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February 2025 Publications

March 4, 2025

Detecting chaos in classical systems? Incomplete discrete choice models? The learnability of knot invariants? A selection of recent publications featuring research using the MGHPCC.

Abbott, Ryan et al (2025), Progress in Normalizing Flows for 4d Gauge Theories, arXiv: 2502.00263 [hep-lat]

Adams, Keir and Connor W. Coley (2025), The impact of conformer quality on learned representations of molecular conformer ensembles, arXiv: 2502.13220 

Bagherian, Hengameh et al (2025), Confronting interacting radiation models for the Hubble tension with Lyman-𝛼 data, Physical Review D, doi: 10.1103/PhysRevD.111.043513

Belhadji, A. et al (2025), Weighted quantization using MMD: From mean field to mean shift via gradient flows, arXiv: 2502.10600 [stat.ML] 

Bishoyi, S.D., Sabharwal, S. & Khanna, G. (2025), Numerical Evidence for Non-Axisymmetric Gravitational “Hair” for Extremal Kerr Black Hole Spacetimes with Hyperboloidal Foliations, Gen Relativ Gravit, doi: 10.1007/s10714-025-03378-1

Brower, Richard C. et al. (2025), Energy-momentum tensor in the 2D Ising CFT in full modular space, arXiv: 2502.00512 [hep-lat] 

Chao, Pengning et al (2025), Sum-of-Squares Bounds on Surface-Enhanced Raman Scattering, arXiv: 2502.09821 [physics.optics] 

Corbeski, Ivan et al (2025), The catalytic mechanism of the RNA methyltransferase METTL3, eLife, doi: 10.7554/eLife.92537.3

Cui, Qiang (2025), Machine learning in molecular biophysics: Protein allostery, multi-level free energy simulations, and lipid phase transitions, Biophysics Reviews, doi: 10.1063/5.0248589

Dolan, Sydney et al (2025), Asynchronous Cooperative Multi-agent Reinforcement Learning with Limited Communication, arXiv: 2502.00558 [cs.MA] 

Fey, Nolan et al (2025), Bridging the Sim-to-Real Gap for Athletic Loco-Manipulation, arXiv:2502.10894 [cs.RO] 

Fishera, B.T. et al (2025), Light-induced reorientation transition in an antiferromagnetic semiconductor, arXiv: 2502.00642  [cond-mat.mtrl-sci]

Joung, Joonyoung F. et al ( 2025), Electron flow matching for generative reaction mechanism prediction obeying conservation law, arXiv: 2502.12979 [cs.LG] 

Kaido, Hiroaki Kaido and Yi Zhang (2025), Universal Inference for Incomplete Discrete Choice Models, arXiv: 2501.17973 [econ.EM]    

Karve, Nachiket et al (2025), Adiabatic Gauge Potential as a Tool for Detecting Chaos in Classical Systems, arXiv: 2502.12046  [nlin.CD]

Koo, B.H. et al (2025), Utilization of Classification Learning Algorithms for Upper-Body Non-Cyclic Motion Prediction, Sensors, doi: 10.3390/s25051297

Le Roy, E.J., & Ummenhofer, C.C. (2025), Past and future modulation of the ENSO teleconnection to Southeast Asian Rainfall by interbasin interactions, Geophysical Research Letters, doi: 10.1029/2024GL111916

Li, Sibei et al (2025), Ground State of the 𝑆=1/2 Heisenberg Spin Chain with Random Ferromagnetic and Antiferromagnetic Couplings, Physical review letters, doi: 10.1103/PhysRevLett.134.086501

Li, Xuhang et al (2025), Enhanced flux potential analysis links changes inenzyme expression to metabolic flux, Molecular Systems Biology, doi: 10.1038/s44320-025-00090-9

Lindsay A. and F. Ruehle (2025), On the Learnability of Knot Invariants: Representation, Predictability, and Neural Similarity, arXiv: 2502.12243 [math.GT] 

Mohammadzadeh, Saeed and Emma Lejeune (2025), Quantifying HIPSC-CM Structural Organization at Scale with Deep Learning-enhanced SARCGRAPH, arXiv: 2501.18714 [q-bio.QM]   

Nevolianis, Thomas et al (2025), Solvation free energies of anions: from new reference data to predictive models, via ChemRxiv, doi: 10.26434/chemrxiv-2025-8bj2t-v2

Nickols, William A. et al (2025), Distinguishing new from persistent infections at the strain level using longitudinal genotyping data, via bioRxiv, doi: 10.1101/2025.02.06.636982

Pandya, Sneh et al (2025), SIDDA: SInkhorn Dynamic Domain Adaptation for Image Classification with Equivariant Neural Networks, arXiv: 2501.14048 [cs.LG] 

Polking, Mark J. et al (2025), Strong long-wave infrared optical response in a topological semiconductor with a Mexican-hat band structure, Phys. Rev. B, doi: 10.1103/PhysRevB.111.085101

McDonald, Matthew A. et al (2025), Bayesian Optimization over Multiple Experimental Fidelities Accelerates Automated Discovery of Drug Molecules, ACS Central Sciences. doi: 10.1021/acscentsci.4c01991

Metzger, Kyle et al (2025), Anomaly preserving contrastive neural embeddings for end-to-end model-independent searches at the LHC, arXiv: 2502.15926 [hep-ex]   

Muraca, M. et al (2025), Integrated Modeling of SPARC H-mode Scenarios: Exploration of the Impact of Modeling Assumptions on Predicted Performance, arXiv: 2502.00187 [physics.plasm-ph] 

Russo, Alessio and Aldo Pacchiano (2025), Adaptive Exploration for Multi-Reward Multi-Policy Evaluation, arXiv: 2502.02516 [cs.LG]

Sokolov, Monja and Qiang Cui (2025), Impact of Fluctuations in the Peridinin-Chlorophyll a-Protein on the Energy Transfer: Insights from Classical and QM/MM Molecular Dynamics Simulations, Biochemistry, doi: 10.1021/acs.biochem.4c00568

Stopper Jr., Michael J. et al (2025), Isolation and Reactivity of Carbene-Stabilized Carbon Disulfide Radical Anions, Inorganic Chemistry, doi: 10.1021/acs.inorgchem.4c05030

Tu, Jia et al (2025), Chemical Vapor Deposition of Monolayer Graphene on Centimeter-Sized Cu(111) for Nanoelectronics Applications, ACS Applied Nano Materials, doi: 10.1021/acsanm.5c00588

Wang, Allen M. et al (2025), Learning Plasma Dynamics and Robust Rampdown Trajectories with Predict-First Experiments at TCV, arXiv: 2502.12327 [physics.plasm-ph] 

Xie, Yu et al (2025), Incongruent Melting and Phase Diagram of SiC from Machine Learning Molecular Dynamics, arXiv: 2502.17804 [cond-mat.mtr-sci]          

Zhang, Ying et al (2025), Emergence of multiple collective motility modes in a physical model of cell chains, via BioRxiv, doi: 10.1101/2025.01.30.635787

Do you have news about research using computing resources at the MGHPCC? If you have an interesting project that you want to tell people about or a paper you would like listed, contact 

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MGHPCC Publications

Research projects

A Future of Unmanned Aerial Vehicles
Yale Budget Lab
Volcanic Eruptions Impact on Stratospheric Chemistry & Ozone
The Rhode Island Coastal Hazards Analysis, Modeling, and Prediction System
Towards a Whole Brain Cellular Atlas
Tornado Path Detection
The Kempner Institute - Unlocking Intelligence
The Institute for Experiential AI
Taming the Energy Appetite of AI Models
Surface Behavior
Studying Highly Efficient Biological Solar Energy Systems
Software for Unreliable Quantum Computers
Simulating Large Biomolecular Assemblies
SEQer - Sequence Evaluation in Realtime
Revolutionizing Materials Design with Computational Modeling
Remote Sensing of Earth Systems
QuEra at the MGHPCC
Quantum Computing in Renewable Energy Development
Pulling Back the Quantum Curtain on ‘Weyl Fermions’
New Insights on Binary Black Holes
NeuraChip
Network Attached FPGAs in the OCT
Monte Carlo eXtreme (MCX) - a Physically-Accurate Photon Simulator
Modeling Hydrogels and Elastomers
Modeling Breast Cancer Spread
Measuring Neutrino Mass
Investigating Mantle Flow Through Analyses of Earthquake Wave Propagation
Impact of Marine Heatwaves on Coral Diversity
IceCube: Hunting Neutrinos
Genome Forecasting
Global Consequences of Warming-Induced Arctic River Changes
Fuzzing the Linux Kernel
Exact Gravitational Lensing by Rotating Black Holes
Evolution of Viral Infectious Disease
Evaluating Health Benefits of Stricter US Air Quality Standards
Ephemeral Stream Water Contributions to US Drainage Networks
Energy Transport and Ultrafast Spectroscopy Lab
Electron Heating in Kinetic-Alfvén-Wave Turbulence
Discovering Evolution’s Master Switches
Dexterous Robotic Hands
Developing Advanced Materials for a Sustainable Energy Future
Detecting Protein Concentrations in Assays
Denser Environments Cultivate Larger Galaxies
Deciphering Alzheimer's Disease
Dancing Frog Genomes
Cyber-Physical Communication Network Security
Avoiding Smash Hits
Analyzing the Gut Microbiome
Adaptive Deep Learning Systems Towards Edge Intelligence
Accelerating Rendering Power
ACAS X: A Family of Next-Generation Collision Avoidance Systems
Neurocognition at the Wu Tsai Institute, Yale
Computational Modeling of Biological Systems
Computational Molecular Ecology
Social Capital and Economic Mobility
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