533 research outputs found
Coulomb Interactions via Local Dynamics: A Molecular--Dynamics Algorithm
We derive and describe in detail a recently proposed method for obtaining
Coulomb interactions as the potential of mean force between charges which are
dynamically coupled to a local electromagnetic field. We focus on the Molecular
Dynamics version of the method and show that it is intimately related to the
Car--Parrinello approach, while being equivalent to solving Maxwell's equations
with freely adjustable speed of light. Unphysical self--energies arise as a
result of the lattice interpolation of charges, and are corrected by a
subtraction scheme based on the exact lattice Green's function. The method can
be straightforwardly parallelized using standard domain decomposition. Some
preliminary benchmark results are presented.Comment: 8 figure
Simulation of a semiflexible polymer in a narrow cylindrical pore
The probability that a randomly accelerated particle in two dimensions has
not yet left a simply connected domain after a time decays as
for long times. The same quantity also determines the
confinement free energy per unit length of a
semiflexible polymer in a narrow cylindrical pore with cross section . From simulations of a randomly accelerated particle we estimate the
universal amplitude of for both circular and rectangular cross
sections.Comment: 10 pages, 2 eps figure
Spatial Constraint Corrections to the Elasticity of dsDNA Measured with Magnetic Tweezers
In this paper, we have studied, within a discrete WLC model, the spatial
constraints in magnetic tweezers used in single molecule experiments. Two
elements are involved: first, the fixed plastic slab on which is stuck the
initial strand, second, the magnetic bead which pulls (or twists) the attached
molecule free end. We have shown that the bead surface can be replaced by its
tangent plane at the anchoring point, when it is close to the bead south pole
relative to the force. We are led to a model with two parallel repulsive
plates: the fixed anchoring plate and a fluctuating plate, simulating the bead,
in thermal equilibrium with the system. The bead effect is a slight upper shift
of the elongation, about four times smaller than the similar effect induced by
the fixed plate. This rather unexpected result, has been qualitatively
confirmed within the soluble Gaussian model. A study of the molecule elongation
versus the countour length exhibits a significant non-extensive behaviour. The
curve for short molecules (with less than 2 kbp) is well fitted by a straight
line, with a slope given by the WLC model, but it does not go through the
origin. The non-extensive offset gives a 15% upward shift to the elongation of
a 2 kbp molecule stretched by a 0.3 pN force.Comment: 28 pages, 6 figures An explanatory figure has been added. The
physical interpretation of the results has been made somewhat more
transparen
Writhing Photons and Berry Phases in Diffusive Wave Scattering
We study theoretically the polarization state of light in multiple scattering
media in the limit of weak gradients in refractive index. Linearly polarized
photons are randomly rotated due to the Berry phase associated with the
scattering path. For circularly polarized light independent speckle patterns
are found for the two helical states. The statistics of the geometric phase is
related to the writhe distribution of semiflexible polymers such as DNA.Comment: 4 pages, 1 figur
Dynamics and Thermodynamics of Systems with Long Range Interactions: an Introduction
We review theoretical results obtained recently in the framework of
statistical mechanics to study systems with long range forces. This fundamental
and methodological study leads us to consider the different domains of
applications in a trans-disciplinary perspective (astrophysics, nuclear
physics, plasmas physics, metallic clusters, hydrodynamics,...) with a special
emphasis on Bose-Einstein condensates.Comment: Chapter of the forthcoming "Lecture Notes in Physics" volume:
``Dynamics and Thermodynamics of Systems with Long Range Interactions'', T.
Dauxois, S. Ruffo, E. Arimondo, M. Wilkens Eds., Lecture Notes in Physics
Vol. 602, Springer (2002). (see http://link.springer.de/series/lnpp/
Twist and writhe dynamics of stiff filaments
This letter considers the dynamics of a stiff filament, in particular the
coupling of twist and bend via writhe. The time dependence of the writhe of a
filament is for a linear filament and for a curved filament. Simulations are used to study the relative
importance of crankshaft motion and tube like motion in twist dynamics.
Fuller's theorem, and its relation with the Berry phase, is reconsidered for
open filamentsComment: 7 Pages with 2 figure
Entropic Elasticity of Double-Strand DNA Subject to Simple Spatial Constraints
The aim of the present paper is the study of the entropic elasticity of the
dsDNA molecule, having a cristallographic length L of the order of 10 to 30
persistence lengths A, when it is subject to spatial obstructions. We have not
tried to obtain the single molecule partition function by solving a
Schodringer-like equation. We prefer to stay within a discretized version of
the WLC model with an added one-monomer potential, simulating the spatial
constraints. We derived directly from the discretized Boltzmann formula the
transfer matrix connecting the partition functions relative to adjacent
"effective monomers". We have plugged adequate Dirac delta-functions in the
functional integral to ensure that the monomer coordinate and the tangent
vector are independent variables. The partition function is, then, given by an
iterative process which is both numerically efficient and physically
transparent. As a test of our discretized approach, we have studied two
configurations involving a dsDNA molecule confined between a pair of parallel
plates.Comment: The most formal developments of Section I have been moved into an
appendix and replaced by a direct derivation of the transfer matrix used in
the applications. of Section II. Two paragraphs and two figures have been
added to clarify the physical interpretation of the result
Entanglement, elasticity and viscous relaxation of actin solutions
We have investigated the viscosity and the plateau modulus of actin solutions
with a magnetically driven rotating disc rheometer. For entangled solutions we
observed a scaling of the plateau modulus versus concentration with a power of
7/5. The measured terminal relaxation time increases with a power 3/2 as a
function of polymer length. We interpret the entanglement transition and the
scaling of the plateau modulus in terms of the tube model for semiflexible
polymers.Comment: 5 pages, 4 figures, published versio
Whole exome sequencing identifies genetic variants in inherited thrombocytopenia with secondary qualitative function defects
Inherited thrombocytopenias are a heterogeneous group of disorders characterised
by abnormally low platelet counts which can be associated with abnormal bleeding.
Next generation sequencing has previously been employed in these disorders for the
confirmation of suspected genetic abnormalities, and more recently in the discovery
of novel disease causing genes. However its full potential has not previously been
utilised. Over the past 6 years we have sequenced the exomes from 55 patients,
including 37 index cases and 18 additional family members, all of whom were
recruited to the UK Genotyping and Phenotyping of Platelets study. All patients had
inherited or sustained thrombocytopenia of unknown aetiology with platelet counts
varying from 11-186x109
/L. Of the 51 patients phenotypically tested, 37 (73%), had
an additional secondary qualitative platelet defect. Using whole exome sequencing
analysis we have identified “pathogenic” or “likely pathogenic” variants in 46%
(17/37) of our index patients with thrombocytopenia. In addition, we report variants
of uncertain significance in 12 index cases which include novel candidate genetic
variants in previously unreported genes in four index cases. These results
demonstrate that whole exome sequencing is an efficient method for elucidating
potential pathogenic genetic variants in inherited thrombocytopenia. Whole exome
sequencing also has the added benefit of discovering potentially pathogenic genetic
variants for further study in novel genes not previously implicated in inherited
thrombocytopenia
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