Protein Structure Prediction Using Basin-Hopping

Associative memory Hamiltonian structure prediction potentials are not overly rugged, thereby suggesting their landscapes are like those of actual proteins. In the present contribution we show how basin-hopping global optimization can identify low-lying minima for the corresponding mildly frustrated energy landscapes. For small systems the basin-hopping algorithm succeeds in locating both lower minima and conformations closer to the experimental structure than does molecular dynamics with simulated annealing. For large systems the efficiency of basin-hopping decreases for our initial implementation, where the steps consist of random perturbations to the Cartesian coordinates. We implemented umbrella sampling using basin-hopping to further confirm when the global minima are reached. We have also improved the energy surface by employing bioinformatic techniques for reducing the roughness or variance of the energy surface. Finally, the basin-hopping calculations have guided improvements in the excluded volume of the Hamiltonian, producing better structures. These results suggest a novel and transferable optimization scheme for future energy function development

EVACUATION ROUTE MODELING AND PLANNING WITH GENERAL PURPOSE GPU COMPUTING

This work introduces a bilevel, stochastic optimization problem aimed at robust, regional evacuation network design and shelter location under uncertain hazards. A regional planner, acting as a Stackelberg leader, chooses among evacuation-route contraflow operation and shelter location to minimize the expected risk exposure to evacuees. Evacuees then seek an equilibrium with respect to risk exposure in the lower level. An example network is solved exactly with a strategy that takes advantage of a fast, low-memory, equilibrium algorithm and general purpose computing on graphical processing units

Realization of Coherent Optically Dense Media via Buffer-Gas Cooling

We demonstrate that buffer-gas cooling combined with laser ablation can be used to create coherent optical media with high optical depth and low Doppler broadening that offers metastable states with low collisional and motional decoherence. Demonstration of this generic technique opens pathways to coherent optics with a large variety of atoms and molecules. We use helium buffer gas to cool 87Rb atoms to below 7 K and slow atom diffusion to the walls. Electromagnetically induced transparency (EIT) in this medium allows for 50% transmission in a medium with initial OD >70 and for slow pulse propagation with large delay-bandwidth products. In the high-OD regime, we observe high-contrast spectrum oscillations due to efficient four-wave mixing.Comment: 4 pages, 4 figures. V2: modified title, abstract, introduction, conclusion; added references; improved theoretical fit in figure 3(b); shortened slow light theory description; clarified simplicity of apparatus. Final version as published in Phys. Rev.

Photonics

Contains reports on seven research projects.Air Force Rome Air Development Center (in collaboration with C.C. Leiby, Jr.)U.S. Air Force-Rome Air Development Center (Contract F19628-80-C-0077)National Science Foundation (Grant PHY79-09739)Joint Services Electronics Program (Contract DAAG29-80-C-0104)U.S. Air Force Geophysics Laboratory (Contract F19628-79-C-0082

Quantum Optics and Photonics

Contains reports on seven research projects.U.S. Air Force Geophysics Laboratory (Contract F19628-70-C-0082)Joint Services Electronics Program (Contract DAAG29-83-K-0003)National Science Foundation (Grant PHY82-10369)U.S. Air Force - Rome Air Development Center (in collaboration with C.C. Leiby, Jr.)U.S. Air Force - Rome Air Development Center (Contract F19628-80-C-0077)U.S. Air Force - Office of Scientific Research (Contract F49620-82-C-0091

The Energy Landscape, Folding Pathways and the Kinetics of a Knotted Protein

The folding pathway and rate coefficients of the folding of a knotted protein are calculated for a potential energy function with minimal energetic frustration. A kinetic transition network is constructed using the discrete path sampling approach, and the resulting potential energy surface is visualized by constructing disconnectivity graphs. Owing to topological constraints, the low-lying portion of the landscape consists of three distinct regions, corresponding to the native knotted state and to configurations where either the N- or C-terminus is not yet folded into the knot. The fastest folding pathways from denatured states exhibit early formation of the N-terminus portion of the knot and a rate-determining step where the C-terminus is incorporated. The low-lying minima with the N-terminus knotted and the C-terminus free therefore constitute an off-pathway intermediate for this model. The insertion of both the N- and C-termini into the knot occur late in the folding process, creating large energy barriers that are the rate limiting steps in the folding process. When compared to other protein folding proteins of a similar length, this system folds over six orders of magnitude more slowly.Comment: 19 page

Nanostructures, Technology, Research, and Applications

Contains reports on twenty research projects and a list of publications.Joint Services Electronics Program Grant DAAH04-95-1-0038National Science Foundation Grant ECS-94-07078Semiconductor Research CorporationU.S. Army Research Office Grant DAAH04-95-1-0564Defense Advanced Research Projects Agency/Naval Air Systems Command Contract N00019-95-K-0131National Aeronautics and Space Administration Contract NAS8-38249National Aeronautics and Space Administration Grant NAGW-2003IBM Corporation Contract 1622National Science Foundation Graduate FellowshipU.S. Navy - Office of Naval Research Grant N00014-95-1-1297U.S. Army Research Office Contract DAAH04-94-G-0377U.S. Air Force - Office of Scientific Research Grant F49620-92-J-0064U.S. Air Force - Office of Scientific Research Grant F49620-95-1-0311National Science Foundation Contract DMR 94-0034U.S. Air Force - Office of Scientific Research Contract F49620-96-0126Harvard-Smithsonian Astrophysical Observatory Contract SV630304National Aeronautics and Space Administration Grant NAG5-5105Los Alamos National Laboratory Contract E57800017-9

Nanostructures Technology, Research, and Applications

Contains reports on twenty-four research projects and a list of publications.Joint Services Electronics Program Grant DAAHO4-95-1-0038Defense Advanced Research Projects Agency/Semiconductor Research Corporation SA1645-25508PGU.S. Army Research Office Grant DAAHO4-95-1-0564Defense Advanced Research Projects Agency/U.S. Navy - Naval Air Systems Command Contract N00019-95-K-0131Suss Advanced Lithography P. O. 51668National Aeronautics and Space Administration Contract NAS8-38249National Aeronautics and Space Administration Grant NAGW-2003Defense Advanced Research Projects Agency/U.S. Army Research Office Grant DAAHO4-951-05643M CorporationDefense Advanced Research Projects Agency/U.S. Navy - Office of Naval Research Contract N66001-97-1-8909National Science Foundation Graduate FellowshipU.S. Army Research Office Contract DAAHO4-94-G-0377National Science Foundation Contract DMR-940034National Science Foundation Grant DMR 94-00334Defense Advanced Research Projects Agency/U.S. Air Force - Office of Scientific Research Contract F49620-96-1-0126Harvard-Smithsonian Astrophysical Observatory Contract SV630304National Aeronautics and Space Administration Grant NAG5-5105Los Alamos National Laboratory Contract E57800017-9GSouthwest Research Institute Contract 83832MIT Lincoln Laboratory Advanced Concepts ProgramMIT Lincoln Laboratory Contract BX-655

Current Understanding of the Earliest Human Occupations in the Americas: Evaluation of Becerra-Valdivia and Higham (2020)

Various chronologies of the earliest Native American occupations have been proposed with varying levels of empirical support and conceptual rigor, yet none is widely accepted. A recent survey of pre-Clovis dated sites (Becerra-Valdivia and Higham 2020) concludes a pre-Last Glacial Maximum (>26,500–19,000 cal yr BP) entry of humans in the Americas, in part based on recent work at Chiquihuite Cave, Mexico. We evaluate the evidence used to develop this inference. To provide clarity, we present three explicit dispersal models for the earliest human dispersals to the Americas: Strict Clovis-First (13,050 cal yr BP), Paleoindian (16,000 cal yr BP, encompassing pre-LGM, preferred by Becerra-Valdivia and Higham (2020)), and we summarize the current genetic and archaeological evidence bearing on each. We regard all purported Pre-Paleoindian sites as equivocal and the Strict Clovis-First model to be equally unsupported at present. We conclude that current data strongly support the Paleoindian Dispersal model, with Native American ancestors expanding into the Americas sometime after 16,000 cal yr BP (and perhaps after 14,800 cal yr BP), consistent with well-dated archaeological sites and with genetic data throughout the western hemisphere. Models of the Americas’ peopling that incorporate Chiquihuite or other claimed Pre-Paleoindian sites remain unsubstantiated.18 month embargo; published online: 23 October 2021This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]