Biological Graphics and Design  ·  Champaign, IL, USA

Bryan
Gworek

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Greetings! I am a Biophysics and Quantitative Biology Doctoral student at the University of Illinois Urbana-Champaign, working under Dr. Kai Zhang and Dr. Taras Pogorelov.

My research focuses on cell signaling and protein/membrane dynamics, with an emphasis on phosphoinositides — a class of signaling lipids critical for membrane-protein interactions. These interactions drive key cellular processes, including proliferation, maturation, and development.

I work with two key protein systems: Arc (activity-regulated cytoskeleton-associated protein), a peripheral protein that forms viral-like capsids to encapsulate mRNA in neurons, and receptor tyrosine kinases (RTKs) such as FGFR3 and TrkA, which are central regulators of the same cellular functions governed by phosphoinositide signaling.

As a Biophysics doctoral researcher co-advised across computational and experimental laboratories, my goal is to bridge theory and experiment by using computational modeling to generate hypotheses and experimental techniques to validate them (and vise versa)! This dual approach allows me to investigate biological phenomena with a rigor and perspective that neither discipline offers alone.

In addition to my academic work, I enjoy designing and creating graphics for scientific publications, and film photography as a side hobby. You can find my various efforts below. Enjoy!

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  • 2023 – Now

    Ph.D., Biophysics and Quantitative Biology

    University of Illinois Urbana-Champaign

  • 2018 - 2023

    B.S., Physics with a dual-minor in Mathematics/Cinema and Television Arts

    California State University, Fullerton

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Biology is full of surprises... so is the toolkit we use to study it. Here are some of the project areas that have kept me busy (or just kept me curious).

  • Protein Trafficking

    Cellular protein recruitment

  • Receptor Tyrosine Kinases

    Signaling across the membrane

  • Protein-Protein Dimerization

    Oligomerization Dynamics

  • Phospholipid Binding Kinetics

    Protein affinities at membrane interfaces

  • Optogenetic Cell Death

    Light-controlled Necroptosis

  • Free energy barriers

    Markov State Modeling, Data Decomposition, Transition Pathways

  • Interaction Free Energies

    Changes in Gibbs, Helmholtz, or Entropy that govern cellular processes

  • Minimal In-Cell Modeling

    Atomstic Cytoplasm Remodeling

  • Small-Molecule Drug Kinetics

    Effects of solvation and vdW dynamics

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Computational Biophysics

Molecular Dynamics
NAMD, GROMACS, AMBER, OpenMM, MARTINI
Docking
HADDOCK & AutoDock
Scientific / ML Analysis
MDAnalysis, MDTraj, VMD, PyTorch, TensorFlow
Protein Prediction & Bioinformatics
DESeq2, edgeR, AlphaFold2/3, ESMFold, OpenFold
Visualization
Blender, PyMOL, VMD, ChimeraX, Fiji (ImageJ)
Enhanced Sampling
Plumed & WESTPA2

Computer Administration

Linux server management/administration (Ubuntu/Arch), SLURM Configuration/Setup, Docker Management, HPC cluster management (DGX Ampere/Grace Hopper)

Programming Languages

Python Expert Tcl Expert Bash Expert C++ Proficient R Proficient HTML/CSS Proficient Perl Novice Julia Novice

Relevant Coursework

Graduate Machine Learning for Bioinformatics (CS 582), Graduate Statistical Thermodynamics (CHEM 544), Graduate Scientific Writing (MCB 540), Physical Biochemistry (MCB 446)

Experimental Techniques

Microscopy
TIRF, epifluorescence, live cell imaging, confocal, MINFLUX super resolution, Electron Microscopy (TEM)
Molecular Biology
PCR, qRT-PCR, molecular cloning, western blot, SDS/Agarose gels, RNA purification, RNA-seq prep, transfection, transduction
Cell Biology
Cell culture, primary neuron culture, lentiviral culture, AAV, cell death assays
Protein Biochemistry
Protein purification, size-exclusion chromatography (SEC), nanodiscs, extracellular vesicle prep, surface plasmon resonance (SPR), Bio-Layer Interferometry (BLI)