Noah Trebesch

2025 CV • Google Scholar • LinkedIn

Postdoctoral Research Associate
Beckman Institute for Advanced Science and Technology
University of Illinois Urbana-Champaign
3151 Beckman Institute, 405 N Matthews Ave
Urbana, IL 61801

Education

University of Illinois Urbana-Champaign, Center for Biophysics and Quantitative Biology (Urbana, IL)

PhD in Biophysics and Computational Biology - December 2023

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 collective variables, driven MD simulations, the string method with swarms of trajectories (SMwST), bias-exchange umbrella sampling (BEUS), and the weighted histogram analysis method (WHAM).
Also utilizes structural modeling and bioinformatics techniques.
Provides key insight to biomedical researchers developing drugs targeting transporters and synthetic bioengineers hoping to develop custom biomachines.

Investigation of the Evolutionary Relationships between Elevator and Rocking Bundle Transporters

Involves developing from scratch a new computational framework to perform topology-corrected structural comparisons between transporters.
Also involves generating a phylogenetic tree to enable visualization of the evolutionary relationships between transporter families.
Constitutes a powerful new evolutionary context in which the fundamental similarities and differences between elevator and rocking bundle transporters and their mechanisms can be investigated and understood

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 models 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 (Primer Part I and Seminar Part I) and A. Fakharzadeh (Primer Part II and Seminar Part II). "Using Advanced Molecular Dynamics Simulation Techniques to Characterize Large-Scale Conformational Transitions in Transporters" Models, Inference & Algorithms (MIA) Initiative at the Broad Institute of MIT and Harvard. Cambridge, MA (23 Oct 2024).

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 Urbana-Champaign, Beckman Institute for Advanced Science and Technology (Urbana, IL)

N. Trebesch, H. S. Hasdemir, T. Chen, P.-C. Wen, and E. Tajkhorshid. "Molecular dynamics simulations of biological membranes and membrane-associated phenomena across scales." Current Opinion in Structural Biology. 93, 103071 (2025).
S. Pant*, S. Dehghani-Ghahnaviyeh*, N. Trebesch, A. Rasouli, T. Chen, K. Kapoor, P.-C. Wen, E. Tajkhorshid. "Dissecting Large-Scale Structural Transitions in Membrane Transporters Using Advanced Simulation Technologies." Journal of Physical Chemistry B. 129:15, 3703-3719 (2025).
N. Trebesch and E. Tajkhorshid. "Enabling Atomistic Modeling and Simulation of Complex Curved Cellular Membranes with xMAS Builder." bioRxiv. 2025.01.14.632907 (2025).
N. Trebesch. "Computational Investigations of the Structure, Function, and Evolution of Complex Membrane Systems." PhD Dissertation. (2023).
N. Trebesch and E. Tajkhorshid. "Structure Reveals Homology in Elevator Transporters." bioRxiv. 2023.06.14.544989 (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).