ABSTRACT

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.

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

Welcome

The Biophysicist: Introductory Editorial

Stochastic Simulation to Visualize Gene Expression and Error Correction in Living Cells

ABSTRACT

Interactive Tools for Teaching Fourier Transforms

ABSTRACT

Liquid–Liquid Phase Separation: Undergraduate Labs on a New Paradigm for Intracellular Organization

ABSTRACT

Hands-on Curriculum in Optics of Microscopy

ABSTRACT

Undergraduate Researchers: Career Choices and Biophysics Training

Eight Suggestions for Future Leaders of Science and Technology

Welcome

The Biophysicist: Introductory Editorial

Stochastic Simulation to Visualize Gene Expression and Error Correction in Living Cells

Interactive Tools for Teaching Fourier Transforms

Liquid–Liquid Phase Separation: Undergraduate Labs on a New Paradigm for Intracellular Organization