Artificial table testing dynamically adaptive systems

Dynamically Adaptive Systems (DAS) are systems that modify their behavior and structure in response to changes in their surrounding environment. Critical mission systems increasingly incorporate adaptation and response to the environment; examples include disaster relief and space exploration systems. These systems can be decomposed in two parts: the adaptation policy that specifies how the system must react according to the environmental changes and the set of possible variants to reconfigure the system. A major challenge for testing these systems is the combinatorial explosions of variants and envi-ronment conditions to which the system must react. In this paper we focus on testing the adaption policy and propose a strategy for the selection of envi-ronmental variations that can reveal faults in the policy. Artificial Shaking Table Testing (ASTT) is a strategy inspired by shaking table testing (STT), a technique widely used in civil engineering to evaluate building's structural re-sistance to seismic events. ASTT makes use of artificial earthquakes that simu-late violent changes in the environmental conditions and stresses the system adaptation capability. We model the generation of artificial earthquakes as a search problem in which the goal is to optimize different types of envi-ronmental variations

A Neural Circuit Model for Prospective Control of Interceptive Reaching

Two prospective controllers of hand movements in catching -- both based on required velocity control -- were simulated. Under certain conditions, this required velocity controlled to overshoots of the future interception point. These overshoots were absent in pertinent experiments. To remedy this shortcoming, the required velocity model was reformulated in terms of a neural network, the Vector Integration To Endpoint model, to create a Required Velocity Integration To Endpoint modeL Addition of a parallel relative velocity channel, resulting in the Relative and Required Velocity Integration To Endpoint model, provided a better account for the experimentally observed kinematics than the existing, purely behavioral models. Simulations of reaching to intercept decelerating and accelerating objects in the presence of background motion were performed to make distinct predictions for future experiments.Vrije Universiteit (Gerrit-Jan van Jngen-Schenau stipend of the Faculty of Human Movement Sciences); Royal Netherlands Academy of Arts and Sciences; Defense Advanced Research Projects Agency and Office of Naval Research (N00014-95-1-0409

Basic principles of temporal dynamics

All ecological disciplines consider temporal dynamics, although relevant concepts have been developed almost independently. We here introduce basic principles of temporal dynamics in ecology. We figured out essential features that describe temporal dynamics by finding similarities among about 60 ecological concepts and theories. We found that considering the hierarchically nested structure of complexity in temporal patterns (i.e. hierarchical complexity) can well describe the fundamental nature of temporal dynamics by expressing which patterns are observed at each scale. Across all ecological levels, driver–response relationships can be temporally variant and dependent on both short- and long-term past conditions. The framework can help with designing experiments, improving predictive power of statistics, and enhancing communications among ecological disciplines

Path Similarity Analysis: a Method for Quantifying Macromolecular Pathways

Diverse classes of proteins function through large-scale conformational changes; sophisticated enhanced sampling methods have been proposed to generate these macromolecular transition paths. As such paths are curves in a high-dimensional space, they have been difficult to compare quantitatively, a prerequisite to, for instance, assess the quality of different sampling algorithms. The Path Similarity Analysis (PSA) approach alleviates these difficulties by utilizing the full information in 3N-dimensional trajectories in configuration space. PSA employs the Hausdorff or Fr\'echet path metrics---adopted from computational geometry---enabling us to quantify path (dis)similarity, while the new concept of a Hausdorff-pair map permits the extraction of atomic-scale determinants responsible for path differences. Combined with clustering techniques, PSA facilitates the comparison of many paths, including collections of transition ensembles. We use the closed-to-open transition of the enzyme adenylate kinase (AdK)---a commonly used testbed for the assessment enhanced sampling algorithms---to examine multiple microsecond equilibrium molecular dynamics (MD) transitions of AdK in its substrate-free form alongside transition ensembles from the MD-based dynamic importance sampling (DIMS-MD) and targeted MD (TMD) methods, and a geometrical targeting algorithm (FRODA). A Hausdorff pairs analysis of these ensembles revealed, for instance, that differences in DIMS-MD and FRODA paths were mediated by a set of conserved salt bridges whose charge-charge interactions are fully modeled in DIMS-MD but not in FRODA. We also demonstrate how existing trajectory analysis methods relying on pre-defined collective variables, such as native contacts or geometric quantities, can be used synergistically with PSA, as well as the application of PSA to more complex systems such as membrane transporter proteins.Comment: 9 figures, 3 tables in the main manuscript; supplementary information includes 7 texts (S1 Text - S7 Text) and 11 figures (S1 Fig - S11 Fig) (also available from journal site

The FF Planning System: Fast Plan Generation Through Heuristic Search

We describe and evaluate the algorithmic techniques that are used in the FF planning system. Like the HSP system, FF relies on forward state space search, using a heuristic that estimates goal distances by ignoring delete lists. Unlike HSP's heuristic, our method does not assume facts to be independent. We introduce a novel search strategy that combines hill-climbing with systematic search, and we show how other powerful heuristic information can be extracted and used to prune the search space. FF was the most successful automatic planner at the recent AIPS-2000 planning competition. We review the results of the competition, give data for other benchmark domains, and investigate the reasons for the runtime performance of FF compared to HSP