A New Algorithm for Protein Design

We apply a new approach to the reverse protein folding problem. Our method uses a minimization function in the design process which is different from the energy function used for folding. For a lattice model, we show that this new approach produces sequences that are likely to fold into desired structures. Our method is a significant improvement over previous attempts which used the energy function for designing sequences.Comment: 10 pages latex 2.09 no figures. Use uufiles to decod

Molecular Mechanism of DNA Topoisomerase I-Dependent rDNA Silencing: Sir2p Recruitment at Ribosomal Genes

Saccharomyces cerevisiae sir2Δ or top1Δ mutants exhibit similar phenotypes involving ribosomal DNA, including (i) loss of transcriptional silencing, resulting in non-coding RNA hyperproduction from cryptic RNA polymerase II promoters; (ii) alterations in recombination; and (iii) a general increase in histone acetylation. Given the distinct enzymatic activities of Sir2 and Top1 proteins, a histone deacetylase and a DNA topoisomerase, respectively, we investigated whether genetic and/or physical interactions between the two proteins could explain the shared ribosomal RNA genes (rDNA) phenotypes. We employed an approach of complementing top1Δ cells with yeast, human, truncated, and chimeric yeast/human TOP1 constructs and of assessing the extent of non-coding RNA silencing and histone H4K16 deacetylation. Our findings demonstrate that residues 115–125 within the yeast Top1p N-terminal domain are required for the complementation of the top1Δ rDNA phenotypes. In chromatin immunoprecipitation and co-immunoprecipitation experiments, we further demonstrate the physical interaction between Top1p and Sir2p. Our genetic and biochemical studies support a model whereby Top1p recruits Sir2p to the rDNA and clarifies a structural role of DNA topoisomerase I in the epigenetic regulation of rDNA, independent of its known catalytic activity

Soliton-dynamical approach to a noisy Ginzburg-Landau model

We present a dynamical description and analysis of non-equilibrium transitions in the noisy Ginzburg-Landau equation based on a canonical phase space formulation. The transition pathways are characterized by nucleation and subsequent propagation of domain walls or solitons. We also evaluate the Arrhenius factor in terms of an associated action and find good agreement with recent numerical optimization studies.Comment: 4 pages (revtex4), 3 figures (eps

Design of Copolymeric Materials

We devise a method for designing materials that will have some desired structural characteristics. We apply it to multiblock copolymers that have two different types of monomers, A and B. We show how to determine what sequence of A's and B's should be synthesised in order to give a particular structure and morphology. %For example in a melt of such %polymers, one may wish to engineer a body-centered %cubic structure. Using this method in conjunction with the theory of microphase separation developed by Leibler, we show it is possible to efficiently search for a desired morphology. The method is quite general and can be extended to design isolated heteropolymers, such as proteins, with desired structural characteristics. We show that by making certain approximations to the exact algorithm, a method recently proposed by Shakhnovich and Gutin is obtained. The problems with this method are discussed and we propose an improved approximate algorithm that is computationally efficient.Comment: 15 pages latex 2.09 and psfig, 1 postscript figure

Orientation and Alignment Echoes

We present what is probably the simplest classical system featuring the echo phenomenon - a collection of randomly oriented free rotors with dispersed rotational velocities. Following excitation by a pair of time-delayed impulsive kicks, the mean orientation/alignment of the ensemble exhibits multiple echoes and fractional echoes. We elucidate the mechanism of the echo formation by kick-induced filamentation of phase space, and provide the first experimental demonstration of classical alignment echoes in a thermal gas of CO_2 molecules excited by a pair of femtosecond laser pulses

Woodworking facilities: Driving efficiency through Automation applied to major process steps

The investment scenario applied to forestry development analyzes the fundamental changes in the production structure, among other things. These changes refer to the priority development of the pulp and paper industry through the chain of large-scale woodworking facilities, where pulp, paper and cardboard manufacturing plants are the key links. Such facilities include sawmilling facilities, wood-processing factories, and timber factories. Those provide a significant economic benefit, so improving them is one of the top priorities. Considering this priority is the purpose of this article. The goal was achieved using common and scientific research methods, including mathematical modeling. Theoretical research resulted in three sets of formulas adapted for evaluating the pulpwood barking from theoretical findings on image recognition. © 2018 Authors

Soft Fermi Surfaces and Breakdown of Fermi Liquid Behavior

Electron-electron interactions can induce Fermi surface deformations which break the point-group symmetry of the lattice structure of the system. In the vicinity of such a "Pomeranchuk instability" the Fermi surface is easily deformed by anisotropic perturbations, and exhibits enhanced collective fluctuations. We show that critical Fermi surface fluctuations near a d-wave Pomeranchuk instability in two dimensions lead to large anisotropic decay rates for single-particle excitations, which destroy Fermi liquid behavior over the whole surface except at the Brillouin zone diagonal.Comment: 12 pages, 2 figures, revised version as publishe

Method of variational calculation of influence of the propulsion plants of forestry machines upon the frozen and thawing soil grounds

The forests, which grow in the conditions of complete expansion of the perpetually frozen ground, are unique forests in accordance with their taxational characteristics, quality indicators of the felled timber, and the ecological functions, which these forests perform in the nature. They are characterised by the low biological productivity, as well as by the high vulnerability due to climatological changes and human economic activities. It is fair to say that conservation of the permafrost is one of the main functions of the forests, which grow within the cryolithozone. Because of this, it is necessary to ensure special regimes for the forestry management and forest exploitation within the forests of the cryolithozone. We formulated the variational problem in order to determine influence of the changeability of the physical and mechanical properties of the thawing soil ground at the boundary with the permafrost ground. © 2019 SERSC

Secure exchange of information by synchronization of neural networks

A connection between the theory of neural networks and cryptography is presented. A new phenomenon, namely synchronization of neural networks is leading to a new method of exchange of secret messages. Numerical simulations show that two artificial networks being trained by Hebbian learning rule on their mutual outputs develop an antiparallel state of their synaptic weights. The synchronized weights are used to construct an ephemeral key exchange protocol for a secure transmission of secret data. It is shown that an opponent who knows the protocol and all details of any transmission of the data has no chance to decrypt the secret message, since tracking the weights is a hard problem compared to synchronization. The complexity of the generation of the secure channel is linear with the size of the network.Comment: 11 pages, 5 figure