Rigorous results on the local equilibrium kinetics of a protein folding model

A local equilibrium approach for the kinetics of a simplified protein folding model, whose equilibrium thermodynamics is exactly solvable, was developed in [M. Zamparo and A. Pelizzola, Phys. Rev. Lett. 97, 068106 (2006)]. Important properties of this approach are (i) the free energy decreases with time, (ii) the exact equilibrium is recovered in the infinite time limit, (iii) the equilibration rate is an upper bound of the exact one and (iv) computational complexity is polynomial in the number of variables. Moreover, (v) this method is equivalent to another approximate approach to the kinetics: the path probability method. In this paper we give detailed rigorous proofs for the above results.Comment: 25 pages, RevTeX 4, to be published in JSTA

Theory of temperature dependence of the Fermi surface-induced splitting of the alloy diffuse-scattering intensity peak

The explanation is presented for the temperature dependence of the fourfold intensity peak splitting found recently in diffuse scattering from the disordered Cu3Au alloy. The wavevector and temperature dependence of the self-energy is identified as the origin of the observed behaviour. Two approaches for the calculation of the self-energy, the high-temperature expansion and the alpha-expansion, are proposed. Applied to the Cu3Au alloy, both methods predict the increase of the splitting with temperature, in agreement with the experimental results.Comment: 4 pages, 3 EPS figures, RevTeX, submitted to J. Phys. Condens. Matter (Letter to the Editor

Exact Renormalization Group Equations. An Introductory Review

We critically review the use of the exact renormalization group equations (ERGE) in the framework of the scalar theory. We lay emphasis on the existence of different versions of the ERGE and on an approximation method to solve it: the derivative expansion. The leading order of this expansion appears as an excellent textbook example to underline the nonperturbative features of the Wilson renormalization group theory. We limit ourselves to the consideration of the scalar field (this is why it is an introductory review) but the reader will find (at the end of the review) a set of references to existing studies on more complex systems.Comment: Final version to appear in Phys. Rep.; Many references added, section 4.2 added, minor corrections. 65 pages, 6 fig

An Introductory Guide to Aligning Networks Using SANA, the Simulated Annealing Network Aligner.

Sequence alignment has had an enormous impact on our understanding of biology, evolution, and disease. The alignment of biological networks holds similar promise. Biological networks generally model interactions between biomolecules such as proteins, genes, metabolites, or mRNAs. There is strong evidence that the network topology-the "structure" of the network-is correlated with the functions performed, so that network topology can be used to help predict or understand function. However, unlike sequence comparison and alignment-which is an essentially solved problem-network comparison and alignment is an NP-complete problem for which heuristic algorithms must be used.Here we introduce SANA, the Simulated Annealing Network Aligner. SANA is one of many algorithms proposed for the arena of biological network alignment. In the context of global network alignment, SANA stands out for its speed, memory efficiency, ease-of-use, and flexibility in the arena of producing alignments between two or more networks. SANA produces better alignments in minutes on a laptop than most other algorithms can produce in hours or days of CPU time on large server-class machines. We walk the user through how to use SANA for several types of biomolecular networks

Electron-acoustic plasma waves: oblique modulation and envelope solitons

Theoretical and numerical studies are presented of the amplitude modulation of electron-acoustic waves (EAWs) propagating in space plasmas whose constituents are inertial cold electrons, Boltzmann distributed hot electrons and stationary ions. Perturbations oblique to the carrier EAW propagation direction have been considered. The stability analysis, based on a nonlinear Schroedinger equation (NLSE), reveals that the EAW may become unstable; the stability criteria depend on the angle $\theta$ between the modulation and propagation directions. Different types of localized EA excitations are shown to exist.Comment: 10 pages, 5 figures; to appear in Phys. Rev.

Search for Second-Generation Scalar Leptoquarks in ppˉ\bm{p \bar{p}} Collisions at s\sqrt{s}=1.96 TeV

Results on a search for pair production of second generation scalar leptoquark in $p \bar{p}$ collisions at $\sqrt{s}$=1.96 TeV are reported. The data analyzed were collected by the CDF detector during the 2002-2003 Tevatron Run II and correspond to an integrated luminosity of 198 pb$^{-1}$. Leptoquarks (LQ) are sought through their decay into (charged) leptons and quarks, with final state signatures represented by two muons and jets and one muon, large transverse missing energy and jets. We observe no evidence for $LQ$ production and derive 95% C.L. upper limits on the $LQ$ production cross sections as well as lower limits on their mass as a function of $\beta$, where $\beta$ is the branching fraction for $LQ \to \mu q$.Comment: 9 pages (3 author list) 5 figure

Combined search for the standard model Higgs boson decaying to a bb pair using the full CDF data set

We combine the results of searches for the standard model Higgs boson based on the full CDF Run II data set obtained from sqrt(s) = 1.96 TeV p-pbar collisions at the Fermilab Tevatron corresponding to an integrated luminosity of 9.45/fb. The searches are conducted for Higgs bosons that are produced in association with a W or Z boson, have masses in the range 90-150 GeV/c^2, and decay into bb pairs. An excess of data is present that is inconsistent with the background prediction at the level of 2.5 standard deviations (the most significant local excess is 2.7 standard deviations).Comment: To be published in Phys. Rev. Lett (v2 contains minor updates based on comments from PRL

Measurement of the ttbar Production Cross Section in ppbar Collisions at sqrt(s) = 1.96 TeV

We present a measurement of the top quark pair production cross section in ppbar collisions at sqrt(s)=1.96 TeV using 318 pb^{-1} of data collected with the Collider Detector at Fermilab. We select ttbar decays into the final states e nu + jets and mu nu + jets, in which at least one b quark from the t-quark decays is identified using a secondary vertex-finding algorithm. Assuming a top quark mass of 178 GeV/c^2, we measure a cross section of 8.7 +-0.9 (stat) +1.1-0.9 (syst) pb. We also report the first observation of ttbar with significance greater than 5 sigma in the subsample in which both b quarks are identified, corresponding to a cross section of 10.1 +1.6-1.4(stat)+2.0-1.3 (syst) pb.Comment: Accepted for publication in Physics Review Letters, 7 page

Electromagnetic Cell Level Calibration for ATLAS Tile Calorimeter Modules

We have determined the electromagnetic calibration constants of 11% TileCal modules exposed to electron beams with incident angles of 20 and 90 degrees. The gain of all the calorimeter cells have been pre-equalized using the radioactive Cs-source that will be also used in situ. The average values for these modules are equal to: for the flat filter method 1.154+/-0.002 pC/GeV and 1.192+/-0.002 pC/GeV for 20 and 90 degrees, for the fit method 1.040+/-0.002 pC/GeV and 1.068+/-0.003 pC/GeV, respectively. These average values for all cells of calibrated modules agree with the weighted average calibration constants for separate modules within the errors. Using the individual calibration constants for every module the RMS spread value of constants will be 1.9+/-0.1 %. In the case of the global constant this value will be 2.6+/-0.1 %. Finally, we present the global constants which should be used for the electromagnetic calibration of the ATLAS Tile hadronic calorimeter data in the ATHENA framework. These constants are equal to 1.15 pC/GeV in the case of the flat filter method and 1.04 pC/GeV for the fit one