Author

Jonathan Fischer

Johns Hopkins UniversityPrimary ORCID profile (0000-0002-1165-9930 · 1 paper)Unclaimed ORCID profile · follow to get notified of new preprints

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Same name, identified by ORCID

Jonathan FischeriD1 paper · University of Florida

Biology Disciplines

Click to filter author papers

Signature Assays, Organisms & Methods

Click to filter · or open tag

Approach:statistical model· 2 Approach:deep learning· 1 Assay:protein structure· 1 Approach:simulation· 1 Research Focus:software / tool· 1

Frequent Co-Authors

Margaret E. JohnsoniD· 2 shared Samuel L. FoleyiD· 2 shared Sho S TakeshitaiD· 2 shared Yue Moon Ying· 2 shared Ezra Greenberg· 1 shared Gabriel AuiD· 1 shared Hannah Roscom· 1 shared Hassan Sohail· 1 shared

Activity by Year

2025-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 40 mutual co-author links

Click any collaborator node to inspect or filter shared papers

Focal author (center)Selected co-authorORCID co-authorUnlinked name

Curved chords = mutual co-authorship

2 shared papersBiophysics

Margaret E. JohnsonORCID

Mutual co-authors in cluster

Author profile →

2 papers

Recent·Most cited

Transforming macromolecular structures into simulations of self-assembly with ioNERDSS

Yue Moon Ying, Mankun Sang, Gabriel Au, Smriti Chhibber, Yufeng Du, Jonathan Fischer, Samuel L. Foley, Si‐Kao Guo, Ian Herzog-Pohl, Zixiu Hugh Liu, Hannah Roscom, Hassan Sohail, Sho S Takeshita, Margaret E. Johnson

The paper introduces ioNERDSS, a Python tool that converts 3D atomic structures into coarse-grained models for simulating macromolecular self-assembly.

bioRxiv · Apr 16, 2026 · PreprintBiophysics

A membrane-driven biochemical oscillator tunable by the volume to surface area ratio

Jonathan Fischer, Ezra Greenberg, Yue Moon Ying, Sho S Takeshita, Samuel L. Foley, Margaret E. Johnson

This paper introduces a membrane-driven biochemical oscillator that uses volume-to-surface area ratio to tune oscillation periods and validates it through computational and simulation studies.

bioRxiv · Nov 14, 2025 · PreprintBiophysics