Noah Trebesch

2023 CV • Google Scholar • LinkedIn
NSF Graduate Research Fellow
Beckman Institute for Advanced Science and Technology
University of Illinois at Urbana-Champaign
3109 Beckman Institute, 405 N Matthews Ave
Urbana, IL 61801
PhD Graduate Student
Center for Biophysics and Quantitative Biology
University of Illinois at Urbana-Champaign
318C Roger Adams Laboratory, 600 S Mathews Ave
Urbana, IL 61801
Education
University of Illinois at Urbana-Champaign, Center for Biophysics and Quantitative Biology (Urbana, IL)
- PhD in Biophysics and Quantitative Biology - December, 2023 (Expected)
University of Minnesota - Twin Cities, College of Science and Engineering (Minneapolis, MN)
- BS in Physics (Biological Physics Emphasis) - May, 2014
- BS in Computer Science (Computational Science Emphasis) - May, 2014
Research Interests
Structural Elucidation and Thermodynamic Characterization of the Mechanisms of Transporters
- Current transporters include NaCT, VcINDY, and LaINDY.
- Uses nonequilibrium driven molecular dynamics, molecular dynamics flexible fitting (MDFF), string method with swarms of trajectories (SMwST), bias-exchange umbrella sampling (BEUS), and other advanced computational techniques.
- Structural modeling and bioinformatics techniques also utilized.
- Provides key insight to biomedical researchers developing drugs targeting transporters and synthetic bioengineers hoping to develop custom biomachines.
Atomistic Modeling, Visualization, and Simulation of Cell-Scale Membrane Structures
- Capabilities encapsulated in xMAS (Experimentally-Derived Membrane of Arbitrary Shape) Builder.
- Analyzes 3D meshes derived from techniques like electron microscopy to determine placement, orientation, and number of lipid molecules.
- Optimizes lipid placement using an MD-based technique, builds atomistic model using a set of lipid conformation libraries, and eliminates complex lipid clashes using an energy minimization simulation technique.
- Current application is a Terasaki ramp, a structural motif from endoplasmic reticula with a complex helicoidal structure like that of a parking ramp.
- Models allow the interplay between atomic-scale biochemistry and cell-scale biophysics to be probed for the first time.
Presentation Recordings
- N. Trebesch, D. B. Sauer, D.-N. Wang, and E. Tajkhorshid. "Mechanistic Insights from Molecular Dynamics Simulations of Large-Scale Conformational Transitions in the INDY Transport Cycle" Biophysical Society 65th Annual Meeting. Virtual (22 Feb 2021).
- N. Trebesch and E. Tajkhorshid. "Incorporating Proteins into Geometrically Complex, Cell-Scale Membrane Models." Blue Waters Symposium 2019. Sunriver, OR (5 Jun 2019).
- N. Trebesch and E. Tajkhorshid. "Simulation of Geometrically Accurate, Multibillion Atom Cellular Membrane Structures." Blue Waters Symposium 2018. Sunriver, OR (6 Jun 2018).
Publications
(*Equal Contribution)
University of Illinois at Urbana-Champaign, Beckman Institute for Advanced Science and Technology (Urbana, IL)
- N. Trebesch and E. Tajkhorshid. "Structure Reveals Homology in Elevator Transporters." bioRxiv. (2023).
- A. Trifan*, D. Gorgun*, M. Salim*, Z. Li*, A. Brace*, M. Zvyagin*, H. Ma*, A. Clyde, D. Clark, D. J. Hardy, T. Burnley, L. Huang, J. McCalpin, M. Emani, H. Yoo, J. Yin, A. Tsaris, V. Subbiah, T. Raza, J. Liu, N. Trebesch, G. Wells, V. Mysore, T. Gibbs, J. Phillips, S. C. Chennubhotla, I. Foster, R. Stevens, A. Anandkumar, V. Vishwanath, J. E. Stone, E. Tajkhorshid, S. A. Harris, and A. Ramanathan. "Intelligent resolution: Integrating Cryo-EM with AI-driven multi-resolution simulations to observe the severe acute respiratory syndrome coronavirus-2 replication-transcription machinery in action." International Journal of High-Performance Computing Applications. 36:5-6, 603-623 (2022).
- D. B. Sauer, N. Trebesch, J. J. Marden, N. Cocco, J. Song, A. Koide, S. Koide, E. Tajkhorshid, and D.-N. Wang. "Structural basis for the reaction cycle of DASS dicarboxylate transporters." eLife. 9, e61350 (2020).
- T. Jiang, P.-C. Wen, N. Trebesch, Z. Zhao, S. Pant, K. Kapoor, M. Shekhar, and E. Tajkhorshid. "Computational Dissection of Membrane Transport at a Microscopic Level." Trends in Biochemical Sciences. 45:3, 202-216 (2020).
- P.-C. Wen*, P. Mahinthichaichan*, N. Trebesch, T. Jiang, Z. Zhao, E. Shinn, Y. Wang, M. Shekhar, K. Kapoor, C. K. Chan, and E. Tajkhorshid. "Microscopic View of Lipids and Their Diverse Biological Functions." Current Opinion in Structural Biology. 51, 177-186 (2018).
- N. Trebesch, J. V. Vermaas, and E. Tajkhorshid. "Computational Characterization of Molecular Mechanisms of Membrane Transporter Function." Computational Biophysics of Membrane Proteins. C. Domene, Ed. 197-236 (Royal Society of Chemistry, Cambridge, 2016).
- J. V. Vermaas, N. Trebesch, C. G. Mayne, S. Thangapandian, M. Shekhar, P. Mahinthichaichan, J. L. Baylon, T. Jiang, Y. Wang, M. P. Muller, E. Shinn, Z. Zhao, P.-C. Wen, and E. Tajkhorshid. "Microscopic Characterization of Membrane Transporter Function by In Silico Modeling and Simulation." Methods in Enzymology: Computational Approaches for Studying Enzyme Mechanism Part B. G. E. Voth, Ed. 578:16 (2016).
University of Minnesota - Twin Cities, College of Science and Engineering (Minneapolis, MN)
- N. Trebesch and J. ViƱals. "A Computational Method for Investigating Bifurcations in Oscillatory Biochemical Reaction Networks." University Honors Program Theses. (2014).
- N. Trebesch. "Updates and Improvements to Hy3S." Hy3S - Hybrid Stochastic Simulation for Supercomputers. (2013).
- N. Trebesch and B. Freund. "Brownian Motion of Ellipsoidal Particles." Methods of Experimental Physics Projects. (2013).
- J. W. Halley, A. Schofield, and B. Berntson. "Use of magnetite as anode for electrolysis of water." Journal of Applied Physics. 111:124911 (2012). (Acknowledgement).