4,699 research outputs found
Simple estimation of absolute free energies for biomolecules
One reason that free energy difference calculations are notoriously difficult
in molecular systems is due to insufficient conformational overlap, or
similarity, between the two states or systems of interest. The degree of
overlap is irrelevant, however, if the absolute free energy of each state can
be computed. We present a method for calculating the absolute free energy that
employs a simple construction of an exactly computable reference system which
possesses high overlap with the state of interest. The approach requires only a
physical ensemble of conformations generated via simulation, and an auxiliary
calculation of approximately equal central-processing-unit (CPU) cost.
Moreover, the calculations can converge to the correct free energy value even
when the physical ensemble is incomplete or improperly distributed. As a "proof
of principle," we use the approach to correctly predict free energies for test
systems where the absolute values can be calculated exactly, and also to
predict the conformational equilibrium for leucine dipeptide in implicit
solvent.Comment: To appear in J. Chem. Phys., 10 pages, 6 figure
The X-ray nebula of the filled center supernova remnant 3C58 and its interaction with the environment
An \xmm observation of the plerionic supernova remnant 3C58 has allowed us to
study the X-ray nebula with unprecedented detail. A spatially resolved spectral
analysis with a resolution of 8\arcsec has yielded a precise determination of
the relation between the spectral index and the distance from the center. We do
not see any evidence for bright thermal emission from the central core. In
contrast with previous ASCA and {\em Einstein} results, we derive an upper
limit to the black-body 0.5-10 keV luminosity and emitting area of \ergsec and cm, respectively, ruling out
emission from the hot surface of the putative neutron star and also excluding
the "outer-gap" model for hot polar caps. We have performed for the first time
a spectral analysis of the outer regions of the X-ray nebula, where most of the
emission is still non-thermal, but where the addition of a soft (kT=0.2-0.3
keV) optically thin plasma component is required to fit the spectrum at
keV. This component provides 6% of the whole remnant observed flux in the
0.5-10.0 keV band. We show that a Sedov interpretation is incompatible with the
SN1181-3C58 association, unless there is a strong deviation from electron-ion
energy equipartition, and that an origin of this thermal emission in terms of
the expansion of the nebula into the ejecta core nicely fits all the radio and
X-ray observations.Comment: 10 pages, 7 figures, accepted for publication in A&
Subdiffusion and cage effect in a sheared granular material
We investigate experimentally the diffusion properties of a bidimensional
bidisperse dry granular material under quasistatic cyclic shear.The comparison
of these properties with results obtained both in computer simulations of hard
spheres systems and Lenard-Jones liquids and experiments on colloidal systems
near the glass transition demonstrates a strong analogy between the behaviour
of granular matter and these systems. More specifically, we study in detail the
cage dynamics responsible for the subdiffusion in the slow relaxation regime,
and obtain the values of relevant time and length scales.Comment: 4 pages, 6 figures, submitted to PR
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In Search of the Solar Wind Nitrogen Isotope Composition: Analysis of a Gold Plate from the Genesis Spacecraft Concentrator
We report N isotope analysis of a gold plate from the Genesis spacecraft concentrator. We did not find evidence for a light N component in the solar wind
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