The overall purpose of this project is to evaluate the biological and economic feasibility of restoring high-quality forests on mined land, and to measure carbon sequestration and wood production benefits that would be achieved from forest restoration procedures. In this quarterly report, we present a preliminary comparison of the carbon sequestration potential of forests growing on 14 mined sites in a seven-state region in the Midwestern and Eastern Coalfields. Carbon contents of these forests were compared to adjacent forests on non-mined land. The study was installed as a 3 x 3 factorial in a random complete block design with three replications at each location. The treatments include three forest types (white pine, hybrid poplar, mixed hardwood) and three silvicultural regimes (competition control, competition control plus tillage, competition control plus tillage plus fertilization). Each individual treatment plot is 0.5 acres. Each block of nine plots requires 4.5 acres, and the complete installation at each site requires 13.5 acres. The plots at all three locations have been installed and the plot corners marked with PVC stakes. GPS coordinates of each plot have been collected. Soil samples were collected from each plot to characterize the sites prior to treatment. Analysis of soil samples …

A protein local substructure (descriptor) is a set of several short non-overlapping fragments of the polypeptide chain. Each descriptor describes local environment of a particular residue and includes only those segments that are located in the proximity of this residue. Similar descriptors from the representative set of proteins were analyzed to reveal links between the substructures and sequences of their segments. Using detected sequence-based fingerprints specific geometrical conformations are assigned to new sequences. The ability of the approach to recognize correct SCOP folds was tested on 273 sequences from the 49 most popular folds. Good predictions were obtained in 85% of cases. No performance drop was observed with decreasing sequence similarity between target sequences and sequences from the training set of proteins.

Achieving efficient and correct synchronization of multiple threads is a difficult and error-prone task at small scale and, as we march towards extreme scale computing, will be even more challenging when the resulting application is supposed to utilize millions of cores efficiently. Transactional Memory (TM) is a promising technique to ease the burden on the programmer, but only recently has become available on commercial hardware in the new Blue Gene/Q system and hence the real benefit for realistic applications has not been studied, yet. This paper presents the first performance results of TM embedded into OpenMP on a prototype system of BG/Q and characterizes code properties that will likely lead to benefits when augmented with TM primitives. We first, study the influence of thread count, environment variables and memory layout on TM performance and identify code properties that will yield performance gains with TM. Second, we evaluate the combination of OpenMP with multiple synchronization primitives on top of MPI to determine suitable task to thread ratios per node. Finally, we condense our findings into a set of best practices. These are applied to a Monte Carlo Benchmark and a Smoothed Particle Hydrodynamics method. In both cases an optimized TM version, …