Sikao Guo
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Sikao Guo, Ph.D.

Computational biophysicist · Research software engineer

Exploring proteins.Building the tools.

I develop computational methods and open-source software to understand how proteins move, interact, and assemble.

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Protein modeling · C++ / Python · High-performance computing

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Portrait of Sikao Guo wearing a blue checked shirt
Sikao Guo, Ph.D.

Research Engineer · Inria

≈90×Faster parallel simulationNERDSS · 96 CPUs · 20,000-particle benchmark44,000+Structures benchmarkedioNERDSS structure-to-simulation workflows9 toolsOne specification. Three interfaces.AutoCLIP · PyMOL, VMD, and the web

Selected work

What I built, and what it achieved.

All projects

Scientific computing

Open source

NERDSS + ioNERDSS

Problem
Building simulation models from molecular structures needed automation, and particle-based simulation needed to scale beyond a single process.
Built
C++/MPI spatial domain decomposition for NERDSS and automated structure-to-model Python workflows in ioNERDSS (co-developed).
Result
≈90× speedup on 96 CPUs (20,000-particle benchmark) · 44,000+ structures benchmarked · validated across 7 benchmark models.
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NERDSS and ioNERDSS workflow from PDB/mmCIF structures through coarse-grained models and reaction rules to parallel simulation.
Conceptual schematic

Research software

Open source

AutoCLIP

Problem
Each scientific tool needed a separate implementation for PyMOL, VMD, and the web.
Built
A specification-driven Python framework with JSON Schema validation, platform generators, and Linux/macOS CI.
Result
9 structural-biology tools deployed across 3 platforms, one specification each.
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Molecular modeling

Ongoing research

Protein conformational sampling

Problem
Fixed-end loop closure limits exploration of fragments and disordered regions, whose endpoints need to move.
Built
Extensions to a C++ sampler (released-endpoint moves, spatial-hash clash detection) plus an OpenMM all-atom validation workflow.
Result
Broader exploration than tested generative samplers on the evaluated systems (ongoing work).
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Computational biophysics

Published research

Biomolecular assembly models

Problem
Why do some molecular lattices stabilize while others fall apart or remodel?
Built
Stochastic reaction-diffusion models of clathrin and HIV Gag lattices.
Result
Reproduced experimental clathrin kinetics · identified an HIV binding-affinity range for stability and remodeling · first-author papers in PLOS Comp Biol and eLife, plus modeling for a Nature Communications study.
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Selected publications

From methods to mechanisms.

Papers & preprints

About me

Physics, biological questions, and the software in between.

My work has grown from mechanochemical models of molecular motors to biomolecular self-assembly, parallel simulation, and protein conformational sampling. Across these problems, I connect method development with numerical validation and reusable software.

More about my background

Research & collaboration

Let’s talk about the next question.

I’m interested in molecular-modeling methods, biomolecular simulation, and reusable scientific software.

sikaoguo@gmail.com