Welcome to my page
Hello! I'm Amith, a researcher at Brandeis University, located in the Boston area. My work involves exploring the dynamics of epigenetic states at the single-cell level—an endeavor that blends molecular biology with computational modeling. I enjoy creating computational models to gain a deeper understanding of the fundamental processes that drive chromatin folding and gene regulation.
From modeling chromatin to collective behavior in active matter, I'm fascinated by the physics of biological systems.
I would love to connect with people who can challenge me into new ways of thinking. If you're interested in theoretical models on how epigenetic patterns allow DNA to artfully change its expression, check out "Painters in chromatin". Or if you prefer a short talk, here is a video.
Some of my works:
- Topological constraints and finite-size effects in quantitative polymer models of chromatin organization, Macromolecules 2023 (arXiv)
- 4D epigenomics: deciphering the coupling between genome folding and epigenomic regulation with biophysical modeling, Curr Opin Genet Dev 2023
- Painters in chromatin: a unified quantitative framework to characterize epigenome regulation and memory, Nulceic Acids Research 2022 (arXiv)
- Dynamical modeling of the H3K27 epigenetic landscape in mouse embryonic stem cells, PLoS CB 2022 (arXiv)
- Contact Force Mediated Rapid Deposition of Colloidal Microspheres Flowing over Microstructured Barriers, Langmuir 2021
- Swimming statistics of cargo-loaded single bacteria, Soft Matter 2020
- Active modulation of surfactant-driven flow instabilities by swarming bacteria, Physical Review E 2020
- Tuning the torque-speed characteristics of the bacterial flagellar motor to enhance swimming speed, Physical Review E 2019
Contact
Feel free to reach out to me at: amithzafal at brandeis dot edu