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This paper proposes a novel curriculum for the microprocessors and microcontrollers laboratory course. The proposed curriculum blends structured laboratory experiments with an open-ended project phase, addressing complex engineering…
Proteins encode diverse functions within complex three-dimensional structures, yet most deep learning representations remain highly entangled, obscuring the biophysical signals that underlie function. Here we introduce ProtDiS, a…
The research presented in this thesis was motivated by the need to improve introductory physics courses. Introductory physics courses are generally the first courses in which students learn to create models to solve complex problems.…
Laboratory courses represent a unique and potentially important component of the undergraduate physics curriculum, which can be designed to allow students to authentically engage with the process of experimental physics. Among other…
Thermodynamic aspects of chemical reactions have a long history in the Physical Chemistry literature. In particular, biochemical cycles - the building-blocks of biochemical systems - require a source of energy to function. However, although…
Deep learning has deeply influenced protein science, enabling breakthroughs in predicting protein properties, higher-order structures, and molecular interactions. This paper introduces DeepProtein, a comprehensive and user-friendly deep…
This paper presents the findings of pedagogical research on the efficacy of a virtual laboratory platform in general education courses on quantum information science. Specifically, a virtual laboratory activity based on the Bell test has…
Molecular biology explains function of molecules by their geometrical and electronical structures that are mainly determined by utilization of quantum effects in chemistry. However, further quantum effects are not thought to play any…
In its most general form, a `secret objective' is any inconsistency between the experimental reality and the information provided to students prior to starting work on an experiment. Students are challenged to identify the secret objectives…
There is a growing recognition of the need to replace "cookbook"-style introductory labs with more-meaningful learning experiences. To identify the strengths and weaknesses of a mix of cookbook-style and inquiry-based labs, an introductory…
Research-validated multiple-choice questions comprise an easy-to-implement instructional tool for scaffolding student learning and providing formative assessment of students' knowledge. We present findings from the implementation of a…
Composed of amino acid chains that influence how they fold and thus dictating their function and features, proteins are a class of macromolecules that play a central role in major biological processes and are required for the structure,…
In experimental physics, lab notebooks play an essential role in the research process. For all of the ubiquity of lab notebooks, little formal attention has been paid to addressing what is considered `best practice' for scientific…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
Predicting the biological function of molecules, be it proteins or drug-like compounds, from their atomic structure is an important and long-standing problem. Function is dictated by structure, since it is by spatial interactions that…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
Artificial chemistry simulations produce many intriguing emergent behaviors, but they are often difficult to steer or control. This paper proposes a method for steering the dynamics of a classic artificial chemistry model, known as AlChemy…
Development of conceptual multiple-choice tests related to a particular physics topic is important for designing research-based learning tools to reduce the difficulties. We explore the difficulties that the advanced undergraduate and…
Recently, there has been increased attention to improving laboratory instruction at all levels. At the introductory level, research results have shown differing levels of success based on the nature of the desired learning outcomes. In…
The process of discovery in the physical, biological and medical sciences can be painstakingly slow. Most experiments fail, and the time from initiation of research until a new advance reaches commercial production can span 20 years. This…