Pak Lab
Pak Lab

Pak Lab

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Welcome to the Pak Lab (Department of Chemical and Biological Engineering, Colorado School of Mines). Our vision is to advance (bio)macromolecular materials design by pioneering multiscale computational methods and elucidating spatiotemporal organization principles

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Our Research

Our research involves the investigation of:

Thermodynamic and kinetic control over (bio)macromolecular assemblies through modification of molecular building blocks (e.g. proteins) and environmental factors

Fundamental structure-dynamics-function relationships in biological systems to inspire emergent biomaterial properties or to identify novel biomedical strategies

Multiscale computational algorithms (e.g. coarse-graining) to enable biomolecular simulations that require time and length scales inaccessible to atomic-resolution simulations

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Our Team

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Our team brings together a diverse group of undergraduate students, graduate researchers, and postdoctoral scholars. Our members span chemical engineering, materials science, chemistry, computer science, applied mathematics, and quantitative biosciences at Colorado School of Mines (Golden, CO).

Recent Publications

Deciphering self-assembly mechanisms of IRMOF-n-inspired three-dimensional cubic-symmetry nanoporous crystals from multiscale simulations
Architecture of the Sap S-layer of Bacillus anthracis revealed by integrative structural biology
Molecular dynamics and machine learning stratify motion-dependent activity profiles of S-layer destabilizing nanobodies
Formalizing coarse-grained representations of anisotropic interactions at multimeric protein interfaces using virtual sites
Computational prediction of coiled-coil protein gelation dynamics and structure
SlyB encapsulates outer membrane proteins in stress-induced lipid nanodomains
OpenMSCG: A software tool for bottom-up coarse-graining
Critical mechanistic features of HIV-1 viral capsid assembly
Bottom-up coarse-graining: Principles and perspectives
Inositol hexakisphosphate (IP6) accelerates immature HIV-1 Gag protein assembly toward kinetically trapped morphologies

Recent News

Alex presents at the Midwest Thermodynamics and Statistical Mechanics conference!
June 6, 2025
Jack joins LMAC as an undergraduate REU student!
May 19, 2025
Katherine and coworkers publish their work on IRMOF-n assembly in Chem. Mater.!
May 16, 2025
Alex presents a seminar at the University of Buffalo!
April 2, 2025
The lab renews its Maximize ACCESS allocation!
March 17, 2025
Alex presents at the 2025 Mesilla Chemistry workshop!
March 11, 2025
Alex presents a seminar at QBE Mines!
March 5, 2025
LMAC joins a pilot program to test out the Google Cloud Platform!
January 8, 2025
Ethan and coworkers publish their work on the Sap S-layer structure in PNAS!
December 9, 2024
Adam and coworkers publish their work on classifying the activities of anti-virulence nanobodies in PNAS Nexus!
November 26, 2024
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