Sikao Guo

Sikao Guo, Ph.D.

Computational Biophysicist | Molecular Modeling and Simulation

  • Protein conformational sampling
  • Molecular dynamics & umbrella sampling
  • Kinetic models of binding & self-assembly
  • C++/Python scientific software
sikaoguo@gmail.comLinkedInGoogle Scholar
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Summary

Portrait of Sikao Guo wearing a blue checked shirt

Computational biophysicist with a Ph.D. in physics and 6+ years developing molecular modeling methods and production-quality C++/Python software for protein structure, dynamics, and assembly. Experience spans protein conformational sampling, all-atom molecular dynamics with umbrella sampling, and structure-resolved kinetic models of protein binding and self-assembly validated against experiment.

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Experience

Jul. 2025 – Dec. 2026

Inria

Research Engineer

Algorithms–Biology–Structure (ABS) team, Sophia Antipolis, France

  • Extended inverse-kinematics sampling to protein loops, fragments, and intrinsically disordered regions, with released-endpoint SE(3) moves, Ramachandran-informed selection, and clash checks.
  • Built AttnPacker/OpenMM workflows for side-chain reconstruction, energy minimization, all-atom assessment, and comparative benchmarking of geometric and generative protein samplers.
  • Designed AutoCLIP, a specification-driven framework that generates PyMOL, VMD, and web interfaces for structural-biology tools; deployed nine tools with testing, CI/CD, and reproducible packaging.
Jan. 2020 – Jun. 2025

Johns Hopkins University

Assistant Research Scientist · January 2025 – June 2025

Postdoctoral Researcher · January 2020 – December 2024

Department of Biophysics, Baltimore, Maryland

  • Identified the binding-affinity range that lets the immature HIV lattice remodel enough for Gag–Pol encounters, supporting protease dimerization, while retaining its large-scale structure.
  • Developed reaction–diffusion models of adaptor-dependent clathrin lattice stability, reproducing experimental kinetics and predicting a critical nucleus of approximately 25 clathrin under cell-like conditions.
  • Led the C++/MPI parallelization of the NERDSS reaction–diffusion simulator using spatial domain decomposition, reaching approximately 90× speedup on 96 CPUs for a 20,000-particle benchmark.
  • Co-developed ioNERDSS workflows that turn macromolecular structures into self-assembly simulations, benchmarked on 44,000+ structures and assemblies of 3–720 subunits.
  • Co-mentored undergraduate and graduate researchers in simulation methods and interpretation of results.
Sep. 2014 – Dec. 2019

Institute of Physics, Chinese Academy of Sciences

Doctoral Researcher

Beijing, China

  • Developed theoretical and numerical models of dimeric kinesin motors, combining stochastic simulation, all-atom molecular dynamics, and umbrella sampling to reproduce experimental motility measurements and explain how the two motor heads coordinate.
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Education

2014–2019

Ph.D. in Condensed Matter Physics

Institute of Physics, Chinese Academy of Sciences, Beijing, China

2010–2014

B.S. in Physics

Nankai University, Tianjin, China

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Contact

sikaoguo@gmail.comLinkedInGoogle Scholar