October 2023: Kayla is honored with AIChE's 35 Under 35 award!
Kayla is selected to be one of the American Institute of Chemical Engineers (AIChE's) 35 Under 35 for her contributions in the field of bioengineering.
September 2023: NSF funds a new collaborative project on sustainable bioplastics!
We are grateful to the NSF's Designing Materials to Revolutionize and Engineer our Future (DMREF) program for funding our team - led by Dr. Eleftheria Roumeli at the University of Washington - to pursue the automated, tunable, and integrated design, processing, and modeling of a new class of sustainable bioplastics sourced from biological cells or tissues! (Award 2323976).
September 2023: The NIH funds our work on designing drugs to treat HIV infection in the brain!
We are so excited to have received a grant from the National Institute of Mental Health (NIMH) at the NIH to combine in vitro and in silico models to investigate antiretroviral drug transport across the blood-brain barrier for the treatment of HIV-1 infection in the brain (Award 1R21MH132159-01A1).
August 2023: Outstanding advisor/mentor nominations
Kayla is nominated for an Outstanding Faculty Advisor Award for the second year in a row, and both Kayla and Daisy Fuchs are also recognized as Outstanding Mentors for their undergraduate research mentorship through the Discovery Learning Apprenticeship (DLA) Program at CU Boulder!
July 2023: David Saeb receives a fellowship from D. E. Shaw!
Congratulations to David Saeb for receiving an Undergraduate and Master's Fellowship from D. E. Shaw Research, which will support his attendance at a virtual event where he will present his latest research!
July 2023: Emily Rhodes receives the Teets Family Endowment in Nano-Technology Graduate Fellowship!
Congratulations to Emily Rhodes on receiving this prestigious graduate fellowship, which supports research at CU Boulder in the area of nano-technology. Way to go Emily!
July 2023: AB Nexus funds a new collaborative project on pericentrin
We're excited to have received a seed grant from AB Nexus to pursue a new collaboration with Dr. Chad Pearson at CU Anschutz, and Drs. Loren Hough and Michael Shirts at CU Boulder! We'll be blending simulations and experimental approaches to investigate how pericentrin self-assembly regulates intracellular trafficking for cilia formation and signaling, and how dysregulation of this process contributes to Down Syndrome.
July 2023: AB Nexus funds our research - again!
The RDI Lab and the lab of Dr. Kimberley Bruce at CU Anschutz are honored to be the first established team to receive another full seed grant from this amazing program! This funding will support us in translating our past mechanistic findings to the design of optimized strategies for co-activating microglial receptors to treat Alzheimer’s disease. We greatly appreciate the co-sponsorship of CU Boulder's College of Engineering & Applied Science and the Chemical and Biological Engineering department!
June 2023: Kern Lipid Conference Roger Davis Award - Runner up!
Kayla is designated a runner up for the Kern Lipid Conference Roger Davis Investigator Award for Transitional Faculty! She'll attend the conference in Vail, Colorado, in August.
May 2023: Emily Rhodes receives a fellowship from D. E. Shaw!
May 2023: Emily Rhodes attends Schrödinger's Catalyzing Gender Equity: Early Careers in Computational Sciences Symposium
Congratulations to Emily Rhodes for being invited to participate in a symposium hosted by Schrödinger in New York, on Catalyzing Gender Equity: Early Careers in Computational Sciences in support of women and non-binary computational scientists!
May 2023: The DOE funds our research!
We are excited to have received an award from the DOE Vehicles Technology Office to work towards the development of next-generation lithium-ion batteries! Working with a fantastic team that includes scientists from CU Boulder (RDI Lab, Dr. Mike Toney), NREL (Dr. Rob Tenent), and NMSU (Dr. Hongmei Luo), our part of the puzzle involves the use of reactive MD to achieve a mechanistic understanding of the cathode-elecrolyte interface.
February 2023: Making connections between antibody framework mutations and flexibility!
Published in Frontiers in Immunology, our simulations showcased the ability of antibody framework mutations to shift the distribution of antibody heavy and light chain interface angles, leading to local changes in antibody flexibility via local changes in the solvent accessible surface area. These results could help to establish design principles for creating antibodies with increased specificity, stability, and breadth!
November 2022: Combining deep learning with agent-based modeling to design vaccines against highly mutable pathogens!
Published in Frontiers in Immunology, we employed deep reinforcement learning to drive a coarse-grained, agent-based model of affinity maturation - the evolutionary process by which antibodies evolve - towards the design of a vaccine that maximizes protective immune responses against highly mutable pathogens like HIV.
August 2022: The RDI Lab grows some more!
Emma Aldrich and Rafael Ferreira de Menezes join the lab as graduate students.
July 2022: The NIH funds another area of our research program!
We are grateful to have received a second grant from the National Institute of Allergy and Infectious Diseases at the NIH to combine computational and experimental tools - in collaboration with Dr. Sara Sawyer at CU Boulder - to develop a new animal model for HIV! (Award 1R01OD034046-01)
July 2022: Elucidating new methods to measure lipoprotein lipase activity!
Published in Frontiers in Cardiovascular Medicine, we describe new experimental methods for measuring the activity of lipoprotein lipase - a protein that regulates lipid and lipoprotein processing in microglia and plays a key role in Alzheimer's disease - using small molecule activators and inhibitors. Our simulation results real the likely way in which these small molecules interact with the surface of lipoprotein lipase.
July 2022: Foundations of Molecular Modeling and Simulation (FOMMS): poster and early career awards!
Congratulations to Emily Rhodes, Daisy Fuchs, and Jon Faris for receiving Early Career Researcher Awards at the FOMMS 2022 conference. Another congratulations to Emily for her poster award!!
May 2022: National Academy of Engineering symposium!
Kayla is invited to attend the National Academy of Engineering (NAE)’s Grainger Foundation Frontiers of Engineering 2022 Symposium!
May 2022: The NIH funds our research!
We are excited to have received an award from the NIH's National Institute of Allergy and Infectious Diseases to develop machine learning-driven agent-based models of the immune response to influenza-based antigens! This work is geared towards informing the design of a universal influenza vaccine! (Award 1R21AI169364-01)
April 2022: RDI Lab graduates its first student!
April 2022: First agent-based model of affinity maturation with amino acid-level resolution!
Published in PLOS Computational Biology, alongside Dr. Arup Chakraborty at MIT and Nobel Laureate Dr. Martin Karplus at Harvard, we employed multi-scale modeling approaches to develop the first agent-based model of the affinity maturation process by which antibodies evolve in vivo that operates at the amino acid level! We utilized this model to uncover a novel mechanism of antibody evolution against highly mutable pathogens like HIV and influenza.
October 2021: Aligned binding of cellulases to cellulose surfaces
Published in the Journal of Physical Chemistry Letters, our simulations - in combination with sum frequency generation spectroscopy performed by our collaborators in Denmark - we provided direct evidence for the aligned binding of cellulases to cellulose surfaces. This work could provide a route to designing new cellulases to breakdown otherwise insoluble cellulose materials, leading to improved biomass conversion into green fuels and chemicals.
October 2021: Faculty Success Program Grant
Kayla receives a Grant, awarded through CU Boulder's Office of Faculty Affairs, to participate in the National Center for Faculty Development and Diversity's (NCFDD) Faculty Success Program in spring 2022! This turned out to be an absolutely fantastic program.
October 2021: Jon Faris receives a poster award at the 21st Annual Meeting of the Rocky Mountain Virology Association
Congratulations to Jon for his 2nd-place poster award at the annual Rocky Mountain National Virology Association meeting, which culminated in Jon's co-authored publication in Viruses that summarized select presentations.
September 2021: NSF funds our research!
We are thrilled to have received an award from the NSF - alongside Drs. Will Medlin, Ryan Hayward, and Mike Toney at CU Boulder and Dr. Andreas Heyden at USC - to understand and optimize hydrogenolysis processes for upcycling of polyesters and mixed plastics! Our piece of the puzzle involves carrying out atomistic simulations of metal oxide depolymerization interfaces. Read about our efforts here!
September 2021: Developing predictive tools for future monoclonal antibody development
Published in a Special Collection in Frontiers in Immunology, our bioinformatics analyses showed framework mutations in existing therapeutic antibodies can be accurately predicted solely from baseline human antibody sequence data! Molecular dynamics simulations revealed the mechanistic basis for the evolutionary selection of these mutations. Collectively, these findings suggest baseline human antibody repertoires may be useful as predictive tools to guide future monoclonal antibody development. This article was deemed among the "top viewed spontaneous articles from 2021 published in the section B Cell Biology of Frontiers in Immunology"!
August 2021: The RDI Lab is growing!
Travis Dong, Bailey Zinger, and Emma Lietzke join the lab as graduate students.
June 2021: AB Nexus funds our research!
We are grateful to the AB Nexus program at the University of Colorado for awarding us a research grant to support our collaborative Alzheimer's disease research with Dr. Kimberley Bruce at CU Anschutz!
January 2021: Women ExceLling in COmputational Molecular Engineering (WELCOME) Seminar Series
I am honored to have been invited to give a talk in the WELCOME Seminar Series, which showcases outstanding research being performed by women chemical engineers in the realm of computational molecular engineering!
August 2020: The RDI Lab is officially in business!
Kayla joins the Chemical and Biological Engineering department at the University of Colorado boulder as an Assistant Professor (read the story here! Brian Petersen, Jon Faris, Daisy Fuchs, and Emily Rhodes join the lab as graduate students.