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One of the reasons large-scale software development is difficult is the number of dependencies that software engineers face. These dependencies create a need for communication and coordination that requires continuous effort by developers. Empirical studies, including our own, suggest that technical dependencies among software components create social(More)
Key Findings We introduce and explicate a novel development paradigm for distributed software engineering development tools, Continuous Coordination. Continuous Coordination constitutes a paradigm for collaborative systems, which combines elements of traditionally formal, process-oriented approaches with those of the more informal, awareness-based(More)
One of the reasons why large-scale software development is difficult is the number of dependencies that software engineers need to face; e.g., dependencies among the software components and among the development tasks. These dependencies create a need for communication and coordination that requires continuous effort by software developers. Empirical(More)
Steered Molecular Dynamics (SMD) has been seen to provide the potential of mean force (PMF) along a peptide unfolding pathway effectively but at significant computational cost, particularly in all-atom solvents. Adaptive steered molecular dynamics (ASMD) has been seen to provide a significant computational advantage by limiting the spread of the(More)
This paper describes Ariadne, a Java tool for the Eclipse IDE, that links technical and social dependencies. Ariadne is based on the observation that technical dependencies among software components create social dependencies among the software developers implementing these components. We describe our approach for creating technical, socio-technical and(More)
Ariadne is a novel visualization tool that allows end users to explore the socio-technical relationships in software development projects. Essentially the visualization is a variant of a social network graph. It is based on the observation that dependencies between software components create dependencies between the developers implementing those components.(More)
Ariadne is a visualization tool that allows end users to explore the socio-technical relationships in software development projects. Essentially the visualization is a variant of a social network graph. It is based on the observation that dependencies between software components create dependencies between the developers implementing those components. This(More)
Neuropeptide Y (NPY) has been found to adopt two stable conformations in vivo: (1) a monomeric form called the PP-fold in which a polyproline tail is folded onto an α-helix via a β-turn and (2) a dimeric form of the unfolded proteins in which the α-helices interact with each other via side chains. The transition pathway and rates between the two(More)
The potential of mean force (PMF) for stretching decaalanine in vacuum was determined earlier by Park and Schulten [J. Chem. Phys. 120, 5946 (2004)] in a landmark article demonstrating the efficacy of combining steered molecular dynamics and Jarzynski's nonequilibrium relation. In this study, the recently developed adaptive steered molecular dynamics (ASMD)(More)
Steered molecular dynamics, SMD, [S. Park and K. Schulten, J. Chem. Phys. 120, 5946 (2004)] combined with Jarzynski's equality has been used widely in generating free energy profiles for various biological problems, e.g., protein folding and ligand binding. However, the calculated averages are generally dominated by "rare events" from the ensemble of(More)