Scalable Adaptive Protein Ensemble Refinement Integrating Flexible Fitting

Recent advances in cryo-electron microscopy (cryo-EM) has enabled modeling macromolecular complexes that are essential components of life. The density maps obtained from cryo-EM experiments is often integrated with ab-initio, knowledge-driven or first principles-based computational methods to build, fit and refine protein structures inside the electron density maps. Going beyond a single stationary-structure determination scheme, it is becoming more common to interpret the experimental data with a set of multiple physical models all of which contributes to the average observation seen by the experiment. Hence, there is a need to decide on the quality of an ensemble of protein structures on-the-fly, while refining them against the density maps. In this work, we demonstrate such adaptive decision making capabilities during flexible fitting of biomolecules. Our solution uses RADICAL tools (RCT) and we test this new implementation in exascale high performance computing environment for two proteins, Adenylate Kinase (ADK) and Carbon Monoxide Dehydrogenase (CODH). Our results indicate that using multiple replicas in flexible fitting with adaptive decision making improves the overall quality of fit and model by 40 % improvement when compared against the traditional flexible fitting approach. These advances are agnostic to system-size and computing environments.

A Dual Role for Behavior in Evolution and Shaping Organismal Selective Environments

The hypothesis that evolved behaviors play a determining role in facilitating and impeding the evolution of other traits has been discussed for more than 100 years with little consensus beyond an agreement that the ideas are theoretically plausible in accord with the Modern Synthesis. Many recent reviews of the genomic, epigenetic, and developmental mechanisms underpinning major behavioral transitions show how facultative expression of novel behaviors can lead to the evolution of obligate behaviors and structures that enhance behavioral function. Phylogenetic and genomic studies indicate that behavioral traits are generally evolutionarily more labile than other traits and that they help shape selective environments on the latter traits. Adaptive decision-making to encounter resources and avoid stress sources requires specific sensory inputs, which behaviorally shape selective environments by determining those features of the external world that are biologically relevant. These recent findings support the hypothesis of a dual role for behavior in evolution and are consistent with current evolutionary theory.

Adaptive Gaze Behavior and Decision Making of Penalty Corner Strikers in Field Hockey

In recent years, studies have increasingly dealt with the interaction of gaze behavior and decision making of team sports athletes. However, there is still a variety of important game situations, for example, in the case of penalty corners in field hockey, in which this interaction has not been investigated in detail yet. Penalty corners present a meaningful goal scoring opportunity by providing a relatively free shot. This paper considers two studies. The first study investigated a possible connection between the gaze behavior and the quality of decisions of experienced field hockey players and evaluated the level of success of different gaze strategies. A preliminary study (Study 1) was designed as a survey questionnaire with the aim of preparing for the main study by obtaining subjective assessments of the individual gaze behavior and decision making of professional athletes. In the second and the main study (Study 2), the gaze behavior of experienced field hockey players was recorded using mobile eye-tracking systems to analyze different strategical approaches in associated gaze behavior and decision making. Study 1 showed that players consider reacting to the defenders' behavior during a penalty corner a promising avenue for improving success at penalty corner attempts. It also indicated that such defense-dependent strategies are currently only rarely employed. Study 2 demonstrated how gaze behavior differs between different strategical approaches of the offense. It was shown that the gaze direction on the ball, the stopper, and the goal area is important to allow for a more optimal adaptation to the tactical behavior of defense. It can be concluded that adaptive decision making (i.e., choosing which variation will be carried out just after the “injection” of the ball) seems promising but requires further training to improve the success rate of penalty corner.

People Adjust Recency Adaptively to Environment Structure

Recency effects—giving exaggerated importance to recent outcomes—are a common aspect of decision tasks. In the current study, we explore two explanations of recency-based decision making, that it is (1) a deliberate strategy for adaptive decision making in real-world environments which tend to be dynamic and autocorrelated, and/or (2) a product of processing limitations of working memory. Supporting explanation 1, we found that participants strategically adjusted their recency levels across trials to achieve optimal levels in a range of tasks. Furthermore, they started with default recency values that had high aggregate performance across environments. However, only some correlations between recency values and WM scores were significant, providing no clear conclusion regarding explanation 2. Ultimately, we propose that recency involves a combination of the two—people can strategically change recency within the limits of WM capacities to adapt to external environments.