Research

Understanding proteins through computation.

I connect molecular models, stochastic simulation, and structural data to study how proteins explore conformations and organize into functional assemblies.

Flexible-endpoint sampling

Conceptual paths · not sampled structures · schematic

Molecular modeling · Ongoing research

Protein conformational sampling

A modular C++/Python sampler for protein loops, fragments, and intrinsically disordered regions, paired with explicit all-atom validation.

C++
Python
Protein sampling
OpenMM

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Interactions → assembly → remodeling

Conceptual assembly · not simulation output · schematic

Computational biophysics · Published research

Biomolecular assembly models

Mechanistic models of clathrin and HIV lattices that connect molecular interactions to experimentally observed assembly behavior.

Stochastic simulation
Self-assembly
Membranes
Kinetics

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Methods that support the science

Models need reliable computational tools.

NERDSS-MPI, ioNERDSS, and AutoCLIP connect simulation, automated model construction, and scientist-facing interfaces. Validation, testing, and documentation are part of the method—not an afterthought.

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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