation of post-methylation repair mechanisms are fundamental to the progression of a tumor cell and hence these mechanisms act as a method for prevention and destruction of cancerous genomes.Comment: 7 pages, 5 figures; Approximation replaced with exact calculation; Minor error corrected; Minor changes to model syste

Yeast autonomously replicating sequence binding factor is involved in nucleotide excision repair

Nucleotide excision repair (NER) in yeast is effected by the concerted action of a large complex of proteins. Recently, we identified a stable subcomplex containing the yeast Rad7 and Rad16 proteins. Here, we report the identification of autonomously replicating sequence binding factor 1 (ABF1) as a component of the Rad7/Rad16 NER subcomplex. Yeast ABF1 protein is encoded by an essential gene required for DNA replication, transcriptional regulation, and gene silencing. We show that ABF1 plays a direct role in NER in vitro. Additionally, consistent with a role of ABF1 protein in NER in vivo, we show that certain temperature-sensitive abf1 mutant strains that are defective in DNA replication are specifically defective in the removal of photoproducts by NER and are sensitive to killing by ultraviolet (UV) radiation. These studies define a novel and unexpected role for ABF1 protein during NER in yeast

A Primer on Metagenomics

Metagenomics is a discipline that enables the genomic study of uncultured microorganisms. Faster, cheaper sequencing technologies and the ability to sequence uncultured microbes sampled directly from their habitats are expanding and transforming our view of the microbial world. Distilling meaningful information from the millions of new genomic sequences presents a serious challenge to bioinformaticians. In cultured microbes, the genomic data come from a single clone, making sequence assembly and annotation tractable. In metagenomics, the data come from heterogeneous microbial communities, sometimes containing more than 10,000 species, with the sequence data being noisy and partial. From sampling, to assembly, to gene calling and function prediction, bioinformatics faces new demands in interpreting voluminous, noisy, and often partial sequence data. Although metagenomics is a relative newcomer to science, the past few years have seen an explosion in computational methods applied to metagenomic-based research. It is therefore not within the scope of this article to provide an exhaustive review. Rather, we provide here a concise yet comprehensive introduction to the current computational requirements presented by metagenomics, and review the recent progress made. We also note whether there is software that implements any of the methods presented here, and briefly review its utility. Nevertheless, it would be useful if readers of this article would avail themselves of the comment section provided by this journal, and relate their own experiences. Finally, the last section of this article provides a few representative studies illustrating different facets of recent scientific discoveries made using metagenomics

Magnetic Properties of a Bose-Einstein Condensate

Three hyperfine states of Bose-condensed sodium atoms, recently optically trapped, can be described as a spin-1 Bose gas. We study the behaviour of this system in a magnetic field, and construct the phase diagram, where the temperature of the Bose condensation $T_{BEC}$ increases with magnetic field. In particular the system is ferromagnetic below $T_{BEC}$ and the magnetization is proportional to the condensate fraction in a vanishing magnetic field. Second derivatives of the magnetisation with regard to temperature or magnetic field are discontinuous along the phase boundary.Comment: 5 pages, 5 figures included, to appear in Phys. Rev.

Bogomol'nyi Equations of Maxwell-Chern-Simons vortices from a generalized Abelian Higgs Model

We consider a generalization of the abelian Higgs model with a Chern-Simons term by modifying two terms of the usual Lagrangian. We multiply a dielectric function with the Maxwell kinetic energy term and incorporate nonminimal interaction by considering generalized covariant derivative. We show that for a particular choice of the dielectric function this model admits both topological as well as nontopological charged vortices satisfying Bogomol'nyi bound for which the magnetic flux, charge and angular momentum are not quantized. However the energy for the topolgical vortices is quantized and in each sector these topological vortex solutions are infinitely degenerate. In the nonrelativistic limit, this model admits static self-dual soliton solutions with nonzero finite energy configuration. For the whole class of dielectric function for which the nontopological vortices exists in the relativistic theory, the charge density satisfies the same Liouville equation in the nonrelativistic limit.Comment: 30 pages(4 figures not included), RevTeX, IP/BBSR/93-6

Oscillons: Resonant Configurations During Bubble Collapse

Oscillons are localized, non-singular, time-dependent, spherically-symmetric solutions of nonlinear scalar field theories which, although unstable, are extremely long-lived. We show that they naturally appear during the collapse of subcritical bubbles in models with symmetric and asymmetric double-well potentials. By a combination of analytical and numerical work we explain several of their properties, including the conditions for their existence, their longevity, and their final demise. We discuss several contexts in which we expect oscillons to be relevant. In particular, their nucleation during cosmological phase transitions may have wide-ranging consequences.Comment: 31 pages Revtex, 20 uufiles-encoded figures. Section "Possible Applications of Oscillons" slightly expande

Distribution of the area enclosed by a 2D random walk in a disordered medium

The asymptotic probability distribution for a Brownian particle wandering in a 2D plane with random traps to enclose the algebraic area A by time t is calculated using the instanton technique.Comment: 4 pages, ReVTeX. Phys. Rev. E (March 1999), to be publishe

Spectral Boundary of Positive Random Potential in a Strong Magnetic Field

We consider the problem of randomly distributed positive delta-function scatterers in a strong magnetic field and study the behavior of density of states close to the spectral boundary at $E=\hbar\omega_{c}/2$ in both two and three dimensions. Starting from dimensionally reduced expression of Brezin et al. and using the semiclassical approximation we show that the density of states in the Lifshitz tail at small energies is proportio- nal to $e^{f-2}$ in two dimensions and to $\exp(-3.14f\ln(3.14f/\pi e)/ \sqrt(2me))$ in three dimensions, where $e$ is the energy and $f$ is the density of scatterers in natural units.Comment: 12 pages, LaTex, 5 figures available upon request, to appear in Phys. Rev.

The emergence of Special and Doubly Special Relativity

Building on our previous work [Phys.Rev.D82,085016(2010)], we show in this paper how a Brownian motion on a short scale can originate a relativistic motion on scales that are larger than particle's Compton wavelength. This can be described in terms of polycrystalline vacuum. Viewed in this way, special relativity is not a primitive concept, but rather it statistically emerges when a coarse graining average over distances of order, or longer than the Compton wavelength is taken. By analyzing the robustness of such a special relativity under small variations in the polycrystalline grain-size distribution we naturally arrive at the notion of doubly-special relativistic dynamics. In this way, a previously unsuspected, common statistical origin of the two frameworks is brought to light. Salient issues such as the role of gauge fixing in emergent relativity, generalized commutation relations, Hausdorff dimensions of representative path-integral trajectories and a connection with Feynman chessboard model are also discussed.Comment: 21 pages, 1 figure, RevTeX4, substantially revised version, accepted in Phys. Rev.