332 research outputs found
Radial Distribution Function for Semiflexible Polymers Confined in Microchannels
An analytic expression is derived for the distribution of the
end-to-end distance of semiflexible polymers in external potentials
to elucidate the effect of confinement on the mechanical and statistical
properties of biomolecules. For parabolic confinement the result is exact
whereas for realistic potentials a self-consistent ansatz is developed, so that
is given explicitly even for hard wall confinement. The
theoretical result is in excellent quantitative agreement with fluorescence
microscopy data for actin filaments confined in rectangularly shaped
microchannels. This allows an unambiguous determination of persistence length
and the dependence of statistical properties such as Odijk's deflection
length on the channel width . It is shown that neglecting the
effect of confinement leads to a significant overestimation of bending
rigidities for filaments
Investigating the effects of laser beams (532 and 660 nm) in annihilation of pistachio mould fungus using spectrophotometry analysis
When moulds are illuminated by visible electromagnetic-EM radiations, several effects on nucleus materials and nucleotides can be detected. These effects have a significant influence on mould generation or destruction. This paper presents the effects and implications of a red diode laser beam (660 nm), a second-harmonics of a Nd:YAG laser emitting green beam (532 nm), or the combination of both, on the eradication of Pistachio mould fungus. Incident doses (ID) of both beams are kept identical throughout the experiment. The absorption spectrums of irradiated mouldy samples and the bright-greenish-yellow-fluorescence (BGYF) of fungus occurring in mould texture due to electronic excitation are investigated. We found that a combination of a green and a red laser beam with an ID of 0.5 J/cm^2 provides the optimal effects on Pistachio mould fungus eradication
Radial distribution function of semiflexible polymers
We calculate the distribution function of the end--to--end distance of a
semiflexible polymer with large bending rigidity. This quantity is directly
observable in experiments on single semiflexible polymers (e.g., DNA, actin)
and relevant to their interpretation. It is also an important starting point
for analyzing the behavior of more complex systems such as networks and
solutions of semiflexible polymers. To estimate the validity of the obtained
analytical expressions, we also determine the distribution function numerically
using Monte Carlo simulation and find good quantitative agreement.Comment: RevTeX, 4 pages, 1 figure. Also available at
http://www.cip.physik.tu-muenchen.de/tumphy/d/T34/Mitarbeiter/frey.htm
New results for virial coefficients of hard spheres in D dimensions
We present new results for the virial coefficients B_k with k <= 10 for hard
spheres in dimensions D=2,...,8.Comment: 10 pages, 5 figures, to appear in conference proceedings of STATPHYS
2004 in Pramana - Journal of Physic
Intrinsic profiles and capillary waves at homopolymer interfaces: a Monte Carlo study
A popular concept which describes the structure of polymer interfaces by
``intrinsic profiles'' centered around a two dimensional surface, the ``local
interface position'', is tested by extensive Monte Carlo simulations of
interfaces between demixed homopolymer phases in symmetric binary (AB)
homopolymer blends, using the bond fluctuation model. The simulations are done
in an LxLxD geometry. The interface is forced to run parallel to the LxL planes
by imposing periodic boundary conditions in these directions and fixed boundary
conditions in the D direction, with one side favoring A and the other side
favoring B. Intrinsic profiles are calculated as a function of the ``coarse
graining length'' B by splitting the system into columns of size BxBxD and
averaging in each column over profiles relative to the local interface
position. The results are compared to predictions of the self-consistent field
theory. It is shown that the coarse graining length can be chosen such that the
interfacial width matches that of the self-consistent field profiles, and that
for this choice of B the ``intrinsic'' profiles compare well with the
theoretical predictions.Comment: to appear in Phys. Rev.
Chromatin: a tunable spring at work inside chromosomes
This paper focuses on mechanical aspects of chromatin biological functioning.
Within a basic geometric modeling of the chromatin assembly, we give for the
first time the complete set of elastic constants (twist and bend persistence
lengths, stretch modulus and twist-stretch coupling constant) of the so-called
30-nm chromatin fiber, in terms of DNA elastic properties and geometric
properties of the fiber assembly. The computation naturally embeds the fiber
within a current analytical model known as the ``extensible worm-like rope'',
allowing a straightforward prediction of the force-extension curves. We show
that these elastic constants are strongly sensitive to the linker length, up to
1 bp, or equivalently to its twist, and might locally reach very low values,
yielding a highly flexible and extensible domain in the fiber. In particular,
the twist-stretch coupling constant, reflecting the chirality of the chromatin
fiber, exhibits steep variations and sign changes when the linker length is
varied.
We argue that this tunable elasticity might be a key feature for chromatin
function, for instance in the initiation and regulation of transcription.Comment: 38 pages 15 figure
Conformational transitions of heteropolymers in dilute solutions
In this paper we extend the Gaussian self-consistent method to permit study
of the equilibrium and kinetics of conformational transitions for
heteropolymers with any given primary sequence. The kinetic equations earlier
derived by us are transformed to a form containing only the mean squared
distances between pairs of monomers. These equations are further expressed in
terms of instantaneous gradients of the variational free energy. The method
allowed us to study exhaustively the stability and conformational structure of
some periodic and random aperiodic sequences. A typical phase diagram of a
fairly long amphiphilic heteropolymer chain is found to contain phases of the
extended coil, the homogeneous globule, the micro-phase separated globule, and
a large number of frustrated states, which result in conformational phases of
the random coil and the frozen globule. We have also found that for a certain
class of sequences the frustrated phases are suppressed. The kinetics of
folding from the extended coil to the globule proceeds through non-equilibrium
states possessing locally compacted, but partially misfolded and frustrated,
structure. This results in a rather complicated multistep kinetic process
typical of glassy systems.Comment: 15 pages, RevTeX, 20 ps figures, accepted for publication in Phys.
Rev.
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