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The weighted ensemble (WE) path sampling approach orchestrates an ensemble of parallel calculations with intermittent communication to enhance the sampling of rare events, such as molecular associations or conformational changes in proteins or peptides. Trajectories are replicated and pruned in a way that focuses computational effort on under-explored regions of configuration space while maintaining rigorous kinetics. To enable the simulation of rare events at any scale (e.g. atomistic, cellular), we have developed an open-source, interoperable, and highly scalable software package for the execution and analysis of WE simulations: WESTPA (The Weighted Ensemble Simulation Toolkit with Parallelization and Analysis). WESTPA scales to thousands of CPU cores and includes a suite of analysis tools that have been implemented in a massively parallel fashion. The software has been designed to interface conveniently with any dynamics engine and has already been used with a variety of molecular dynamics (e.g. GROMACS, NAMD, OpenMM, AMBER) and cell-modeling packages (e.g. BioNetGen, MCell). WESTPA has been in production use for over a year, and its utility has been demonstrated for a broad set of problems, ranging from atomically detailed host-guest associations to non-spatial chemical kinetics of cellular signaling networks. The following describes the design and features of WESTPA, including the facilities it provides for running WE simulations, storing and analyzing WE simulation data, as well as examples of input and output.

Articular cartilage is an avascular connective tissue that exhibits little intrinsic capacity for repair. Articular cartilage exists in a reduced oxygen ( approximately 5%) environment in vivo; therefore, oxygen tension may be an important factor that regulates the metabolism of chondrocyte progenitors. A number of recent studies have developed tissue engineering approaches for promoting cartilage repair using undifferentiated progenitor cells seeded on biomaterial scaffolds, but little is known about how oxygen might influence these engineered tissues. Human adipose-derived adult stem (hADAS) cells isolated from the stroma of subcutaneous fat were suspended in alginate beads and cultured in control or chondrogenic media in either low oxygen (5%) or atmospheric oxygen tension (20%) for up to 14 days. Under chondrogenic conditions, low oxygen tension significantly inhibited the proliferation of hADAS cells, but induced a two-fold increase in the rate of protein synthesis and a three-fold increase in total collagen synthesis. Low oxygen tension also increased glycosaminoglycan synthesis at certain timepoints. Immunohistochemical analysis showed significant production of cartilage-associated matrix molecules, including collagen type II and chondroitin-4-sulfate. These findings suggest oxygen tension may play an important role in regulating the proliferation and metabolism of hADAS cells as they undergo chondrogenesis, and the exogenous control of oxygen tension may provide a means of increasing the overall accumulation of matrix macromolecules in tissue-engineered cartilage.

A new wind-input and wind-breaking dissipation for phase-averaged spectral models of wind-generated surface waves is presented. Both are based on recent field observations in Lake George, New South Wales, Australia, at moderate-to-strong wind-wave conditions. The respective parameterizations are built on quantitative measurements and incorporate new observed physical features, which until very recently were missing in source terms employed in operational models. Two novel features of the wind-input source function are those that account for the effects of full airflow separation (and therefore relative reduction of the input at strong wind forcing) and for nonlinear behavior of this term. The breaking term also incorporates two new features evident from observational studies; the dissipation consists of two parts-a strictly local dissipation term and a cumulative term-and there is a threshold for wave breaking, below which no breaking occurs. Four variants of the dissipation term are selected for evaluation, with minimal calibration to each. These four models are evaluated using simple calculations herein. Results are generally favorable. Evaluation for more complex situations will be addressed in a forthcoming paper.

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