1,121 research outputs found
Casting Polymer Nets to Optimize Noisy Molecular Codes
Life relies on the efficient performance of molecular codes, which relate
symbols and meanings via error-prone molecular recognition. We describe how
optimizing a code to withstand the impact of molecular recognition noise may be
approximated by the statistics of a two-dimensional network made of polymers.
The noisy code is defined by partitioning the space of symbols into regions
according to their meanings. The "polymers" are the boundaries between these
regions and their statistics defines the cost and the quality of the noisy
code. When the parameters that control the cost-quality balance are varied, the
polymer network undergoes a first-order transition, where the number of encoded
meanings rises discontinuously. Effects of population dynamics on the evolution
of molecular codes are discussed.Comment: PNAS 200
Remarks on Bootstrap Percolation in Metric Networks
We examine bootstrap percolation in d-dimensional, directed metric graphs in
the context of recent measurements of firing dynamics in 2D neuronal cultures.
There are two regimes, depending on the graph size N. Large metric graphs are
ignited by the occurrence of critical nuclei, which initially occupy an
infinitesimal fraction, f_* -> 0, of the graph and then explode throughout a
finite fraction. Smaller metric graphs are effectively random in the sense that
their ignition requires the initial ignition of a finite, unlocalized fraction
of the graph, f_* >0. The crossover between the two regimes is at a size N_*
which scales exponentially with the connectivity range \lambda like_* \sim
\exp\lambda^d. The neuronal cultures are finite metric graphs of size N \simeq
10^5-10^6, which, for the parameters of the experiment, is effectively random
since N<< N_*. This explains the seeming contradiction in the observed finite
f_* in these cultures. Finally, we discuss the dynamics of the firing front
Protein-DNA computation by stochastic assembly cascade
The assembly of RecA on single-stranded DNA is measured and interpreted as a
stochastic finite-state machine that is able to discriminate fine differences
between sequences, a basic computational operation. RecA filaments efficiently
scan DNA sequence through a cascade of random nucleation and disassembly events
that is mechanistically similar to the dynamic instability of microtubules.
This iterative cascade is a multistage kinetic proofreading process that
amplifies minute differences, even a single base change. Our measurements
suggest that this stochastic Turing-like machine can compute certain integral
transforms.Comment: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC129313/
http://www.pnas.org/content/99/18/11589.abstrac
Molecular Model of the Contractile Ring
We present a model for the actin contractile ring of adherent animal cells.
The model suggests that the actin concentration within the ring and
consequently the power that the ring exerts both increase during contraction.
We demonstrate the crucial role of actin polymerization and depolymerization
throughout cytokinesis, and the dominance of viscous dissipation in the
dynamics. The physical origin of two phases in cytokinesis dynamics ("biphasic
cytokinesis") follows from a limitation on the actin density. The model is
consistent with a wide range of measurements of the midzone of dividing animal
cells.Comment: PACS numbers: 87.16.Ka, 87.16.Ac
http://www.ncbi.nlm.nih.gov/pubmed/16197254
http://www.weizmann.ac.il/complex/tlusty/papers/PhysRevLett2005.pd
Thermodynamics and structure of self-assembled networks
We study a generic model of self-assembling chains which can branch and form
networks with branching points (junctions) of arbitrary functionality. The
physical realizations include physical gels, wormlike micells, dipolar fluids
and microemulsions. The model maps the partition function of a solution of
branched, self-assembling, mutually avoiding clusters onto that of a Heisenberg
magnet in the mathematical limit of zero spin components. The model is solved
in the mean field approximation. It is found that despite the absence of any
specific interaction between the chains, the entropy of the junctions induces
an effective attraction between the monomers, which in the case of three-fold
junctions leads to a first order reentrant phase separation between a dilute
phase consisting mainly of single chains, and a dense network, or two network
phases. Independent of the phase separation, we predict the percolation
(connectivity) transition at which an infinite network is formed that partially
overlaps with the first-order transition. The percolation transition is a
continuous, non thermodynamic transition that describes a change in the
topology of the system. Our treatment which predicts both the thermodynamic
phase equilibria as well as the spatial correlations in the system allows us to
treat both the phase separation and the percolation threshold within the same
framework. The density-density correlation correlation has a usual
Ornstein-Zernicke form at low monomer densities. At higher densities, a peak
emerges in the structure factor, signifying an onset of medium-range order in
the system. Implications of the results for different physical systems are
discussed.Comment: Submitted to Phys. Rev.
Phonons in a one-dimensional microfluidic crystal
The development of a general theoretical framework for describing the
behaviour of a crystal driven far from equilibrium has proved difficult1.
Microfluidic crystals, formed by the introduction of droplets of immiscible
fluid into a liquid-filled channel, provide a convenient means to explore and
develop models to describe non-equilibrium dynamics2, 3, 4, 5, 6, 7, 8, 9, 10,
11. Owing to the fact that these systems operate at low Reynolds number (Re),
in which viscous dissipation of energy dominates inertial effects, vibrations
are expected to be over-damped and contribute little to their dynamics12, 13,
14. Against such expectations, we report the emergence of collective normal
vibrational modes (equivalent to acoustic 'phonons') in a one-dimensional
microfluidic crystal of water-in-oil droplets at Reapprox10-4. These phonons
propagate at an ultra-low sound velocity of approx100 mum s-1 and frequencies
of a few hertz, exhibit unusual dispersion relations markedly different to
those of harmonic crystals, and give rise to a variety of crystal instabilities
that could have implications for the design of commercial microfluidic systems.
First-principles theory shows that these phonons are an outcome of the
symmetry-breaking flow field that induces long-range inter-droplet
interactions, similar in nature to those observed in many other systems
including dusty plasma crystals15, 16, vortices in superconductors17, 18,
active membranes19 and nucleoprotein filaments20.Comment: https://www.weizmann.ac.il/complex/tlusty/papers/NaturePhys2006.pd
On the stability of high-speed milling with spindle speed variation
Spindle speed variation is a well-known technique to suppress regenerative machine tool vibrations, but it is usually considered to be effective only for low spindle speeds. In this paper, the effect of spindle speed variation is analyzed in the high-speed domain for spindle speeds corresponding to the first flip (period doubling) and to the first Hopf lobes. The optimal amplitudes and frequencies of the speed modulations are computed using the semidiscre- tization method. It is shown that period doubling chatter can effectively be suppressed by spindle speed variation, although, the technique is not effective for the quasiperiodic chatter above the Hopf lobe. The results are verified by cutting tests. Some special cases are also discussed where the practical behavior of the system differs from the predicted one in some ways. For these cases, it is pointed out that the concept of stability is understood on the scale of the principal period of the system—that is, the speed modulation period for variable spindle speed machining and the tooth passing period for constant spindle speed machining
Model and parameter dependence of heavy quark energy loss in a hot and dense medium
Within the framework of the Langevin equation, we study the energy loss of
heavy quark due to quasi-elastic multiple scatterings in a quark-gluon plasma
created by relativistic heavy-ion collisions. We investigate how the initial
configuration of the quark-gluon plasma as well as its properties affect the
final state spectra and elliptic flow of D meson and non-photonic electron. We
find that both the geometric anisotropy of the initial quark-gluon plasma and
the flow profiles of the hydrodynamic medium play important roles in the heavy
quark energy loss process and the development of elliptic flow. The relative
contribution from charm and bottom quarks is found to affect the transverse
momentum dependence of the quenching and flow patterns of heavy flavor decay
electron; such influence depends on the interaction strength between heavy
quark and the medium.Comment: 16 pages, 7 figure
Electromagnetic Calorimeter for HADES
We propose to build the Electromagnetic calorimeter for the HADES di-lepton
spectrometer. It will enable to measure the data on neutral meson production
from nucleus-nucleus collisions, which are essential for interpretation of
dilepton data, but are unknown in the energy range of planned experiments (2-10
GeV per nucleon). The calorimeter will improve the electron-hadron separation,
and will be used for detection of photons from strange resonances in elementary
and HI reactions.
Detailed description of the detector layout, the support structure, the
electronic readout and its performance studied via Monte Carlo simulations and
series of dedicated test experiments is presented.
The device will cover the total area of about 8 m^2 at polar angles between
12 and 45 degrees with almost full azimuthal coverage. The photon and electron
energy resolution achieved in test experiments amounts to 5-6%/sqrt(E[GeV])
which is sufficient for the eta meson reconstruction with S/B ratio of 0.4% in
Ni+Ni collisions at 8 AGeV. A purity of the identified leptons after the hadron
rejection, resulting from simulations based on the test measurements, is better
than 80% at momenta above 500 MeV/c, where time-of-flight cannot be used.Comment: 40 pages, 38 figures version2 - the time schedule added, information
about PMTs in Sec.III update
Domain regime in two-dimensional disordered vortex matter
A detailed numerical study of the real space configuration of vortices in
disordered superconductors using 2D London-Langevin model is presented. The
magnetic field is varied between 0 and for various pinning
strengths . For weak pinning, an inhomogeneous disordered vortex matter
is observed, in which the topologically ordered vortex lattice survives in
large domains. The majority of the dislocations in this state are confined to
the grain boundaries/domain walls. Such quasi-ordered configurations are
observed in the intermediate fields, and we refer it as the domain regime (DR).
The DR is distinct from the low-field and the high-fields amorphous regimes
which are characterized by a homogeneous distribution of defects over the
entire system. Analysis of the real space configuration suggests domain wall
roughening as a possible mechanism for the crossover from the DR to the
high-field amorphous regime. The DR also shows a sharp crossover to the high
temperature vortex liquid phase. The domain size distribution and the roughness
exponent of the lattice in the DR are also calculated. The results are compared
with some of the recent Bitter decoration experiments.Comment: 9 pages, 9 figure
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