Subbarrier interactions of the oxygen isotopes

We derive a unified description of the low-energy elastic, inelastic, neutron transfer, and fusion cross sections of systems involving two stable oxygen isotopes. Coupled channels equations with an incoming wave boundary condition are employed, as is the no-recoil approximation; the adiabatic approximation, which violates unitarity, is avoided. A calculation with phenomenologically determined 16O + 16O and 16O-n potentials reproduces the measured cross sections within the limitations of the model. A possible error in the data analysis for 16O + 17O by Thomas et al. is pointed out

Stabilization of a (3+1)D soliton in a Kerr medium by a rapidly oscillating dispersion coefficient

Using the numerical solution of the nonlinear Schroedinger equation and a variational method it is shown that (3+1)-dimensional spatiotemporal optical solitons can be stabilized by a rapidly oscillating dispersion coefficient in a Kerr medium with cubic nonlinearity. This has immediate consequence in generating dispersion-managed robust optical soliton in communication as well as possible stabilized Bose-Einstein condensates in periodic optical-lattice potential via an effective-mass formulation. We also critically compare the present stabilization with that obtained by a rapid sinusoidal oscillation of the Kerr nonlinearity parameter.Comment: 6 pages, 6 ps figures, New figure 4 added, Physical Review

An insect picornavirus may have genome organization similar to that of caliciviruses

AbstractComputer-assisted analysis of the amino acid sequence of the product encoded by the sequenced 3′ portion of the cricket paralysis virus (CrPV), an insect picornavirus, genome showed that this protein is homologous not to the RNA-directed RNA polymerases, as originally suggested, but to the capsid proteins of mammalian picornaviruses. Alignment of the CrPV protein sequence with those of picornavirus and calicivirus capsid proteins demonstrated that the sequenced portion of the insect picornavirus genome encodes the C-terminal part of VP3 and the entire VP1. Thus CrPV seems to have a genome organization distinct from that of other picornaviruses but closely resembling that of caliciviruses, with the capsid proteins encoded in the 3′ part of the genome. On the other hand, the tentative phylogenetic trees generated from the VP3 alignment revealed grouping of CrPV with hepatitis A virus, a true picornavirus, not with caliciviruses. Thus CrPV may be a picornavirus with a calicivirus-like genome organization. Different options for CrPV genome expression are discussed

Deformations and dilations of chaotic billiards, dissipation rate, and quasi-orthogonality of the boundary wavefunctions

We consider chaotic billiards in d dimensions, and study the matrix elements M_{nm} corresponding to general deformations of the boundary. We analyze the dependence of |M_{nm}|^2 on \omega = (E_n-E_m)/\hbar using semiclassical considerations. This relates to an estimate of the energy dissipation rate when the deformation is periodic at frequency \omega. We show that for dilations and translations of the boundary, |M_{nm}|^2 vanishes like \omega^4 as \omega -> 0, for rotations like \omega^2, whereas for generic deformations it goes to a constant. Such special cases lead to quasi-orthogonality of the eigenstates on the boundary.Comment: 4 pages, 3 figure

Quantum versus Classical Dynamics in a driven barrier: the role of kinematic effects

We study the dynamics of the classical and quantum mechanical scattering of a wave packet from an oscillating barrier. Our main focus is on the dependence of the transmission coefficient on the initial energy of the wave packet for a wide range of oscillation frequencies. The behavior of the quantum transmission coefficient is affected by tunneling phenomena, resonances and kinematic effects emanating from the time dependence of the potential. We show that when kinematic effects dominate (mainly in intermediate frequencies), classical mechanics provides very good approximation of quantum results. Moreover, in the frequency region of optimal agreement between classical and quantum transmission coefficient, the transmission threshold, i.e. the energy above which the transmission coefficient becomes larger than a specific small threshold value, is found to exhibit a minimum. We also consider the form of the transmitted wave packet and we find that for low values of the frequency the incoming classical and quantum wave packet can be split into a train of well separated coherent pulses, a phenomenon which can admit purely classical kinematic interpretation

Estimation of prokaryotic supergenome size and composition from gene frequency distributions

BACKGROUND: Because prokaryotic genomes experience a rapid flux of genes, selection may act at a higher level than an individual genome. We explore a quantitative model of the distributed genome whereby groups of genomes evolve by acquiring genes from a fixed reservoir which we denote as supergenome. Previous attempts to understand the nature of the supergenome treated genomes as random, independent collections of genes and assumed that the supergenome consists of a small number of homogeneous sub-reservoirs. Here we explore the consequences of relaxing both assumptions. RESULTS: We surveyed several methods for estimating the size and composition of the supergenome. The methods assumed that genomes were either random, independent samples of the supergenome or that they evolved from a common ancestor along a known tree via stochastic sampling from the reservoir. The reservoir was assumed to be either a collection of homogeneous sub-reservoirs or alternatively composed of genes with Gamma distributed gain probabilities. Empirical gene frequencies were used to either compute the likelihood of the data directly or first to reconstruct the history of gene gains and then compute the likelihood of the reconstructed numbers of gains. CONCLUSIONS: Supergenome size estimates using the empirical gene frequencies directly are not robust with respect to the choice of the model. By contrast, using the gene frequencies and the phylogenetic tree to reconstruct multiple gene gains produces reliable estimates of the supergenome size and indicates that a homogeneous supergenome is more consistent with the data than a supergenome with Gamma distributed gain probabilities

Nonlocal evolution of weighted scale-free networks

We introduce the notion of globally updating evolution for a class of weighted networks, in which the weight of a link is characterized by the amount of data packet transport flowing through it. By noting that the packet transport over the network is determined nonlocally, this approach can explain the generic nonlinear scaling between the strength and the degree of a node. We demonstrate by a simple model that the strength-driven evolution scheme recently introduced can be generalized to a nonlinear preferential attachment rule, generating the power-law behaviors in degree and in strength simultaneously.Comment: 4 pages, 4 figures, final version published in PR

AAA+: A class of chaperone-like ATPases associated with the assembly, operation, and disassembly of protein complexes

Using a combination of computer methods for iterative database searches and multiple sequence alignment, we show that protein sequences related to the AAA family of ATPases are far more prevalent than reported previously. Among these are regulatory components of Lon and Clp proteases, proteins involved in DNA replication, recombination, and restriction (including subunits of the origin recognition complex, replication factor C proteins, MCM DNA-licensing factors and the bacterial DnaA, RuvB, and McrB proteins), prokaryotic NtrC-related transcription regulators, the Bacillus sporulation protein SpoVJ, Mg2+, and Co2+ chelatases, the Halobacterium GvpN gas vesicle synthesis protein, dynein motor proteins, TorsinA, and Rubisco activase. Alignment of these sequences, in light of the structures of the clamp loader delta' subunit of Escherichia coli DNA polymerase III and the hexamerization component of N-ethylmaleimide-sensitive fusion protein, provides structural and mechanistic insights into these proteins, collectively designated the AAA+ class. Whole-genome analysis indicates that this class is ancient and has undergone considerable functional divergence prior to the emergence of the major divisions of life. These proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes. The hexameric architecture often associated with this class can provide a hole through which DNA or RNA can be thread; this may be important for assembly or remodeling of DNA-protein complexes

Quantum dissipation due to the interaction with chaotic degrees-of-freedom and the correspondence principle

Both in atomic physics and in mesoscopic physics it is sometimes interesting to consider the energy time-dependence of a parametrically-driven chaotic system. We assume an Hamiltonian ${\cal H}(Q,P;x(t))$ where $x(t)=Vt$. The velocity $V$ is slow in the classical sense but not necessarily in the quantum-mechanical sense. The crossover (in time) from ballistic to diffusive energy-spreading is studied. The associated irreversible growth of the average energy has the meaning of dissipation. It is found that a dimensionless velocity $v_{PR}$ determines the nature of the dynamics, and controls the route towards quantal-classical correspondence (QCC). A perturbative regime and a non-perturbative semiclassical regime are distinguished.Comment: 4 pages, clear presentation of the main poin

Phase transition in ultrathin magnetic films with long-range interactions: Monte Carlo simulation of the anisotropic Heisenberg model

Ultrathin magnetic films can be modeled as an anisotropic Heisenberg model with long-range dipolar interactions. It is believed that the phase diagram presents three phases: An ordered ferromagnetic phase I, a phase characterized by a change from out-of-plane to in-plane in the magnetization II, and a high-temperature paramagnetic phase III. It is claimed that the border lines from phase I to III and II to III are of second order and from I to II is first order. In the present work we have performed a very careful Monte Carlo simulation of the model. Our results strongly support that the line separating phases II and III is of the BKT type.Comment: 7 page