SGSikao Guo
Contact

Computational biophysics × scientific computing

I build validated molecular-modeling methods and the software that makes them usable at scale.

Research scientist and software engineer working across protein conformational sampling, biomolecular self-assembly, structural bioinformatics, and high-performance simulation.

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Open to U.S.-based Research Scientist and Research Software Engineer rolesNo sponsorship required
Sampled protein backbone conformations.01Protein conformationsDiagram showing a Qt interface and CLI metadata transformed into JSON and then into VMD, PyMOL, and web applications.02Scientific interfacesEight simulation snapshots showing membrane-associated assemblies growing as molecular concentration increases, above a stylized membrane.03Mechanistic assembly

Hiring snapshot

Two role paths. One scientific-computing profile.

Choose the lens most relevant to your team; the evidence is the same, while project priority and the recommended resume adapt.

Mechanistic modeling, method development, and scientific validation appear first.

Best-fit downloadResearch Scientist resume

Target roles

Research Scientist · Research Software Engineer

Mechanistic research and production-minded scientific computing in one profile.

Core methods

Molecular modeling · structural bioinformatics

Protein conformational sampling, biomolecular self-assembly, reaction-diffusion, and quantitative validation.

Engineering stack

C++17 · Python · MPI · OpenMM

Parallel algorithms, scientific pipelines, testing, CI/CD, packaging, visualization, and researcher-facing interfaces.

Location & work status

No sponsorship required

Open to U.S.-based roles.
≈90× speedup

MPI NERDSS on 96 CPUs

44,000+ structures

ioNERDSS benchmarking across the PDB

9 applications · 3 platforms

One specification to VMD, PyMOL, and web

Selected work

Research methods developed as reusable infrastructure.

The three strongest case studies for the selected role appear first. Change the hiring perspective above without changing the underlying evidence.

Priority for Research Scientist

Sampled protein backbone conformations.Ongoing work
Molecular modeling2026 – Present

Protein backbone sampling

An extension of tripeptide loop-closure sampling that releases terminal constraints, introduces SE(3) motions and shifted sampling frames, and couples broad backbone geometric exploration to all-atom structural validation.

My roleExtended and optimized the C++ sampler and built its all-atom validation workflow.

  • C++
  • Inverse kinematics
  • SE(3)
  • Hit-and-Run
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Eight simulation snapshots showing membrane-associated assemblies growing as molecular concentration increases, above a stylized membrane.Published
Computational biophysics2020 – 2024

Biomolecular assembly models

PaperClathrin assembly paperPaperHIV-1 lattice paperPaperDynamin nanocluster paper

Structure-resolved stochastic and kinetic models of clathrin lattices, HIV-1 Gag assembly, and dynamin recruitment that integrate experimental constraints and produce testable system-level predictions.

My roleDesigned and analyzed the clathrin and HIV-1 models and contributed quantitative modeling to collaborative studies.

  • NERDSS
  • Stochastic simulation
  • Kinetic modeling
  • Membranes
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Conceptual path from particle-based reaction–diffusion models to parallel NERDSS simulation.Open source
Scientific infrastructure2022 – 2025

NERDSS + ioNERDSS infrastructure

PaperioNERDSS preprintPaperMPI paperCodeioNERDSS repository

A connected software stack that transforms PDB or mmCIF structures into simulation-ready coarse-grained models and runs explicit particle-based reaction-diffusion and self-assembly at larger spatial and computational scales.

My roleCo-developed ioNERDSS and led the MPI design, implementation, validation, and benchmarking for NERDSS.

  • C++
  • Python
  • MPI
  • PDB/mmCIF
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More work

Diagram showing a Qt interface and CLI metadata transformed into JSON and then into VMD, PyMOL, and web applications.Open source
Research software2025 – 2026

Cross-platform GUI generation

PaperFramework preprintCodeAutoCLIP repositoryDocumentationDocumentation

A Python framework that converts a designed interface and CLI metadata into a validated, platform-independent JSON specification, then generates consistent scientific applications for desktop molecular viewers and web environments.

My roleDesigned the framework architecture and implemented the specification, validation, and platform generators.

  • Python
  • Qt
  • JSON Schema
  • VMD
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Selected publications

Mechanistic modeling, molecular structure and dynamics, and scientific computing.

A focused selection of work in protein assembly, structural workflows, high-performance simulation, and research software.

View publication list

Collaboration

Physics training, biological questions, engineering execution.

I work with experimental scientists, modelers, and software teams to turn research questions into testable methods—and those methods into maintainable systems others can validate, scale, and reuse.

2025–now

Research Engineer · Inria

Developing inverse-kinematics protein-backbone samplers and a cross-platform framework for automatically generating VMD, PyMOL, and web applications.

2020–2025

Johns Hopkins University · Biophysics

Built NERDSS and ioNERDSS infrastructure and led computational studies of clathrin, retroviral Gag, and membrane-associated assembly.

Ph.D.

Institute of Physics, Chinese Academy of Sciences

Developed quantitative models connecting molecular conformational changes and chemical transitions to the emergent mechanics of kinesin motors.

Contact

Building a molecular-modeling method or scientific platform?

I am open to U.S.-based Research Scientist and Research Software Engineer roles. No sponsorship required.

Email me Scientist resume Engineer resume