2,511 research outputs found
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
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
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
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
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
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
Domain wall propagation and nucleation in a metastable two-level system
We present a dynamical description and analysis of non-equilibrium
transitions in the noisy one-dimensional Ginzburg-Landau equation for an
extensive system based on a weak noise canonical phase space formulation of the
Freidlin-Wentzel or Martin-Siggia-Rose methods. We derive propagating nonlinear
domain wall or soliton solutions of the resulting canonical field equations
with superimposed diffusive modes. The transition pathways are characterized by
the nucleations and subsequent propagation of domain walls. We discuss the
general switching scenario in terms of a dilute gas of propagating domain walls
and evaluate the Arrhenius factor in terms of the associated action. We find
excellent agreement with recent numerical optimization studies.Comment: 28 pages, 16 figures, revtex styl
Magnetic susceptibility, exchange interactions and spin-wave spectra in the local spin density approximation
Starting from exact expression for the dynamical spin susceptibility in the
time-dependent density functional theory a controversial issue about exchange
interaction parameters and spin-wave excitation spectra of itinerant electron
ferromagnets is reconsidered. It is shown that the original expressions for
exchange integrals based on the magnetic force theorem (J. Phys. F14 L125
(1984)) are optimal for the calculations of the magnon spectrum whereas static
response function is better described by the ``renormalized'' magnetic force
theorem by P. Bruno (Phys. Rev. Lett. 90, 087205 (2003)). This conclusion is
confirmed by the {\it ab initio} calculations for Fe and Ni.Comment: 12 pages, 2 figures, submitted to JPC
Self-reported pregnancy exposures and placental DNA methylation in the MARBLES prospective autism sibling study.
Human placenta is a fetal-derived tissue that offers a unique sample of epigenetic and environmental exposures present in utero. In the MARBLES prospective pregnancy study of high-risk younger siblings of children with autism spectrum disorder (ASD), pregnancy and environmental factors collected by maternal interviews were examined as predictors of placental DNA methylation, including partially methylated domains (PMDs), an embryonic feature of the placental methylome. DNA methylation data from MethylC-seq analysis of 47 placentas of children clinically diagnosed at 3 years with ASD or typical development using standardized assessments were examined in relation to: child's gestational age, birth-weight, and diagnosis; maternal pre-pregnancy body mass index, smoking, education, parity, height, prenatal vitamin and folate intake; home ownership; pesticides professionally applied to lawns or gardens or inside homes, pet flea/tick pouches, collars, or soaps/shampoos used in the 3 months prior to or during pregnancy. Sequencing run, order, and coverage, and child race and sex were considered as potential confounders. Akaike information criterion was used to select the most parsimonious among candidate models. Final prediction models used sandwich estimators to produce homoscadisticity-robust estimates of the 95% confidence interval (CI) and P-values controlled the false discovery rate at 5%. The strongest, most robust associations were between pesticides professionally applied outside the home and higher average methylation over PMDs [0.45 (95% CI 0.17, 0.72), P = 0.03] and a reduced proportion of the genome in PMDs [-0.42 (95% CI - 0.67 to -0.17), P = 0.03]. Pesticide exposures could alter placental DNA methylation more than other factors
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