398 research outputs found
Quantum point contact due to Fermi-level pinning and doping profiles in semiconductor nanocolumns
We show that nanoscale doping profiles inside a nanocolumn in combination
with Fermi-level pinning at the surface give rise to the formation of a
saddle-point in the potential profile. Consequently, the lateral confinement
inside the channel varies along the transport direction, yielding an embedded
quantum point contact. An analytical estimation of the quantization energies
will be given
Anomalous self-diffusion in the ferromagnetic Ising chain with Kawasaki dynamics
We investigate the motion of a tagged spin in a ferromagnetic Ising chain
evolving under Kawasaki dynamics. At equilibrium, the displacement is Gaussian,
with a variance growing as . The temperature dependence of the
prefactor is derived exactly. At low temperature, where the static
correlation length is large, the mean square displacement grows as
in the coarsening regime, i.e., as a finite fraction of the
mean square domain length. The case of totally asymmetric dynamics, where
(resp. ) spins move only to the right (resp. to the left), is also
considered. In the steady state, the displacement variance grows as . The temperature dependence of the prefactor is derived exactly,
using the Kardar-Parisi-Zhang theory. At low temperature, the displacement
variance grows as in the coarsening regime, again proportionally to
the mean square domain length.Comment: 22 pages, 8 figures. A few minor changes and update
Glauber dynamics in a single-chain magnet: From theory to real systems
The Glauber dynamics is studied in a single-chain magnet. As predicted, a
single relaxation mode of the magnetization is found. Above 2.7 K, the
thermally activated relaxation time is mainly governed by the effect of
magnetic correlations and the energy barrier experienced by each magnetic unit.
This result is in perfect agreement with independent thermodynamical
measurements. Below 2.7 K, a crossover towards a relaxation regime is observed
that is interpreted as the manifestation of finite-size effects. The
temperature dependences of the relaxation time and of the magnetic
susceptibility reveal the importance of the boundary conditions.Comment: Submitted to PRL 10 May 2003. Submitted to PRB 12 December 2003;
published 15 April 200
Nyquist method for Wigner-Poisson quantum plasmas
By means of the Nyquist method, we investigate the linear stability of
electrostatic waves in homogeneous equilibria of quantum plasmas described by
the Wigner-Poisson system. We show that, unlike the classical Vlasov-Poisson
system, the Wigner-Poisson case does not necessarily possess a Penrose
functional determining its linear stability properties. The Nyquist method is
then applied to a two-stream distribution, for which we obtain an exact,
necessary and sufficient condition for linear stability, as well as to a
bump-in-tail equilibrium.Comment: 6 figure
Delocalization of states in two component superlattices with correlated disorder
Electron and phonon states in two different models of intentionally
disordered superlattices are studied analytically as well as numerically. The
localization length is calculated exactly and we found that it diverges for
particular energies or frequencies, suggesting the existence of delocalized
states for both electrons and phonons. Numerical calculations for the
transmission coefficient support the existence of these delocalized states.Comment: RevTeX, 12 pages, 2 PS figures adde
Patterns of subnet usage reveal distinct scales of regulation in the transcriptional regulatory network of Escherichia coli
The set of regulatory interactions between genes, mediated by transcription
factors, forms a species' transcriptional regulatory network (TRN). By
comparing this network with measured gene expression data one can identify
functional properties of the TRN and gain general insight into transcriptional
control. We define the subnet of a node as the subgraph consisting of all nodes
topologically downstream of the node, including itself. Using a large set of
microarray expression data of the bacterium Escherichia coli, we find that the
gene expression in different subnets exhibits a structured pattern in response
to environmental changes and genotypic mutation. Subnets with less changes in
their expression pattern have a higher fraction of feed-forward loop motifs and
a lower fraction of small RNA targets within them. Our study implies that the
TRN consists of several scales of regulatory organization: 1) subnets with more
varying gene expression controlled by both transcription factors and
post-transcriptional RNA regulation, and 2) subnets with less varying gene
expression having more feed-forward loops and less post-transcriptional RNA
regulation.Comment: 14 pages, 8 figures, to be published in PLoS Computational Biolog
From Nonspecific DNA–Protein Encounter Complexes to the Prediction of DNA–Protein Interactions
©2009 Gao, Skolnick. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.doi:10.1371/journal.pcbi.1000341DNA–protein interactions are involved in many essential biological activities. Because there is no simple mapping code between DNA base pairs and protein amino acids, the prediction of DNA–protein interactions is a challenging problem. Here, we present a novel computational approach for predicting DNA-binding protein residues and DNA–protein interaction modes without knowing its specific DNA target sequence. Given the structure of a DNA-binding protein, the method first generates an ensemble of complex structures obtained by rigid-body docking with a nonspecific canonical B-DNA. Representative models are subsequently selected through clustering and ranking by their DNA–protein interfacial energy. Analysis of these encounter complex models suggests that the recognition sites for specific DNA binding are usually favorable interaction sites for the nonspecific DNA probe and that nonspecific DNA–protein interaction modes exhibit some similarity to specific DNA–protein binding modes. Although the method requires as input the knowledge that the protein binds DNA, in benchmark tests, it achieves better performance in identifying DNA-binding sites than three previously established methods, which are based on sophisticated machine-learning techniques. We further apply our method to protein structures predicted through modeling and demonstrate that our method performs satisfactorily on protein models whose root-mean-square Ca deviation from native is up to 5 Å from their native structures. This study provides valuable structural insights into how a specific DNA-binding protein interacts with a nonspecific DNA sequence. The similarity between the specific DNA–protein interaction mode and nonspecific interaction modes may reflect an important sampling step in search of its specific DNA targets by a DNA-binding protein
A self-organized model for cell-differentiation based on variations of molecular decay rates
Systemic properties of living cells are the result of molecular dynamics
governed by so-called genetic regulatory networks (GRN). These networks capture
all possible features of cells and are responsible for the immense levels of
adaptation characteristic to living systems. At any point in time only small
subsets of these networks are active. Any active subset of the GRN leads to the
expression of particular sets of molecules (expression modes). The subsets of
active networks change over time, leading to the observed complex dynamics of
expression patterns. Understanding of this dynamics becomes increasingly
important in systems biology and medicine. While the importance of
transcription rates and catalytic interactions has been widely recognized in
modeling genetic regulatory systems, the understanding of the role of
degradation of biochemical agents (mRNA, protein) in regulatory dynamics
remains limited. Recent experimental data suggests that there exists a
functional relation between mRNA and protein decay rates and expression modes.
In this paper we propose a model for the dynamics of successions of sequences
of active subnetworks of the GRN. The model is able to reproduce key
characteristics of molecular dynamics, including homeostasis, multi-stability,
periodic dynamics, alternating activity, differentiability, and self-organized
critical dynamics. Moreover the model allows to naturally understand the
mechanism behind the relation between decay rates and expression modes. The
model explains recent experimental observations that decay-rates (or turnovers)
vary between differentiated tissue-classes at a general systemic level and
highlights the role of intracellular decay rate control mechanisms in cell
differentiation.Comment: 16 pages, 5 figure
A comparison of sunlight exposure in men with prostate cancer and basal cell carcinoma
Ultraviolet radiation exposure increases basal cell carcinoma (BCC) risk, but may be protective against prostate cancer. We attempted to identify exposure patterns that confer reduced prostate cancer risk without increasing that of BCC. We used a questionnaire to assess exposure in 528 prostate cancer patients and 442 men with basal cell carcinoma, using 365 benign prostatic hypertrophy patients as controls. Skin type 1 (odds ratio (OR)=0.47, 95% CI=0.26–0.86), childhood sunburning (OR=0.38, 95% CI=0.26–0.57), occasional/frequent sunbathing (OR=0.21, 95% CI=0.14–0.31), lifetime weekday (OR=0.85, 95% CI=0.80–0.91) and weekend exposure (OR=0.79, 95% CI=0.73–0.86) were associated with reduced prostate cancer risk. Skin type 1 (OR=4.00, 95% CI=2.16–7.41), childhood sunburning (OR=1.91, 95% CI=1.36–2.68), regular foreign holidays (OR=6.91, 95% CI=5.00-9.55) and weekend (OR=1.17, 95% CI=1.08–1.27) but not weekday exposure were linked with increased BCC risk. Combinations of one or two parameters were associated with a progressive decrease in the ORs for prostate cancer risk (OR=0.54–0.25) with correspondingly increased BCC risk (OR=1.60–2.54). Our data do not define exposure patterns that reduce prostate cancer risk without increasing BCC risk
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