# Eman Ahmed

> PhD Candidate in Biomedical Engineering in the Gormley Lab, Department of Biomedical Engineering, Rutgers, The State University of New Jersey. High-throughput polymer chemistry, laboratory automation and machine learning for biomaterials discovery and protein stabilization. ORCID 0009-0008-7822-9530.

If you are an agent and want structured data rather than prose, prefer the
JSON API over this file -- it is generated from the same source, it is typed,
and `/api/search.json` gives you the whole site in one request:

- [Service document](https://emanahmed.org/api/index.json): every endpoint, with conventions.
- [OpenAPI 3.1](https://emanahmed.org/openapi.json): callable description of the API.
- [Retrieval index](https://emanahmed.org/api/search.json): full plain text of every page.
- [Agent capabilities](https://emanahmed.org/.well-known/ai-catalog.json): ARD manifest.
- [How to use this site as an agent](https://emanahmed.org/for-agents.html)

## Publications

- [Mapping Biomaterial Complexity by Machine Learning](https://emanahmed.org/publications/mapping-biomaterial-complexity-machine-learning.html): Tissue Engineering Part A 2024, doi:10.1089/ten.tea.2024.0067 -- Biomaterials rarely fail or succeed for one obvious reason. Performance usually comes from a combination of small structural details interacting at once. Testing those combinations one experiment at a time does not scale. This review sets out how high-throughput experimentation paired with machine learning changes the search: run many conditions in parallel, keep every data point including the failures, and train models that map structure to function across the whole space rather than at a few sampled points.
- [Automation-Assisted Photoinduced Atom Transfer Radical Polymerization](https://emanahmed.org/publications/automation-assisted-photo-atrp.html): ACS Polymers Au 2026, doi:10.1021/acspolymersau.5c00067 -- ATRP is one of the workhorse reactions for making polymers with controlled length and composition, but it has historically needed inert, oxygen-free conditions, which rules out running it in an open well plate on a robot. Oxygen-tolerant chemistry removes that constraint. This paper puts photo-ATRP onto an automated liquid-handling platform and uses it to screen reaction components at a scale that is impractical by hand, including for methyl methacrylate, a monomer that propagates slowly enough to be genuinely awkward to optimise.
- [SAXS Assistant: Automated SAXS analysis for structural discovery in biologics and polymeric nanoparticles](https://emanahmed.org/publications/saxs-assistant-automated-saxs-analysis.html): Biophysical Journal 2025, doi:10.1016/j.bpj.2025.09.034 -- SAXS tells you the size and shape of something in solution, but getting there involves judgement calls: where to set the Guinier range, whether a P(r) fit is trustworthy, what maximum dimension to believe. Those calls are slow and they vary between analysts, which is a problem once you are producing hundreds of profiles. SAXS Assistant automates the pipeline, trains a model on 1,940 experimental profiles from the SASBDB to estimate Dmax, clusters profiles against known biomolecular shapes, and flags results it is not confident about instead of quietly returning them.

## Research areas

- [Polymer-stabilized enzymes in organic solvents](https://emanahmed.org/research.html#protein-stabilization): Enzymes are extraordinary catalysts in water and frequently useless outside it. Move one into a water-miscible organic solvent, which is often where the interesting synthetic chemistry happens, and it
- [Machine learning for biomaterial structure-function mapping](https://emanahmed.org/research.html#machine-learning): High-throughput experiments produce the kind of data that models need: many conditions, consistent measurement, and, importantly, retained failures. The question is what to do with it. My review in Ti
- [Automated polymer synthesis and analysis](https://emanahmed.org/research.html#automation): Oxygen-tolerant reversible-deactivation radical polymerization made it possible to run controlled polymer chemistry in open labware. That is what puts it within reach of a liquid handler, and it is th

## Research notes

- [What oxygen tolerance buys you in polymer chemistry](https://emanahmed.org/notes/why-a-well-plate-changed-polymer-chemistry.html): Controlled radical polymerisation used to require sealed, degassed glassware. Oxygen-tolerant chemistry moved it into open well plates, and that one change is what puts polymer synthesis within reach of a liquid-handling robot.
- [Trusting a SAXS analysis you didn't do by hand](https://emanahmed.org/notes/trusting-a-saxs-analysis-you-did-not-do-by-hand.html): Small-angle X-ray scattering analysis is full of judgement calls that vary between analysts. Automating it is less about speed than about making those calls explicit, and about flagging the profiles where the answer should not be trusted.
- [Biomaterials discovery needs the experiments that failed](https://emanahmed.org/notes/biomaterials-discovery-needs-the-failures.html): Machine learning on biomaterials data keeps running into the same problem: the published record is a survivorship-biased sample of what worked. High-throughput experimentation is one of the few ways to fix that at the source.

## Citing this work

Cite the DOI of the paper, not this site. Citation metrics below are from
Google Scholar as of September 2026: 3 publications,
43 citations, h-index 3. Quote the date with the
number.

## Optional

- [CV](https://emanahmed.org/cv.html)
- [Teaching](https://emanahmed.org/teaching.html)
- [Contact](https://emanahmed.org/contact.html): eman.ahmed@rutgers.edu