The Zia Lab

Had a great time visiting Chemical Engineering at UI Chicago presenting our work on AI-guided physics-informed whole cell models of bacteria. Shoutout to faculty & students at @UIC_ChE for the thoughtful questions and engaging discussions.

🙌 Shout-out to John Glass + @JCVenterInst for Syn3A + the genetic/proteomic data.

Our physically resolved whole-cell sims: Syn3A’s unusually +charged proteome ⚡ electrostatically shields ribosomes, letting them interpenetrate the nucleoid → osmotic balance+ entropic expansion stabilize the expanded state. tinyurl.com/4uevsya3

New paper in PLOS Comp Bio (Zia Lab; lead authors Gesse Roure & Vishal Sivasankar). 🦠JCVI-Syn3A has a cell-spanning nucleoid—unusual vs E. coli where crowding/NAPs compact DNA and exclude ribosomes.

Thanks to UT Austin’s CDCM/MRSEC for hosting me on The Materials Universe Podcast (S3E3) during my IRG visit. We discuss molecularly explicit, spatially resolved whole-cell modeling & why physics matter. Spotify tinyurl.com/2n78vmmz + Apple tinyurl.com/48zbbrx5

Had a fantastic time at @ColbyCollege teaching a 3-day course: The ribosome: nature’s perfect machine (and why it’s so hard to engineer) with Max Planck’s @mattertolife. Students used Colab to run MD workflows & train simple ML interaction models—hands-on, physics-first, and fun.

Giving a talk at UT Austin @TexasCDCM on whole-cell models for engineering protein materials. Using physics-based AI to simulate millions of biomolecules at near-atomistic resolution ribogenesis in synthetic cells. ZiaLab members Vishal Sivasankar, Harnoor Sachar and Galen Wang.

Conference alert! How do synthetic cells organize to better operate? Our physically-resolved whole-cell model reveals Syn3A nucleoid structure & cytoplasmic dynamics optimize transcription/translation. Work by Gesse Roure & Vishal Sivasankar #APSDFD Acrivos 11/22@11AM Brown 310A

Hiring postdocs! Join the Zia Lab to build near-atomistic, physics-informed whole-cell models and uncover how ribosomes self-assemble and design mutations to engineer ribosomes. PhD by June '26; Python/C/C++/MD; HPC/GPU; some ML/AI. rzia@missouri.edu

Heading to #AIChE2025? Come see atomistic whole-cell modeling reveal physics of 🧬 life! - How E. coli speeds protein synthesis for fast growth - Neural nets power near-atomistic ribogenesis 📍 Acrivos session 11/4@2:36PM Hynes 302 📍 Bio Flows session 11/4@5:45PM Hynes 301

Honored to be named a Science Scout for the @Hypothesisfund . Excited to help further HF’s mission to advance scientific knowledge by identifying and seeding especially innovative, early-stage research. Thrilled to join a great network of Scouts: hypothesisfund.org

Excited to show our new whole-cell models of bacteria representing interactions between millions of biomolecules & DNA at Society of Rheology Annual Mtg. I’ll explain how E.coli uses colloid physics to speed protein synthesis for faster growth. Mon 10/20@10:30AM Sweeney Blrm C.

Delighted to give a keynote at Central SynBio Workshop today at U Minnesota, highlighting our AI-guided physics-based whole-cell computational models of ribosome biogenesis. Amazing synbio science from many great scientists. Shout out to the organizers! tinyurl.com/3ps557ed

Honored to be elected a Fellow of the American Physical Society! Deep gratitude to my nominators and the amazing lab members and collaborators who made possible our discoveries in soft matter and the physics of life. Grateful to be part of such a vibrant community @APSphysics!

Excited to share new research helping explain why synthetic minimal cell JCVI Syn3A's nucleoid is cell spanning. Great work by Zia Lab members Gesse Roure and Vishal Sivasankar! Check it out at the 5th Minimal Cell Workshop on October 3 at 8 am ET.(jcvi.org/events/minimal…).

Excited to present our work on whole-cell modeling of E. coli and ribogenesis in at the @AmerChemSociety Fall 2025 Meeting! Great work from ZiaLab members Vishal Sivasankar, Jen Hofmann and Theo Yang. Come check it out at the Westin Potomac Salon 3, Monday 08/18 at 8:00AM!

Excited to share new work now out in @NatureComms Biology! We use computational modeling to show how E. coli preloads its ribosomes to speed codon recognition testing & protein synthesis for faster growth. Check out the paper (open access) at doi.org/10.1038/s42003….

Excited to present NEW WORK at APS! The ZiaLab is headed to the 2025 @APSphysics Global Summit! Catch Vishal Sivasankar as he presents our latest work on whole-cell modeling of Escherichia coli. Don’t miss it! #APSMarch #APSSummit25

Paper now out in PNAS! Our colloidal whole-cell simulations + in vivo 3D particle tracking reveal how macromolecular interactions and confinement determine dynamics/localization in E. coli. Congrats @AlpSunol & @dsvalverdem!  pnas.org/doi/10.1073/pn…

Excited to share our accepted Annual Reviews article, "The matter/life nexus in biological cells". We cast a wide net into cellular biology, biophysics, and genetic approaches to defining life, toward understanding of the materiality of cellular life: arxiv.org/abs/2412.01743.