Eleutherodactylus martinicensis

Number of Pages: 4Integrative BiologyGeological Science

Refined Genetic Algorithms for Polypeptide Structure Prediction

Accurate and reliable prediction of macromolecular structures has eluded researchers for nearly 40 years. Prediction via energy minimization assumes the native conformation has the globally minimal energy potential. An exhaustive search is impossible since for molecules of normal size, the size of the search space exceeds the size of the universe. Domain knowledge sources, such as the Brookhaven PDB can be mined for constraints to limit the search space. Genetic algorithms (GAs) are stochastic, population based, search algorithms of polynomial (P) time complexity that can produce semi-optimal solutions for problems of nondeterministic polynomial (NP) time complexity such as PSP. Three refined GAs are presented: A farming model parallel hybrid GA (PHGA) preserves the effectiveness of the serial algorithm with substantial speed up. Portability across distributed and MPP platforms is accomplished with the Message Passing Interface (MPI) communications standard. A Real-valved GA system, real-valued Genetic Algorithm, Limited by constraints (REGAL), exploiting domain knowledge. Experiments with the pentapeptide Met-enkephalin have identified conformers with lower energies (CHARMM) than the accepted optimal conformer (Scheraga, et al), -31.98 vs -28.96 kcals/mol. Analysis of exogenous parameters yields additional insight into performance. A parallel version (Para-REGAL), an island model modified to allow different active constraints in the distributed subpopulations and novel concepts of Probability of Migration and Probability of Complete Migration

Nonminimal Couplings in the Early Universe: Multifield Models of Inflation and the Latest Observations

Models of cosmic inflation suggest that our universe underwent an early phase of accelerated expansion, driven by the dynamics of one or more scalar fields. Inflationary models make specific, quantitative predictions for several observable quantities, including particular patterns of temperature anistropies in the cosmic microwave background radiation. Realistic models of high-energy physics include many scalar fields at high energies. Moreover, we may expect these fields to have nonminimal couplings to the spacetime curvature. Such couplings are quite generic, arising as renormalization counterterms when quantizing scalar fields in curved spacetime. In this chapter I review recent research on a general class of multifield inflationary models with nonminimal couplings. Models in this class exhibit a strong attractor behavior: across a wide range of couplings and initial conditions, the fields evolve along a single-field trajectory for most of inflation. Across large regions of phase space and parameter space, therefore, models in this general class yield robust predictions for observable quantities that fall squarely within the "sweet spot" of recent observations.Comment: 17pp, 2 figs. References added to match the published version. Published in {\it At the Frontier of Spacetime: Scalar-Tensor Theory, Bell's Inequality, Mach's Principle, Exotic Smoothness}, ed. T. Asselmeyer-Maluga (Springer, 2016), pp. 41-57, in honor of Carl Brans's 80th birthda