Author

Yue Moon Ying

Johns Hopkins University

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

Biology Disciplines

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Biophysics· 3

Signature Assays, Organisms & Methods

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

Frequent Co-Authors

Margaret E. JohnsoniD· 3 shared Jonathan Fischer· 2 shared Mankun SangiD· 2 shared Samuel L. FoleyiD· 2 shared Sho S TakeshitaiD· 2 shared Si‐Kao GuoiD· 2 shared Adip JhaveriiD· 1 shared Ezra Greenberg· 1 shared

Activity by Year

2025-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 35 mutual co-author links

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3 shared papersBiophysics

Margaret E. JohnsonORCID

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3 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

Parallelization of particle-based reaction-diffusion simulations using MPI

Si‐Kao Guo, Nenad Korolija, Kent F. Milfeld, Adip Jhaveri, Mankun Sang, Yue Moon Ying, Margaret E. Johnson

This paper presents a parallel implementation of the NERDSS software using MPI, achieving near-linear scaling for particle-based reaction-diffusion simulations up to 96 processors.

Journal of Computational Chemistry · May 22, 2025Peer-reviewedBiophysics