2,729 research outputs found
Mapping of mutation-sensitive sites in protein-like chains
In this work we have studied, with the help of a simple on-lattice model, the
distribution pattern of sites sensitive to point mutations ('hot' sites) in
protein-like chains. It has been found that this pattern depends on the
regularity of the matrix that rules the interaction between different kinds of
residues. If the interaction matrix is dominated by the hydrophobic effect
(Miyazawa Jernigan like matrix), this distribution is very simple - all the
'hot' sites can be found at the positions with maximum number of closest
nearest neighbors (bulk).
If random or nonlinear corrections are added to such an interaction matrix
the distribution pattern changes. The rising of collective effects allows the
'hot' sites to be found in places with smaller number of nearest neighbors
(surface) while the general trend of the 'hot' sites to fall into a bulk part
of a conformation still holds.Comment: 15 pages, 6 figure
Collapse of Randomly Self-Interacting Polymers
We use complete enumeration and Monte Carlo techniques to study
self--avoiding walks with random nearest--neighbor interactions described by
, where is a quenched sequence of ``charges'' on the
chain. For equal numbers of positive and negative charges (), the
polymer with undergoes a transition from self--avoiding behavior to a
compact state at a temperature . The collapse temperature
decreases with the asymmetry Comment: 8 pages, TeX, 4 uuencoded postscript figures, MIT-CMT-
Thermodynamics of protein folding: a random matrix formulation
The process of protein folding from an unfolded state to a biologically
active, folded conformation is governed by many parameters e.g the sequence of
amino acids, intermolecular interactions, the solvent, temperature and chaperon
molecules. Our study, based on random matrix modeling of the interactions,
shows however that the evolution of the statistical measures e.g Gibbs free
energy, heat capacity, entropy is single parametric. The information can
explain the selection of specific folding pathways from an infinite number of
possible ways as well as other folding characteristics observed in computer
simulation studies.Comment: 21 Pages, no figure
Discrete Breathers in a Realistic Coarse-Grained Model of Proteins
We report the results of molecular dynamics simulations of an off-lattice
protein model featuring a physical force-field and amino-acid sequence. We show
that localized modes of nonlinear origin (discrete breathers) emerge naturally
as continuations of a subset of high-frequency normal modes residing at
specific sites dictated by the native fold. In the case of the small
-barrel structure that we consider, localization occurs on the turns
connecting the strands. At high energies, discrete breathers stabilize the
structure by concentrating energy on few sites, while their collapse marks the
onset of large-amplitude fluctuations of the protein. Furthermore, we show how
breathers develop as energy-accumulating centres following perturbations even
at distant locations, thus mediating efficient and irreversible energy
transfers. Remarkably, due to the presence of angular potentials, the breather
induces a local static distortion of the native fold. Altogether, the
combination of this two nonlinear effects may provide a ready means for
remotely controlling local conformational changes in proteins.Comment: Submitted to Physical Biolog
Finite size effects on thermal denaturation of globular proteins
Finite size effects on the cooperative thermal denaturation of proteins are
considered. A dimensionless measure of cooperativity, Omega, scales as N^zeta,
where N is the number of amino acids. Surprisingly, we find that zeta is
universal with zeta = 1 + gamma, where the exponent gamma characterizes the
divergence of the susceptibility for a self-avoiding walk. Our lattice model
simulations and experimental data are consistent with the theory. Our finding
rationalizes the marginal stability of proteins and substantiates the earlier
predictions that the efficient folding of two-state proteins requires the
folding transition temperature to be close to the collapse temperature.Comment: 3 figures. Physical Review Letters (in press
Parallelization of Markov chain generation and its application to the multicanonical method
We develop a simple algorithm to parallelize generation processes of Markov
chains. In this algorithm, multiple Markov chains are generated in parallel and
jointed together to make a longer Markov chain. The joints between the
constituent Markov chains are processed using the detailed balance. We apply
the parallelization algorithm to multicanonical calculations of the
two-dimensional Ising model and demonstrate accurate estimation of
multicanonical weights.Comment: 15 pages, 5 figures, uses elsart.cl
Sequence Dependence of Self-Interacting Random Chains
We study the thermodynamic behavior of the random chain model proposed by
Iori, Marinari and Parisi, and how this depends on the actual sequence of
interactions along the chain. The properties of randomly chosen sequences are
compared to those of designed ones, obtained through a simulated annealing
procedure in sequence space. We show that the transition to the folded phase
takes place at a smaller strength of the quenched disorder for designed
sequences. As a result, folding can be relatively fast for these sequences.Comment: 14 pages, uuencoded compressed postscript fil
Introduction to protein folding for physicists
The prediction of the three-dimensional native structure of proteins from the
knowledge of their amino acid sequence, known as the protein folding problem,
is one of the most important yet unsolved issues of modern science. Since the
conformational behaviour of flexible molecules is nothing more than a complex
physical problem, increasingly more physicists are moving into the study of
protein systems, bringing with them powerful mathematical and computational
tools, as well as the sharp intuition and deep images inherent to the physics
discipline. This work attempts to facilitate the first steps of such a
transition. In order to achieve this goal, we provide an exhaustive account of
the reasons underlying the protein folding problem enormous relevance and
summarize the present-day status of the methods aimed to solving it. We also
provide an introduction to the particular structure of these biological
heteropolymers, and we physically define the problem stating the assumptions
behind this (commonly implicit) definition. Finally, we review the 'special
flavor' of statistical mechanics that is typically used to study the
astronomically large phase spaces of macromolecules. Throughout the whole work,
much material that is found scattered in the literature has been put together
here to improve comprehension and to serve as a handy reference.Comment: 53 pages, 18 figures, the figures are at a low resolution due to
arXiv restrictions, for high-res figures, go to http://www.pabloechenique.co
Comparisons of binary black hole merger waveforms
This a particularly exciting time for gravitational wave physics.
Ground-based gravitational wave detectors are now operating at a sensitivity
such that gravitational radiation may soon be directly detected, and recently
several groups have independently made significant breakthroughs that have
finally enabled numerical relativists to solve the Einstein field equations for
coalescing black-hole binaries, a key source of gravitational radiation. The
numerical relativity community is now in the position to begin providing
simulated merger waveforms for use by the data analysis community, and it is
therefore very important that we provide ways to validate the results produced
by various numerical approaches. Here, we present a simple comparison of the
waveforms produced by two very different, but equally successful
approaches--the generalized harmonic gauge and the moving puncture methods. We
compare waveforms of equal-mass black hole mergers with minimal or vanishing
spins. The results show exceptional agreement for the final burst of radiation,
with some differences attributable to small spins on the black holes in one
case.Comment: Revtex 4, 5 pages. Published versio
An elliptical tiling method to generate a 2-dimensional set of templates for gravitational wave search
Searching for a signal depending on unknown parameters in a noisy background
with matched filtering techniques always requires an analysis of the data with
several templates in parallel in order to ensure a proper match between the
filter and the real waveform. The key feature of such an implementation is the
design of the filter bank which must be small to limit the computational cost
while keeping the detection efficiency as high as possible. This paper presents
a geometrical method which allows one to cover the corresponding physical
parameter space by a set of ellipses, each of them being associated to a given
template. After the description of the main characteristics of the algorithm,
the method is applied in the field of gravitational wave (GW) data analysis,
for the search of damped sine signals. Such waveforms are expected to be
produced during the de-excitation phase of black holes -- the so-called
'ringdown' signals -- and are also encountered in some numerically computed
supernova signals.Comment: Accepted in PR
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