1,274 research outputs found
The effect of local thermal fluctuations on the folding kinetics: a study from the perspective of the nonextensive statistical mechanics
Protein folding is a universal process, very fast and accurate, which works
consistently (as it should be) in a wide range of physiological conditions. The
present work is based on three premises, namely: () folding reaction is a
process with two consecutive and independent stages, namely the search
mechanism and the overall productive stabilization; () the folding kinetics
results from a mechanism as fast as can be; and () at nanoscale
dimensions, local thermal fluctuations may have important role on the folding
kinetics. Here the first stage of folding process (search mechanism) is focused
exclusively. The effects and consequences of local thermal fluctuations on the
configurational kinetics, treated here in the context of non extensive
statistical mechanics, is analyzed in detail through the dependence of the
characteristic time of folding () on the temperature and on the
nonextensive parameter .The model used consists of effective residues
forming a chain of 27 beads, which occupy different sites of a D infinite
lattice, representing a single protein chain in solution. The configurational
evolution, treated by Monte Carlo simulation, is driven mainly by the change in
free energy of transfer between consecutive configurations. ...Comment: 19 pages, 3 figures, 1 tabl
Scattering of scalar perturbations with cosmological constant in low-energy and high-energy regimes
We study the absorption and scattering of massless scalar waves propagating
in spherically symmetric spacetimes with dynamical cosmological constant both
in low-energy and high-energy zones. In the former low-energy regime, we solve
analytically the Regge-Wheeler wave equation and obtain an analytic absorption
probability expression which varies with , where is the
central mass and is cosmological constant. The low-energy absorption
probability, which is in the range of , increases monotonically
with increase in . In the latter high-energy regime, the scalar
particles adopt their geometric optics limit value. The trajectory equation
with effective potential emerges and the analytic high-energy greybody factor,
which is relevant with the area of classically accessible regime, also
increases monotonically with increase in , as long is less
than or of the order of . In this high-energy case, the null cosmological
constant result reduces to the Schwarzschild value .Comment: 12 pages, 6 figure
Static Rouse Modes and Related Quantities: Corrections to Chain Ideality in Polymer Melts
Following the Flory ideality hypothesis intrachain and interchain excluded
volume interactions are supposed to compensate each other in dense polymer
systems. Multi-chain effects should thus be neglected and polymer conformations
may be understood from simple phantom chain models. Here we provide evidence
against this phantom chain, mean-field picture. We analyze numerically and
theoretically the static correlation function of the Rouse modes. Our numerical
results are obtained from computer simulations of two coarse-grained polymer
models for which the strength of the monomer repulsion can be varied, from full
excluded volume (`hard monomers') to no excluded volume (`phantom chains'). For
nonvanishing excluded volume we find the simulated correlation function of the
Rouse modes to deviate markedly from the predictions of phantom chain models.
This demonstrates that there are nonnegligible correlations along the chains in
a melt. These correlations can be taken into account by perturbation theory.
Our simulation results are in good agreement with these new theoretical
predictions.Comment: 9 pages, 7 figures, accepted for publication in EPJ
Nonextensive statistical mechanics applied to protein folding problem: kinetics aspects
A reduced (stereo-chemical) model is employed to study kinetic aspects of globular protein folding process, by Monte Carlo simulation. Nonextensive statistical approach is used: transition probability p i j between configurations i → j is given by p i j =[1 +(1 - q)ΔGi j/kB T ]1/(1-q), where q is the nonextensive (Tsallis) parameter. The system model consists of a chain of 27 beads immerse in its solvent; the beads represent the sequence of amino acids along the chain by means of a 10-letter stereo-chemical alphabet; a syntax (rule) to design the amino acid sequence for any given 3D structure is embedded in the model. The study focuses mainly kinetic aspects of the folding problem related with the protein folding time, represented in this work by the concept of first passage time (FPT). Many distinct proteins, whose native structures are represented here by compact self avoiding (CSA) configurations, were employed in our analysis, although our results are presented exclusively for one representative protein, for which a rich statistics was achieved. Our results reveal that there is a specific combinations of value for the nonextensive parameter q and temperature T, which gives the smallest estimated folding characteristic time (t). Additionally, for q = 1.1, (t) stays almost invariable in the range 0.9 < T < 1.3, slightly oscillating about its average value <img border=0 width=32 height=32 src="../../../../../../../img/revistas/bjp/v39n2a/a16txt01.gif" align=absmiddle > or = 27 ±σ, where σ = 2 is the standard deviation. This behavior is explained by comparing the distribution of the folding times for the Boltzmann statistics (q → 1), with respect to the nonextensive statistics for q = 1.1, which shows that the effect of the nonextensive parameter q is to cut off the larger folding times present in the original (q → 1) distribution. The distribution of natural logarithm of the folding times for Boltzmann statistics is a triple peaked Gaussian, while, for q = 1.1 (Tsallis), it is a double peaked Gaussian, suggesting that a log-normal process with two characteristic times replaced the original process with three characteristic times. Finally we comment on the physical meaning of the present results, as well its significance in the near future works
Medida de condutividade elétrica do solo adaptada a uma plantadeira.
bitstream/CNPDIA-2009-09/11888/1/CiT46_2008.pd
Soil condutivity electrical measurement system suited to an agricultural implement (subsoiler).
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