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The processes by which protein sidechains reach equilibrium during a folding reaction are investigated using both lattice and all-atom simulations. We find that rates of sidechain relaxation exhibit a distribution over the protein structure, with the fastest relaxing sidechains being involved in kinetically important positions. Traversal of the major folding transition state corresponds to the freezing of a small number of residues, while the rest of the chain proceeds towards equilibrium via backbone fluctuations around the native fold. The post-nucleation processes by which sidechains relax are characterized by very slow dynamics, and many barrier crossings, and thus resemble the behavior of a glass. At optimal temperature, however, the nucleated ensemble is energetically very close to equilibrium; slow relaxation is still observed. At lower temperatures, sidechain relaxation becomes a significant and very noticeable part of the folding reaction.

We present a novel Monte Carlo simulation of protein folding, in which all heavy atoms are represented as interacting hard spheres. This model includes all degrees of freedom relevant to folding - all sidechain and backbone torsions - and uses a Go potential. In this study, we focus on the 46 residue alpha-beta protein crambin and two of its structural components, the helix and helix hairpin. For a wide range of temperatures, we have recorded multiple folding events of these three structures from random coils to native conformations that differ by less than 1 A dRMS from their crystal structure coordinates. The thermodynamics and kinetic mechanism of the helix-coil transition obtained from our simulation shows excellent agreement with currently available experimental and molecular dynamics data. Based on insights obtained from folding its smaller structural components, a possible folding mechanism for crambin is proposed. We observe that the folding occurs via a cooperative, first order-like process, and that many folding pathways to the native state exist. One particular sequence of events constitutes a ``fast-folding'' pathway where kinetic traps are avoided. At very low temperatures, a kinetic trap arising from the incorrect packing of sidechains was observed. These results demonstrate that folding to the native state can be observed in a reasonable amount of time on desktop computers even when an all-atom representation is used, provided the energetics sufficiently stabilize the native state., Comment: 43 pages (including figures), 9 figures, submitted to Journal of Molecular Biology

NASADEM (NASA Digital Elevation Model) is a near-global elevation model that is being produced primarily by completely reprocessing the Shuttle Radar Topography Mission (SRTM) radar data and then merging it with refined ASTER (Advanced Spaceborne Thermal Emission and Reflection Radiometer) GDEM (Global Digital Elevation Model) elevations. The new and improved SRTM elevations in NASADEM result from better vertical control of each SRTM data swath via reference to ICESat (Ice, Cloud, and land Elevation Satellite) elevations and from SRTM void reductions using advanced interferometric unwrapping algorithms. Remnant voids will be filled primarily by GDEM3, but with reduction of GDEM glitches (mostly related to clouds) and therefore with only minor need for secondary sources of fill.

This paper outlines the ASF (Alaska SAR[synthetic aperture radar] Facility) Radarsat data processing requirements as driven by the science users and describes the Radarsat processing system design and implementaiton approach to meet the challenge of providing ASF with and integrated operational SAR image production facility. Design and implementation attributes that facilitate syswtem growth in handling future SAR missions such as Envisat and HIROS are also addressed.

The paper describes the status of a comprehensive synthetic aperture radar (SAR) software package developed specifically to aid the calibration of a multifrequency and multipolarization radar like the Shuttle Imaging Radar, SIR-C. The primary data types processed are engineering telemetry, point targets (corner reflectors and polarimetric active radar calibrators), distributed targets (clutter), tone-generators, and ground receivers. The parameters derived to aid the calibration of the production processor include measurements of relative radiometric channel to channel imbalance, absolute calibration constants, antenna pattern corrections, noise levels, polarimetric cross-talk, and geometric offsets. The software reports standard performance measurements such as resolution, peak and integrated sidelobes, radiometric response accuracy, and geometrical distortions such as scale errors, position bias and standard deviation, and image skew. Furthermore, the inclusion of software to allow updates of the shuttle-state vector (position and velocity) is considered.