One of the basic goals of the CTBP is the training of a new generation of young physicists who can lead the field over the next decade. This training must be cognizant of the fact that scientists working on living systems must be comfortable with biology and biologists even while bringing new physical science based techniques to bear on the most critical problems. The basic features of our program include:
- Encouraging students and postdocs to talk to and work directly with experimentalists to better be able to understand how theory can contribute to the field.
- Creating weekly seminars, multiple weekly group meetings, and running conferences and workshop. All of these serve to expose our trainees to the breadth of the field and to different approaches, both experimental and theoretical.
- Participation in the physics of the living systems student research network; Rice is the lead node of this network. This network uses real and virtual meetings of students from a range of participating institutions to help create a world wide community of young researchers who can provide needed mutual guidance as to how to make progress in this highly interdisciplinary field.
- Finally we regularly host visitors with varying residency periods as yet another path to expose trainees to new ideas in the field.
The second part of our education/outreach program is devoted to outreach. This effort consists of two distinct parts. On the one hand we employ multiple strategies to spread the concepts of physics of living systems as a frontier topic to the broad scientific community. We regularly run specialized meetings for the NSF to help focus the physics community on newly emerging opportunities. And through our individual PI efforts we bring the excitement of the living systems frontier to such organizations as the APS DBIO division, the National Academy of Sciences, the American Chemical Society, the Biomedical Engineering Society and most recently, the American Association for Cancer Research.Our final effort concerns using the draw of working at a physics frontier to bring in undergraduate students from underrepresented groups. Our Frontiers in Science (FIS) program works with local minority serving institutions to identify promising science majors who then spend summers at the CTBP to learn about life as a scientific researcher. This program has been successful in convincing some of these students to go on to graduate school in the sciences, bringing into our community a more diverse population.
2022 CTBP ORBITS summer research program best poster winners
The ORBITS program encompasses multiple undergraduate research programs at CTBP, including the Frontiers in Science Program at Rice, UH, or Northeastern, mentorship from TSU under the PERM program, efforts in the Aiden lab at BCM, and other individual efforts by CTBP faculty. The ORBITS program culminated in a poster session that included 17 posters, developed by undergraduate mentees over a 10 week period under the direction of their mentor. There was a best poster competition, and the best posters from the three main ORBITS sites (Rice, Northeastern, and BCM) are below.
Samirina Acharya - Best poster Rice University site (Houston TX), Overall Best Poster winner. Mentor: Ananya Mondal
Poster Title: Buckling of Active Semi-flexible Polymer Chains.
This project was focused on assessing the mechanical properties of actin filaments in the presence of active myosin motors. We used an existing coarse-grained model of asingle buckled semi flexible polymer and tested the effect of activity on the polymer using molecular dynamics simulations. Our findings suggest that activity reduces the buckling transition, increases the flexibility of the polymer chain, and creates complex local statistics, such as sharp localized bends, compared to a passive buckled polymer.
Britney Cid - Best poster Northeastern site (Boston, MA). Mentor: Alex Moffett
Poster Title: Adding Correlations to Gene Regulatory Network Models
RACIPE is a method for generating ensemble models of gene regulatory networks with randomly sampled parameters. Our goal was to extend RACIPE to allow for correlations in random parameters, which we achieved using copulas. Applying our method to a synthetic gene regulatory network , we found that we could shift the ensemble of models towards different levels of multi-stability by introducing correlations between parameters in a principled manner.
Ayesha Saved - Best Poster Baylor College of Medicine site (Houston, TX). Mentor: Ruqayya Khan
Poster Title: Jumping Through Hoops for Mammalian Loops
Hi-C is an experimental technique for studying the structure of the chromosome in cells. A new method of Hi-C, known as intact Hi-C, allows for more precise DNA loop mapping. To aid the DNA Zoo Project in studying the evolution of functional elements in mammals, I completed intact Hi-C experiments on one representative species from five different mammalian orders.
My work in the May-MIDAS lab focuses on developing in-silico models of bacterial stress response. More specifically, I combine mathematical differential equation-based models and statistical gene models to study bacterial response to environmental or host-induced iron and hydrogen peroxide stress. Along this line, I am also developing models for multi-phenotype parametrization and optimization of dynamical system models.