Modeling two-state cooperativity in protein folding

A protein model with the pairwise interaction energies varying as local environment changes, i.e., including some kinds of collective effect between the contacts, is proposed. Lattice Monte Carlo simulations on the thermodynamical characteristics and free energy profile show a well-defined two-state behavior and cooperativity of folding for such a model. As a comparison, related simulations for the usual G\={o} model, where the interaction energies are independent of the local conformations, are also made. Our results indicate that the evolution of interactions during the folding process plays an important role in the two-state cooperativity in protein folding.Comment: 5 figure

A comparative analysis of the value of information in a continuous time market model with partial information: the cases of log-utility and CRRA

We study the question what value an agent in a generalized Black-Scholes model with partial information attributes to the complementary information. To do this, we study the utility maximization problems from terminal wealth for the two cases partial information and full information. We assume that the drift term of the risky asset is a dynamic process of general linear type and that the two levels of observation correspond to whether this drift term is observable or not. Applying methods from stochastic filtering theory we derive an analytical tractable formula for the value of information in the case of logarithmic utility. For the case of constant relative risk aversion (CRRA) we derive a semianalytical formula, which uses as an input the numerical solution of a system of ODEs. For both cases we present a comparative analysis

2D Raman band splitting in graphene: charge screening and lifting of the K-point Kohn anomaly

Pristine graphene encapsulated in hexagonal boron nitride has transport properties rivalling suspended graphene, while being protected from contamination and mechanical damage. For high quality devices, it is important to avoid and monitor accidental doping and charge fluctuations. The 2D Raman double peak in intrinsic graphene can be used to optically determine charge density, with decreasing peak split corresponding to increasing charge density. We find strong correlations between the 2D 1 and 2D 2 split vs 2D line widths, intensities, and peak positions. Charge density fluctuations can be measured with orders of magnitude higher precision than previously accomplished using the G-band shift with charge. The two 2D intrinsic peaks can be associated with the “inner” and “outer” Raman scattering processes, with the counterintuitive assignment of the phonon closer to the K point in the KM direction (outer process) as the higher energy peak. Even low charge screening lifts the phonon Kohn anomaly near the K point for graphene encapsulated in hBN, and shifts the dominant intensity from the lower to the higher energy peak.This work was supported by the United States National Science Foundation (DMR 1411008, DMR 1308659). J.C. thanks the Department of Defence (DoD), Air Force Office of Scientific Research for its support through the National Defence Science and Engineering Graduate (NDSEG) Fellowship, 32 CFR 168a. The authors would like to thank Cory Dean and Carlos Forsythe for the graphene encapsulated hBN sample. (DMR 1411008 - United States National Science Foundation; DMR 1308659 - United States National Science Foundation; 32 CFR 168a - Department of Defence (DoD), Air Force Office of Scientific Research through the National Defence Science and Engineering Graduate (NDSEG) Fellowship

Dynamical coupled-channel study of K* K*bar and omega phi states in a chiral quark model

A dynamical coupled-channel study of K* K*bar state with isospin 0 and omega phi state is performed within both the chiral SU(3) quark model and the extended chiral SU(3) quark model by solving a resonating group method (RGM) equation. The model parameters are taken from our previous work, which gave a satisfactory description of the energies of the octet and decuplet baryon ground states, the binding energy of the deuteron, the nucleon-nucleon (NN) scattering phase shifts, and the hyperon-nucleon (YN) cross sections. The results show that the interactions of K* K*bar states are attractive, which consequently result in K* K*bar bound states with the binding energies of about 10-70 MeV, and contrarily, no omega phi bound state is obtained. The channel coupling effect of K* K*bar and omega phi is found to be considerably large, which makes the binding of K* K*bar 5-45 MeV deeper. The plausible interpretation of f_0(1710) and X(1812) being K* K*bar dominated states is briefly discussed.Comment: 7 pages, 4 figure

Stopping powers and cross sections due to two-photon processes in relativistic nucleus-nucleus collision

The radiation dose received from high energy galactic cosmic rays (GCR) is a limiting factor in the design of long duration space flights and the building of lunar and martian habitats. It is of vital importance to have an accurate understanding of the interactions of GCR in order to assess the radiation environment that the astronauts will be exposed to. Although previous studies have concentrated on the strong interaction process in GCR, there are also very large effects due to electromagnetic (EM) interactions. In this report we describe our first efforts at understanding these EM production processes due to two-photon collisions. More specifically, we shall consider particle production processes in relativistic heavy ion collisions (RHICs) through two-photon exchange

Jastrow-Correlated Wavefunctions for Flat-Band Lattices

The electronic band structure of many compounds, e.g., carbon-based structures, can exhibit essentially no dispersion. Models of electrons in flat-band lattices define non-perturbative strongly correlated problems by default. We construct a set of Jastrow-correlated ansatz wavefunctions to capture the low energy physics of interacting particles in flat bands. We test the ansatz in a simple Coulomb model of spinless electrons in a honeycomb ribbon. We find that the wavefunction accurately captures the ground state in a transition from a crystal to a uniform quantum liquid.Comment: 5 pages, 4 figures, update context, references and publication informatio

A Physical Theory of the Competition that Allows HIV to Escape from the Immune System

Competition within the immune system may degrade immune control of viral infections. We formalize the evolution that occurs in both HIV-1 and the immune system quasispecies. Inclusion of competition in the immune system leads to a novel balance between the immune response and HIV-1, in which the eventual outcome is HIV-1 escape rather than control. The analytical model reproduces the three stages of HIV-1 infection. We propose a vaccine regimen that may be able to reduce competition between T cells, potentially eliminating the third stage of HIV-1.Comment: 5 pages, 2 figures, to appear in Phys. Rev. Let