Coarse-graining the Dynamics of a Driven Interface in the Presence of Mobile Impurities: Effective Description via Diffusion Maps

Developing effective descriptions of the microscopic dynamics of many physical phenomena can both dramatically enhance their computational exploration and lead to a more fundamental understanding of the underlying physics. Previously, an effective description of a driven interface in the presence of mobile impurities, based on an Ising variant model and a single empirical coarse variable, was partially successful; yet it underlined the necessity of selecting additional coarse variables in certain parameter regimes. In this paper we use a data mining approach to help identify the coarse variables required. We discuss the implementation of this diffusion map approach, the selection of a similarity measure between system snapshots required in the approach, and the correspondence between empirically selected and automatically detected coarse variables. We conclude by illustrating the use of the diffusion map variables in assisting the atomistic simulations, and we discuss the translation of information between fine and coarse descriptions using lifting and restriction operators.Comment: 28 pages, 10 figure

Kinetic distance and kinetic maps from molecular dynamics simulation

Characterizing macromolecular kinetics from molecular dynamics (MD) simulations requires a distance metric that can distinguish slowly-interconverting states. Here we build upon diffusion map theory and define a kinetic distance for irreducible Markov processes that quantifies how slowly molecular conformations interconvert. The kinetic distance can be computed given a model that approximates the eigenvalues and eigenvectors (reaction coordinates) of the MD Markov operator. Here we employ the time-lagged independent component analysis (TICA). The TICA components can be scaled to provide a kinetic map in which the Euclidean distance corresponds to the kinetic distance. As a result, the question of how many TICA dimensions should be kept in a dimensionality reduction approach becomes obsolete, and one parameter less needs to be specified in the kinetic model construction. We demonstrate the approach using TICA and Markov state model (MSM) analyses for illustrative models, protein conformation dynamics in bovine pancreatic trypsin inhibitor and protein-inhibitor association in trypsin and benzamidine

Spinoza

"Spinoza", second edition. Encyclopedia entry for the Springer Encyclopedia of EM Phil and the Sciences, ed. D. Jalobeanu and C. T. Wolfe

Connecting up strategy: are senior strategy directors a missing link?

With companies being exhorted to become more strategically agile and internally connected, this article examines the role of the Senior Strategy Director, the executive tasked specifically with internal strategy. In particular, it explores what they do, what specific capabilities they deploy to enable effective contribution to the company, and in what ways they facilitate the connectedness of strategy. An analysis of multiple interviews over time with Senior Strategy Directors of large companies shows the vital and challenging role these executives play in both shaping, connecting up, and executing strategy. This article identifies the particular capabilities necessary for Senior Strategy Directors to perform their role and shows how it all depends upon their skilful deployment. These findings have significant implications for understanding unfolding micro-processes of strategy in large organizations, for assumptions about the skills and capabilities necessary to be an effective Senior Strategy Director, and for business schools in terms of the content and style of strategy courses they provide

Variable-free exploration of stochastic models: a gene regulatory network example

Finding coarse-grained, low-dimensional descriptions is an important task in the analysis of complex, stochastic models of gene regulatory networks. This task involves (a) identifying observables that best describe the state of these complex systems and (b) characterizing the dynamics of the observables. In a previous paper [13], we assumed that good observables were known a priori, and presented an equation-free approach to approximate coarse-grained quantities (i.e, effective drift and diffusion coefficients) that characterize the long-time behavior of the observables. Here we use diffusion maps [9] to extract appropriate observables ("reduction coordinates") in an automated fashion; these involve the leading eigenvectors of a weighted Laplacian on a graph constructed from network simulation data. We present lifting and restriction procedures for translating between physical variables and these data-based observables. These procedures allow us to perform equation-free coarse-grained, computations characterizing the long-term dynamics through the design and processing of short bursts of stochastic simulation initialized at appropriate values of the data-based observables.Comment: 26 pages, 9 figure

Generalized Ensemble and Tempering Simulations: A Unified View

From the underlying Master equations we derive one-dimensional stochastic processes that describe generalized ensemble simulations as well as tempering (simulated and parallel) simulations. The representations obtained are either in the form of a one-dimensional Fokker-Planck equation or a hopping process on a one-dimensional chain. In particular, we discuss the conditions under which these representations are valid approximate Markovian descriptions of the random walk in order parameter or control parameter space. They allow a unified discussion of the stationary distribution on, as well as of the stationary flow across each space. We demonstrate that optimizing the flow is equivalent to minimizing the first passage time for crossing the space, and discuss the consequences of our results for optimizing simulations. Finally, we point out the limitations of these representations under conditions of broken ergodicity.Comment: 11 pages Latex, 2 eps figures, revised version, typos corrected, PRE in pres

Presenting video recordings of newborn resuscitations in debriefings for teamwork training

Background: The Neonatal Resuscitation Program (NRP) and similar courses have been used to train clinicians. However, formal teamwork training was not included in these courses, and their effectiveness has been questioned. In adult resuscitation, debriefings using video recordings have improved outcomes, but recordings of neonatal resuscitation have been used primarily for research