Generalized Fractal Kinetics in Complex Systems (Application to Biophysics and Biothechnology)

We derive a universal function for the kinetics of complex systems. This kinetic function unifies and generalizes previous theoretical attempts to describe what has been called "fractal kinetic".The concentration evolutionary equation is formally similar to the relaxation function obtained in the stochastic theory of relaxation, with two exponents a and n. The first one is due to memory effects and short-range correlations and the second one finds its origin in the long-range correlations and geometrical frustrations which give rise to ageing behavior. These effects can be formally handled by introducing adequate probability distributions for the rate coefficient. We show that the distribution of rate coefficients is the consequence of local variations of the free energy (energy landscape) appearing in the exponent of the Arrhenius formula. We discuss briefly the relation of the (n,a) kinetic formalism with the Tsallis theory of nonextensive systems.Comment: 15 pages, 3 figures, submitted to Physica

Structure of Extremely Nanosized and Confined In-O Species in Ordered Porous Materials

Perturbed-angular correlation, x-ray absorption, and small-angle x-ray scattering spectroscopies were suitably combined to elucidate the local structure of highly diluted and dispersed InOx species confined in porous of ZSM5 zeolite. These novel approach allow us to determined the structure of extremely nanosized In-O species exchanged inside the 10-atom-ring channel of the zeolite, and to quantify the amount of In2O3 crystallites deposited onto the external zeolite surface.Comment: 4 pages, 5 postscript figures, REVTEX4, published in Physical Review Letter

p-Adic description of characteristic relaxation in complex systems

This work is a further development of an approach to the description of relaxation processes in complex systems on the basis of the p-adic analysis. We show that three types of relaxation fitted into the Kohlrausch-Williams-Watts law, the power decay law, or the logarithmic decay law, are similar random processes. Inherently, these processes are ultrametric and are described by the p-adic master equation. The physical meaning of this equation is explained in terms of a random walk constrained by a hierarchical energy landscape. We also discuss relations between the relaxation kinetics and the energy landscapes.Comment: AMS-LaTeX (+iopart style), 9 pages, submitted to J.Phys.

Universal behavior of localization of residue fluctuations in globular proteins

Localization properties of residue fluctuations in globular proteins are studied theoretically by using the Gaussian network model. Participation ratio for each residue fluctuation mode is calculated. It is found that the relationship between participation ratio and frequency is similar for all globular proteins, indicating a universal behavior in spite of their different size, shape, and architecture.Comment: 4 pages, 3 figures. To appear in Phys. Rev.

Protein sequence and structure: Is one more fundamental than the other?

We argue that protein native state structures reside in a novel "phase" of matter which confers on proteins their many amazing characteristics. This phase arises from the common features of all globular proteins and is characterized by a sequence-independent free energy landscape with relatively few low energy minima with funnel-like character. The choice of a sequence that fits well into one of these predetermined structures facilitates rapid and cooperative folding. Our model calculations show that this novel phase facilitates the formation of an efficient route for sequence design starting from random peptides.Comment: 7 pages, 4 figures, to appear in J. Stat. Phy

Efficient Analysis of High Dimensional Data in Tensor Formats

In this article we introduce new methods for the analysis of high dimensional data in tensor formats, where the underling data come from the stochastic elliptic boundary value problem. After discretisation of the deterministic operator as well as the presented random fields via KLE and PCE, the obtained high dimensional operator can be approximated via sums of elementary tensors. This tensors representation can be effectively used for computing different values of interest, such as maximum norm, level sets and cumulative distribution function. The basic concept of the data analysis in high dimensions is discussed on tensors represented in the canonical format, however the approach can be easily used in other tensor formats. As an intermediate step we describe efficient iterative algorithms for computing the characteristic and sign functions as well as pointwise inverse in the canonical tensor format. Since during majority of algebraic operations as well as during iteration steps the representation rank grows up, we use lower-rank approximation and inexact recursive iteration schemes

Recoilless Resonant Absorption of Monochromatic Neutrino Beam for Measuring Delta m^2_{31} and theta_{13}

We discuss, in the context of precision measurement of Delta m^2_{31} and theta_{13}, physics capabilities enabled by the recoilless resonant absorption of monochromatic antineutrino beam enhanced by the M\"ossbauer effect recently proposed by Raghavan. Under the assumption of small relative systematic error of a few tenth of percent level between measurement at different detector locations, we give analytical and numerical estimates of the sensitivities to Delta m^2_{31} and sin^2 2theta_{13}. The accuracies of determination of them are enormous; The fractional uncertainty in Delta m^2_{31} achievable by 10 point measurement is 0.6% (2.4%) for sin^2 2theta_{13} = 0.05, and the uncertainty of sin^2 2theta_{13} is 0.002 (0.008) both at 1 sigma CL with the optimistic (pessimistic) assumption of systematic error of 0.2% (1%). The former opens a new possibility of determining the neutrino mass hierarchy by comparing the measured value of Delta m^2_{31} with the one by accelerator experiments, while the latter will help resolving the theta_{23} octant degeneracy.Comment: 23 pages, 3 figures, version to appear in New Journal of Physic

Quantum dynamics in strong fluctuating fields

A large number of multifaceted quantum transport processes in molecular systems and physical nanosystems can be treated in terms of quantum relaxation processes which couple to one or several fluctuating environments. A thermal equilibrium environment can conveniently be modelled by a thermal bath of harmonic oscillators. An archetype situation provides a two-state dissipative quantum dynamics, commonly known under the label of a spin-boson dynamics. An interesting and nontrivial physical situation emerges, however, when the quantum dynamics evolves far away from thermal equilibrium. This occurs, for example, when a charge transferring medium possesses nonequilibrium degrees of freedom, or when a strong time-dependent control field is applied externally. Accordingly, certain parameters of underlying quantum subsystem acquire stochastic character. Herein, we review the general theoretical framework which is based on the method of projector operators, yielding the quantum master equations for systems that are exposed to strong external fields. This allows one to investigate on a common basis the influence of nonequilibrium fluctuations and periodic electrical fields on quantum transport processes. Most importantly, such strong fluctuating fields induce a whole variety of nonlinear and nonequilibrium phenomena. A characteristic feature of such dynamics is the absence of thermal (quantum) detailed balance.Comment: review article, Advances in Physics (2005), in pres

Homological Mirror Symmetry for Calabi-Yau hypersurfaces in projective space

We prove Homological Mirror Symmetry for a smooth d-dimensional Calabi-Yau hypersurface in projective space, for any d > 2 (for example, d = 3 is the quintic three-fold). The main techniques involved in the proof are: the construction of an immersed Lagrangian sphere in the `d-dimensional pair of pants'; the introduction of the `relative Fukaya category', and an understanding of its grading structure; a description of the behaviour of this category with respect to branched covers (via an `orbifold' Fukaya category); a Morse-Bott model for the relative Fukaya category that allows one to make explicit computations; and the introduction of certain graded categories of matrix factorizations mirror to the relative Fukaya category.Comment: 133 pages, 17 figures. Changes to the argument ruling out sphere bubbling in the relative Fukaya category, and dealing with the behaviour of the symplectic form under branched covers. Other minor changes suggested by the referee. List of notation include

Neuer Kopf, alte Ideen? : "Normalisierung" des Front National unter Marine Le Pen

In this article, it is investigated whether vibrational entropy (VE) is an important contribution to the free energy of globular proteins at ambient conditions. VE represents the major configurational-entropy contribution of these proteins. By definition, it is an average of the configurational entropies of the protein within single minima of the energy landscape, weighted by their occupation probabilities. Its large part originates from thermal motion of flexible torsion angles giving rise to the finite peak widths observed in torsion angle distributions. While VE may affect the equilibrium properties of proteins, it is usually neglected in numerical calculations as its consideration is difficult. Moreover, it is sometimes believed that all well-packed conformations of a globular protein have similar VE anyway. Here, we measure explicitly the VE for six different conformations from simulation data of a test protein. Estimates are obtained using the quasi-harmonic approximation for three coordinate sets, Cartesian, bond-angle-torsion (BAT), and a new set termed rotamer-degeneracy lifted BAT coordinates by us. The new set gives improved estimates as it overcomes a known shortcoming of the quasi-harmonic approximation caused by multiply populated rotamer states, and it may serve for VE estimation of macromolecules in a very general context. The obtained VE values depend considerably on the type of coordinates used. However, for all coordinate sets we find large entropy differences between the conformations, of the order of the overall stability of the protein. This result may have important implications on the choice of free energy expressions used in software for protein structure prediction, protein design, and NMR refinement