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/synthetic)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/synthetic)macromolecular assemblies through modification of molecular building blocks (e.g. proteins or polymers) and environmental factors

Fundamental structure-dynamics-function relationships in biological and soft matter systems to inspire emergent material properties or to identify novel technological strategies

Multiscale computational algorithms (e.g. coarse-graining) to enable macromolecular 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

Probabilistic forecasting for coarse-grained molecular dynamics
Active subspace learning for coarse-grained molecular dynamics
Interactions of common synthesis solvents with MOFs studied via free energies of solvation: Implications on stability and polymorph selection
Machine learning to design metal-organic frameworks: progress and challenges from a data efficiency perspective
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

Recent News

Alex is awarded an NSF CAREER award!
April 28, 2026
Anna passes her thesis proposal defense!
April 27, 2026
Adam passes his thesis defense!
April 17, 2026
Luc and coworkers publish the probabilistic forecasting method in J. Chem. Theory Comput.!
April 13, 2026
Anna and coworkers publish the active subspace coarse-graining method in J. Chem. Phys.!
April 13, 2026
Helen joins the group!
April 13, 2026
Madeline joins the group!
January 12, 2026
Alex presents at Pacifichem 2025!
December 17, 2025
Tariq passes his thesis proposal defense!
November 14, 2025
Alex presents at the AIChE Annual Meeting 2025 in Boston!
November 2, 2025
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