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 $1.8\times 10^{32}$ \ergsec and $1.3\times 10^{10}$ cm$^2$, 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 $E<1$ 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

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