1,166 research outputs found
Four-states phase diagram of proteins
A four states phase diagram for protein folding as a function of temperature
and solvent quality is derived from an improved 2-d lattice model taking into
account the temperature dependence of the hydrophobic effect. The phase diagram
exhibits native, globule and two coil-type regions. In agreement with
experiment, the model reproduces the phase transitions indicative of both warm
and cold denaturations. Finally, it predicts transitions between the two coil
states and a critical point.Comment: 7 pages, 5 figures. Accepted for publication in Europhysics Letter
Growth of fat slits and dispersionless KP hierarchy
A "fat slit" is a compact domain in the upper half plane bounded by a curve
with endpoints on the real axis and a segment of the real axis between them. We
consider conformal maps of the upper half plane to the exterior of a fat slit
parameterized by harmonic moments of the latter and show that they obey an
infinite set of Lax equations for the dispersionless KP hierarchy. Deformation
of a fat slit under changing a particular harmonic moment can be treated as a
growth process similar to the Laplacian growth of domains in the whole plane.
This construction extends the well known link between solutions to the
dispersionless KP hierarchy and conformal maps of slit domains in the upper
half plane and provides a new, large family of solutions.Comment: 26 pages, 6 figures, typos correcte
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
Simplicity of eigenvalues in Anderson-type models
We show almost sure simplicity of eigenvalues for several models of
Anderson-type random Schr\"odinger operators, extending methods introduced by
Simon for the discrete Anderson model. These methods work throughout the
spectrum and are not restricted to the localization regime. We establish
general criteria for the simplicity of eigenvalues which can be interpreted as
separately excluding the absence of local and global symmetries, respectively.
The criteria are applied to Anderson models with matrix-valued potential as
well as with single-site potentials supported on a finite box.Comment: 20 page
Proteinlike behavior of a spin system near the transition between ferromagnet and spin glass
A simple spin system is studied as an analog for proteins. We investigate how
the introduction of randomness and frustration into the system effects the
designability and stability of ground state configurations. We observe that the
spin system exhibits protein-like behavior in the vicinity of the transition
between ferromagnet and spin glass.
Our results illuminate some guiding principles in protein evolution.Comment: 12 pages, 4 figure
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
A new estimation of the recent tropospheric molecular hydrogen budget using atmospheric observations and variational inversion
This paper presents an analysis of the recent tropospheric molecular hydrogen (H2) budget with a particular focus on soil uptake and European surface emissions. A variational inversion scheme is combined with observations from the RAMCES and EUROHYDROS atmospheric networks, which include continuous measurements performed between mid-2006 and mid-2009. Net H2 surface flux, then deposition velocity and surface emissions and finally, deposition velocity, biomass burning, anthropogenic and N2 fixation-related emissions were simultaneously inverted in several scenarios. These scenarios have focused on the sensibility of the soil uptake value to different spatio-temporal distributions. The range of variations of these diverse inversion sets generate an estimate of the uncertainty for each term of the H2 budget. The net H2 flux per region (High Northern Hemisphere, Tropics and High Southern Hemisphere) varies between −8 and +8 Tg yr−1. The best inversion in terms of fit to the observations combines updated prior surface emissions and a soil deposition velocity map that is based on bottom-up and top-down estimations. Our estimate of global H2 soil uptake is −59±9 Tg yr−1. Forty per cent of this uptake is located in the High Northern Hemisphere and 55% is located in the Tropics. In terms of surface emissions, seasonality is mainly driven by biomass burning emissions. The inferred European anthropogenic emissions are consistent with independent H2 emissions estimated using a H2/CO mass ratio of 0.034 and CO emissions within the range of their respective uncertainties. Additional constraints, such as isotopic measurements would be needed to infer a more robust partition of H2 sources and sinks
Thermodynamics of Heat Shock Response
Production of heat shock proteins are induced when a living cell is exposed
to a rise in temperature. The heat shock response of protein DnaK synthesis in
E.coli for temperature shifts from temperature T to T plus 7 degrees,
respectively to T minus 7 degrees is measured as function of the initial
temperature T. We observe a reversed heat shock at low T. The magnitude of the
shock increases when one increase the distance to the temperature , thereby mimicking the non monotous stability of proteins at low
temperature. Further we found that the variation of the heat shock with T
quantitatively follows the thermodynamic stability of proteins with
temperature. This suggest that stability related to hot as well as cold
unfolding of proteins is directly implemented in the biological control of
protein folding. We demonstrate that such an implementation is possible in a
minimalistic chemical network.Comment: To be published in Physical Review Letter
A possible mechanism for cold denaturation of proteins at high pressure
We study cold denaturation of proteins at high pressures. Using
multicanonical Monte Carlo simulations of a model protein in a water bath, we
investigate the effect of water density fluctuations on protein stability. We
find that above the pressure where water freezes to the dense ice phase
( kbar), the mechanism for cold denaturation with decreasing
temperature is the loss of local low-density water structure. We find our
results in agreement with data of bovine pancreatic ribonuclease A.Comment: 4 pages for double column and single space. 3 figures Added
references Changed conten
Lower Spectral Branches of a Spin-Boson Model
We study the structure of the spectrum of a two-level quantum system weakly
coupled to a boson field (spin-boson model). Our analysis allows to avoid the
cutoff in the number of bosons, if their spectrum is bounded below by a
positive constant. We show that, for small coupling constant, the lower part of
the spectrum of the spin-boson Hamiltonian contains (one or two) isolated
eigenvalues and (respectively, one or two) manifolds of atom -boson states
indexed by the boson momentum . The dispersion laws and generalized
eigenfunctions of the latter are calculated
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