A unified, cross-platform framework for automatic GUI and plugin generation in structural bioinformatics and beyond
arXiv 2602.16047, 2026 · preprint · first author
Sikao Guo, Ph.D., Computational Biophysics & Scientific Software
- Biomolecular self-assembly
- Protein conformational sampling
- Reaction–diffusion & kinetic models
- Scientific software & HPC
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Short Bio
I am a computational biophysicist and Research Engineer in the Algorithms–Biology–Structure (ABS) team at Inria Sophia Antipolis, working with Frédéric Cazals. I extend inverse-kinematics sampling in the Structural Bioinformatics Library to flexible protein fragments and intrinsically disordered regions, and build AutoCLIP, which generates PyMOL, VMD, and web interfaces for structural-biology tools from one specification.
From 2020 to 2025 I was a postdoctoral researcher and then Assistant Research Scientist in the T. C. Jenkins Department of Biophysics at Johns Hopkins University with Margaret E. Johnson, modeling clathrin and immature HIV lattices and leading the C++/MPI parallelization of the NERDSS reaction–diffusion simulator. I received my Ph.D. in condensed matter physics from the Institute of Physics, Chinese Academy of Sciences (advisor: Ping Xie), working on models of dimeric kinesin motors, and my B.S. in physics from Nankai University.
Parallelization of particle-based reaction–diffusion simulations using MPI
Journal of Computational Chemistry 46(14), e70132, 2025 · first author
Structure of the HIV immature lattice allows for essential lattice remodeling within budded virions
eLife 12, e84881, 2023 · first author
Large self-assembled clathrin lattices spontaneously disassemble without sufficient adaptor proteins
PLOS Computational Biology 18(3), e1009969, 2022 · first author
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Contact
I am interested in molecular-modeling methods, biomolecular simulation, and reusable scientific software. Reach me at sikaoguo@gmail.com.