ChE 2026 Spring Seminar Series – Alexander Pak, PhD

Details

Speaker: Alexander Pak, PhD
Assistant Professor in the Department of Chemical and Biological Engineering, Quantitative Biosciences and Engineering Program, and Materials Science Program
Colorado School of Mines

Title: Mechanisms of Morphological Transitions in Self-Organizing Molecular Systems

Abstract: Elucidating how microscopic molecular interactions give rise to macroscopic function remains a central challenge in soft and biological materials. Many self-organizing supra- and macromolecular systems admit multiple accessible morphologies under similar chemical conditions. Subtle changes in interaction strength, flexibility, or environment can redirect assembly or trigger disassembly, leading to distinct structural and functional outcomes. In this context, the traditional structure-function paradigm is incomplete without a dynamical perspective on how collective molecular motions govern morphology selection. In this seminar, I will present a multiscale computational framework, augmented by data-driven analysis, to uncover the thermodynamic and dynamical mechanisms underlying morphological transitions in select systems. I will show how effective free energy landscapes derived from quantum-to-coarse-grained simulations identify thermodynamic windows and pathways for metal-organic framework assembly. I will then demonstrate how competing morphologies in bacterial microcompartment shell proteins are selected through linker-mediated collective dynamics and how machine learning applied to molecular dynamics trajectories reveals motion-dependent mechanisms that promote controlled depolymerization of surface-layer lattices. Finally, I will introduce machine-learning-enhanced coarse-grained models that preserve structural fidelity while retaining key dynamical signatures, which will enable systematic distinction between thermodynamically and kinetically governed transitions. Together, these studies illustrate how integrating statistical mechanics with data-driven modeling provides mechanistic insight into structure-dynamics-function relationships and establishes a foundation for predictive control of morphology in complex soft materials.

Bio: Alex is currently an Assistant Professor of Chemical and Biological Engineering at Colorado School of Mines, where he has been since January of 2021. He received his B.S. in Chemical Engineering from M.I.T and his Ph.D. in Chemical Engineering from UT Austin. His graduate research focused on fundamental charge storage mechanisms using carbon-based nanomaterials for supercapacitor applications. As a postdoc, Alex received the F32 NIH Postdoctoral National Research Service Award, which supported his transition into computational biophysics as part of the Chemistry Department at the University of Chicago. Alex is the recipient of the R35 MIRA award from the NIH. His group focuses on the development of multiscale simulation techniques and their application toward both fundamental understanding and engineered control of self-assembled complexes, including for macromolecules, polymers, and porous crystals.