SGSikao Guo
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Curriculum vitae

Computational biology and molecular simulation.

Research engineer developing scalable C++ and Python systems spanning MPI-based high-performance computing, computational geometry, molecular simulation, and scientific workflows—transforming research algorithms into reusable software infrastructure.

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Experience

Research and engineering

Inria

Jul. 2025 – Present
Research Engineer · Sophia Antipolis, France
  • Developed a cross-platform GUI code-generation framework that automated interface generation for 9+ computational biology applications across VMD, PyMOL, and web platforms.
  • Engineered a C++ protein backbone sampler that generalized inverse-kinematics loop sampling to backbone and intrinsically disordered region conformational sampling using SE(3)-based rigid-body moves.
  • Built an automated structural validation pipeline integrating AttnPacker, OpenMM, and PhiSiCal for reproducible evaluation and benchmarking of sampled protein conformations.
C++PythonPanelQtOpenMMVMDPyMOL

Johns Hopkins University

Jan. 2020 – Jun. 2025
Postdoctoral Researcher, Assistant Research Scientist · Baltimore, MD
  • Parallelized the C++ NERDSS reaction-diffusion simulator using MPI domain decomposition, achieving near-linear strong scaling to 96 CPU cores for large-scale biomolecular self-assembly simulations.
  • Developed structure-resolved computational models of clathrin-mediated endocytosis and HIV-1 assembly, revealing mechanisms governing critical nucleus formation, adaptor stoichiometry, and Gag-Pol dimerization.
  • Developed ioNERDSS, a Python toolkit that automates conversion of PDB/mmCIF structures into simulation-ready coarse-grained reaction-diffusion models, substantially reducing manual model preparation.
  • Implemented computational geometry and machine-learning algorithms for interface detection, reaction-network generation, and binding-affinity estimation to automate simulation parameterization.
C++PythonMPIPDB/mmCIFCoarse-grainingReaction-diffusionStochastic simulationHPC

Education

Physics training

Ph.D. Physics

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

Sept. 2014 – Dec. 2019

B.S. Physics

Nankai University · Tianjin, China

Sept. 2010 – Jun. 2014

Selected publications

Research output

Selected work

Open-source software

Technical strengths

Methods and tools

Software engineering

Python · C++ · Scientific software development · Algorithm development

High-performance computing

MPI · Parallel computing

Computational science

Computational biophysics · Structural bioinformatics · Protein modeling