Welcome to the Computational BioSystems Lab

at the University of Alberta

We study questions at the interface between cell biology, physiology and engineering using a range of computational and theoretical techniques. Often, these questions require the development of new methods for simulating complex systems across disparate length and time scales. More detailed descriptions of our research can be found here.

Information about our research team can be found here. If you are interested in joining the Computational BioSystems Lab, more information can be found here.

Meet the Team

Principal Investigator

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Wylie Stroberg

Assistant Professor of Mechanical Engineering

Computational Biology, Multiscale Simulation, Material Science

Graduate Students

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Ali Bigdeli

PhD Student, Mechanical Engineering

Multiscale modeling of GLAD-based enzymatic nanosensors

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Emad Ghazizadeh

PhD Student, Mechanical Engineering

Protein-based modulation of endoplasmic reticulum shape

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Faiyaz Bin Naser Chowdhury

MSc Student, Mechanical Engineering (joint w/ Prof. McDonald)

Development of machine learning-based coarse grained models for high-entropy alloys.

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Nashit Jalal

PhD Student, Mechanical Engineering (joint w/ Prof. McDonald)

Simulation of high-entropy alloys for thermal-spray deposition

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Sara Sheikhi

PhD Student, Mechanical Engineering (joint w/ Prof. Hogan)

Development of new interatomic potentials for advanced ceramics using machine learning

Alumni

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Alexander Detkov

BSc Student, Engineering Physics (2024), now PhD student at Caltech

Nanoscale flow of polymeric solutions

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Md. Zobayer Hossein

MSc Student (2023)

Thesis Title - Bilayer tension-induced clustering fo the UPR sensor IRE1

Projects

The overarching aim of our lab is to bring new quantitative techniques to problems in biology and nanotechnology. Below you will find examples of our research projects.

Systems Biology of Proteostasis and the Unfolded Protein Response

We are deciphering the control mechanism of the unfolded protein response and protein homeostasis to open new therapeutic avenues for age-associated and protein folding diseases

Reactions in Crowded Cellular Compartments

The study of macromolecular crowding is indispensable for understanding cellular physiology and biochemistry. We are investigating how crowding affects quantitatively the cellular biochemistry, and qualitatively cellular physiology.

Wetting Phenomena of Nanoscale Structures

We are using mesoscopic simulations to investigate wetting and transport properties of complex fluids at the nanoscale.

Recent Publications

List of all publications by the Computational BioSystems Lab

W. Stroberg, S. Schnell (2020). Manuscript Title: Concentration Sensing in Crowded Environments Concentration Sensing in Crowded Environments. bioRxiv.

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J. Eilertsen, W. Stroberg, S. Schnell (2019). Characteristic, completion or matching timescales? An analysis of temporary boundaries in enzyme kinetics. Journal of Theoretical Biology.

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W. Stroberg, J. Eilertsen, S. Schnell (2019). Information processing by endoplasmic reticulum stress sensors. bioRxiv.

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J. Eilertsen, W. Stroberg, S. Schnell (2018). Theory of the reactant-stationary kinetics for a coupled auxiliary enzyme assay. ChemRxiv.

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J. Eilertsen, W. Stroberg, S. Schnell (2018). Characteristic, completion or matching timescales? an analysis of temporary boundaries in enzyme kinetics. arXiv.

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See all publications

Open Positions

Available positions in the Computational BioSystems Lab

  1. Postdoctoral Fellow - There is an opening for a postdoctoral fellow focusing on multiscale modeling and algorithm development for reaction-diffusion simulations in nanoconfined environments. See here for the full job posting and application process.
  2. PhD Research Assistanceship - There is an opening for a PhD student position in Biomedical or Mechanical Engineering focusing on modeling diffusion processes within the endoplasmic reticulum. See here for the full job posting and application process.

Additionally, inquiries from exceptional or self-funded candidates are always welcome. For more information, send a email to Prof. Stroberg with the subject line Interested Candidate for the CBSL, and include a CV and description of why you would like to join our team.

Contact

  • Donadeo Innovation Centre for Engineering, 9211-116 Street NW, Edmonton, AB T6G 1H9