Epithelial mechanics and mechanobiology have become 2 important research fields in life sciences and bioengineering. These fields investigate how physical factors induced by cell adhesion and collective behaviors can directly regulate biologic processes, such as organ development and disease progression. Cell mechanics and mechanobiology thus make exciting biophysics education topics to illustrate how fundamental physics principles play a role in regulating cell biology. However, the field currently lacks hands-on activities that engage students in learning science and outreach programs in these topics. One such area is the development of robust hands-on modules that allow students to observe features of cell shape and mechanics and connect them to fundamental physics principles. Here, we demonstrate a workflow that engages students in studying epithelial cell mechanics by using commercial histology slides of frog skin. We show that by using recently developed artificial intelligence–based image-segmentation tools, students can easily quantify different cell morphologic features in a high-throughput manner. Using our workflow, students can reproduce 2 essential findings in cell mechanics: the common gamma distribution of normalized cell aspect ratio in jammed epithelia and the constant ratio between the nuclear and cellular area. Importantly, because the only required instrument for this active learning module is a readily available light microscope and a computer, our module is relatively low cost, as well as portable. These features make the module scalable for students at various education levels and outreach programs. This highly accessible education module provides a fun and engaging way to introduce students to the world of epithelial tissue mechanics.ABSTRACT
The analysis of particles bound to surfaces by tethers can facilitate understanding of biophysical phenomena (e.g., DNA–protein or protein–ligand interactions and DNA extensibility). Modeling such systems theoretically aids in understanding experimentally observed motions, and the limitations of such models can provide insight into modeling complex systems. The simulation of tethered particle motion (TPM) allows for analysis of complex behaviors exhibited by such systems; however, this type of experiment is rarely taught in undergraduate science classes. We have developed a MATLAB simulation package intended to be used in academic contexts to concisely model and graphically represent the behavior of different tether–particle systems. We show how analysis of the simulation results can be used in biophysical research using single-molecule force spectroscopy (SMFS). Students in physics, engineering, and chemistry will be able to make connections with principles embedded in the field of study and understand how those principles can be used to create meaningful conclusions in a multidisciplinary context. The simulation package can model any given tether–particle system and allows the user to generate a parameter space with static and dynamic model components. Our simulation was successfully able to recreate generally observed experimental trends by using acoustic force spectroscopy (AFS). Further, the simulation was validated through consideration of the conservation of energy of the tether–bead system, trend analyses, and comparison of particle positional data from actual TPM in silico experiments conducted to simulate data with a parameter space similar to the AFS experimental setup. Overall, our TPM simulator and graphical user interface is primarily for demonstrating behaviors characteristic to TPM in a classroom setting but can serve as a template for researchers to set up TPM simulations to mimic a specific SMFS experimental setup.ABSTRACT
Students beginning the study of biochemistry or biophysics at the undergraduate or even early graduate level are often overwhelmed by the complexity of the systems and the nomenclature. By comparison, chemical systems appear simple, as students can more easily relate to introductory chemistry courses, where the molecules are smaller and bind yet smaller ions. This allows students to write the structure of the entire molecule on a piece of paper and see exactly to which functional groups an ion, such as a proton (H+) in the simplest case, binds. Yet, concepts that are fundamental in biochemical macromolecules, namely proteins, can perfectly well be taught at the undergraduate or beginning graduate level, and probably be more easily understood, by using simpler, familiar chemical examples. The concept of interacting binding sites, which is at the root of cooperativity in protein binding reactions and conformational changes, is already present in simple molecules, such as ethylenediaminetetraacetic acid (EDTA). In this article, we show how to teach these topics by using the idea of the partition function, rather than a formal algebraic approach, to treat the binding of protons to EDTA. Profound concepts, such as that of interacting sites, appear naturally in a small molecule, where the origin can be easily ascribed, in this case, mainly to electrostatic interactions. Equipped with this understanding and this approach, students will be able to tackle more complicated biochemical systems, in which the molecules are larger, but the concepts are the same.ABSTRACT
Microscopy is crucial to much of biophysics. The variety of approaches to imaging exemplified by contemporary microscopes is remarkable, yet this breadth is generally unknown to students, limiting perceptions of biology, physics, and related fields and of potential career paths. We therefore created and implemented an outreach activity as part of a day camp that especially targeted low-income high school students. The students engaged with 3 very different microscopes: a simple transmitted light microscope; a light sheet fluorescence microscope; and a newly invented multicamera array microscope. With these instruments, we examined subjects such as transgenic zebrafish larvae with fluorescent immune cells, contrasting the various instruments’ capabilities, including resolution and field of view. Pre- and postactivity questions showed that the activity succeeded in expanding students’ understanding and appreciation of the varied aims and abilities of modern microscopes and moreover led to discussions of model organisms, biophysics, and science funding. Additional activities briefly illustrated the nature of digital images and mathematic manipulation. I describe here the activities and goals, as well as ways they can be generalized and implemented at other institutions with access to different sorts of imaging tools.ABSTRACT
Since the Force Concept Inventory in 1992, many concept inventories have been developed to cover classical scientific fields. However, there is a lack of concept inventories for interdisciplinary fields, such as biophysics. We introduce a Biophysics Concept Inventory Survey (BCIS), a 20-question, multiple-choice survey to measure student gains in biophysical concepts. The BCIS contains 5 question classifications: remember, understand, apply, analyze, and create, as well as question concepts divided into primarily physics or primarily biology questions. We administered the BCIS to 3 cohorts of students over 4 years. Each cohort participated in a 10-week summer Research Experience for Undergraduates (REU) in biophysics. We compared the presurvey (before REU) and postsurvey (after REU) scores to determine the fraction of the maximum possible gain or loss realized. Our analysis of the results suggests that the BCIS shows no biases based on sex or ethnicity. Further, we used the BCIS to show that 69% of the REU participants showed gains in biophysics concepts, with most of the total participant mean of gain occurring at higher levels of Bloom’s taxonomy: create and analyze. Overall, participants obtain slightly higher scores in physics (8% increase) than biology (5% increase) when comparing the pre- and postscores. The coronavirus disease 2019 pandemic allows a splitting of prepandemic and postpandemic cohorts, with the postpandemic cohort showing significantly larger gains than the prepandemic students. These results show that the BCIS, with question classifications and concepts, probes the students’ ability to apply knowledge to various biophysical science topics without underlying biases and enables instructors to obtain answers to important questions about the effectiveness of the educational programs. The BCIS fills a gap for interdisciplinary concept inventories.ABSTRACT
We present the implementation of a computer simulation laboratory for the calculation of the heat capacity of the folding-unfolding pseudo phase transition of a polyalanine Ala30 α-helix, using molecular dynamics simulations. Unlike conventional calorimetry experiments, which provide a macroscopic interpretation of the heat capacity, the computer laboratory additionally offers a molecular perspective of the energy exchange processes that lead to the peak of the heat capacity at the phase transition, as well as the statistical mechanical interpretation of the phase transition. The exercise is targeted toward 1st- or 2nd-year students of biophysics in the context of an undergraduate physical chemistry course. We use a graphical web interface to overcome the steep learning barriers associated with command line interactions in commonly used molecular dynamics protocols. The web interface (VIKING) also handles communication with computing hardware in the background, so that students with limited or no programming experience can launch and analyze the simulations easily. A collaboration between the VIKING support team and responsible teachers is required to set up VIKING. We also present a solution in which simulations can be launched on students’ own computers, if some command line knowledge can be expected. The laboratory can also be repurposed for students of various backgrounds (physics, chemistry, biology, or engineering) and scholastic levels (undergraduate or graduate).ABSTRACT