Scott S. Douglas

Effects of pulling forces, osmotic pressure, condensing agents and viscosity on the thermodynamics and kinetics of DNA ejection from bacteriophages to bacterial cells: a computational study

In this work, we report on simulations of double-stranded DNA (dsDNA) ejection from bacteriophage φ29 into a bacterial cell. The ejection was studied with a coarse-grained model, in which viral dsDNA was represented by beads on a torsion-less string. The bacteriophages capsid and the bacterial cell were defined by sets of spherical constraints. To account for the effects of the viscous medium inside the bacterial cell, the simulations were carried out using a Langevin dynamics protocol. Our simplest simulations (involving constant viscosity and no external biasing forces) produced results compatible with the push-pull model of DNA ejection, with an ejection rate significantly higher in the first part of ejection than in the latter parts. Additionally, we performed more complicated simulations, in which we included additional factors such as external forces, osmotic pressure, condensing agents and ejection-dependent viscosity. The effects of these factors (independently and in combination) on the thermodynamics and kinetics of DNA ejection were studied. We found that, in general, the dependence of ejection forces and ejection rates on the amount of DNA ejected becomes more complex if the ejection is modeled with a broader, more realistic set of parameters and influences (such as variation in the solvents viscosity and the application of an external force). However, certain combinations of factors and numerical parameters led to the opposition of some ejection-driving and ejection-inhibiting influences, ultimately causing an apparent simplification of the ejection profiles.

Integrating Numerical Computation into the Modeling Instruction Curriculum

Numerical computation (the use of a computer to solve, simulate, or visualize a physical problem) has fundamentally changed the way scientific research is done. Systems that are too difficult to solve in closed form are probed using computation. Experiments that are impossible to perform in the laboratory are studied numerically. Consequently, in modern science and engineering, computation is widely considered to be as important as theory and experiment.

Do-It-Yourself Whiteboard-Style Physics Video Lectures

Video lectures are increasingly being used in physics instruction. For example, video lectures can be used to “flip” the classroom, i.e., to deliver, via the Internet, content that is traditionally transmitted by in-class lectures (e.g., presenting concepts, working examples, etc.), thereby freeing up classroom time for more interactive instruction. To date, most video lectures are live lecture recordings or screencasts. The hand-animated “whiteboard” video is an alternative to these more common styles and affords unique creative opportunities such as stop-motion animation or visual “demonstrations” of phenomena that would be difficult to demo in a classroom. In the spring of 2013, a series of whiteboard-style videos were produced to provide video lecture content for Georgia Tech introductory physics instruction, including flipped courses and a MOOC. This set of videos (which also includes screencasts and live recordings) can be found on the “Your World is Your Lab” YouTube channel. In this article, we de...

Peer Assessment of Student-Produced Mechanics Lab Report Videos.

We examine changes in students’ rating behavior during a semester-long sequence of peer evaluation laboratory exercises in an introductory mechanics course. We perform a quantitative analysis of the ratings given by students to peers’ physics lab reports, and conduct interviews with students. We find that peers persistently assign higher ratings to lab reports than do experts, that peers begin the semester by giving high ratings most frequently and end the semester with frequent middle ratings, and that peers go through the semester without much change in the frequency of low ratings. We then use student interviews to develop a model for student engagement with peer assessment. This model is based on two competing influences which appear to shape peer evaluation behavior: a strong disinclination to give poor ratings with a complementary preference to give high ratings when in doubt, and an attempt to develop an expertlike criticality when assessing peers’ work.

Exploring physics students’ engagement with online instructional videos in an introductory mechanics course

The advent of new educational technologies has stimulated interest in using online videos to deliver content in university courses. We examined student engagement with 78 online videos that we created and were incorporated into a one-semester flipped introductory mechanics course at the Georgia Institute of Technology. We found that students were more engaged with videos that supported laboratory activities than with videos that presented lecture content. In particular, the percentage of students accessing laboratory videos was consistently greater than 80% throughout the semester. On the other hand, the percentage of students accessing lecture videos dropped to less than 40% by the end of the term. Moreover, the fraction of students accessing the entirety of a video decreases when videos become longer in length, and this trend is more prominent for the lecture videos than the laboratory videos. The results suggest that students may access videos based on perceived value: students appear to consider the laboratory videos as essential for successfully completing the laboratories while they appear to consider the lecture videos as something more akin to supplemental material. In this study, we also found that there was little correlation between student engagement with the videos and their incoming background. There was also little correlation found between student engagement with the videos and their performance in the course. An examination of the in-video content suggests that students engaged more with concrete information that is explicitly required for assignment completion (e.g., actions required to complete laboratory work, or formulas or mathematical expressions needed to solve particular problems) and less with content that is considered more conceptual in nature. It was also found that students’ in-video accesses usually increased toward the embedded interaction points. However, students did not necessarily access the follow-up discussion of these interaction points. The results of the study suggest ways in which instructors may revise courses to better support student learning. For example, external intervention that helps students see the value of accessing videos may be required in order for this resource to be put to more effective use. In addition, students may benefit more from a clicker question that reiterates important concepts within the question itself, rather than a clicker question that leaves some important concepts to be addressed only in the discussion afterwards.