Author

Si‐Kao Guo

Johns Hopkins UniversityORCID 0000-0002-7680-8060Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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

Frequent Co-Authors

Mankun SangiD· 2 shared Margaret E. JohnsoniD· 2 shared Yue Moon Ying· 2 shared Adip JhaveriiD· 1 shared Gabriel AuiD· 1 shared Hannah Roscom· 1 shared Hassan Sohail· 1 shared Ian Herzog-Pohl· 1 shared

Activity by Year

2025-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 35 mutual co-author links

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2 shared papersBiophysics

Mankun SangORCID

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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

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