News Snippets

Alex is awarded the CAREER award from the National Science Foundation (NSF) for $0.84M! This 5-year grant will support the lab’s work on path entropy and path complexity for self-organizing biomolecules.

Anna presented her thesis proposal on “Leveraging Deep Learning to Elucidate Kinetic Factors in Biological Self-Assembly”. Congrats to Anna for passing!

Adam defended his thesis titled “From binding to function: A multiscale framework for mechanism discovery and engineering of antivirulence nanobodies targeting B. anthracis S-layers”. Congratulations to Dr. Adam Cecil!

Luc and Anna published their manuscript entitled “Probabilistic forecasting for coarse-grained molecular dynamics” in the Journal of Chemical Theory and Computation. Congrats to them all!

Anna published her manuscript entitled “Active subspace learning for coarse-grained molecular dynamics” in the Journal of Chemical Physics. Congrats to all!

Welcome to Helen, a 3rd year PhD student in the Materials Science program! Helen joins us from the Toberer group, where she had been working on high-entropy alloys. She will be working on random heteropolymer-based nanoparticles and patchy particle assembly. Looking forward to working together!

Welcome to Madeline, a new PhD student in Chemical and Biological Engineering (CBE)! Madeline is co-advised by both Alex and Prof. Diego Gomez-Gualdron (also in CBE). She will be working on machine learning models to create chemically-transferable models for peptides, polymers, and metal-organic frameworks. Looking forward to working together!

Alex attended Pacifichem 2025 in Hawaii and gave three talks to represent the lab. The talks featured the probabilistic forecasting work from Luc and Anna, the bacterial microcompartment shell assembly work from Emiel, and the anti-virulence nanobody engineering work from Adam.

Tariq presented his thesis proposal on “Learning Supramolecular Coiled-Coil Self-Assembly” to ultimately design coiled-coil-based biomaterials by leveraging both multiscale simulations and machine learning. Congrats to Tariq for passing!

Alex attended the AIChE Annual Meeting 2025 in Boston and gave three talks to represent the lab. The talks featured the probabilistic forecasting work from Luc and Anna, the bacterial microcompartment shell assembly work from Emiel, and the anti-virulence nanobody engineering work from Adam.

Luc defended his thesis titled “Development of data-driven coarse-grained models for stimuli-responsive proteins”. Congratulations to Dr. Luc Christians!

Alex is awarded the R35 (Maximizing Investigators’ Research Award or MIRA) from the National Institutes of Health (NIH) for $1.7M. This is a 5-year award that provides broad support for the lab’s research on self-assembling protein complexes. We will specifically look at two families of proteins (bacterial microcompartments and surface-layer proteins) investigating how combinatorial and conformational complexity regulate assembly outcomes.

Alex attended MTSM 2025 hosted at the University of Wisconsin-Madison. He presented his talk entitled “Advancing coarse-graining methods using statistical mechanical principles and probabilistic machine learning.” Thanks to Rosy Cersonsky for the invitation!

Jack joined the group as a summer undergraduate researcher as part of the ICECRM REU program. He will be working on engineering linker proteins for artificial pyrenoids.

Katherine published her manuscript entitled “Deciphering self-assembly mechanisms of IRMOF-n-inspired three-dimensional cubic-symmetry nanoporous crystals from multiscale simulations” in Chemistry of Materials. Congrats to all!

Alex visited the Department of Chemical and Biological Engineering at the University of Buffalo to give a seminar! His seminar is titled "Data-driven molecular dynamics simulations of self-organizing complexes.”

LMAC was awarded a renewed allocation on NSF-funded HPC resources through the Maximize ACCESS program. With the group growing, our compute needs have also grown and this renewal now supports all of our research programs (leveraging both CPUs and GPUs). The new project is entitled “Multiscale Simulations of Macromolecular Assemblies.” We are thankful for the support!

Alex presented his invited talk entitled “Probabilistic forecasting for coarse-grained molecular dynamics” at the 2025 Mesilla Chemistry workshop.

Alex visited the Quantitative Biosciences and Engineering (QBE) program at Colorado School of Mines to give a seminar! His seminar is titled "Combining molecular dynamics and machine learning to study biomolecular complexes.”

The lab was invited by the Research Computing team at Mines to participate in a pilot of the Google Cloud Platform (GCP). Cloud computing may offer us the infrastructure that we need as our compute requirements grow and continue to push toward GPU and hybrid GPU/CPU workflows. Looking forward to the pilot!

Ethan and Adam, in collaboration with the Remaut and Kudryashev groups, published their manuscript entitled “Architecture of the Sap S-layer of Bacillus anthracis revealed by integrative structural biology” in PNAS. Congrats to them all!

Adam, Mukund, and Kaylee published their manuscript entitled “Molecular dynamics and machine learning stratify motion-dependent activity profiles of S-layer destabilizing nanobodies” in PNAS Nexus. Congrats to them all!

Mia, a FIRST undergraduate scholar in QBE, has joined the lab to study the dynamics of coiled-coil proteins under the influence of small molecule drugs. Looking forward to learning together!

Alex visited the Materials Science program at University of Wyoming to give a seminar! His seminar is titled "Data-driven molecular dynamics simulations of self-organizing complexes.”

In honor of the 2024 Nobel Prize in Chemistry, Alex organized a student competition for de novo protein design. Students will be tasked with designing stable proteins (or oligomers) that form the shape of the Mines reuleaux. The contest will run for a month and winners will receive cash prizes. Thanks to Suzy, Duncan, Christian, and Josh for their feedback!

We welcome our most recent GPU workstation addition to the lab, affectionately named Shannon.

Alex attended the 2024 AIChE Annual Meeting in San Diego, CA. He presented a talk entitled “Holistic framework for coarse-graining and back-mapping through active subspace learning.”

Welcome to Sanjib, our newest postdoc to join LMAC! Sanjib will be working on coarse-grained modeling and simulation of pH-dependent protein assemblies.

Emiel successfully defended his PhD thesis proposal entitled “Modeling and designing stoichiometry and morphology of bacterial microcompartments.” Congrats to Emiel!

Alex was invited to give a talk entitled “Promoting educational and outreach activities throughout the HDR institutes via a centralized repository” at the 2024 HDR Institutes meeting.

Gabe, an undergraduate in QBE, will be investigating the ion-dependent dynamics of the EA1 S-layer protein. Looking forward to learning together!

Three undergraduate students (Mimi, Ben, and Byron) and one Master’s student (Kyle) join the group to continue the work on the active subspace coarse-graining method (in collaboration with Steve Pankavich in AMS). Looking forward to learning together!

Emiel was awarded the Outstanding Student Poster Award for Exemplary Research (Division of Physical Chemistry) at the ACS Fall 2024 meeting! His poster is entitled “Elucidating self-assembly principles of a model bacterial microcompartment through molecular dynamics simulations.”

The group attended ACS Fall 2024 in Denver, CO! Luc, Adam, Katherine, and Meagan all gave excellent talks while Emiel presented his poster on BMCs.

Alex went to his first Foundations of Molecular Modeling and Simulation (FOMMS) conference. This year, FOMMS was hosted in Snowbird, UT. While there, Alex presented a poster entitled “Advancing coarse-graining methods using statistical mechanical principles and machine learning.”

Alex (in collaboration with the NSF ID4 center) hosted a 2-day workshop on “Integration of data fluency into 6th-12th grade education” from July 11-12. The goal of the workshop is to bring together 6th-12th grade teachers, educators, pedagogy specialists, district administrators, scientists, and engineers to design curricular materials and learning modules (via a hackathon style environment) to increase data fluency and data analytic skills. Thanks to Emily, Brad, and Matthew for helping to organize!

Alex attended his first Gordon Research Conference (GRC) for Systems Chemistry. He was invited to give a lightning talk entitled “Coarse-grained modeling and simulation of pleomorphic assemblies.”

Alex and Joe represented CBE for the SUMMET 2024 cohort at Mines. They shared a general overview of Chemical and Biological Engineering before going deeper into our specific research interests. Both Alex and Joe led hands-on activities for computational and experimental research, respectively. Thanks to Anna for helping out!

Hayley, an undergraduate in BME, will be joining LMAC to study the permeation of small molecules through BMC hexamers. Her project is supported by an NSF REU. Looking forward to learning together!

Alex served as a judge for the technical pitches and poster symposium at the 2024 Rocky Mountain MESA (Math, Engineering, and Science Achievement) Jamboree hosted at Mines’ campus. Teams of high school students presented their engineering pitches and demos that each targeted a challenge or need of their choice.

Alex visited CSU for the 2024 Front Range Microbiome Symposium in his role as a member of the steering committee. Thanks to Tiffany and Susan for organizing!

Alex attended ACS Spring 2024 in New Orleans, LA to give an invited talk entitled “Integrating molecular dynamics simulations and deep learning models to investigate S-layer depolymerization.”

We welcome two new GPU workstations into the lab. They are affectionately named Langevin and Kubo.

Luc, Ethan, Emiel, and Evan published their manuscript entitled “Formalizing coarse-grained representations of anisotropic interactions at multimeric protein interfaces using virtual sites” in the Journal of Physical Chemistry B. Congrats to them all!

Bea is a MS student in Data Science who will be doing research with us as part of an independent study. Her project is a collaboration with Terry Lowe (MME) and will focus on machine learning classifiers to distinguish the formability of sheet metal used in biomedical devices. Looking forward to learning together!

Welcome to our new PhD students, Anna and Tariq! Anna will be working on machine learning methods for molecular simulations while Tariq will be working on machine learning methods for protein assembly prediction.

Luc’s work on coiled-coil protein hydrogels (in collaboration with the Montclare group at NYU) was published in Biomacromolecules. The manuscript is entitled “Computational prediction of coiled–coil protein gelation dynamics and structure.”

Adam’s work on the oligomeric lipoprotein SlyB (in collaboration with the Remaut group at VIB) was published in Nature. The manuscript is entitled “SlyB encapsulates outer membrane proteins in stress-induced lipid nanodomains.”

Alex visited the Department of Chemical Engineering at University of Washington to give a seminar! His seminar is titled "Probing the dynamics of macromolecular assemblies using data-driven coarse-grained modeling and simulation.”

Katherine presented her thesis proposal entitled “Exploring self-assembly dynamics in porous crystals: insights, mechanisms, and implications for synthesis.” She successfully defended her thesis proposal!