A semi-empirical method for prediction of antigenic determinants on protein antigens

AbstractAnalysis of data from experimentally determined antigenic sites on proteins has revealed that the hydrophobic residues Cys, Leu and Val, if they occur on the surface of a protein, are more likely to be a part of antigenic sites. A semi-empirical method which makes use of physicochemical properties of amino acid residues and their frequencies of occurrence in experimentally known segmental epitopes was developed to predict antigenic determinants on proteins. Application of this method to a large number of proteins has shown that our method can predict antigenic determinants with about 75% accuracy which is better than most of the known methods. This method is based on a single parameter and thus very simple to use

Characteristic distributions of finite-time Lyapunov exponents

We study the probability densities of finite-time or \local Lyapunov exponents (LLEs) in low-dimensional chaotic systems. While the multifractal formalism describes how these densities behave in the asymptotic or long-time limit, there are significant finite-size corrections which are coordinate dependent. Depending on the nature of the dynamical state, the distribution of local Lyapunov exponents has a characteristic shape. For intermittent dynamics, and at crises, dynamical correlations lead to distributions with stretched exponential tails, while for fully-developed chaos the probability density has a cusp. Exact results are presented for the logistic map, $x \to 4x(1-x)$. At intermittency the density is markedly asymmetric, while for `typical' chaos, it is known that the central limit theorem obtains and a Gaussian density results. Local analysis provides information on the variation of predictability on dynamical attractors. These densities, which are used to characterize the {\sl nonuniform} spatial organization on chaotic attractors are robust to noise and can therefore be measured from experimental data.Comment: To be appear in Phys. Rev

A thermodynamic framework to develop rate-type models for fluids without instantaneous elasticity

In this paper, we apply the thermodynamic framework recently put into place by Rajagopal and co-workers, to develop rate-type models for viscoelastic fluids which do not possess instantaneous elasticity. To illustrate the capabilities of such models we make a specific choice for the specific Helmholtz potential and the rate of dissipation and consider the creep and stress relaxation response associated with the model. Given specific forms for the Helmholtz potential and the rate of dissipation, the rate of dissipation is maximized with the constraint that the difference between the stress power and the rate of change of Helmholtz potential is equal to the rate of dissipation and any other constraint that may be applicable such as incompressibility. We show that the model that is developed exhibits fluid-like characteristics and is incapable of instantaneous elastic response. It also includes Maxwell-like and Kelvin-Voigt-like viscoelastic materials (when certain material moduli take special values).Comment: 18 pages, 5 figure

Interruption of torus doubling bifurcation and genesis of strange nonchaotic attractors in a quasiperiodically forced map : Mechanisms and their characterizations

A simple quasiperiodically forced one-dimensional cubic map is shown to exhibit very many types of routes to chaos via strange nonchaotic attractors (SNAs) with reference to a two-parameter $(A-f)$ space. The routes include transitions to chaos via SNAs from both one frequency torus and period doubled torus. In the former case, we identify the fractalization and type I intermittency routes. In the latter case, we point out that atleast four distinct routes through which the truncation of torus doubling bifurcation and the birth of SNAs take place in this model. In particular, the formation of SNAs through Heagy-Hammel, fractalization and type--III intermittent mechanisms are described. In addition, it has been found that in this system there are some regions in the parameter space where a novel dynamics involving a sudden expansion of the attractor which tames the growth of period-doubling bifurcation takes place, giving birth to SNA. The SNAs created through different mechanisms are characterized by the behaviour of the Lyapunov exponents and their variance, by the estimation of phase sensitivity exponent as well as through the distribution of finite-time Lyapunov exponents.Comment: 27 pages, RevTeX 4, 16 EPS figures. Phys. Rev. E (2001) to appea

Multicloud solutions with massless and massive monopoles

Certain spontaneously broken gauge theories contain massless magnetic monopoles. These are realized classically as clouds of non-Abelian fields surrounding one or more massive monopoles. In order to gain a better understanding of these clouds, we study BPS solutions with four massive and six massless monopoles in an SU(6) gauge theory. We develop an algebraic procedure, based on the Nahm construction, that relates these solutions to previously known examples. Explicit implementation of this procedure for a number of limiting cases reveals that the six massless monopoles condense into four distinct clouds, of two different types. By analyzing these limiting solutions, we clarify the correspondence between clouds and massless monopoles, and infer a set of rules that describe the conditions under which a finite size cloud can be formed. Finally, we identify the parameters entering the general solution and describe their physical significance.Comment: 58 pages, 5 figure

Non-Abelian Vortices in Supersymmetric Gauge Field Theory via Direct Methods

Vortices in supersymmetric gauge field theory are important constructs in a basic conceptual phenomenon commonly referred to as the dual Meissner effect which is responsible for color confinement. Based on a direct minimization approach, we present a series of sharp existence and uniqueness theorems for the solutions of some non-Abelian vortex equations governing color-charged multiply distributed flux tubes, which provide an essential mechanism for linear confinement. Over a doubly periodic domain, existence results are obtained under explicitly stated necessary and sufficient conditions that relate the size of the domain, the vortex numbers, and the underlying physical coupling parameters of the models. Over the full plane, existence results are valid for arbitrary vortex numbers and coupling parameters. In all cases, solutions are unique.Comment: 38 pages, late

Prevalence and risk of hepatitis e virus infection in the HIV population of Nepal

Background: Infection with the hepatitis E virus (HEV) can cause acute hepatitis in endemic areas in immune-competent hosts, as well as chronic infection in immune-compromised subjects in non-endemic areas. Most studies assessing HEV infection in HIV-infected populations have been performed in developed countries that are usually affected by HEV genotype 3. The objective of this study is to measure the prevalence and risk of acquiring HEV among HIV-infected individuals in Nepal. Methods: We prospectively evaluated 459 Human Immunodeficiency Virus (HIV)-positive individuals from Nepal, an endemic country for HEV, for seroprevalence of HEV and assessed risk factors associated with HEV infection. All individuals were on antiretroviral therapy and healthy blood donors were used as controls. Results: We found a high prevalence of HEV IgG (39.4%) and HEV IgM (15.3%) in HIV-positive subjects when compared to healthy HIV-negative controls: 9.5% and 4.4%, respectively (OR: 6.17, 95% CI 4.42-8.61, p < 0.001 and OR: 3.7, 95% CI 2.35-5.92, p < 0.001, respectively). Individuals residing in the Kathmandu area showed a significantly higher HEV IgG seroprevalance compared to individuals residing outside of Kathmandu (76.8% vs 11.1%, OR: 30.33, 95% CI 18.02-51.04, p = 0.001). Mean CD4 counts, HIV viral load and presence of hepatitis B surface antigen correlated with higher HEV IgM rate, while presence of hepatitis C antibody correlated with higher rate of HEV IgG in serum. Overall, individuals with HEV IgM positivity had higher levels of alanine aminotransferase (ALT) than IgM negative subjects, suggesting active acute infection. However, no specific symptoms for hepatitis were identified. Conclusions: HIV-positive subjects living in Kathmandu are at higher risk of acquiring HEV infection as compared to the general population and to HIV-positive subjects living outside Kathmandu

Multiorder coherent Raman scattering of a quantum probe field

We study the multiorder coherent Raman scattering of a quantum probe field in a far-off-resonance medium with a prepared coherence. Under the conditions of negligible dispersion and limited bandwidth, we derive a Bessel-function solution for the sideband field operators. We analytically and numerically calculate various quantum statistical characteristics of the sideband fields. We show that the multiorder coherent Raman process can replicate the statistical properties of a single-mode quantum probe field into a broad comb of generated Raman sidebands. We also study the mixing and modulation of photon statistical properties in the case of two-mode input. We show that the prepared Raman coherence and the medium length can be used as control parameters to switch a sideband field from one type of photon statistics to another type, or from a non-squeezed state to a squeezed state and vice versa.Comment: 12 pages, 7 figures, to be published in Phys. Rev.