Below is a list of publications acknowledging UChicago Compute Infrastructure, support, and services.

2025

• On the effectiveness and generalization of race representations for debiasing high-stakes decisions
  Nguyen, D., & Tan, C.
• Entailment Progressions: A Robust Approach to Evaluating Reasoning Within Larger Discourse
  Shastry, R., Chiril, P., Charney, J., & Uminsky, D.
• Can AI Weather Models Predict the 2024 Dubai Rainfall, a Regional Grey Swan?
  Sun, Y. Q., Hassanzadeh, P., & Shaw, T. A.
• A Century of Inflation Narratives
  Heddaya, M., Tan, C., Voigt, R., Zeng, Q., & Zentefis, A.
• Deep Learning and Non-Invertible Symmetries in Gauge Theories
  Apte, A.
• Cer-Eval: Certifiable and Cost-Efficient Evaluation Framework for LLMs
  Wang, G., Chen, Z., Li, B., & Xu, H.
• The content, structure, and history of English trait words
  Liu, Y., Charlesworth, T., Koch, A., Luttrell, A., & Jackson, J. C.
• Efficient Distributed Optimization under Heavy-Tailed Noise
  Lee, S. H., Zaheer, M., & Li, T.
• Humans and convolutional neural networks prioritize similar visual features in intuitive physics judgments
  Calabro, R., Bhattacharyya, K., Bainbridge, W., & Leong, Y. C.
• Predicting whole-brain neural dynamics from prefrontal cortex functional near-infrared spectroscopy signal during movie-watching
  Gao, S., Nash, R., Burns, S., & Leong, Y. C.
• A Multimodal Seq2Seq Transformer for Predicting Brain Responses to Naturalistic Stimuli
  He, Q., & Leong, Y. C.
• Automated scoring of the Ambiguous Intentions Hostility Questionnaire using fine-tuned large language models.
  Lyu, Y., Combs, D., Neumann, D., & Leong, Y. C.
• Emotional arousal enhances narrative memories through functional integration of large-scale brain networks
  Park, J. S., Gollapudi, K., Ke, J., Nau, M., Pappas, I., & Leong, Y. C.
• Linear representations of political perspective emerge in large language models
  Kim, J., Evans, J., & Schein, A.
• Unraveling Misinformation Propagation in LLM Reasoning
  Feng, Y., Wang, Y., Cui, S., Faltings, B., Lee, M., & Zhou, J.
• AbsenceBench: Language Models Can’t Tell What’s Missing
  Fu, H. Y., Shrivastava, A., Moore, J., West, P., Tan, C., & Holtzman, A.
• Linearly Decoding Refused Knowledge in Aligned Language Models
  Shrivastava, A., & Holtzman, A.
• Data assimilation with machine learning surrogate models: A case study with FourCastNet
  Adrian, M., Sanz-Alonso, D., & Willett, R.
• Evaluating the Goal-Directedness of Large Language Models
  Everitt, T., Garbacea, C., Bellot, A., Richens, J., Papadatos, H., Campos, S., & Shah, R.
• HyPerAlign: Interpretable Personalized LLM Alignment via Hypothesis Generation
  Garbacea, C., & Tan, C.
• MOFA: Discovering Materials for Carbon Capture with a GenAI-and Simulation-Based Workflow
  Yan, X., Hudson, N., Park, H., Grzenda, D., Pauloski, J. G., Schwarting, M., Harb, H., Foreman, S., Knight, C., Gibbs, T., Chard, K., Chaudhuri, S., Tajkhorshid, E., Foster, I., Moosavi, M., Ward, L., & Huerta, E. A.
• Cartesian Equivariant Representations for Learning and Understanding Molecular Orbitals
  King, D., Grzenda, D., Zhu, R., Hudson, N., Foster, I., Cheng, B., & Gagliardi, L.
• Historical Polarization in Legislative Support for Civil Rights in the United States
  Jackson, J. C., Liu, Y., & Kteily, N. S.
• Prejudice Tied to State Centralization in Historical Societies
  Dillion, D., Liu, Y., Chen, Y., Watts, J., Zhao, C., Baral, S., Bucker, W., Atari, M., Kteily, N., & Jackson, J. C.
• Rising Moralization in Social Media Discourse
  Puryear, C., Brady, W., Jackson, J. C., Leong, Y., & Kteily, N.
• Seeds of Discourse: A Multilingual Corpus of Direct Quotations from African Media on Agricultural Biotechnologies
  Chiril, P., Spreadbury, T., Rock, J. S., Dowd-Uribe, B., & Uminsky, D.
• A Century of Inflation Narratives
  Heddaya, M., Tan, C., Voigt, R., Zeng, Q., & Zentefis, A.
• A machine learning model using clinical notes to identify physician fatigue
  Hsu, C.-C., Obermeyer, Z., & Tan, C.
• Hypobench: Towards systematic and principled benchmarking for hypothesis generation
  Liu, H., Huang, S., Hu, J., Zhou, Y., & Tan, C.
• Relu neural networks with linear layers are biased towards single-and multi-index models
  Parkinson, S., Ongie, G., & Willett, R.
• Prediction-Powered Adaptive Shrinkage Estimation
  Li, S., & Ignatiadis, N.
• Stein’s unbiased risk estimate and Hyvärinen’s score matching
  Ghosh, S., Ignatiadis, N., Koehler, F., & Lee, A.
• Introspective Growth: Automatically Advancing LLM Expertise in Technology Judgment
  Wu, S., Bao, H., Kunievsky, N., & Evans, J. A.
• Language models surface the unwritten code of science and society
  Bao, H., Wu, S., Choi, J., Mao, Y., & Evans, J. A.
• Layers at similar depths generate similar activations across llm architectures
  Wolfram, C., & Schein, A.
• Broad Spectrum Structure Discovery in Large-Scale Higher-Order Networks
  Hood, J., De Bacco, C., & Schein, A.
• Modeling Latent Underdispersion with Discrete Order Statistics
  Lederman, J., & Schein, A.
• Private Retrieval Augmented Generation with Random Projection
  Yao, D., & Li, T.
• Multiple Streams of Relation Extraction: Enriching and Recalling in Transformers
  Nief, T., Reber, D., Richardson, S., & Holtzman, A.
• HypoEval: Hypothesis-Guided Evaluation for Natural Language Generation
  Li, M., Li, H., & Tan, C.
• Multi-frequency progressive refinement for learned inverse scattering
  Melia, O., Tsang, O., Charisopoulos, V., Khoo, Y., Hoskins, J., & Willett, R.
• Hardware Acceleration for HPS Algorithms in Two and Three Dimensions
  Melia, O., Fortunato, D., Hoskins, J., & Willett, R.
• Incorporating Hierarchical Semantics in Sparse Autoencoder Architectures
  Muchane, M., Richardson, S., Park, K., & Veitch, V.
• Concept Incongruence: An Exploration of Time and Death in Role Playing
  Bai, X., Peng, I., Singh, A., & Tan, C.
• Grounded Persuasive Language Generation for Automated Marketing
  Wu, J., Yang, C., Mahns, S., Wang, C., Zhu, H., Fang, F., & Xu, H.
• Tokenized Bandit for LLM Decoding and Alignment
  Shin, S., Yang, C., Xu, H., & Hajiaghayi, M. T.
• How Alignment Shrinks the Generative Horizon
  Yang, C., & Holtzman, A.
• Hierarchical Implicit Neural Emulators
  Jiang, R., Zhang, X., Jakhar, K., Lu, P. Y., Hassanzadeh, P., Maire, M., & Willett, R.
• CLEAR: A Clinically-Grounded Tabular Framework for Radiology Report Evaluation
  Jiang, Y., Chen, C., Wang, S., Li, F., Tang, Z., Mervak, B. M., Chelala, L., Straus, C. M., Chahine, R., Armato, S. G. III, & Tan, C.
• The geometry of categorical and hierarchical concepts in large language models
  Park, K., Choe, Y. J., Jiang, Y., & Veitch, V.
• RATE: Causal Explainability of Reward Models with Imperfect Counterfactuals
  Reber, D., Richardson, S. M., Nief, T., Garbacea, C., & Veitch, V.
• Solving Inverse Problems with Deep Linear Neural Networks: Global Convergence Guarantees for Gradient Descent with Weight Decay
  Laus, H., Parkinson, S., Charisopoulos, V., Krahmer, F., & Willett, R.
• Nonlinear tomographic reconstruction via nonsmooth optimization
  Charisopoulos, V., & Willett, R.
• Limits on the computational expressivity of non-equilibrium biophysical processes
  Carlos Floyd, Aaron R. Dinner, Arvind Murugan, and Suriyanarayanan Vaikuntanathan
• Symmetry breaking-induced N-body electrodynamic forces in optical matter systems
  John Parker, Spoorthi Nagasamudram, Curtis Peterson, Yanzeng Li, Sina Soleimanikahnoj, Stuart A. Rice, and Norbert F. Scherer
• Structural reconfiguration of interacting multi-particle systems through parametric pumping
  Qinghao Mao, Brady Wu, Bryan VanSaders, and Heinrich M. Jaeger
• Symmetry is the Key to the Design of Reticular Frameworks
  Andrea Darù, John S. Anderson, Davide M. Proserpio, and Laura Gagliardi
• Topography Dominates the Hemispheric Asymmetry of Stratospheric Sudden Warmings
  Siming Liu, Tiffany Shaw, and Chaim I. Garfinkel
• A Portfolio Approach to Massively Parallel Bayesian Optimization
  Mickael Binois, Nicholson Collier, and Jonathan Ozik
• Temporal Contrastive Learning through implicit non-equilibrium memory
  Martin J. Falk, Adam T. Strupp, Benjamin Scellier, and Arvind Murugan
• Ribosomal protein phylogeography offers quantitative insights into the efficacy of genome-resolved surveys of microbial communities
  Matthew S. Schechter, Florian Trigodet, Iva A. Veseli, Samuel E. Miller, Matthew L. Klein, Metehan Sever, Loïs Maignien, Tom O. Delmont, Samuel H. Light, and A. Murat Eren
• An NV− center in magnesium oxide as a spin qubit for hybrid quantum technologies
  Vrindaa Somjit, Joel Davidsson, Yu Jin, and Giulia Galli

2024

• Causal Micro-Narratives
  Zentefis, A., Tan, C., Heddaya, M., Voigt, R., & Zeng, Q.
• Casesumm: a large-scale dataset for long-context summarization from us supreme court opinions
  Heddaya, M., MacMillan, K., Malani, A., Mei, H., & Tan, C.
• Inconsistency of cross-validation for structure learning in Gaussian graphical models
  Lyu, Z., Tai, W. M., Kolar, M., & Aragam, B.
• Efficient adaptive federated optimization
  Lee, S. H., Sharma, S., Zaheer, M., & Li, T.
• Tilted Sharpness-Aware Minimization
  Li, T., Zhou, T., & Bilmes, J. A.
• Tree Bandits for Generative Bayes
  O’Hagan, S., Kim, J., & Rockova, V.
• Does Editing Provide Evidence for Localization?
  Wang, Z., & Veitch, V.
• Hostile attribution bias shapes neural synchrony in the left ventromedial prefrontal cortex during ambiguous social narratives
  Lyu, Y., Su, Z., Neumann, D., Meidenbauer, K. L., & Leong, Y. C.
• Residual connections harm self-supervised abstract feature learning
  Zhang, X., Jiang, R., Gao, W., Willett, R., & Maire, M.
• Latent intrinsics emerge from training to relight
  Zhang, X., Gao, W., Jain, S., Maire, M., Forsyth, D., & Bhattad, A.
• The linear representation hypothesis and the geometry of large language models
  Park, K., Choe, Y. J., & Veitch, V.
• An Empirical Investigation of Container Building Strategies and Warm Times to Reduce Cold Starts in Scientific Computing Serverless Functions
  Bauer, A., Gonthier, M., Pan, H., Chard, R., Grzenda, D., Straesser, M., Pauloski, J. G., Kamatar, A., Baughman, M., Hudson, N., Foster, I., & Chard, K.
• Sok: On finding common ground in loss landscapes using deep model merging techniques
  Khan, A., Nief, T., Hudson, N., Sakarvadia, M., Grzenda, D., Ajith, A., Pettyjohn, J., Chard, K., & Foster, I.
• Deep Model Merging: The Sister of Neural Network Interpretability–A Survey
  Khan, A., Nief, T., Hudson, N., Sakravadia, M., Grzenda, D., Ajith, A., Pettyjohn, J., Chard, K., & Foster, I.
• BioMAISx: A Corpus for Aspect-Based Sentiment Analysis of Media Representations of Agricultural Biotechnologies in Africa
  Chiril, P., Spreadbury, T., Rock, J. S., Dowd-Uribe, B., & Uminsky, D.
• Quantifying the uniqueness and divisiveness of presidential discourse
  Zhou, K., Meitus, A. A., Chase, M., Wang, G., Mykland, A., Howell, W., & Tan, C.
• Hypothesis generation with large language models
  Zhou, Y., Liu, H., Srivastava, T., Mei, H., & Tan, C.
• The ALCORE Tensor Decomposition for Sparse Count Data
  Hood, J., & Schein, A. J.
• Nested diffusion models using hierarchical latent priors
  Zhang, X., Jiang, R., Willett, R., & Maire, M.
• Deep learning lattice gauge theories
  Apte, A., Córdova, C., Huang, T.-C., & Ashmore, A.
• Literature Meets Data: A Synergistic Approach to Hypothesis Generation
  Liu, H., Zhou, Y., Li, M., Yuan, C., & Tan, C.
• Neural entropy
  Premkumar, A.
• Diffusion Density Estimators
  Premkumar, A.
• Identifying Self-Disclosures of Use, Misuse and Addiction in Community-based Social Media Posts (NAACL 2024 Findings)
  Yang, C., Chakrabarty, T., Hochstatter, K. R., Slavin, M. N., El‑Bassel, N., & Muresan, S.
• When Hindsight is Not 20/20: Testing Limits on Reflective Thinking in Large Language Models (NAACL 2024 Findings)
  Li, Y., Yang, C., & Ettinger, A.
• Training Machine Learning Emulators to Preserve Invariant Measures of Chaotic Attractors
  Lu, P., Jiang, R., Orlova, E., & Willett, R.
• Embed and Emulate: Contrastive representations for simulation-based inference
  Jiang, R., Lu, P. Y., & Willett, R.
• Bonbon alignment for large language models and the sweetness of best-of-n sampling
  Gui, L., Gârbacea, C., & Veitch, V.
• Stabilizing black-box model selection with the inflated argmax.
  Adrian, M., Soloff, J. A., & Willett, R.
• Gpt-4v cannot generate radiology reports yet
  Jiang, Y., Chen, C., Nguyen, D., Mervak, B. M., & Tan, C.
• Beyond reverse KL: Generalizing direct preference optimization with diverse divergence constraints
  Wang, C., Jiang, Y., Yang, C., Liu, H., & Chen, Y.
• On the origins of linear representations in large language models
  Jiang, Y., Rajendran, G., Ravikumar, P. K., Aragam, B., & Veitch, V.
• Unlocking Mesoscopic Disorder in Graphitic Carbon with Spectroelectrochemistry
  Ry Papadopoulos, Benjamin Masters, Dr. Arpan Kundu, Nicholas Maldonado, Dr. Alexander S. Filatov, Dr. Yuzi Liu, Taemin Kim, Prof. Giulia Galli, and Prof. Anna Wuttig
• A dynamic subset of network interactions underlies tuning to natural movements in marmoset sensorimotor cortex
  Dalton D. Moore, Jason N. MacLean, Jeffrey D. Walker, and Nicholas G. Hatsopoulos
• Redox-Tunable Ring Expansion Enabled By A Single-Component Electrophilic Nitrogen Atom Synthon
  Patrick Q. Kelly, Nikki R. Keramati, Kate R. Kaplin, Tessa Lynch-Colameta, James P. Phelan, and Mark D. Levin
• Synthesis of a potassium capped terminal cobalt–oxido complex
  Sophie W. Anferov, Alexandra Krupinski, and John S. Anderson
• Constraints on compact objects from the Dark Energy Survey five-year supernova sample
  P. Shah, T. M. Davis, M. Vincenzi, P. Armstrong, D. Brout, R. Camilleri, L. Galbany, J. García-Bellido, M. S. S. Gill, O. Lahav, J. Lee, C. Lidman, A. Möller, M. Sako, B. O. Sánchez, M. Sullivan, L. Whiteway, P. Wiseman, S. Allam, M. Aguena, S. Bocquet, D. Brooks, D. L. Burke, A. Carnero Rosell, L. N. da Costa, M. E. S. Pereira, S. Desai, S. Dodelson, P. Doel, I. Ferrero, B. Flaugher, J. Frieman, E. Gaztanaga, D. Gruen, R. A. Gruendl, G. Gutierrez, K. Herner, S. R. Hinton, D. L. Hollowood, K. Honscheid, D. J. James, K. Kuehn, S. Lee, J. L. Marshall, J. Mena-Fernández, R. Miquel, J. Myles, A. Palmese, A. Pieres, A. A. Plazas Malagón, A. Roodman, S. Samuroff, E. Sanchez, I. Sevilla-Noarbe, M. Smith, E. Suchyta, M. E. C. Swanson, G. Tarle, C. To, V. Vikram, and N. Weaverdyck
• Mesomeric control of the optoelectronic properties of polymerized small molecule acceptors
  Diego Sorbelli, Yilei Wu, Zhenan Bao, and Giulia Galli
• Charge Scaling in Classical Force Fields for Lithium Ions in Polymers
  Dongyue Liang, Yuxi Chen, Chuting Deng, and Juan J. de Pablo
• Quantitative insights into the mechanism of proton conduction and selectivity for the human voltage-gated proton channel Hv1
  Yu Liu, Chenghan Li, J. Alfredo Freites, Douglas J. Tobias, and Gregory A. Voth
• Ion Transport at Polymer–Argyrodite Interfaces
  Yuxi Chen, Dongyue Liang, Elizabeth M. Y. Lee, Sokseiha Muy, Maxime Guillaume, Marc-David Braida, Antoine A. Emery, Nicola Marzari, and Juan J. de Pablo
• Structural, Ionic, and Electronic Properties of Solid-State Phthalimide-Containing Polymers for All-Organic Batteries
  Riccardo Alessandri, Cheng-Han Li, Sheila Keating, Khirabdhi T. Mohanty, Aaron Peng, Jodie L. Lutkenhaus, Stuart J. Rowan, Daniel P. Tabor, and Juan J. de Pablo
• The simplicity of protein sequence-function relationships
  Yeonwoo Park, Brian P. H. Metzger, and Joseph W. Thornton
• Climate, demography, immunology, and virology combine to drive two decades of dengue virus dynamics in Cambodia
  Cara E. Brook, Carly Rozins, Jennifer A. Bohl, Vida Ahyong, Sophana Chea, Liz Fahsbender, Rekol Huy, Sreyngim Lay, Rithea Leang, Yimei Li, Chanthap Lon, Somnang Man, Mengheng Oum, Graham R. Northrup, Fabiano Oliveira, Andrea R. Pacheco, Daniel M. Parker, Katherine Young, Michael Boots, Cristina M. Tato, Joseph L. DeRisi, Christina Yek, and Jessica E. Manning
• Quantum-Inspired Classical Algorithm for Graph Problems by Gaussian Boson Sampling
  Changhun Oh, Bill Fefferman, Liang Jiang, and Nicolás Quesada
• Pattern formation in odd viscoelastic fluids
  Carlos Floyd, Aaron R. Dinner, and Suriyanarayanan Vaikuntanathan
• Transport coefficient approach for characterizing nonequilibrium dynamics in soft matter
  HongRui He, Heyi Liang, Miaoqi Chu, Zhang Jiang, Juan J. de Pablo, Matthew V. Tirrell, Suresh Narayanan, and Wei Chen
• Exact Results for a Boundary-Driven Double Spin Chain and Resource-Efficient Remote Entanglement Stabilization
  Andrew Lingenfelter, Mingxing Yao, Andrew Pocklington, Yu-Xin Wang, Abdullah Irfan, Wolfgang Pfaff, and Aashish A. Clerk
• Hyper-diverse antigenic variation and resilience to transmission-reducing intervention in falciparum malaria
  Qi Zhan, Qixin He, Kathryn E. Tiedje, Karen P. Day, and Mercedes Pascual
• Phylogeny structures species’ interactions in experimental ecological communities
  Paula Lemos-Costa, Zachary R. Miller, and Stefano Allesina
• Native mass spectrometry and structural studies reveal modulation of MsbA–nucleotide interactions by lipids
  Tianqi Zhang, Jixing Lyu, Bowei Yang, Sangho D. Yun, Elena Scott, Minglei Zhao, and Arthur Laganowsky
• A robust model for cell type-specific interindividual variation in single-cell RNA sequencing data
  Minhui Chen and Andy Dahl
• Electrodynamic Interference and Induced Polarization in Nanoparticle-Based Optical Matter Arrays
  Curtis Peterson, John Parker, Emmanuel Valenton, Yuval Yifat, Shiqi Chen, Stuart A. Rice, and Norbert F. Scherer
• A digital twin of the infant microbiome to predict neurodevelopmental deficits
  Nicholas Sizemore, Kaitlyn Oliphant, Ruolin Zheng, Camilia R. Martin, Erika C. Claud, and Ishanu Chattopadhyay
• Prediction of the essential intermolecular contacts for side-binding of VASP on F-actin
  Fikret Aydin, Harshwardhan H. Katkar, Alisha Morganthaler, Alyssa J. Harker, David R. Kovar, and Gregory A. Voth
• Trans-eQTL mapping in gene sets identifies network effects of genetic variants
  Lili Wang, Nikita Babushkin, Zhonghua Liu, and Xuanyao Liu
• Shaping immunity: The influence of natural selection on population immune diversity
  Haley E. Randolph, Katherine A. Aracena, Yen-Lung Lin, Zepeng Mu, and Luis B. Barreiro
• Molecular dynamics simulations of HIV-1 matrix-membrane interactions at different stages of viral maturation
  Puja Banerjee, Kun Qu, John A.G. Briggs, and Gregory A. Voth
• Uncooled High Detectivity Mid-Infrared Photoconductor Using HgTe Quantum Dots and Nanoantennas
  Augustin Caillas and Philippe Guyot-Sionnest
• Motor crosslinking augments elasticity in active nematics
  Steven A. Redford, Jonathan Colen, Jordan L. Shivers, Sasha Zemsky, Mehdi Molaei, Carlos Floyd, Paul V. Ruijgrok, Vincenzo Vitelli, Zev Bryant, Aaron R. Dinner, and Margaret L. Gardel
• HIV-1 capsid shape, orientation, and entropic elasticity regulate translocation into the nuclear pore complex
  Arpa Hudait and Gregory A. Voth
• PySAGES: flexible, advanced sampling methods accelerated with GPUs
  Pablo F. Zubieta Rico, Ludwig Schneider, Gustavo R. Pérez-Lemus, Riccardo Alessandri, Siva Dasetty, Trung D. Nguyen, Cintia A. Menéndez, Yiheng Wu, Yezhi Jin, Yinan Xu, Samuel Varner, John A. Parker, Andrew L. Ferguson, Jonathan K. Whitmer, and Juan J. de Pablo
• Dynamics of activation in the voltage-sensing domain of Ciona intestinalis phosphatase Ci-VSP
  Spencer C. Guo, Rong Shen, Benoît Roux, and Aaron R. Dinner
• Fluorination promotes lithium salt dissolution in borate esters for lithium metal batteries
  Peiyuan Ma, Ritesh Kumar, Minh Canh Vu, Ke-Hsin Wang, Priyadarshini Mirmira, and  Chibueze V. Amanchukwu
• AI Can Identify Solar System Instability Billions of Years in Advance
  Dorian S. Abbot, J. D. Laurence-Chasen, Robert J. Webber, David M. Hernandez, and Jonathan Weare
• Donor-acceptor pairs in wide-bandgap semiconductors for quantum technology applications
  Anil Bilgin, Ian N. Hammock, Jeremy Estes, Yu Jin, Hannes Bernien, Alexander A. High, and Giulia Galli

2023

• Measurement in the age of llms: An application to ideological scaling
  O’Hagan, S., & Schein, A.
• Clinical Notes Reveal Physician Fatigue
  Hsu, C.-C., Obermeyer, Z., & Tan, C.
• Training neural operators to preserve invariant measures of chaotic attractors
  Jiang, R., Lu, P. Y., Orlova, E., & Willett, R.
• Rotation-invariant random features provide a strong baseline for machine learning on 3D point clouds
  Melia, O., Jonas, E., & Willett, R.
• Can You Follow Me? Testing Situational Understanding in ChatGPT (EMNLP 2023)
  Yang, C., & Ettinger, A.
• Deep Stochastic Mechanics
  Orlova, E., Ustimenko, A., Jiang, R., Lu, P. Y., & Willett, R.
• Concept algebra for (score-based) text-controlled generative models
  Wang, Z., Gui, L., Negrea, J., & Veitch, V.
• Uncovering meanings of embeddings via partial orthogonality
  Jiang, Y., Aragam, B., & Veitch, V.
• Learning nonparametric latent causal graphs with unknown interventions
  Jiang, Y., & Aragam, B.
• Why Are Mountaintops Cold? The Transition of Surface Lapse Rate on Dry Planets
  Malte F. Jansen, Michael A. Mischna, and Edwin S. Kite
• Entropic Penalty Switches Li+ Solvation Site Formation and Transport Mechanisms in Mixed Polarity Copolymer Electrolytes
  Chuting Deng, Peter Bennington, Regina J. Sánchez-Leija, Shrayesh N. Patel, Paul F. Nealey, and Juan J. de Pablo
• OpenMSCG: A Software Tool for Bottom-Up Coarse-Graining
  Yuxing Peng, Alexander J. Pak, Aleksander E. P. Durumeric, Patrick G. Sahrmann, Sriramvignesh Mani, Jaehyeok Jin, Timothy D. Loose, Jeriann Beiter, and Gregory A. Voth
• Denoising Autoencoder Trained on Simulation-Derived Structures for Noise Reduction in Chromatin Scanning Transmission Electron Microscopy
  Walter Alvarado, Vasundhara Agrawal, Wing Shun Li, Vinayak P. Dravid, Vadim Backman, Juan J. de Pablo, and Andrew L. Ferguson
• Monte Carlo Simulations of Water Adsorption in Aluminum Oxide Rod-Based Metal–Organic Frameworks
  Saumil Chheda, WooSeok Jeong, Nikita Hanikel, Laura Gagliardi, and J. Ilja Siepmann
• Theoretical Investigation of Single-Molecule-Magnet Behavior in Mononuclear Dysprosium and Californium Complexes
  Debmalya Ray, Meagan S. Oakley, Arup Sarkar, Xiaojing Bai, and Laura Gagliardi
• Non-Covalent Interactions Mimic the Covalent: An Electrode-Orthogonal Self-Assembled Layer
  Deepak Badgurjar, Madison Huynh, Benjamin Masters, and Anna Wuttig
• Acidic Conditions Impact Hydrophobe Transfer across the Oil–Water Interface in Unusual Ways
  Sijia Chen, Zhefu Li, and Gregory A. Voth
• Statistical Mechanical Design Principles for Coarse-Grained Interactions across Different Conformational Free Energy Surfaces
  Jaehyeok Jin and Gregory A. Voth
• Fast and Robust Geometric Two-Qubit Gates for Superconducting Qubits and beyond
  F. Setiawan, Peter Groszkowski, and Aashish A. Clerk
• Turbulence through sustained vortex ring collisions
  Takumi Matsuzawa, Noah P. Mitchell, Stéphane Perrard, and William T. M. Irvine
• Entanglements via Slip Springs with Soft, Coarse-Grained Models for Systems Having Explicit Liquid–Vapor Interfaces
  Ludwig Schneider and Juan J. de Pablo
• Generalizations of the Jaccard index and Sørensen index for assessing agreement across multiple readers in object detection and instance segmentation in biomedical imaging
  Madeleine S. Durkee, Kyle Lleras, Karen Drukker, Junting Ai, Thao Cao, Gabriel Casella, Deepjyoti Ghosh, Marcus R. Clark, and Maryellen L. Giger
• Metacognition bridges experiences and beliefs in Sense of Agency
  John Veillette, Letitia Ho, and Howard Nusbaum
• Permutation-based group sequential analyses for cognitive neuroscience
  John P. Veillette, Letitia Ho, and Howard C. Nusbaum
• Fast upper-level jet stream winds get faster under climate change
  Tiffany A. Shaw and Osamu Miyawaki
• GoM DE: interpreting structure in sequence count data with differential expression analysis allowing for grades of membership
  Peter Carbonetto, Kaixuan Luo, Abhishek Sarkar, Anthony Hung, Karl Tayeb, Sebastian Pott, and Matthew Stephens
• Functional brain connectivity predicts sleep duration in youth and adults
  Anurima Mummaneni, Omid Kardan, Andrew J. Stier, Taylor A. Chamberlain, Alfred F. Chao, Marc G. Berman, and Monica D. Rosenberg
• What We Teach About Race and Gender: Representation in Images and Text of Children’s Books
  Anjali Adukia, Alex Eble, Emileigh Harrison, Hakizumwami Birali Runesha, and Teodora Szasz
• Challenge of Small Energy Differences in Metal–Organic Framework Reactivity
  Noah Dohrmann, Daniel S. King, Carlo A. Gaggioli, and Laura Gagliardi
• All-photonic Gottesman-Kitaev-Preskill–qubit repeater using analog-information-assisted multiplexed entanglement ranking
  Filip Rozpędek, Kaushik P. Seshadreesan, Paul Polakos, Liang Jiang, and Saikat Guha
• Measuring response functions of active materials from data
  Mehdi Molaei, Steven A. Redford, Wen-Hung Chou, Danielle Scheff, Juan J. de Pablo, Patrick W. Oakes, and Margaret L. Gardel
• Electrochemical Reduction of N2O with a Molecular Copper Catalyst
  Jorge L. Martinez, Joseph E. Schneider, Sophie W. Anferov, and John S. Anderson
• A new Bayesian factor analysis method improves detection of genes and biological processes affected by perturbations in single-cell CRISPR screening
  Yifan Zhou, Kaixuan Luo, Lifan Liang, Mengjie Chen, and Xin He
• Engineering the formation of spin-defects from first principles
  Cunzhi Zhang, Francois Gygi, and Giulia Galli
• Binning is Sinning: Redemption for Hubble Diagram Using Photometrically Classified Type Ia Supernovae
  R. Kessler, M. Vincenzi, and P. Armstrong
• Large-scale neural dynamics in a shared low-dimensional state space reflect cognitive and attentional dynamics
  Hayoung Song, Won Mok Shim, and Monica D Rosenberg
• Single-cell genomics improves the discovery of risk variants and genes of atrial fibrillation
  Alan Selewa, Kaixuan Luo, Michael Wasney, Linsin Smith, Xiaotong Sun, Chenwei Tang, Heather Eckart, Ivan P. Moskowitz, Anindita Basu, Xin He, and Sebastian Pott
• Thermal Conductivity of Water at Extreme Conditions
  Cunzhi Zhang, Marcello Puligheddu, Linfeng Zhang, Roberto Car, and Giulia Galli
• Elucidating the Molecular Mechanism of CO2 Capture by Amino Acid Ionic Liquids
  Bohak Yoon and Gregory A. Voth
• A flexible empirical Bayes approach to multivariate multiple regression, and its improved accuracy in predicting multi-tissue gene expression from genotypes
  Fabio Morgante, Peter Carbonetto, Gao Wang, Yuxin Zou, Abhishek Sarkar, Matthew Stephens
• Robust Relationship Between Midlatitudes CAPE and Moist Static Energy Surplus in Present and Future Simulations
  Ziwei Wang and Elisabeth J. Moyer
• Quantum Vibronic Effects on the Electronic Properties of Molecular Crystals
  Arpan Kundu and Giulia Galli
• Isotopic Enrichment Resulting from Differential Condensation of Methane Isotopologues Involving Non-equilibrium Gas–Surface Collisions Modeled with Molecular Dynamics Simulations
  Michelle R. Brann, Xinyou Ma, and S. J. Sibener
• CUDA-aware MPI implementation of Gibbs sampling for an IRT model
  William S. Welling, Yanyan Sheng, & Michelle M. Zhu
• Unveiling the catalytic mechanism of GTP hydrolysis in microtubules
  Daniel Beckett and Gregory A. Voth
• Learning to learn by using nonequilibrium training protocols for adaptable materials
  Martin J. Falk, Jiayi Wu, Ayanna Matthews, Vedant Sachdeva, Nidhi Pashine, Margaret L. Gardel, Sidney R. Nagel, and Arvind Murugan
• The structure of phosphatidylinositol remodeling MBOAT7 reveals its catalytic mechanism and enables inhibitor identification
  Kun Wang, Chia-Wei Lee, Xuewu Sui, Siyoung Kim, Shuhui Wang, Aidan B. Higgs, Aaron J. Baublis, Gregory A. Voth, Maofu Liao, Tobias C. Walther & Robert V. Farese Jr
• A unified model for the dynamics of ATP-independent ultrafast contraction
  Carlos Floyd, Arthur T. Molines, Xiangting Lei, Jerry E. Honts, Fred Chang, Mary Williard Elting, Suriyanarayanan Vaikuntanathan, Aaron R. Dinner, and M. Saad Bhamla
• Neutral vs. non-neutral genetic footprints of Plasmodium falciparum multiclonal infections
  Labbé, Frédéric; He, Qixin; Zhan, Qi; Tiedje, Kathryn E.; Argyropoulos, Dionne C.; Tan, Mun Hua; Ghansah, Anita; et al.
• Density Matrix Embedding Using Multiconfiguration Pair-Density Functional Theory
  Abhishek Mitra, Matthew R. Hermes, and Laura Gagliardi
• Toward improved loading, cooling, and trapping of molecules in magneto-optical traps
  T K Langin and D DeMille
• Narrow range of early habitable Venus scenarios permitted by modeling of oxygen loss and radiogenic argon degassing
  Alexandra O. Warren, Edwin S. Kite
• Inequality constrained stochastic nonlinear optimization via active-set sequential quadratic programming
  Sen Na, Mihai Anitescu, Mladen Kolar
• Computational design of self-assembling peptide chassis materials for synthetic cells
  Y. Ma, R. Kapoor, B. Sharma, A.P. Liu, A.L. Ferguson
• Propagating motor cortical patterns of excitability are ubiquitous across human and non-human primate movement initiation
  Karthikeyan Balasubramanian, Fritzie I. Arce-McShane, Brian M. Dekleva, Jennifer L. Collinger, and Nicholas G. Hatsopoulos

2022

• A Unified Causal View of Domain Invariant Representation Learning
  Wang, Z., & Veitch, V.
• Accurate pKa Calculations in Proteins with Reactive Molecular Dynamics Provide Physical Insight Into the Electrostatic Origins of Their Values
  Joshua Zuchniarz, Yu Liu, Chenghan Li, and Gregory A. Voth
• Preparation of metrological states in dipolar-interacting spin systems
  Tian-Xing Zheng, Anran Li, Jude Rosen, Sisi Zhou, Martin Koppenhöfer, Ziqi Ma, Frederic T. Chong, Aashish A. Clerk, Liang Jiang, and Peter C. Maurer
• Evolutionary insights into primate skeletal gene regulation using a comparative cell culture model
  Housman, Genevieve; Briscoe, Emilie; Gilad, Yoav
• Modeling hepatitis C micro-elimination among people who inject drugs with direct-acting antivirals in metropolitan Chicago
  Tatara, Eric; Gutfraind, Alexander; Collier, Nicholson T.; Echevarria, Desarae; Cotler, Scott J.; Major, Marian E.; et al.
• Analysis of the extent of limbic system changes in multiple sclerosis using FreeSurfer and voxel-based morphometry approaches
  Abuaf, Amanda Frisosky; Bunting, Samuel R.; Klein, Sara; Carroll, Timothy; Carpenter-Thompson, Jake; et al.
• Differences in the functional brain architecture of sustained attention and working memory in youth and adults
  Kardan, Omid; Stier, Andrew J.; Cardenas-Iniguez, Carlos; Schertz, Kathryn E.; Pruin, Julia C.; Deng, Yuting; et al.
• Fine-mapping from summary data with the “Sum of Single Effects” model
  Yuxin Zou, Peter Carbonetto, Gao Wang, Matthew Stephens
• Empirical evaluation of fully Bayesian information criteria for mixture IRT models using NUTS
  Rehab AlHakmani, Yanyan Sheng
• Influence of Excess Charge on Water Adsorption on the BiVO4(010) Surface
  Wennie Wang, Marco Favaro, Emily Chen, Lena Trotochaud, Hendrik Bluhm, Kyoung-Shin Choi, Roel van de Krol, David E. Starr, and Giulia Galli
• Evolution of pi-peptide assembly: from understanding to prediction and control
  A.L. Ferguson and J.D. Tovar
• Hybrid computational-experimental data-driven design of self-assembling π-conjugated peptides
  K. Shmilovich, S.S. Panda, A. Stouffer, J.D. Tovar, and A.L. Ferguson
• Computational discovery of high charge mobility self-assembling π-conjugated peptides
  K. Shmilovich, Y. Yao, J.D. Tovar, H.E. Katz, A. Schleife, and A.L. Ferguson
• Data-driven discovery of cardiolipin-selective small molecules by computational active learning
  B. Mohr, K. Shmilovich, I.S. Kleinwächter, D. Schneider, A.L. Ferguson*, and T. Bereau
• Active learning of polarizable nanoparticle phase diagrams for the guided design of triggerable self-assembling superlattices
  S. Dasetty, I. Coropceanu, J. Porter, J. Li, J.J. de Pablo, D. Talapin, and A.L. Ferguson
• Hierarchical self-assembly pathways of polypeptoid helices and sheets
  M. Zhao, K.J. Lachowski, S. Alamdari, J. Sampath, P. Mu, C.J. Mundy, J. Pfaendtner, C.-L. Chen, L.D. Pozzo, and A.L. Ferguson
• Hydrodynamic Coupling Melts Acoustically Levitated Crystalline Rafts
  Brady Wu, Bryan VanSaders, Melody X. Lim, and Heinrich M. Jaeger
• Structural basis for lipid and copper regulation of the ABC transporter MsbA
  Lyu J, Liu C, Zhang T, Schrecke S, Elam NP, Packianathan C, Hochberg GKA, Russell D, Zhao M, Laganowsky A. S
• Multiscale rheology model for entangled Nylon 6 melts
  Heyi Liang, Kenji Yoshimoto, Masahiro Kitabata, Umi Yamamoto, Juan J. de Pablo

2021

• Using Constrained Density Functional Theory to Track Proton Transfers and to Sample Their Associated Free Energy Surface
  Chenghan Li and Gregory A. Voth
• Inverse Conformational Selection in Lipid–Protein Binding
  Amélie Bacle, Pavel Buslaev, Rebeca Garcia-Fandino, Fernando Favela-Rosales, Tiago Mendes Ferreira, Patrick F. J. FuchsIvan Gushchin, Matti Javanainen, Anne M. Kiirikki, Jesper J. Madsen, Josef Melcr, Paula Milán Rodríguez, Markus S. Miettinen, O. H. Samuli Ollila, Chris G. Papadopoulos, Antonio Peón,Thomas J. Piggot, Ángel Piñeiro, and Salla I. Virtanen
• Learning to control active matter
  Martin J. Falk, Vahid Alizadehyazdi, Heinrich Jaeger, and Arvind Murugan
• Analytic Design of Accelerated Adiabatic Gates in Realistic Qubits: General Theory and Applications to Superconducting Circuits
  F. Setiawan, Peter Groszkowski, Hugo Ribeiro, and Aashish A. Clerk
• Probing the Coherence of Solid-State Qubits at Avoided Crossings
  Mykyta Onizhuk, Kevin C. Miao, Joseph P. Blanton, He Ma, Christopher P. Anderson, Alexandre Bourassa, David D. Awschalom, and Giulia Galli
• A strong nonequilibrium bound for sorting of cross-linkers on growing biopolymers
  Yuqing Qiu, Michael Nguyen, Glen M. Hocky, Aaron R. Dinner, and Suriyanarayanan Vaikuntanathan
• Phylogeny of the damselfishes (Pomacentridae) and patterns of asymmetrical diversification in body size and feeding ecology
  McCord, Charlene L.; Nash, Chloe M.; Cooper, W. James; Westneat, Mark W.
• An antigenic diversification threshold for falciparum malaria transmission at high endemicity
  Qixin He, Mercedes Pascual
• RNA-binding protein syncrip regulates starvation-induced hyperactivity in adult Drosophila
  Wanhao Chi, Wei Liu, Wenqin Fu, Shengqian Xia, Ellie S. Heckscher, Xiaoxi Zhuang
• Quantum repeaters based on concatenated bosonic and discrete-variable quantum codes
  Filip Rozpędek, Kyungjoo Noh, Qian Xu, Saikat Guha, Liang Jiang
• Kinetics of Phenol Escape from the Insulin R6 Hexamer
  Adam Antoszewski, Chatipat Lorpaiboon, John Strahan, and Aaron R. Dinner
• Structural Ensemble of the Insulin Monomer
  Luis Busto-Moner, Chi-Jui Feng, Adam Antoszewski, Andrei Tokmakoff, and Aaron R. Dinner
• Spatiotemporal control of liquid crystal structure and dynamics through activity patterning
  Zhang, R., Redford, S.A., Ruijgrok, P.V. et al.
• Determining sequence-dependent DNA oligonucleotide hybridization and dehybridization mechanisms using coarse-grained molecular simulation, Markov state models, and infrared spectroscopy
  M.S. Jones, B. Ashwood, A. Tokmakoff, and A.L. Ferguson
• Computationally guided tuning of peptide-conjugated perylene diimide self-assembly 
  S.S. Panda, K. Shmilovich, S.M. Herringer, N.J. Marin, A.L. Ferguson, and J.D. Tovar
• Tetranucleosome interactions drive chromatin folding 
  W. Alvarado, J. Moller, A.L. Ferguson*, and J.J. de Pablo
• Inverse design of self-assembling diamond photonic lattices from anisotropic colloidal clusters
  Y. Ma, J. Aulicino, and A.L. Ferguson 
• Autobahn: Automorphism-based Graph Neural Nets
  Erik Thiede, Wenda Zhou, Risi Kondor
• Stressed Lipid Droplets: How Neutral Lipids Relieve Surface Tension and Membrane Expansion Drives Protein Association
  Siyoung Kim, Myong In Oh, and Jessica M. J. Swanson
• Physical Characterization of Triolein and Implications for Its Role in Lipid Droplet Biogenesis
  Siyoung Kim, Gregory A. Voth

2020

• Effect of directed aging on nonlinear elasticity and memory formation in a material
  Daniel Hexner, Nidhi Pashine, Andrea J. Liu, and Sidney R. Nagel
• A Unification of the Holstein Polaron and Dynamic Disorder Pictures of Charge Transport in Organic Crystals
  Jonathan H. Fetherolf, Denis Golež, and Timothy C. Berkelbach
• Continual Learning of Multiple Memories in Mechanical Networks
  Menachem Stern, Matthew B. Pinson, and Arvind Murugan
• Chromatin-enriched RNAs mark active and repressive cis-regulation: An analysis of nuclear RNA-seq
  Sun, Xiangying; Wang, Zhezhen; Hall, Johnathon M.; Perez-Cervantes, Carlos; Ruthenburg, Alexander J.; et al.
• Practical considerations for measuring the effective reproductive number, Rt
  Katelyn M. Gostic, Lauren McGough, Edward B. Baskerville, Sam Abbott, Keya Joshi, Christine Tedijanto, Rebecca Kahn, Rene Niehus, James A. Hay, Pablo M. De Salazar, Joel Hellewell, Sophie Meakin, James D. Munday, Nikos I. Bosse, Katharine Sherrat, Robin N. Thompson, Laura F. White, Jana S. Huisman, Jérémie Scire, Sebastian Bonhoeffer, Tanja Stadler, Jacco Wallinga, Sebastian Funk, Marc Lipsitch, Sarah Cobey
• A human-machine partnered approach for identifying social media signals of elevated traumatic grief in Chicago gang territories
  Forrest Stuart, Alicia Riley, Hossein Pourreza
• A Fast Algorithm for Maximum Likelihood Estimation of Mixture Proportions Using Sequential Quadratic Programming
  Youngseok Kim, Peter Carbonetto, Matthew Stephens & Mihai Anitescu
• Evidence for H2 Dissociation and Recombination Heat Transport in the Atmosphere of KELT-9b
  Megan Mansfield et al.
• MARTINI-compatible coarse-grained model for the mesoscale simulation of peptoids
  M. Zhao, J. Sampath, S. Alamdari, G. Shen, C.-L. Chen, C.J. Mundy, J. Pfaendtner, and A.L. Ferguson
• Computationally guided tuning of amino acid configuration influences the chiroptical properties of supramolecular peptide-π-peptide nanostructures
  S. Panda, K. Shmilovich, A.L. Ferguson, and J.D. Tovar
• Free-energy calculations of the functional selectivity of 5-HT2B G protein coupled receptor
  B.L. Peters, J. Deng, and A.L. Ferguson
• Effect of core oligomer length on the phase behavior and assembly of π-conjugated peptides
  E. Jira, K. Shmilovich, T. Kale, A.L. Ferguson, J.D. Tovar, and C. Schroeder
• Discovery of self-assembling π-conjugated peptides by active learning-directed coarse-grained molecular simulation
  K. Shmilovich, R.A. Mansbach, H. Sidky, O.E. Dunne, S.S. Panda, J.D. Tovar, and A.L. Ferguson 
• Lorentz Group Equivariant Neural Network for Particle Physics
  Alexander Bogatskiy, Brandon Anderson, Jan T. Offermann, Marwah Roussi, David W. Miller, and Risi Kondor
• The Surface and Hydration Properties of Lipid Droplets
  Siyoung Kim, Jessica M.J. Swanson

2019

• Reproducible big data science: A case study in continuous FAIRness
  Madduri, Ravi; Chard, Kyle; D’Arcy, Mike; Jung, Segun C.; Rodriguez, Alexis; Sulakhe, Dinanath; Deutsch, Eric; et al.
• A modeling framework to inform preexposure prophylaxis initiation and retention scale-up in the context of ‘Getting to Zero’ initiatives
  Khanna, Aditya et al.,
• Ab Initio Linear and Pump-Probe Spectroscopy of Excitons in Molecular Crystals
  Alan M. Lewis and Timothy C. Berkelbach
• Alternative polyadenylation mediates genetic regulation of gene expression
  Briana Mittleman, Sebastian Pott, Shane Warland, Tony Zeng, Mayher Kaur,Yoav Gilad, Yang I Li
• An Embarrassingly Parallel Method for Large-Scale Stochastic Programs
  Burhaneddin Sandıkçı, Osman Y. Özaltın
• Assessing Fit in Ordinal Factor Analysis Models: SRMR vs. RMSEA
  Dexin Shi, Alberto Maydeu-Olivares & Yves Rosseel
• Community Collections: A Framework for Openly Sharing Software Stacks Across Research Computing Centers Using Singularity and Lmod
  Kevin Manalo et al.
• Compatible observable decompositions for coarse-grained representations of real molecular systems
  Thomas Dannenhoffer-Lafage, Jacob W. Wagner, Aleksander E. P. Durumeric, and Gregory A.Voth
• Comprehensive estimate of the sensitivity of ANITA to tau neutrinos
  Stephanie Wissel et al
• Concept Study for the Beamforming Elevated Array for Cosmic Neutrinos
  Stephanie Wissel et al
• Constraints on the ultrahigh-energy cosmic neutrino flux from the fourth flight of ANITA
  P. W. Gorham et al.
• Design and learning in multi-stable mechanical networks
  Stern, Menachem; Pinson, Matthew; Murugan, Arvind
• Design patterns for data-driven research acceleration
  Rachana Ananthakrishnan, Kyle Chard, and Ian Foster
• Developing and Testing of Lipid Force Fields with Applications toModeling Cellular Membranes
  Alison N. Leonard, Eric Wang, Viviana Monje-Galvan, and Jeffery B. Klauda
• Emulating Satellite Drag from Large Simulation Experiments
  Furong  Sun, Robert B.  Gramacy, Benjamin  Haaland, Earl  Lawrence, and Andrew Walker
• Experimental Evidence for pKa‑Driven Asynchronicity in C−HActivation by a Terminal Co(III)−Oxo Complex
  McKenna K. Goetz and John S. Anderson
• Semi–Synthetic Dataset for the Evaluation of Motion Compensation Approaches for Voltage Sensitive Dye Imaging
  Philipp Flotho, Lars Haab, David Eckert, Kazutaka Takahashi, Karsten Schwerdtfeger, Daniel J. Strauss
• Performance of T2 Maps in the Detection of Prostate Cancer
  A. Chatterjee, A. Devaraj, M. Mathew, T. Szasz, T. Antic, G.S. Karczmar and A. Oto
• Machine Learning Prediction of Accurate Atomization Energies of Organic Molecules from Low-Fidelity Quantum Chemical Calculations
  L. Ward, B. Blaiszik, I. Foster, R. S. Assary, B. Narayanan, and L. Curtiss
• Optimized Compilation of Aggregated Instructions for Realistic Quantum Computers
  Y.Shi et al., 
• Discovery and characterization of variance QTLs in human induced pluripotent stem cells
  A. K. Sarkar  , P-Y. Tung , J. D. Blischak, J. E. Burnett, Y. I. Li, M. Stephens, and Y. Gilad
• Characterization and valuation of uncertainty of calibrated parameters in stochastic decision models
  F. A.-Escudero, A. B. Knudsen, J. Ozik, N. Collier, and K. M. Kuntz
• Reversible homolytic activation of water via metal–ligand cooperativity in a T-shaped Ni(II) complex
  M-C. Chang, K. A. Jesse, A. S. Filatov, and J. S. Anderson
• Script of Scripts: A pragmatic workflow system for daily computational research
  G. Wang, and B. Peng
• Vertex Corrections to the Polarizability Do Not Improve the GW Approximation for the Ionization Potential of Molecules
  Quantifying in situ adaptive immune cell cognate interactions in humans
  V. M. Liarski et al.,
• The histone methyltransferase EZH2 primes the early differentiation of follicular helper T cells during acute viral infection
  X. Chen et al.,
• First cosmology results using Type IA supernovae from the dark energy survey: effects of chromatic corrections to supernova photometry on measurements of cosmological parameters
  J. Lasker et al., 
• A Search for Optical Emission from Binary Black Hole Merger GW170814 with the Dark Energy Camera
  Z. Doctor et al., 
• Superheavy Dark Matter and ANITA’s Anomalous Events
  D. Hooper, S. Wegsman, C. Deaconu, and  A. Vieregg
• Qresp, a tool for curating, discovering, and exploring reproducible scientific papers
  M. Govoni, M. Munakami, A. Tanikanti, J. H. Skone, H. B. Runesha, F. Giberti, J. de Pablo and G. Galli
• Vertex Corrections to the Polarizability Do Not Improve the GW Approximation for the Ionization Potential of Molecules 
  A.M. Lewis and T. C. Berkelbach
• Ab Initio Lifetime and Concomitant Double-Excitation Character of Plasmons at Metallic Densities
  A.M. Lewis and T. C. Berkelbach
• Nanocrystals in Molten Salts and Ionic Liquids: Experimental Observation of Ionic Correlations Extending beyond the Debye Length. 
  V. Kamysbayev et al.,
• The XENON1T Data Distribution and Processing Scheme
  D. Ahlin et al., 
• Effects of Radius and Gravity on the Inner Edge of the Habitable Zone
  H. Yang, T. D. Komacek, and D. S. Abbot
• Design and performance of an interferometric trigger array for radio detection of high-energy neutrinos
  P.Allison et al.,
• Propagating patterns of activity across motor cortex facilitate movement initiation
  K. Balasubramanian, V. Papadourakis, W. Liang,  K. Takahashi, M. D Best, A. J Suminski, and N. G. Hatsopoulos
• A Spatial Knowledge Economy
  D. R. Davis and J. I. Dingel
• Perfection in Nucleation and Growth of Blue-Phase Single Crystals: Small Free-Energy Required to Self-Assemble at Specific Lattice Orientation
  X. Li et al., 
• How Segregated Is Urban Consumption?
  D. R. Davis, J. I. Dingel, J. Monras and E. Morales
• Orientational Dynamics of Transition Dipoles and Exciton Relaxation in LH2 from Ultrafast Two-Dimensional Anisotropy
  S.C. Massey et al., 
• Multiscale model of integrin adhesion assembly
  T. C Bidone, A. V Skeeters, P. W Oakes, G. A Voth
• Directed aging, memory and Nature’s greed
  N. Pashine, D. Hexner, A  J. Liu and S. R. Nagel
• Simulations of Water Vapor and Clouds on Rapidly Rotating and Tidally Locked Planets: A 3D Model Intercomparison
  J. Yang et al., 
• Parsl: Pervasive Parallel Programming in Python
  Y. Babuji et al.,
• The self-tuned sensitivity of circadian clocks
  K. Husain, W. Pittayakanchit, G. Pattanayak, M. J Rust, and A. Murugan
• icemc: A Monte Carlo Simulation for Cosmogenic Neutrinos interacting in the Antarctic ice as viewed by the Antarctic Impulsive Transient Antenna (ANITA)
  L. Cremonesi et al.,
• Ena/VASP processive elongation is modulated by avidity on actin filaments bundled by the filopodia crosslinker fascin
  A. J. Harker et al.,
• Tidally-Distorted, Iron-Enhanced Exoplanets Closely Orbiting Their Stars
  E. M. Price and L. A. Rogers
• Mycolactone Toxin Membrane Permeation: Atomistic versus Coarse-Grained MARTINI Simulations
  F. Aydin, R. Sun, J.M.J. Swanson
• First cosmology results using Type Ia supernova from the Dark Energy Survey: simulations to correct supernova distance biases
  R. Kessler et al.,
• Swampland conjectures and late-time cosmology
  M. Raveri,  W. Hu, and S. Sethi
• Acoustic Dark Energy: Potential Conversion of the Hubble Tension
  M -X.  Lin, G. Benevento, W. Hu, M. Raveri
• The Atmospheric Circulation and Climate of Terrestrial Planets Orbiting Sun-like and M Dwarf Stars over a Broad Range of Planetary Parameters
  T. D. Komacek and D. S. Abbot
• Challenges in delivering digital content in archival and production environments
  Dunham, Brittan; Ming, Candace
• Fluctuations and phase transitions of uniaxial and biaxial liquid crystals using a theoretically informed Monte Carlo and a Landau free energy density
  S. Villada-Gil, V. Palacio-Betancur, J. C Armas-Pérez, J. J de Pablo and J. P Hernández-Ortiz
• OH-Stretch Raman Multivariate Curve Resolution Spectroscopy of HOD/H2O Mixtures
  A. A. Kananenka, N. J. Hestand, and J. L. Skinner
• Understanding the anharmonic vibrational structure of the carbon dioxide dimer
  S. Maystrovsky,   M. Keçeli, and O. Sode
• Future climate emulations using quantile regressions on large ensembles
  M. A. Haugen, M. L. Stein, R. L. Sriver, and E. J. Moyer
• Non-uniform spontaneous surface curvature gives limited shape control in simulated single-polymer micelles
  B. Moths
• THE BUZZARD FLOCK: DARK ENERGY SURVEY SYNTHETIC SKY CATALOGS
  J. DeRose et al., 
• Beyond Walkers in Stochastic Quantum Chemistry: Reducing Error using Fast Randomized Iteration
  S. M. Greene, R. J. Webber, J. Weare, and T. C. Berkelbach
• Practical rare event sampling for extreme mesoscale weather
  R. J. Webber, D. A. Plotkin, M. E O’Neill, D. S. Abbot, and J.Weare
• Multiconfigurational Coarse-Grained Molecular Dynamics
  M.E. Sharp et al., 
• Maximizing Simulated Tropical Cyclone Intensity With Action Minimization
  D. A. Plotkin et al.,
• Synthesis, Characterization, and Theoretical Investigation of a Transition State Analogue for Proton Transfer during C−H Activation by a Rhodium-Pincer Complex
  J.J, Gair et al.,
• Extracting collective motions underlying nucleosome dynamics via nonlinear manifold learning
  A. Z. Guo,   J. Lequieu, and J. J. de Pablo
• Predicting Returns with Text Data
  Z.T. Ke, B.T. Kelly, D. Xiu
• Temporal Pattern Recognition through Analog Molecular Computation
  J. O’Brien and A. Murugan
• What Sets the Slope of the Molecular Kennicutt–Schmidt Relation?
  V. A. Semenov, A. V. Kravtsov, and N. Y. Gnedin
• Kinetic simulations of mildly relativistic shocks – I. Particle acceleration in high Mach number shocks
  P. Crumley,  D. Caprioli, S. Markoff and  A. Spitkovsky
• First Cosmology Results Using SNe Ia from the Dark Energy Survey: Analysis, Systematic Uncertainties, and Validation
  D. Brout et al.,
• Simultaneous Inference for Pairwise Graphical Models with Generalized Score Matching
  Ming Yu, Varun Gupta, and Mladen Kolar
• The Free Energy Landscape of Internucleosome Interactions and Its Relation to Chromatin Fiber Structure
  J. Moller, J. Lequieu, and J. J. de Pablo
• Fault-tolerant preparation of approximate GKP states
  Y. Shi, C. Chamberland, and A. Cross
• Full proximity treatment of topological superconductors in Josephson-junction architectures
  F. Setiawan, Chien-Te Wu, and K. Levin
• Persistence of intense, climate-driven runoff late in Mars history
  E.S. Kite et al., 
• Bottom-up Acceleration of Ultra-High-Energy Cosmic Rays in the Jets of Active Galactic Nuclei
  R. Mbarek, and D. Caprioli
• Coarse-graining involving virtual sites: Centers of symmetry coarse-graining
  J. Jina, Y. Hana, and G. A. Voth
• Lensing covariance on cut sky and SPT-Planck lensing tensions
  P. Motloch and W. Hu
• Mid-IR spectroscopy of supercritical water: From dilute gas to dense fluid
  N. J. Hestand,   S. E. Strong, L. Shi, and J. L. Skinner
• Sculpting stable structures in pure liquids
  T. Emeršič et al.,
• Two-sample inference for high-dimensional Markov networks
  B. Kim,  S. Liu, and  M. Kolar
• Adversarial-Residual-Coarse-Graining: Applying machine learning theory to systematic molecular coarse-graining
  A. E. P. Durumeric, and G. A. Voth
• Spatial Correlation, Trade, and Inequality: Evidence from the Global Climate
  J. I. Dingel, K. C. Meng, S. M. Hsiang
• Learned multi-stability in mechanical networks
  Menachem Stern, Matthew B. Pinson, Arvind Murugan
• Phenomenology of modified gravity at recombination
  Meng-Xiang Lin, Marco Raveri, and Wayne Hu
• Concordance and discordance in cosmology
  Marco Raveri and Wayne Hu
• Experimental Evidence for pKa‑Driven Asynchronicity in C−H Activation by a Terminal Co(III)−Oxo Complex
  McKenna K. Goetz and John S. Anderson
• Systematic Coarse-Grained Lipid Force Fields with Semiexplicit Solvation via Virtual Sites
  A.J. Pak et al.
• Reconstructing Gravity on Cosmological Scales
  M. Raveri
• All-electron density functional calculations for electron and nuclear spin interactions in molecules and solid
  K. Ghosh, H. Ma, V. Gavini, and G. Galli
• Controlling supramolecular chirality in peptide-π-peptide networks by variation of alkyl spacer length
  Panda, K. Shmilovich, A.L. Ferguson, J.D. Tovar
• Cormorant: Covariant Molecular Neural Networks
  Brandon Anderson, Truong Son Hy, Risi Kondor

2018

• Accurate calculation of side chain packing and free energy with applications to protein molecular dynamics
  Jumper, John M.; Faruk, Nabil F.; Freed, Karl F.; Sosnick, Tobin R.
  Using pseudoalignment and base quality to accurately quantify microbial community composition
  Reppell, Mark; Novembre, John
• Large-scale genome-wide enrichment analyses identify new trait-associated genes and pathways across 31 human phenotypes
  X. Zhu and M. Stephens
• Ab Initio Lifetime and Concomitant Double-Excitation Character of Plasmons at Metallic Densities
  A.M. Lewis and T.C. Berkelbach
• Vertex corrections to the polarizability do not improve the GW approximation for molecules
  A.M. Lewis and T.C. Berkelbach
• Estimating city-level travel patterns using street imagery: A case study of using Google Street View in Britain
  R. Goel , L. M. T. Garcia, A.Goodman, R. Johnson, R. Aldred, M. Murugesan, S. Brage, K. Bhalla and J. Woodcock
• Umbrella sampling: a powerful method to sample tails of distributions
  C. Matthews, J. Weare, A. Kravtsov and E. Jennings
• A two per cent Hubble constant measurement from standard sirens within five years
  H-Y. Chen, M. Fishbach and D.E. Holz
• Crater Mound Formation by Wind Erosion on Mars
  L.J. Steele, E.S. Kite and T.I. Michaels
• A Comparative Assessment of Human and Chimpanzee iPSC-derived Cardiomyocytes with Primary Heart Tissues
  B.J. Pavlovic, L.E. Blake, J. Roux, C. Chavarria & Yoav Gilad
• Amphiphile-Induced Phase Transition of Liquid Crystals at Aqueous Interfaces
  H. Ramezani-Dakhel, M. Rahimi, J. Pendery, Y-K. Kim , S. Thayumanava , B. Roux , N.L. Abbott , and J.J.de Pablo
• Evolutionary strategy for inverse charge measurements of dielectric particles
  X. Jiang, J. Li, V. Lee, H.M. Jaeger, O.G. Heinonen, and J.J. de Pablo
• Molecular transport through membranes: Accurate permeability coefficients from multidimensional potentials of mean force and local diffusion constants
  R. Sun,   Y. Han, J. M. J. Swanson, J. S. Tan, J. P. Rose, and  G. A. Voth
• DES Y1 Results: Validating cosmological parameter estimation using simulated Dark Energy Surveys
  Maccrann, De Rose et.al.,
• Testing Latitudinally Dependent Explanations of the Circulation Response to Increased CO2 Using Aquaplanet Models
  T. A. Shaw and Z. Tan
• Gating Mechanisms during Actin Filament Elongation by Formins
  F. Aydin, N. Courtemanche, T.D. Pollard, and G.A. Voth
• Mars obliquity history constrained by elliptic crater orientations
  S.J.Holo, E.S.Kite and S.J.Robbins
• Shaping the topology of folding pathways in mechanical systems
  M. Stern, V. Jayaram, and A. Murugan
• Inflationary versus reionization features from Planck 2015 data
  G. Obied, C. Dvorkin, C. Heinrich, W. Hu, and V. Miranda
• Diffusive shock re-acceleration
  D. Caprioli, H. Zhang, and A. Spitkovsky
• Microsimulation Model Calibration using Incremental Mixture Approximate Bayesian Computation
  C. Rutter, J. Ozik, M. DeYoreo, and N. Collier
• Neuroanatomical Correlates of Impulsive Action in Excoriation (Skin-Picking) Disorder
  A. W. Blum., S.l R. Chamberlain, M.l D. Harries, B. L. Odlaug, S. A. Redden and J. E. Grant
• Describing screening in dense ionic fluids with a charge-frustrated Ising model
  N. B. Ludwig, K. Dasbiswas, D. V. Talapin, and S. Vaikuntanathan
• Nonequilibrium phase diagrams for actomyosin networks
  S.L. Freedman, G.M. Hocky,  S. Banerjee and A.R. Dinner
• Global patterns of crop yield stability under additional nutrient and water inputs
  C. Müller , J. Elliott,  et al.,
• Constraints On Duty Cycles Of Quasars At Z ∼ 6
  H. Chen and N. Y. Gnedin
• VC3: A Virtual Cluster Service for Community Computation
  L. Bryant, J. Van, B. Riedel, R.W. Gardner, et al. ,
• A membrane burial potential with H-bonds and applications to curved membranes and fast simulations
  W. Zongan;J. M.Jumper; W. Sheng; K. F. Freed and T.R. Sosnick
• Coupling First Principles Calculations of Electron-Electron and Electron-Phonon Scattering, and Applications to Carbon-based Nanostructures
  R.L. McAvoy, M.Govoni, and G.Galli
• Ligand‐Based Storage of Protons and Electrons in Dihydrazonopyrrole Complexes of Nickel
  M‐C. Chang,  A. J. McNeece,  E. A. Hill, A. S. Filatov, and J. S. Anderson
• Influenza incidence prediction for the United States: an update for the 2018-2019 season
  X. Du, Y.  Peng, M. Liu and M. Pascual
• Exploring the phenotypic consequences of tissue specific gene expression variation inferred from GWAS summary statistics
  A. N. Barbeira, S. P. Dickinson, R. Bonazzola, J. Zheng, et al.,
• A Novel Channel‐Synthesizing Method for Reducing Uncertainties in Satellite Radiative Transfer Modeling
  Y. Lu  and F. Zhang
• Sterically controlled mechanochemistry under hydrostatic pressure
  H. Yan, F. Yang, D. Pan et al.,
• Dielectric properties of condensed systems composed of fragments
  D. Pan, M. Govoni, and G. Galli
• Incidence Prediction for the 2017-2018 Influenza Season in the United States with an Evolution-informed Model
  X. Du and M. Pascual
• Reactive optical matter: light-induced motility in electrodynamically asymmetric nano-scale scatterers
  Y. Yifat, D. Coursault, C. W. Peterson, J. Parker, Y. Bao, S. K. Gray, S. A. Rice, and N. F. Scherer
• Optical magnetism in core-satellite nanostructures excited by vector beams
  J. Parker, S. Gray, N.F. Scherer
• Evolutionary conservation of the allosteric activation of factor VIIa by tissue factor in lamprey: comment
  J. J. Madsen  E. Persson O. H. Olsen
• Travel Time to Clinic but not Neighborhood Crime Rate is Associated with Retention in Care Among HIV-Positive Patients
  J. P. Ridgway, E. A. Almirol, J. Schmitt, T.Schuble, and J. A. Schneider
• Thickness dependence of forming single crystal by liquid-crystalline blue phase on chemically patterned surface
  X. Li, J. A. Martinez-Gonzalez, J. J. de Pablo,  and P. Nealey
• Simultaneous segmentation and classification of multichannel immuno-fluorescently labeled confocal microscopy images using deep convolutional neural networks
  A. R. Sibley, V. Liarski, M. Clark, and M. L. Giger
• Mineral-Water Interface Structure of Xenotime
  A.G. Stack,  J.E. Stubbs, S. Roy, S.G. Srinivasan, S. Roy, V.S. Bryantsev,  P.J. Eng, R. Custelcean, A.D. Gordon, and C.R. Hexel.
• Using Partially-Observed Facebook Networks to Develop a Peer-Based HIV Prevention Intervention: Case Study
  A.S. Khanna, S.M. Goodreau, S. Michaels, and J. A. Schneider
• Enhanced configurational sampling with hybrid non-equilibrium molecular dynamics–Monte Carlo propagator
  D. Suh,  B. K. Radak, C. Chipot, and B. Roux
• Entropic Forces Drive Clustering and Spatial Localization of Influenza A M2 During Viral Budding
  J. J. Madsen, J. M. A. Grime, J. S. Rossman, and G. A. Voth
• Dynamics of optically directed assembly and disassembly of plasmonic nanoplatelet arrays
  D. Coursault, N. Sule, J. Parker, Y. Bao and N. F. Scherer
• Influenza Season in the United States with an Evolution-informed Model 
  X. Du, M. Pascual
• Characterizing agricultural impacts of recent large-scale US droughts and changing technology and management
  J. Elliott, M. Glotter, A. C. Ruane, K. J.Boote, J. L.Hatfield, J. W.Jones, C. Rosenzweig, L. A.Smith, and I. Foster
• Enforcing the Courant-Friedrichs-Lewy Condition in Explicitly Conservative Local Time Stepping Schemes
  N. Y.Gnedin, V. A.Semenov, and A. V.Kravtsov
• A Catalytically Disabled Double Mutant of Src Tyrosine Kinase Can Be Stabilized into an Active-Like Conformation
  Y. Meng , L.G. Ahuja ,  A.P. Kornev, S.S.Taylor, and B. Roux.
• Multipolar analysis of electric and magnetic modes excited by vector beams in core-satellite nano-structures
  J. Parker, S. Gray, and N. Scherer
• Mechanism and Determinants of Amphipathic Helix-Containing Protein Targeting to Lipid Droplets
  C.Prévost,  M. E. Shar , N. Kory,  Q. Lin , G.A.Voth, R.V.Farese Jr., and T.C. Walther
• How Common Are Intentional GAAP Violations? Estimates from a Dynamic Model
  A.A. ZAKOLYUKINA

2017

• The Complexity of Folding Self-Folding Origami
  Menachem Stern, Matthew B. Pinson, and Arvind Murugan
• Economic development, flow of funds, and the equilibrium interaction of financial frictions
  Benjamin Moll, Robert M. Townsend, and Victor Zhorin
• Proton movement and coupling in the POT family of peptide transporters
  Joanne L. Parker, Chenghan Li, Allete Brinth, Zhi Wang, Lutz Vogeley, Nicolae Solcan, Gregory Ledderboge-Vucinic, Jessica M. J. Swanson, Martin Caffrey, Gregory A. Voth, and Simon Newstead
• Uniform Inference for High-Dimensional Quantile Regression: Linear Functionals and Regression Rank Scores
  J. Bradic and M. Kolar
• Comparative Study of the Collective Dynamics of Proteins and Inorganic Nanoparticles
  E.J. Haddadian, H. Zhang, K.F. Freed, and J.F. Douglas
• Glacial Ocean Circulation and Stratification Explained by Reduced Atmospheric Temperature
  M.F. Jansen
• Highly Coarse-Grained Representations of Transmembrane Proteins
  J.J. Madsen, A.V. Sinitskiy, J.Li, and G.A. Voth
• Kepler-108: A Mutually Inclined Giant Planet System
  S.M. Mills and D.C. Fabrycky
• Karp: Accurate and Fast Taxonomic Classification Using Pseudoalignment
  M. Reppell and J. Novembre
• Encoding of Both Reaching and Grasping Kinematics in Dorsal and Ventral Premotor Cortices
  K. Takahashi, M.D. Best, N. Huh, K.A. Brown, A.A. Tobaa, and N.G. Hatsopoulos.
• Communication: Improved Ab Initio Molecular Dynamics by Minimally Biasing with Experimental Data
  A.D. White, C.Knight, G.M. Hocky, and G.A. Voth
• Stable Colloids in Molten Inorganic Salts
  H. Zhang, K.Dasbiswas, N.B. Ludwig, G. Han, B. Lee, S. Vaikuntanathan, and D. V. Talapin
• Balancing Performance and Lifetime of Mlc Pcm by Using a Regionretention Monitor
  M.Z. Zhang, L.K. Zhang, L. Jiang, Z.Y. Liu, and F.T. Chong

2016

• Directed Evolution of RebH for Catalyst-Controlled Halogenation of Indole C-H bonds
  M.C. Andorfer, H.J. Park, J. Vergara-Coll, and J.C. Lewis
• Primary Motor and Sensory Cortical Areas Communicate via Spatiotemporally Coordinated Networks at Multiple Frequencies
  F.I. Arce-McShane, C.F. Ross, K. Takahashi, B.J. Sessle, and N.G. Hatsopoulos
• The Origin and Evolution of LIGO’s First Gravitational-Wave Source
  K. Belczynski, D.E. Holz, T. Bulik, and R. O’Shaughnessy
• Is The Gamma-Ray Source 3FGL J2212.5+0703 a Dark Matter Subhalo?
  B. Bertoni, D. Hooper, and T. Linden
• Spatio-Temporal Patterning in Primary Motor Cortex at Movement Onset
  M.D. Best, A.J. Suminski, K. Takahashi, K.A. Brown, and N.G. Hatsopoulos
• Observation of the Pressure Effect in Simulations of Droplets Splashing on a Dry Surface
  A. Boelens, A. Latka, and J. de Pablo
• A New N-Acyl Homoserine Lactone Synthase in an Uncultured Symbiont of the Red Sea Sponge Theonella swinhowei
  M. Britstein, G. Devescovi, K.M. Handley, A. Malik, M. Haber, K. Saurav, R. Teta, V. Costantino, I. Burgsdorf, and J.A. Gilbert
• Improved Cosmic-Ray Injection Models and the Galactic Center Gamma-Ray Excess
  E. Carlson, T. Linden, and S. Profumo
• Changes in Spatio-temporal Precipitation Patterns in Changing Climate Conditions
  W. Chang, M. Stein, J. Wang, V.R. Kotamarthi, and E. Moyer
• A Multiple Time-Step Dual-Hamiltonian Hybrid Molecular Dynamics-Monte Carlo Canonical Propagation Algorithm
  Y. Chen, S. Kale, J. Weare, A.R. Dinner, and B. Roux
• Search for Kilonovae in Dark Energy Survey Supernova Fields
  Z. Doctor
• Multi-model Cross Pollination in Time
  H. Du and L.A. Smith
• Convergence of Economic Growth and the Great Recession as Seen From a Celestial Observatory
  E. Duede and V. Zhorin
• Disturbance Regimes Predictably Alter Diversity in an Ecologically Complex Bacterial System
  S.M. Gibbons, M. Scholz, A.L. Hutchison, A.R. Dinner, J.A. Gilbert, and M.L. Coleman
• Cosmic Reionization on Computers: Numerical and Physical Convergence
  N.Y. Gnedin
• Cosmic Reionization on Computers: The Faint End of the Galaxy Luminosity Function
  N.Y. Gnedin
• On the Proper Use of the Reduced Speed of Light Approximation
  N.Y. Gnedin
• The Turbulent Circulation of a Snowball Earth Ocean
  M.F. Jansen
• Pre-Exposure Prophylaxis (PrEP) Awareness and Use in a Population-based Sample of Young Black Men Who Have Sex with Men
  A.S. Khanna, S. Michaels, B. Skaathun, E. Morgan, K. Green, L. Young, and J.A. Schneider
• Computationally Efficient Multiscale Reactive Molecular Dynamics to Describe Amino Acid Deprotonation in Proteins
  S. Lee, R. Liang, G.A. Voth, and J.M. Swanson
• The Origin of Coupled Chloride and Proton Transport in a Cl(–)/H(+) Antiporter
  S. Lee, H.B. Mayes, J.M. Swanson, and G.A. Voth
• Multiscale Simulations Reveal Key Aspects of the Proton Transport Mechanism in the ClC-ec1 Antiporter
  S. Lee, J.M. Swanson, and G.A. Voth
• The Composition of the Microbiota Modulates Allograft Rejection
  Y.M. Lei, et al.
• The F-actin Bundler ?-actinin Ain1 is Tailored for Ring Assembly and Constriction during Cytokinesis in Fission Yeast
  Y. Li, J.R. Christensen, K.E. Homa, G.M. Hocky, A. Fok, J.A. Sees, G.A. Voth, and D.R. Kovar
• Multiscale Simulations Reveal Key Features of the Proton Pumping Mechanism in Cytochrome c Oxidase
  R. Liang, J.M. Swanson, Y. Peng, M. Wikstrom, and G. Voth
• The High-Energy Tail of the Galactic Center Gamma-Ray Excess
  T. Linden, N.L. Rodd, B.R. Safdi, and T.R. Slatyer
• Workflow Performance Improvement Using Model-Based Scheduling over Multiple Clusters and Clouds
  K. Maheshwari, E.-S. Jung, J. Meng, V. Morozov, V. Vishwanath, and R. Kettimuthu
• Differential and Enhanced Response to Climate Forcing in Diarrheal Disease Due to Rotavirus across a Megacity of the Developing World
  P.P. Martinez, A.A. King, M. Yunus, A.S.G. Faruque, and M. Pascua
• Comparing Offline Decoding Performance in Physiologically Defined Neuronal Classes
  D.B. Matthew, T. Kazutaka, J.S. Aaron, E. Christian, E.M. Lee, and G.H. Nicholas
• Spatial Scale Drives Patterns in Soil Bacterial Diversity
  S.L. O’Brien, S.M. Gibbons, S.M. Owens, J. Hampton-Marcell, E.R. Johnston, J.D. Jastrow, J.A. Gilbert, F. Meyer, and D.A. Antonopoulos
• Temperatures in Transient Climates: Improved Methods for Simulations with Evolving Temporal Covariances
  A. Poppick, D.J. McInerney, E.J. Moyer, and M.L. Stein
• A Theory of Interactions between Polarizable Dielectric Spheres
  J. Qin, J. Li, V. Lee, H. Jaeger, J.J. de Pablo, and K.F. Freed
• Optimal Prediction in the Retina and Natural Motion Statistics
  J.M. Salisbury and S.E. Palmer
• Design of Defect Spins in Piezoelectric Aluminum Nitride for Solid-State Hybrid Quantum Technologies
  H. Seo, M. Govoni, and G. Galli
• Quantum Decoherence Dynamics of Divacancy Spins in Silicon Carbide
  H. Seo, A.L. Falk, P.V. Klimov, K.C. Miao, G. Galli, and D.D. Awschalom
• Necessity of Capillary Modes in a Minimal Model of Nanoscale Hydrophobic Solvation
  S. Vaikuntanathan, G. Rotskoff, A. Hudson, and P.L. Geissler
• A Technique for Detection of PeV Neutrinos Using a Phased Radio Array
  A. Vieregg, K. Bechtol, and A. Romero-Wolf
• Explaining the Geographic Origins of Seasonal Influenza A (H3N2)
  F. Wen, T. Bedford, and S. Cobey
• Crystal Structure of Zwitterionic 2-[bis (2-methoxyphenyl) Phosphaniumyl]-4-methylbenzenesulfonate Monohydrate Dichloromethane Monosolvate
  H. Zhang, G. Feng, A.S. Filatov, and R.F. Jordan
• Lattice Boltzmann Simulation of Asymmetric Flow in Nematic Liquid Crystals with Finite Anchoring
  R. Zhang, T. Roberts, I.S. Aranson, and J.J. de Pablo
• Dynamic Structure of Active Nematic Shells
  Rui Zhang, Ye Zhou, Mohammad Rahimi, and Juan J. de Pablo
• Bayesian Large-scale Multiple Regression with Summary Statistics from Genome-Wide Association Studies
  X. Zhu and M. Stephens

2015

• Towards Anatomic Scale Agent-Based Modeling with a Massively Parallel Spatially Explicit General-Purpose Model of Enteric Tissue (SEGMEnT_HPC)
  Cockrell, Robert Chase; Christley, Scott; Chang, Eugene; An, Gary
• On the Interplay between Star Formation and Feedback in Galaxy Formation Simulations
  O. Agertz and A.V. Kravtsov
• Principal Component Estimation of a Large Covariance Matrix with High-Frequency Data
  Y. A•t-Sahalia and D. Xiu
• Globus Platform-as-a-service for Collaborative Science Applications
  R. Ananthakrishnan, K. Chard, I. Foster, and S. Tuecke
• The Genotype-Tissue Expression (GTEx) Pilot Analysis: Multitissue Gene Regulation in Humans
  K.G. Ardlie et al.
• Theoretically Informed Monte Carlo Simulation of Liquid Crystals by Sampling of Alignment-Tensor Fields
  J.C. Armas-Perez, A. Londono-Hurtado, O. Guzman, J.P. Hernandez-Ortiz, and J.J de Pablo
• Type I Planet Migration in a Magnetized Disk. II. Effect of Vertical Angular Momentum Transport
  A. Bans, A. Konigl, and A. Uribe
• ROCKET: Robust Confidence Intervals via Kendall’s Tau for Transelliptical Graphical Models
  R.F. Barber and M. Kolar
• Eight New Milky Way Companions Discovered in First-year Dark Energy Survey Data
  K. Bechtol et al.
• Cosmic Shear Measurements with DES Science Verification Data
  M. Becker et al.
• Role of Presolvation and Anharmonicity in Aqueous Phase Hydrated Proton Solvation and Transport
  R. Biswas, Y.-L. S. Tse, A. Tokmakoff, and G.A. Voth
• A New Reduction of the Blanco Cosmology Survey: An Optically Selected Galaxy Cluster Catalog and a Public Release of Optical Data Products
  L. Bleem, B. Stalder, M. Brodwin, M. Busha, M. Gladders, F. High, A. Rest, and R. Wechsler
• Graphoepitaxial Assembly of Cylinder Forming Block Copolymers in Cylindrical Holes
  Brandon L. Peters, Mark Somervell, Takeo Nakano, Gerard Schmid, and Juan J. de Pablo
• Lifestyle Evolution in Cyanobacterial Symbionts of Sponges
  I. Burgsdorf, B.M. Slaby, K.M. Handley, M. Haber, J. Blom, C.W. Marshall, J.A. Gilbert, U. Hentschel, and L. Steindler
• Hydrated Proton Structure and Diffusion at Platinum Surfaces
  Z. Cao, R. Kumar, Y. Peng, and G.A. Voth
• Ion Transport through Ultrathin Electrolyte under Applied Voltages
  Z. Cao, Y. Peng, and G.A. Voth
• The Multiscale Coarse-Graining Method. XI. Accurate Interactions Based on the Centers of Charge of Coarse-Grained Sites
  Z. Cao and G.A. Voth
• Hydroxide Solvation and Transport in Anion Exchange Membranes
  C. Chen, Y.-L.S. Tse, G.E. Lindberg, C. Knight, and G.A. Voth
• Versioned Distributed Arrays for Resilience in Scientific Applications: Global View Resilience
  A. Chien, P. Balaji, P. Beckman, N. Dun, A. Fang, H. Fujita, K. Iskra, Z. Rubenstein, Z. Zheng, and R. Schreiber
• Fibrillar Dimer Formation of Islet Amyloid Polypeptides
  C.-c. Chiu and J.J. de Pablo
• The Galactic Center GeV Excess from a Series of Leptonic Cosmic-ray Outbursts
  I. Cholis, C. Evoli, F. Calore, T. Linden, C. Weniger, and D. Hooper
• Towards Anatomic Scale Agent-Based Modeling with a Massively Parallel Spatially Explicit General-Purpose Model of Enteric Tissue (SEGMEnT_HPC)
  R.C. Cockrell, S. Christley, E. Chang, and G. An
• Coherent Neutrino-Nucleus Scattering Detection with a CsI [Na] Scintillator at the SNS Spallation Source
  J. Collar, N. Fields, M. Hai, T. Hossbach, J. Orrell, C. Overman, G. Perumpilly, B. Scholz
• What Drives Home Market Advantage?
  A.K. Cosar, P.L. Grieco, S. Li, and F. Tintelnot
• Tunable Molecular Orientation and Elevated Thermal Stability of Vapor-deposited Organic Semiconductors
  S.S. Dalal, D.M. Walters, I. Lyubimov, J.J. de Pablo, and M.D. Ediger
• Exploring Valleys without Climbing Every Peak: More Efficient and Forgiving Metabasin Metadynamics via Robust On-the-Fly Bias Domain Restriction
  J.F. Dama, G.M. Hocky, R. Sun, and G.A. Voth
• A Universal Model for Halo Concentrations
  B. Diemer and A.V. Kravtsov
• Eight Ultra-faint Galaxy Candidates Discovered in Year Two of the Dark Energy Survey
  A. Drlica-Wagner et al.
• Data Decomposition in Monte Carlo Neutron Transport Simulations Using Global View Arrays
  N. Dun, H. Fujita, J.R. Tramm, A.A. Chien, and A.R. Siegel
• The AgMIP GRIDded Crop Modeling Initiative (AgGRID) and the Global Gridded Crop Model Intercomparison (GGCMI)
  J. Elliott and C. Muller
• Many Resident Task Computing in Support of Dynamic Ensemble Computations
  J. Ozik, N.T. Collier, and J.M. Wozniak
• The High-Frequency Trading Arms Race: Frequent Batch Auctions as a Market Design Response
  Eric Budish and John Shim
• Uncertainties in Scaling-Up Crop Models for Large-Area Climate Change Impact Assessments
  F. Ewert et al.
• Incorporating Global Industrial Classification Standard into Portfolio Allocation: A Simple Factor-based Large Covariance Matrix Estimator with High Frequency Data
  J. Fan, A. Furger, and D. Xiu
• High-energy Neutrino Signatures of Newborn Pulsars in the Local Universe
  K. Fang
• Anisotropy of the Extragalactic Radio Background from Dark Matter Annihilation
  K. Fang and T. Linden
• Cluster Mergers and the Origin of the ARCADE-2 Excess
  K. Fang and T. Linden
• Phenotypic Variation in Overwinter Environmental Transmission of a Baculovirus and the Cost of Virulence
  A.E. Fleming-Davies and G. Dwyer
• Effects of Host Heterogeneity on Pathogen Diversity and Evolution
  A.E. Fleming-Davies, V. Dukic, V. Andreasen, and G. Dwyer
• A Conserved Bicycle Model for Circadian Clock Control of Membrane Excitability
  M. Flourakis et al.
• An Analysis of Biomolecular Force Fields for Simulations of Polyglutamine in Solution
  A.M. Fluitt and J.J. de Pablo
• A Framework for the Cross-Sectoral Integration of Multi-Model Impact Projections: Land Use Decisions under Climate Impacts Uncertainties
  K. Frieler et al.
• Optimal Variable Selection in Multi-Group Sparse Discriminant Analysis
  I. Gaynanova and M. Kolar
• Ecological Succession and Viability of Human-Associated Microbiota on Restroom Surfaces
  S.M. Gibbons, T. Schwartz, J. Fouquier, M. Mitchell, N. Sangwan, J.A. Gilbert, and S.T. Kelley
• CEO Personality and Firm Policies
  I. Gow., S.N. Kaplan, D.F. Larcker, and A.A. Zakolyukina
• Speeding Up Neighborhood Search in Local Gaussian Process Prediction
  R.B. Gramacy and B. Haaland
• Coarse-Grained Ions for Nucleic Acid Modeling
  D.M. Hinckley and J.J. de Pablo
• A Molecular View of the Role of Chirality in Charge-Driven Polypeptide Complexation
  K.Q. Hoffmann, S.L. Perry, L. Leon, D. Priftis, M. Tirrell, and J.J. de Pablo
• Molecular Pathways for Defect Annihilation in Directed Self-Assembly
  S.M. Hur, V. Thapar, A. Ramirez-Hernandez, G. Khaira, T. Segal-Peretz, P.A. Rincon-Delgadillo, W. Li, M. Muller, P.F. Nealey, and J.J. de Pablo
• Velocity and Mass Bias in the Distribution of Dark Matter Haloes
  E. Jennings, C.M. Baugh, and D. Hatt
• Non-linear Stochastic Growth Rates and Redshift Space Distortions
  E. Jennings and D. Jennings
• Disentangling Redshift-Space Distortions and Nonlinear Bias Using the 2D Power Spectrum
  E. Jennings, R.H. Wechsler, S.W. Skillman, and M.S. Warren
• Radiative Return Capabilities of a High-Energy, High-Luminosity e⁺e^– Collider
  M. Karliner, M. Low, J.L. Rosner, and L.-T. Wang
• The Difference Imaging Pipeline for the Transient Search in the Dark Energy Survey
  R. Kessler et al.
• Identifying Peer Change Agents on a Large Social Network
  A.S. Khanna, S.D. Jacobs, S. Michaels, B. Skaathun, E. Morgan, L.E. Young, and J.A. Schneider
• Preexposure Prophylaxis Awareness and Use in a Population-Based Sample of Young Black Men Who Have Sex With Men
  A.S. Khanna, S. Michaels, B. Skaathun, E. Morgan, K. Green, L. Young, and J.A. Schneider
• Stratigraphy of Aeolis Dorsa, Mars: Stratigraphic Context of the Great River Deposits
  E.S. Kite, A.D. Howard, A.S. Lucas, J.C. Armstrong, O. Aharonson, and M.P. Lamb
• How Superfluid Vortex Knots Untie
  D. Kleckner, L.H. Kauffman, and W. Irvine
• Deciphering Thermal Phase Curves of Dry, Tidally Locked Terrestrial Planets
  D.D. Koll and D.S. Abbot
• Effects of Diurnal Variation of Gut Microbes and High-Fat Feeding on Host Circadian Clock Function and Metabolism
  V. Leone et al.
• A Molecular View of DNA-Conjugated Nanoparticle Association Energies
  J.P. Lequieu, D.M. Hinckley, and J.J. de Pablo
• Separate Universe Consistency Relation and Calibration of Halo Bias
  Y. Li, W. Hu, and M. Takada
• Column Density Profiles of Multi-Phase Gaseous Halos
  C.J. Liang, A.V. Kravtsov, and O. Agertz
• Metabolic Potential of Fatty Acid Oxidation and Anaerobic Respiration by Abundant Members of Thaumarchaeota and Thermoplasmata in Deep Anoxic Peat
  X. Lin, K.M. Handley, J.A. Gilbert, and J.E. Kostka
• Known Radio Pulsars Do Not Contribute to the Galactic Center Gamma-Ray Excess
  T. Linden
• Mesoscale Study of Proton Transport in Proton Exchange Membranes: Role of Morphology
  S. Liu, J. Savage, and G.A. Voth
• Homeotropic Nano-particle Assembly on Degenerate Planar Nematic Interfaces: Films and Droplets
  A. Londono-Hurtado, J.C. Armas-Perez, J.P. Hernandez-Ortiz, and J.J. de Pablo
• Post-regularization Inference for Dynamic Nonparanormal Graphical Models
  J. Lu, M. Kolar, and H. Liu
• Orientational Anisotropy in Simulated Vapor-Deposited Molecular Glasses
  I. Lyubimov, L. Antony, D.M. Walters, D. Rodney, M.D. Ediger, and J.J. de Pablo
• Blue-phase Liquid Crystal Droplets
  J.A. Martinez-Gonzalez, Y. Zhou, M. Rahimi, E. Bukusoglu, N.L. Abbott, and J.J. de Pablo
• Classification of Magnetized Star-Planet Interactions: Bow Shocks, Tails, and Inspiraling Flows
  T. Matsakos, A. Uribe, and A. Konigl
• Polarization Predictions for Inflationary CMB Power Spectrum Features
  V. Miranda, W. Hu, and C. Dvorkin
• The Splashback Radius as a Physical Halo Boundary and the Growth of Halo Mass
  S. More, B. Diemer, and A.V. Kravtsov
• Predictive Information in a Sensory Population
  S.E. Palmer, O. Marre, M.J. Berry, and W. Bialek
• Hydrated Excess Protons Can Create Their Own Water Wires
  Y. Peng, J.M.J. Swanson, S.-G. Kang, R. Zhou, and G.A. Voth
• Chirality-selected Phase Behaviour in Ionic Polypeptide Complexes
  S.L. Perry et al.
• Design, Synthesis, and Characterization of a Bifunctional Chelator with Ultrahigh Capacity for Uranium Uptake from Seawater Simulant
  M. Piechowicz, C.W. Abney, X. Zhou, N.C. Thacker, Z. Li, and W. Lin
• FUV Variability of HD 189733. Is the Star Accreting Material from its Hot Jupiter?
  I. Pillitteri, A. Maggio, G. Micela, S. Sciortino, S. Wolk, and T. Matsakos
• Nanoparticle Self-assembly at the Interface of Liquid Crystal Droplets
  M. Rahimi, T.F. Roberts, J.C. Armas-Perez, X. Wang, E. Bukusoglu, N.L. Abbott, and J.J. de Pablo
• Supercal: Cross-Calibration of Multiple Photometric Systems to Improve Cosmological Measurements with Type Ia Supernovae
  D. Scolnic et al.
• Decoding Thalamic Afferent Input Using Microcircuit Spiking Activity
  A.J. Sederberg, S.E. Palmer, and J.N. MacLean
• Distributed Multinomial Regression
  M. Taddy
• Document Classification by Inversion of Distributed Language Representations
  M. Taddy
• Bayesian and Empirical Bayesian Forests
  M. Taddy, C.S. Chen, J. Yun
• Global Production with Export Platforms
  F. Tintelnot
• Propensity of Hydrated Excess Protons and Hydroxide Anions for the Air-Water Interface 
  Y.-L.S. Tse, C. Chen, G.E. Lindberg, R. Kumar, and G.A. Voth
• An Analysis of Hydrated Proton Diffusion in Ab Initio Molecular Dynamics
  Y.L. Tse, C. Knight, and G.A. Voth
• Type I Planet Migration in a Magnetized Disk. I. Effect of Large-scale Vertical and Azimuthal Field Components
  A. Uribe, A. Bans, and A. Konigl
• A New Technique for Detection of PeV Neutrinos Using a Phased Radio Array
  A. Vieregg, K. Bechtol, and A. Romero-Wolf
• Predicting the Sensitivity of Multiscale Coarse-Grained Models to their Underlying Fine-Grained Model Parameters
  J.W. Wagner, J.F. Dama, and G.A. Voth
• Designing Free Energy Surfaces That Match Experimental Data with Metadynamics
  A.D. White, J.F. Dama, and G.A. Voth
• Sculpting Bespoke Mountains: Determining Free Energies with Basis Expansions
  J.K. Whitmer, A.M. Fluitt, L. Antony, J. Qin, M. McGovern, and J.J. de Pablo
• Fin Ray Sensation Participates in the Generation of Normal Fin Movement in the Hovering Behavior of the Bluegill Sunfish (Lepomis macrochirus)
  R. Williams and M.E. Hale
• Intergenerational Continuity of Cell Shape Dynamics in Caulobacter crescentus
  C.S. Wright, S. Banerjee, S. Iyer-Biswas, S. Crosson, A.R. Dinner, and N.F. Scherer
• Extreme Data Compression for the CMB
  A. Zablocki and S. Dodelson
• The Soil Microbiome Influences Grapevine-Associated Microbiota
  I. Zarraonaindia et al.
• CosmoSIS: Modular Cosmological Parameter Estimation
  J. Zuntz, M. Paterno, E. Jennings, D. Rudd, A. Manzotti, S. Dodelson, S. Bridle, S. Sehrish, and J.  Kowalkowski

2014

• Memory Maintenance in Synapses with Calcium-Based Plasticity in the Presence of Background Activity
  Higgins, David; Graupner, Michael; Brunel, Nicolas
• Hydrated Excess Protons Can Create Their Own Water Wires
  Yuxing Peng, Jessica M. J. Swanson, Seung-gu Kang, Ruhong Zhou, Gregory A. Voth
• Dependence of the Outer Density Profiles of Halos on Their Mass Accretion Rate
  Benedikt Diemer and Andrey V. Kravtsov
• Dynamic Spatiotemporal Brain Analyses Using High Performance Electrical Neuroimaging: Theoretical Framework and Validation
  Stephanie Cacioppo, Robin M. Weiss, Hakizumwami Birali Runesha, and John T. Cacioppo
• Proton Transport Under External Applied Voltage
  Zhen Cao, Revati Kumar, Yuxing Peng, Gregory A. Voth
• Neutrinos Help Reconcile Planck Measurements with Both the Early and Local Universe
  Cora Dvorkin, Mark Wyman, Douglas H. Rudd, and Wayne Hu
• Measuring Liquid Crystal Elastic Constants with Free Energy Perturbations
  Abhijeet A. Joshi, Jonathan K. Whitmer, Orlando Guzmán, Nicholas L. Abbott, and Juan J. de Pablo
• Interactions of Protein Kinase C-α C1A and C1B Domains with Membranes: A Combined Computational and Experimental Study
  Jianing Li, Brian P. Ziemba, Joseph J. Falke, Gregory A. Voth
• Strong Dependence of the Inner Edge of the Habitable Zone on Planetary Rotation Rate
  Author: Jun Yang, Gwenaël Boué, Daniel C. Fabrycky, and Dorian S. Abbot
• Chloride Enhances Fluoride Mobility in Anion Exchange Membrane/Polycationic Systems
  Ying-Lung Steve Tse, Himanshu N. Sarode, Gerrick E. Lindberg, Thomas A. Witten, Yuan Yang, Andrew M. Herring, Gregory A. Voth
• Graph Estimation from Multi-Attribute Data
  Mladen Kolar, Han Liu, and Eric P. Xing
• Unraveling the Mystery of ATP Hydrolysis in Actin Filaments
  Martin McCullagh, Marissa G. Saunders, Gregory A. Voth
• Longitudinal Analysis of Microbial Interaction Between Humans and the Indoor Environment
  Simon Lax, Daniel P. Smith, Jarrad Hampton-Marcell, Sarah M. Owens, Kim M. Handley, Nicole M. Scott, Sean M. Gibbons, Peter Larsen, Benjamin D. Shogan, Sophie Weiss, Jessica L. Metcalf, Luke K. Ursell, Yoshiki Vázquez-Baeza, Will Van Treuren, Nur A. Hasan, Molly K. Gibson, Rita Colwell, Gautam Dantas, Rob Knight, and Jack A. Gilbert
• Super-Sample Covariance in Simulations
  Yin Li, Wayne Hu, and Masahiro Takada
• Multiscale Simulation Reveals a Multifaceted Mechanism of Proton Permeation through the Influenza A M2 Proton Channel
  Ruibin Liang, Hui Li,  Jessica M. J. Swanson, and Gregory A. Voth
• Inflationary Steps in the Planck Data
  Vinícius Miranda and Wayne Hu
• Cosmological Parameter Uncertainties from SALT-II Type Ia Supernova Light Curve Models
  J. Mosher, J. Guy, R. Kessler, P. Astier, J. Marriner, M. Betoule, M. Sako, P. El-Hage, R. Biswas, R. Pain, S. Kuhlmann, N. Regnault, J. A. Frieman, D. P. Schneider
• Cosmic Reionization on Computers. I. Design and Calibration of Simulations
  Nickolay Y. Gnedin
• Cosmic Reionization on Computers. II. Reionization History and Its Back-reaction on Early Galaxies
  Nickolay Y. Gnedin and Alexander A. Kaurov
• Neutrinos Help Reconcile Planck Measurements with the Local Universe
  Mark Wyman, Douglas H. Rudd, R. Ali Vanderveld, and Wayne Hu
• Strong Dependence of the Inner Edge of the Habitable Zone on Planetary Rotation Rate
  Jun Yang, Gwenaël Boué, Daniel C. Fabrycky, and  Dorian S. Abbot

2013

• Weak Lensing Simulations for Large-Area Sky Surveys and Second-Order Effects in Cosmic Shear Power Spectra
  Matthew R. Becker
• A Quantitative Meta-Analysis of Functional Imaging Studies of Social Rejection
  Stephanie Cacioppo, Chris Frum, Erik Asp, Robin M. Weiss, James W. Lewis, and John T. Cacioppo
• On the Evolution of Cluster Scaling Relations
  Benedikt Diemer, Andrey V. Kravtsov, and Surhud More
• Constraints and Potentials of Future Irrigation Water Availability on Agricultural Production under Climate Change
  Joshua Elliott, Delphine Deryng, Christoph Müller, Katja Frieler, Markus Konzmann, Dieter Gerten, Michael Glotter, Martina Flörke, Yoshihide Wada, and Neil Best
• Predicting Agricultural Impacts of Large-Scale Drought: 2012 and the Case for Better Modeling
  Joshua Elliott, Michael Glotter, Neil Best, Ken Boote, Jim Jones, Jerry Hatfield, Cynthia Rosenzweig, Leonard A, Smith, and Ian Foster
• Massively Parallel Approximate Gaussian Process Regression
  Robert B. Gramacy, Jarad Niemi, and Robin Weiss
• The Abundance of Voids and the Excursion Set Formalism
  Elise Jennings, Yin Li, and Wayne Hu
• The AGORA High-Resolution Galaxy Simulations Comparison Project
  Ji-hoon Kim, Tom Abel, Oscar Agertz, Greg L. Bryan, Daniel Ceverino, Charlotte Christensen, Charlie Conroy, Avishai Dekel, Nickolay Y. Gnedin, and Nathan J. Goldbaum
• Multi-state Approach to Chemical Reactivity in Fragment Based Quantum Chemistry Calculations
  Adrian W. Lange and Gregory A. Voth
• Precipitation in a Surface-Energy Budget Context in Transient and Equilibrium Climates
  Shanshan Sun and Elisabeth Moyer
• Dynamical Simulations of Coarse Grain Polymeric Systems: Rouse and Entangled Dynamics
  Abelardo Ramírez-Hernández, François A. Detcheverry, Brandon L. Peters, Verónica C. Chappa, Kenneth S. Schweizer, Marcus Müller, and Juan J. de Pablo
• Autoinhibition of Endophilin in Solution via Interdomain Interactions
  Francisco X. Vázquez, Vinzenz M. Unger, and Gregory A. Voth
• Nematic-Field-Driven Positioning of Particles in Liquid Crystal Droplets
  Jonathan K. Whitmer, Xiaoguang Wang, Frederic Mondiot, Daniel S. Miller, Nicholas L. Abbott, and Juan J. de Pablo
• Simulations of Galileon Modified Gravity: Clustering Statistics in Real and Redshift Space
  Mark Wyman, Elise Jennings, and Marcos Lima
• Measuring Intentional Manipulation: A Structural Approach
  Anastasia Zakolyukina