Physics-based protein structure refinement through multiple molecular dynamics trajectories and structure averaging.

We used molecular dynamics (MD) simulations for structure refinement of Critical Assessment of Techniques for Protein Structure Prediction 10 (CASP10) targets. Refinement was achieved by selecting structures from the MD-based ensembles followed by structural averaging. The overall performance of this method in CASP10 is described, and specific aspects are analyzed in detail to provide insight into key components. In particular, the use of different restraint types, sampling from multiple short simulations versus a single long simulation, the success of a quality assessment criterion, the application of scoring versus averaging, and the impact of a final refinement step are discussed in detail.

Open Resources for Biology Education (ORBE): a resource collection.

In undergraduate life sciences education, open educational resources (OERs) increase accessibility and retention for students, reduce costs, and save instructors time and effort. Despite increasing awareness and utilization of these resources, OERs are not centrally located, and many undergraduate instructors describe challenges in locating relevant materials for use in their classes. To address this challenge, we have designed a resource collection (referred to as Open Resources for Biology Education, ORBE) with 89 unique resources that are primarily relevant to undergraduate life sciences education. To identify the resources in ORBE, we asked undergraduate life sciences instructors to list what OERs they use in their teaching and curated their responses. Here, we summarize the contents of the ORBE and describe how educators can use this resource as a tool to identify suitable materials to use in their classroom context. By highlighting the breadth of unique resources openly available for undergraduate biology education, we intend for the ORBE to increase instructors' awareness and use of OERs.

Examining and Supporting Mechanistic Explanations Across Chemistry and Biology Courses.

Causal mechanistic reasoning is a thinking strategy that can help students explain complex phenomena using core ideas commonly emphasized in separate undergraduate courses, as it requires students to identify underlying entities, unpack their relevant properties and interactions, and link them to construct mechanistic explanations. As a crossdisciplinary group of biologists, chemists, and teacher educators, we designed a scaffolded set of tasks that require content knowledge from biology and chemistry to construct nested hierarchical mechanistic explanations that span three scales (molecular, macromolecular, and cellular). We examined student explanations across seven introductory and upper-level biology and chemistry courses to determine how the construction of mechanistic explanations varied across courses and the relationship between the construction of mechanistic explanations at different scales. We found non-, partial, and complete mechanistic explanations in all courses and at each scale. Complete mechanistic explanation construction was lowest in introductory chemistry, about the same across biology and organic chemistry, and highest in biochemistry. Across tasks, the construction of a mechanistic explanation at a smaller scale was associated with constructing a mechanistic explanation for larger scales; however, the use of molecular scale disciplinary resources was only associated with complete mechanistic explanations at the macromolecular, not cellular scale.

How Do Instructors Explain The Mechanism by which ATP Drives Unfavorable Processes?

Concerns regarding students' difficulties with the concept of energy date back to the 1970s. They become particularly apparent for systems involving adenosine triphosphate (ATP), which plays a central role in maintaining the nonequilibrium state of biological systems and in driving energetically unfavorable processes. One of the most well-documented misconceptions related to ATP is the idea that breaking bonds releases energy, when the opposite is true. This misconception is often attributed to language used in biology referring to the "high-energy bonds" in ATP. We interviewed chemistry, biology, and biochemistry instructors to learn how they think about and teach the mechanism(s) by which ATP is used as an energy source in biological systems. Across 15 interviews, we found that instructors relied primarily on two mechanisms to explain the role of ATP: 1) energy release, focused on ATP hydrolysis and bond energies; and/or 2) energy transfer, focused on phosphorylation and common intermediates. Many instructors shared negative and uncomfortable experiences related to teaching ATP and energy release. Based on these findings, we suggest instructional strategies that: 1) aim to ease the concerns expressed by introductory biology instructors, and 2) emphasize the role of ATP so as to support students' understanding of molecular mechanisms.