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Publications

The Research Computing Center's (RCC) resources and staff support a number of faculty projects that have resulted in published academic papers. See below for a list of papers acknowledging the RCC for providing computational resources, support, and services.

If you have published a paper that acknowledged RCC and it is not listed below please contact us with the appropriate citation information.  For information on how to cite or acknowledge RCC in your publications see Acknowledging the RCC.

2024

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

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

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

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

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

S. 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

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