How do proteins find their native state so fast?
Levinthal's paradox, revisited with exascale sampling. We combine enhanced-sampling MD with transition-path theory to map folding funnels for β-rich domains.
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Meridian University · Faraday Hall
The physics of living matter, computed from first principles
We build multiscale models of proteins, membranes, and molecular machines — pairing long-timescale molecular dynamics with machine learning to explain how living systems move, fold, and compute. Everything we publish ships with open data and runnable code.
Explore our research Read the papers
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Research
Five questions we are trying to answer
Our program spans from femtosecond bond vibrations to the collective mechanics of whole organelles. The threads below are deliberately interconnected.
What sets the mechanics of a living bilayer?
Coarse-grained models of lipid rafts and curvature-sensing proteins, validated against neutron-scattering form factors.
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How do molecular motors convert chemistry into motion?
Free-energy landscapes for ATP-driven conformational cycles in kinesin and the F1-ATPase.
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Can we predict allosteric pathways from structure alone?
Graph-neural surrogates trained on perturbation-response scanning across kinase families.
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How far can ML force fields be trusted?
Uncertainty-aware neural potentials with active learning in the loop, benchmarked against gold-standard coupled-cluster references.
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What is the right coarse-graining for life?
Information-theoretic bounds on how much microscopic detail a predictive mesoscale model can safely discard.
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Reproducibility pledge. Every figure in every paper links to the exact commit, container image, and input deck that produced it. If you cannot re-run it, we consider it a bug and we want to hear about it.
Selected result
Fluorescence recovery across a 96-well plate
Recovery half-times cluster into two populations, consistent with a two-state model of chromophore maturation. The full analysis notebook is in the dataset release.
The recovery curve follows .
People
The lab
Twenty-three researchers across physics, chemistry, computer science, and biology.
Priya Nandakumar
Principal Investigator
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Senior Research Scientist
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Research Scientist, ML
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Postdoctoral Fellow
XXx_clippath_circle0_xXXAiko Tanaka
Postdoctoral Fellow
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PhD Candidate
XXx_clip_legacy_rect_xXXDaniel Okonkwo
PhD Candidate
XXx_ancestor_clippath_xXXMei Lin
PhD Candidate
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Publications
Recent papers
Nature Methods (2026)
Uncertainty-aware neural potentials for long-timescale molecular dynamics
Ostrowski L., Nandakumar P., et al.
DOI: 10.1038/s41592-026-01847-2 · Data & code
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PNAS (2026)
Curvature sensing emerges from lipid-tail entropy in coarse-grained bilayers
Ferreira M., Tanaka A., Nandakumar P.
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Biophysical Journal (2025)
Transition paths of the F1-ATPase rotary cycle from adaptive sampling
Herrera T., Ricci S., Nandakumar P.
DOI: 10.1016/j.bpj.2025.09.014
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JCTC (2025)
Active-learning force fields with calibrated coupled-cluster references
Okonkwo D., Lin M., Ostrowski L.
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Show our full 2020–2026 bibliography (128 entries)
The complete list, including preprints and conference proceedings, is maintained in our public Zotero group and mirrored as BibTeX in the lab's data repository. Highlights include three Nature-family papers, the CEBL Folding-Trajectory Benchmark, and the open-source meridian-md simulation toolkit.
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Seminars
Weekly seminar series
Thursdays, 4:00 PM, Faraday Hall 220. Fall term focuses on machine learning for structural biology, with three external speakers from national labs.
Spring term covered membrane biophysics and included our annual student lightning-talk session.
Recordings back to 2019 are available to the university community through the media portal.
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Facilities
Compute & instrumentation
| Resource | Detail | Access |
|---|---|---|
| Meridian GPU cluster | 512× H100, 200 Gb/s IB | Fair-share queue |
| Cryo-EM (Krios G4) | 300 kV, cold FEG | By proposal |
| Confocal microscopy | Spinning-disk, FRAP | Core facility |
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For the record
Notes & corrections
We post errata and clarifications here as they arise. Nothing outstanding this term.
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Datasets
Open reproducibility packages
Everything below is released under CC-BY-4.0 with a permanent DOI.
CEBL Folding-Trajectory Benchmark v3
2.1 TB · 4,096 trajectories · HDF5
Long-timescale trajectories for 40 fast-folding proteins with matched neural-potential baselines.
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640 GB · coarse-grained · GROMACS
Curvature-sensing free-energy profiles across 60 lipid compositions.
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Allosteric Pathway Graphs
18 GB · JSON graphs
Perturbation-response graphs for 220 kinase structures.
XXx_dangerous_scheme_xXXRotary-Motor Transition Paths
95 GB · DCD + metadata
Committor-annotated transition paths for the F1-ATPase catalytic cycle.
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Printed copy — canonical links: Benchmark v3 https://doi.org/10.5281/zenodo.1029384 · Curvature Atlas https://doi.org/10.5281/zenodo.1029411 · © 2026 Meridian University.
News
Recent milestones
- Jul 2026 — Benchmark v3 crosses 10,000 downloads.
- May 2026 — Ostrowski & Nandakumar published in Nature Methods.
- Mar 2026 — New H100 partition online for lab members.
- Jan 2026 — Annual open house.
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Now recruiting
We have two funded PhD positions starting Fall 2027 in ML force fields and membrane mechanics. Applications open in October.
Identity
Visual system
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Bay C status:
Contact
Get in touch
Center for Computational Biophysics & Living-Systems
220 Faraday Hall, 1400 Science Drive
Meridian, CA 94040
General: info@cebl.example.edu
Press: press@cebl.example.edu