News Snippets

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!

LMAC was awarded time on the Anton 2 machine hosted at PSC. Anton 2 is a specialized supercomputer that is capable of biomolecular simulations on the scale of micro- to milliseconds. Our award will allow us to study a conformational switch that we hypothesize regulates the assembly of bacterial surface layers.

The group traveled to Orlando, FL to present at the 2023 AIChE Annual Meeting. Luc, Adam, and Katherine all gave excellent talks!

LMAC renews its allocation on NSF-funded HPC machines through the Maximize ACCESS program. These resources are a central lifeblood for the group. We are thankful for the support!

Alex visited the Department of Chemical and Biological Engineering at Colorado State University (CSU) to give a seminar! His seminar is titled "Probing the dynamics of biomolecular assemblies through coarse-grained modeling and simulation.”

Ethan presented and successfully defended his Master’s thesis entitled “Elucidating protein-protein interactions that regulate the structure of bacterial protein assemblies using multiscale modeling methods.” Congrats to Ethan! Best of luck to him as he continues his graduate studies as a PhD student at Northwestern University.

Mukund (QBE), Kaylee (CS), Carla (CS), and Philip (ME) have joined the lab for the summer as undergraduate researchers. The cohort is a mix of students supported by an REU and by the SURF program. Mukund and Kaylee will be working on machine learning methods to predict nanobody epitopes while Carla and Philip will be working on machine learning methods to predict coiled-coil protein properties. Looking forward to learning together!

Adam presented his thesis proposal entitled “Computational design of therapeutic nanobodies to target S-layer virulence factors.” He successfully defended his thesis proposal!

Emiel is a PhD student in CBE who will be working on engineering the self-assembly of bacterial microcompartments. Looking forward to learning together!

Meagan is a part-time MST student in Chemistry / part-time NREL researcher who is joining LMAC. Specifically, her project will be on supra-coarse-grained model development of cellulose. Looking forward to learning together!

Alex visited the Department of Applied Mathematics and Statistics at Colorado School of Mines to give a seminar! His seminar is titled "Coarse-Graining as a Hypothesis Testing Framework to Bridge the Microscale to Macroscale.”

Alex visited the Department of Chemistry at the University of Colorado Denver to give a seminar! His seminar is titled "Probing the Dynamics of Viral Assemblies andBeyond Through Coarse-Grained Modeling.”

LMAC successfully renewed its NSF-funded HPC allocation, now under the Maximize ACCESS program. This allocation is absolutely essential as it supports the majority of the group’s compute needs. We are thankful for the support!

Ethan, a former undergraduate research in LMAC, officially joins as a Master's Thesis student! He will be continuing his work on S-layers and bacterial microcompartments.

Leah (CBE/AMS), Cavan (CBE), Sophia (QBE), and Noor (CBE) have joined the group as undergraduate researchers. Leah will investigate reaction-diffusion models as an alternative to molecular dynamics simulations. Cavan will investigate the free energies of BMC hexamer binding. Noor and Sophia will investigate peptides as viral inhibitors, e.g., for SARS-CoV-2. Looking forward to learning together!

Our computational resources have expanded with 9x new A5000 GPUs! These machines are shared with the Gomez-Gualdron group and will enable more high-throughput molecular dynamics simulations and ML/AI model training. We have affectionately named the machines after Ada Lovelace.

Luc passes his thesis proposal defense with flying colors! Congrats, Luc! Luc’s thesis proposal is titled “Development of coarse-grained modeling and deep learning framework to design stimuli-responsive peptide-based hydrogels.”

We set up a new GPU workstation today (affectionately named Helmholtz). This latest computer joins our in-house GPU workstation ensemble (Maxwell, Boltzmann, and Gibbs). Plenty more names to go!‍

Laura is a rising high-school junior who has joined LMAC for the summer as part of the CS@Mines program. Laura will be working on Python code development for data-driven coarse-graining methodologies. Looking forward to learning together!

Hana graduates from Mines (and LMAC) and finishes her MSNT in QBE. Hana is now an Associate Project Engineer at Automated Engineering Services, Inc. We wish you the best!

Alex has been awarded a NIH R21 grant through NIAID. The grant (R21-AI168838) is titled “Multiscale Modeling of B. Anthracis Surface Layer Assembly and Depolymerization by Nanobodies.”

Cosette presents her work on BMCs at the Undergraduate Research Symposium. This was also Alex’s first time at the UR Symposium. Fun to see all the neat UG research happening at Mines!

Alex has been awarded a NSF Engineering Research Initiation (ERI) grant (also, his first independent grant). The grant (NSF 2138620) is titled “ERI: Modeling Bacterial Microcompartment Assembly Using a Data-Driven Multiscale Framework.”

Luc has won the inaugural Mines VPRTT Materials Science Graduate Fellowship Program award. The fellowship is funded in part by the ID4 NSF HDR center and recognizes graduate students at the intersection of materials science and data science.

LMAC was awarded a new XSEDE allocation to gain access to NSF-funded supercomputers around the nation. The allocation request entitled “Coarse-grained molecular dynamics simulations of biomolecular assemblies” will support most of the current research activities in the group.

Katie (CBE) and Isabella (CBE) have joined the group to investigate the dynamics of coiled-coil proteins for drug delivery applications. Looking forward to learning together!

Katie and Isabella are undergraduate researchers in CBE who have joined LMAC. Both Katie and Isabella will be working on protein-based hydrogels. Looking forward to learning together!

Adam and Katherine (co-advised by Prof. Diego Gomez-Gualdron) are new PhD students joining LMAC. Adam will be working on SLPs and nanobody engineering while Katherine will be working on MOF self-assembly. Looking forward to learning together!

Mitch graduates from Mines (and LMAC) with a MSNT in QBE. Mitch will be working on his startup Amalgam as CTO. Best of luck!

Alex and Diego present a vision to integrate machine learning into the CBE curriculum at the West/Southwest CBE Department Head meeting.

Alex presented a talk at ACS Fall 2021 entitled “Investigating cooperative SARS-CoV-2 spike glycoprotein and ACE2 receptor binding using coarse-grained modeling and simulation.”

Ethan, Evan, and Cosette are undergraduate researchers (from CBE, CBE/Chemistry, and Chemistry, respectively) who have joined LMAC. Ethan will be working on SLPs, while both Evan and Cosette will be working on BMCs. Looking forward to learning together!

Alex is teaching a new module on Sustainability and Health during this summer’s SUMMET program at Mines. The modules are focused on Python programming integrated with computational molecular sciences. Students will have a chance to play around with interactive code and simulation data.

Our dedicated A100 GPUs have finally arrived after some supply chain/shipping delays. These will be situated in Wendian, the high-performance computing (HPC) cluster at Mines, and supported by our colleagues at CIARC. They will take a few more weeks to setup but these nodes will exponentially increased our computing capabilities :)

Alex presented a talk at the 2021 BPS Annual Meeting entitled “Exploring the diverse morphological landscape of self-assembled HIV-1 proteins from a coarse-grained perspective.”

LMAC received its first batch of GPU Workstations today! We’ll be busy setting these up so that we can finally get started on our research. These high performance workstations will help bridge the time until our HPC cluster nodes (currently delayed) become available.

Welcome to our new graduate students, Hana Mawlawi (QBE), Luc Christians (CBE), and Mitch Hale (QBE). We’re excited to have them! These brave students will help shape LMAC from its inception. Hana is interested in metal-ion-binding proteins, such as S-layer proteins, Luc in coarse-graining theory and self-assembling peptides, and Mitch in bacterial microcompartments. We have a lot to do!

Alex begins his first day at Mines! This marks the start of the Laboratory for Multiscale Modeling of Macromolecular Assembly and Control (LMAC). Alex will be busy recruiting students, setting up the lab, and teaching graduate stat mech (CBEN 624) this term.