AI: Beyond AlphaFold
We are leveraging the latest breakthroughs in AI, generative models, and integrative simulation that go well beyond proteins. RNA is the next frontier.
Los Alamos National Laboratory
Decoding the Language of RNA
We combine cutting-edge AI, computer simulations, and experimental approaches to reveal the mechanisms of drugs that target ribosomes, riboswitches, and non-coding RNAs at atomic resolution.
Research Focus
Ribosome Dynamics
Large-scale molecular simulations reveal the energy landscape of tRNA selection and translocation, uncovering how the ribosome achieves remarkable accuracy in protein synthesis.
Riboswitch Mechanisms
Joint computational and experimental studies illuminate how riboswitches—nature's genetic switches—sense small molecules and regulate gene expression with exquisite precision.
Non-coding RNAs
Pioneering structural studies of lncRNAs reveal their complex architecture and key roles in development, disease, and epigenetic mechanisms.
Our Team
Our interdisciplinary team combines expertise in AI, computational biophysics, structural biology, high-performance computing, and experimental biochemistry.
Principal Investigator
Karissa Sanbonmatsu, Ph.D.
Leading research on RNA structure and dynamics through innovative computational approaches. Pioneer in billion-atom molecular simulations and structural studies of long non-coding RNAs.
Postdoc
Nathan Jespersen
Cryo-EM, AI, MD
Postdoc
Jignesh Prajapati
MD simulation, RNA modeling and folding, structural biology
Collaborators
Joachim Frank
Columbia University
Cryo-EM
Nicholas Lubbers
Los Alamos, AI Division
AI
José Onuchic
Rice University, CTBP
Protein/RNA folding
Anna Lappala
Harvard University
AI, Computational Physics
Jeannie Lee
Massachusetts General Brigham (MGB)
X Chromosome Inactivation
Alumni
Jignesh Prajapati
Birla Institute of Technology And Science (BITS)
Assistant Professor
Ankush Singhal
Eli Lilly, AI Division
Scientist
Dylan Girodat
University of Lethbrige
Assistant Professor
Doo Nam Kim
Pacific Northwest National Laboratory
Scientist
Ashutosh Dharap
University of South Florida
Assistant Professor
Serdal Kirmizialtin
NYU Abu Dhabi
Associate Professor
Irina Novikova
Pacific Northwest National Laboratory
Scientist
Paul Whitford
Northeastern University
Associate Professor
Scott Hennelly
Los Alamos
Principal Investigator
Andrea Vaiana
NTX/UNM
Scientist
Publications
Human protein synthesis requires aminoacyl-tRNA pivoting during proofreading
Nature CommunicationsStatistical relationships across epigenomes using large-scale hierarchical clustering
Bioinformatics AdvancesSupercomputing in the biological sciences: Toward Zettascale and Yottascale simulations
Current Opinion In Structural BiologyGeometric alignment of aminoacyl-tRNA relative to catalytic centers of the ribosome underpins accurate mRNA decoding
Nature CommunicationsZinc-finger protein CNBP alters the 3-D structure of lncRNA Braveheart in solution
Nature CommunicationsFour-dimensional chromosome reconstruction elucidates the spatiotemporal reorganization of the mammalian X chromosome
Proceedings of the National Academy of SciencesScaling molecular dynamics beyond 100,000 processor cores for large‐scale biophysical simulations
Journal of Computational ChemistryCOOLAIR Antisense RNAs Form Evolutionarily Conserved Elaborate Secondary Structures
Cell ReportsA G-Rich Motif in the LncRNA Braveheart Interacts with a Zinc-Finger Transcription Factor to Specify the Cardiovascular Lineage
Molecular CellRegulation of the Mammalian Elongation Cycle by Subunit Rolling: A Eukaryotic-Specific Ribosome Rearrangement
CellExcited States of Ribosome Translocation Revealed through Integrative Molecular Modeling
Proceedings of the National Academy of SciencesHead Swivel on the Ribosome Facilitates Translocation Via Intra-Subunit tRNA Hybrid Sites
NatureSimulating Movement of tRNA Into the Ribosome During Decoding
Proceedings of the National Academy of SciencesNews
COOLAIR Paper Published in Cell Reports
Our research on COOLAIR antisense RNAs revealing evolutionarily conserved elaborate secondary structures has been published.
Read more →Braveheart LncRNA Study in Molecular Cell
New findings on how a G-Rich motif in the lncRNA Braveheart specifies cardiovascular lineage development.
Read more →Cell Publication on Ribosome Dynamics
Landmark study reveals eukaryotic-specific ribosome rearrangement mechanism for regulating protein synthesis.
Read more →Media and Resources
Videos
Molecular simulations, research presentations, and scientific visualizations of RNA dynamics.
Watch Videos →Images
Gallery of molecular structures, simulation snapshots, and scientific illustrations.
View Gallery →Jobs
Join our team! Current openings for postdocs, graduate students, and research positions.
View Openings →Contact
Los Alamos National Laboratory
Theoretical Biology and Biophysics GroupTheoretical Division
P.O. Box 1663
Los Alamos, NM 87545
New Mexico Consortium
Biological Laboratory100 Entrada Drive
Los Alamos, NM 87544 newmexicoconsortium.org