2,410 research outputs found
Opening of DNA double strands by helicases. Active versus passive opening
Helicase opening of double-stranded nucleic acids may be "active" (the
helicase directly destabilizes the dsNA to promote opening) or "passive" (the
helicase binds ssNA available due to a thermal fluctuation which opens part of
the dsNA). We describe helicase opening of dsNA, based on helicases which bind
single NA strands and move towards the double-stranded region, using a discrete
``hopping'' model. The interaction between the helicase and the junction where
the double strand opens is characterized by an interaction potential. The form
of the potential determines whether the opening is active or passive. We
calculate the rate of passive opening for the helicase PcrA, and show that the
rate increases when the opening is active. Finally, we examine how to choose
the interaction potential to optimize the rate of strand separation. One
important result is our finding that active opening can increase the unwinding
rate by 7 fold compared to passive opening.Comment: 13 pages, 3 figure
Velocity and processivity of helicase unwinding of double-stranded nucleic acids
Helicases are molecular motors which unwind double-stranded nucleic acids
(dsNA) in cells. Many helicases move with directional bias on single-stranded
(ss) nucleic acids, and couple their directional translocation to strand
separation. A model of the coupling between translocation and unwinding uses an
interaction potential to represent passive and active helicase mechanisms. A
passive helicase must wait for thermal fluctuations to open dsNA base pairs
before it can advance and inhibit NA closing. An active helicase directly
destabilizes dsNA base pairs, accelerating the opening rate. Here we extend
this model to include helicase unbinding from the nucleic-acid strand. The
helicase processivity depends on the form of the interaction potential. A
passive helicase has a mean attachment time which does not change between ss
translocation and ds unwinding, while an active helicase in general shows a
decrease in attachment time during unwinding relative to ss translocation. In
addition, we describe how helicase unwinding velocity and processivity vary if
the base-pair binding free energy is changed.Comment: To appear in special issue on molecular motors, Journal of Physics -
Condensed Matte
Error of an arbitrary single-mode Gaussian transformation on a weighted cluster state using a cubic phase gate
In this paper, we propose two strategies for decreasing the error of
arbitrary single-mode Gaussian transformations implemented using one-way
quantum computation on a four-node linear cluster state. We show that it is
possible to minimize the error of the arbitrary single-mode Gaussian
transformation by a proper choice of the weight coefficients of the cluster
state. We modify the computation scheme by adding a non-Gaussian state obtained
using a cubic phase gate as one of the nodes of the cluster. This further
decreases the computation error. We evaluate the efficiencies of the proposed
optimization schemes comparing the probabilities of the error correction of the
quantum computations with and without optimizations. We have shown that for
some transformations, the error probability can be reduced by up to 900 times.Comment: 14 pages, 8 figure
Genetic drift suppresses bacterial conjugation in spatially structured populations
Conjugation is the primary mechanism of horizontal gene transfer that spreads
antibiotic resistance among bacteria. Although conjugation normally occurs in
surface-associated growth (e.g., biofilms), it has been traditionally studied
in well-mixed liquid cultures lacking spatial structure, which is known to
affect many evolutionary and ecological processes. Here we visualize spatial
patterns of gene transfer mediated by F plasmid conjugation in a colony of
Escherichia coli growing on solid agar, and we develop a quantitative
understanding by spatial extension of traditional mass-action models. We found
that spatial structure suppresses conjugation in surface-associated growth
because strong genetic drift leads to spatial isolation of donor and recipient
cells, restricting conjugation to rare boundaries between donor and recipient
strains. These results suggest that ecological strategies, such as enforcement
of spatial structure and enhancement of genetic drift, could complement
molecular strategies in slowing the spread of antibiotic resistance genes
Guided random walk calculation of energies and <\sq {r^2} > values of the state of H_2 in a magnetic field
Energies and spatial observables for the state of the hydrogen
molecule in magnetic fields parallel to the proton-proton axis are calculated
with a guided random walk Feynman-Kac algorithm. We demonstrate that the
accuracy of the results and the simplicity of the method may prove it a viable
alternative to large basis set expansions for small molecules in applied
fields.Comment: 10 pages, no figure
Competing anisotropy in the (TmxPr1-x)2Fe17 system
The magnetization curves of magnetically aligned finely powdered samples of the (TmxPr1-x)2Fe17 compounds have been measured at 4 K. The easy magnetization axis is oriented in the basal plane or along the hexagonal axis for the compounds with x = 0-0.3 and 0.7-1, respectively. This is because of the absence of magnetic ordering in the Tm and Pr subsystems in these ranges, respectively, and because of competing anisotropy of the subsystems. For the compositions with x = 0.4-0.6, both rare-earth subsystems are magnetically ordered and the easy magnetization axis is oriented between the basal plane and the hexagonal axis. The critical fields of FOMPs decrease quickly as the Pr or Tm content decreases in the ranges 0-0.3 and 0.7-1, respectively. The magnetization anisotropy also diminishes as the Tm content becomes smaller than x = 0.7. No influence of the intrinsic microdeformations on the magnetization of the compounds was detected. © 2018 The Authors, published by EDP Sciences
Unconventional magnetism of non-uniform distribution of Co in TiO2 nanoparticles
High-resolution transmission electron microscopy (HRTEM), X-ray diffraction (XRD) analysis, electron paramagnetic resonance (EPR), X-ray absorption spectroscopy (XAS), magnetic methods, and density-functional theory (DFT) calculations were applied for the investigations of Co-doped anatase TiO2 nanoparticles (∼20 nm). It was found that high-spin Co2+ ions prefer to occupy the interstitial positions in the TiO2 lattice which are the most energetically favourable in compare to the substitutional those. A quantum mechanical model which operates mainly on two types of Co2+ – Co2+ dimers with different negative exchange interactions and the non-interacting paramagnetic Co2+ ions provides a satisfactorily description of magnetic properties for the TiO2:Co system. © 2020 Elsevier B.V.Russian Foundation for Basic Research. Ministry of Science and Higher Education of the Russian Federatio
Femtosecond photonic viral inactivation probed using solid-state nanopores
We report on detection of virus inactivation using femtosecond laser radiation by measuring the
conductance of a solid state nanopore designed for detecting single particles. Conventional methods
of assaying for viral inactivation based on plaque forming assays require 24–48 h for bacterial growth.
Nanopore conductance measurements provide information on morphological changes at a single
virion level.We show that analysis of a time series of nanopore conductance can quantify the detection
of inactivation, requiring only a few minutes from collection to analysis. Morphological changes were
verified by dynamic light scattering. Statistical analysis maximizing the information entropy provides
a measure of the log reduction value. This work provides a rapid method for assaying viral inactivation
with femtosecond lasers using solid-state nanopores.First author draf
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