On behalf of the Biophysical Society, I am pleased to welcome you to the inaugural issue of our new educational journal, The Biophysicist. Over the years of discussion and planning that led to this new journal, there were many questions about just what the scope of articles would be. Here we find the first installment of that answer, but by no means the last. As our Editor-in-Chief, Sam Safran, describes in his introductory editorial, the eventual scope of the journal will be built around information that the community of biophysicists provides and finds useful. This first issue hints
Together with our entire Editorial Board, I am very happy to welcome you, the readership, to the first issue of the new Biophysical Society publication on biophysics education, The Biophysicist. The journal focuses on all levels at which biophysics learning and teaching take place—formally or informally: secondary education and community colleges, 4-year colleges, and university settings (including undergraduate, graduate, and postgraduate learners) as well as active researchers in the field. Scholarly communities in chemistry, physics, and biology education are well established. However, the uniquely interdisciplinary, pedagogical challenges of biophysics—for both students and teachers—have not yet been addressed from
Stochastic simulation can make the molecular processes of cellular control more vivid than the traditional differential equation approach by generating typical system histories, instead of just statistical measures such as the mean and variance of a population. Simple simulations are now easy for students to construct from scratch—that is, without recourse to black-box packages. In some cases, their results can also be compared directly with single-molecule experimental data. After introducing the stochastic simulation algorithm, this article gives two case studies involving gene expression and error correction, respectively. For gene expression, stochastic simulation results are compared with experimental data, an important research exercise for biophysics students. For error correction, several proofreading models are compared to find the minimal components necessary for sufficient accuracy in translation. Animations of the stochastic error correction models provide insight into the proofreading mechanisms. Code samples and resulting animations showing results are given in the online Supplemental Material.ABSTRACT
Fourier transforms (FT) are universal in chemistry, physics, and biology. Despite FTs being a core component of multiple experimental techniques, undergraduate courses typically approach FTs from a mathematical perspective, leaving students with a lack of intuition on how an FT works. Here, I introduce interactive teaching tools for upper-level undergraduate courses and describe a practical lesson plan for FTs. The materials include a computer program to capture video from a webcam and display the original images side-by-side with the corresponding plot in the Fourier domain. Several patterns are included to be printed on paper and held up to the webcam as input. During the lesson, students are asked to predict the features observed in the FT and then place the patterns in front of the webcam to test their predictions. This interactive approach enables students with limited mathematical skills to achieve a certain level of intuition for how FTs translate patterns from real space into the corresponding Fourier space.ABSTRACT
Recent work has shown that the intracellular environment is organized not only through membrane-bound organelles but also through fluid droplets that emerge through liquid–liquid phase separation (LLPS). Intracellular LLPS has attracted recent attention because these fluid droplets, termed biomolecular condensates or membraneless organelles, seem to play important roles in cells' responses to stress, gene regulation, and pathologies. Our understanding of intracellular LLPS has advanced through many quantitative biophysical techniques. Here, we describe a set of undergraduate lab activities that highlight these biophysical techniques. We use various optical microscopy methods and quantitative image analysis to characterize the physical properties of a model aqueous system that exhibits liquid–liquid phase separation. These lab activities can form a multiweek module that exposes students to this exciting new and interdisciplinary field that investigates how phase transitions organize the cell interior.ABSTRACT
Optics is an important subfield of physics required for instrument design and used in a variety of other disciplines, especially subjects that intersect the life sciences. Students from a variety of disciplines and backgrounds should be educated in the basics of optics to train the next generation of interdisciplinary researchers and instrumentalists who will push the boundaries of discovery or create inexpensive optical-based diagnostics. We present an experimental curriculum developed to teach students the basics of geometric optics, including ray and wave optics. The students learn these concepts in an active, hands-on manner through designing, building, and testing a homebuilt light microscope made from component parts. We describe the experimental equipment and basic measurements students can perform to learn these basic optical principles focusing on good optical design techniques, testing, troubleshooting, and iterative design. Students are also exposed to fundamental concepts of measurement uncertainty inherent in all experimental systems. The project students build is open and versatile to allow advanced projects, such as epifluorescence. We also describe how the equipment and curriculum can be flexibly used for an undergraduate level optics course, an advanced laboratory course, and graduate-level training modules or short courses.ABSTRACT
In this report, two undergraduate researchers with different career goals explain how biophysics relates to choices and summarize their advice to undergraduates interested in biophysics. Kelsey Jackson (Bachelor of Science in Physics and Data Science in 2021) and Molly Myers (Bachelor of Science in Business Administration in Economics with a minor in Mathematics 2020) are at Creighton University in Omaha, Nebraska. Under the guidance of their mentor, Michael Nichols, of the physics department at Creighton University, the students use biophysical optics to develop diagnostic tools to distinguish cancer cells from normal cells metabolically and architecturally. What is your career goal
Encouraging our high school and college students to gain experience and specialize in science, technology, engineering, and math (STEM) fields has never been more important. These fields are central to our countries' health, wealth, and security. They also provide numerous opportunities for employment and stability for our young people. In contrast to doctors and lawyers, whose functions are familiar, being a scientist, mathematician, or engineer may be elusive to youngsters not exposed to these specialties at home. Counselors and parents encourage students to acquire technical knowledge in these fields through course and research experiences; thus we often see today hard-working