2,658 research outputs found
A model for the accidental catalysis of protein unfolding in vivo
Activated processes such as protein unfolding are highly sensitive to
heterogeneity in the environment. We study a highly simplified model of a
protein in a random heterogeneous environment, a model of the in vivo
environment. It is found that if the heterogeneity is sufficiently large the
total rate of the process is essentially a random variable; this may be the
cause of the species-to-species variability in the rate of prion protein
conversion found by Deleault et al. [Nature, 425 (2003) 717].Comment: 5 pages, 2 figure
A refined hydrogen bond potential for flexible protein models
One of the major disadvantages of coarse-grained hydrogen bond potentials, for their use in protein folding simulations, is the appearance of abnormal structures when these potentials are used in flexible chain models, and no other geometrical restrictions or energetic contributions are defined into the system.We have efficiently overcome this problem, for chains of adequate size in a relevant temperature range, with a refined coarse-grained hydrogen bond potential. With it, we have been able to obtain nativelike alpha-helices and beta-sheets in peptidic systems, and successfully reproduced the competition between the populations of these secondary structure elements by the effect of temperature and concentration changes. In this manuscript we detail the design of the interaction potential and thoroughly examine its applicability in energetic and structural terms, considering factors such as chain length, concentration, and temperature
Lattice model for cold and warm swelling of polymers in water
We define a lattice model for the interaction of a polymer with water. We
solve the model in a suitable approximation. In the case of a non-polar
homopolymer, for reasonable values of the parameters, the polymer is found in a
non-compact conformation at low temperature; as the temperature grows, there is
a sharp transition towards a compact state, then, at higher temperatures, the
polymer swells again. This behaviour closely reminds that of proteins, that are
unfolded at both low and high temperatures.Comment: REVTeX, 5 pages, 2 EPS figure
Response of the Brazilian gravitational wave detector to signals from a black hole ringdown
It is assumed that a black hole can be disturbed in such a way that a
ringdown gravitational wave would be generated. This ringdown waveform is well
understood and is modelled as an exponentially damped sinusoid. In this work we
use this kind of waveform to study the performance of the SCHENBERG
gravitational wave detector. This first realistic simulation will help us to
develop strategies for the signal analysis of this Brazilian detector. We
calculated the signal-to-noise ratio as a function of frequency for the
simulated signals and obtained results that show that SCHENBERG is expected to
be sensitive enough to detect this kind of signal up to a distance of .Comment: 5 pages, 4 figures, Amaldi 5 Conference Proceedings contribution.
Submitted to Class. Quantum Gra
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
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
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
Observational Limit on Gravitational Waves from Binary Neutron Stars in the Galaxy
Using optimal matched filtering, we search 25 hours of data from the LIGO
40-meter prototype laser interferometric gravitational-wave detector for
gravitational-wave chirps emitted by coalescing binary systems within our
Galaxy. This is the first test of this filtering technique on real
interferometric data. An upper limit on the rate R of neutron star binary
inspirals in our Galaxy is obtained: with 90% confidence, R< 0.5/hour. Similar
experiments with LIGO interferometers will provide constraints on the
population of tight binary neutron star systems in the Universe.Comment: RevTeX, minor revisions, exactly as published in PRL 83 (1999) p1498,
4 pages, 2 figures include
Black Hole Area in Brans-Dicke Theory
We have shown that the dynamics of the scalar field
in Brans-Dicke theories of gravity makes the surface area of the black hole
horizon {\it oscillatory} during its dynamical evolution. It explicitly
explains why the area theorem does not hold in Brans-Dicke theory. However, we
show that there exists a certain non-decreasing quantity defined on the event
horizon which is proportional to the black hole entropy for the case of
stationary solutions in Brans-Dicke theory. Some numerical simulations have
been demonstrated for Oppenheimer-Snyder collapse in Brans-Dicke theory.Comment: 12 pages, latex, 5 figures, epsfig.sty, some statements clarified and
two references added, to appear in Phys. Rev.
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