Publications
The publications are organized by year and tag. Please use Ctrl-F to search for a tag of interest.
Tag-1 = XFELs/Crystallography
Tag-2 = Electronic Structure
Tag-3 = Tomography
Tag-4 = Ptychography
Tag-5 = Workflow/Software Infrastructure
Tag-6 = Image Analysis, Computer Vision
Tag-7 =Machine Learning/Optimization
Tag-8 = GPU/High Performance Implementations
Tag-9 = CAMERA
Tag-10 = GISAXS. WAXS, SAXS
Tag-11 = Quantum Computation
Tag-12 = Chemical/Material Informatics
Tag-13 = X-Ray Photon Correlation Spectroscopy
Tag-14 = Self-Driving Autonomous Experiments
Tag-15 = Multiple Scattering
2024
AI@ ALS Workshop Report: Machine Learning Needs at the Advanced Light Source [Tag-6, Tag-7]
2024, Taylor & Francis
Parkinson, Dilworth Y, Chavez, Tanny, Choudhary, Monika, English, Damon, Hao, Guanhua, Hellert, Thorsten, Leemann, Simon C, Nemsak, Slavomir, Rotenberg, Eli, Taylor, Andrea
qlty: Handling large tensors in scientific imaging deep-learning workflows [Tag-6, Tag-7]
2024, Software Impacts
Zwart, Petrus H
Towards Autonomous Synchrotron Fourier Transform Infrared Microscopy [Tag-14]
2024, Microscopy and Microanalysis
Zwart, Petrus, Tas, Neslihan, Noack, Marcus, Holman, HoiYing
Long-Term, Non-Invasive Detection of Low-Dose Ionizing Radiation Exposure [Tag-6]
2024, Electrochemical Society Meeting Abstracts 245
Inman, Jamie, Wu, Yulun, Chen, Liang, Ghosh, Dhruba, Wan, Kenneth, DeChant, Jared, Obst-Huebl, Lieselotte, Nakamura, Kei, Ralston, Corie, Celniker, Susan
DLSIA: Deep Learning for Scientific Image Analysis [Tag-6, Tag-7]
2024, Journal of Applied Crystallography
Roberts, Eric J, Chavez, Tanny, Hexemer, Alexander, Zwart, Petrus H
Benchmarking topic models on scientific articles using BERTeley [Tag-7]
2024, Journal of Natural Language Processing
Chagnon, E., Pandolfi, R., Donatelli, J., Ushizima, D.
RhizoNet segments plant roots to assess biomass and growth for enabling self-driving labs [Tag-7,14]
2024, Nature Scientific Reports
Sordo, Z., Andeer, P., Sethian, J., Northen, T., Ushizima, D.
Optimizing and Scaling the 3D Reconstruction of Single-Particle Imaging [Tag-1]
2024 IEEE International Parallel and Distributed Processing Symposium
N. Shah, C. Sweeney, V. Ramakrishnaiah, J. Donatelli, W.C. Feng.
Methods and Applications of Autonomous Experimentation [Tag-7,14]
2024, CRC Press
Noack, Marcus M and Ushizima, Daniela
A substitutional quantum defect in WS2 discovered by high-throughput computational screening and fabricated by site-selective STM manipulation [Tag-14]
2024, Nature Communications
John C Thomas, Wei Chen, Yihuang Xiong, Bradford A Barker, Junze Zhou, Weiru Chen, Antonio Rossi, Nolan Kelly, Zhuohang Yu, Da Zhou, Shalini Kumari, Edward S Barnard, Joshua A Robinson, Mauricio Terrones, Adam Schwartzberg, D Frank Ogletree, Eli Rotenberg, Marcus M Noack, Sinéad Griffin, Archana Raja, David A Strubbe, Gian-Marco Rignanese, Alexander Weber-Bargioni, Geoffroy HautierZ
A unifying perspective on non-stationary kernels for deeper Gaussian processes [Tag-7]
2024, APL Machine Learning
Noack, Marcus M and Luo, Hengrui and Risser, Mark D
Benchmarking topic models on scientific articles using BERTeley [Tag-7]
Natural Language Processing Journal
E. Chagnon, R. Pandolfi, J. Donatelli, D. Ushizima
tomoCAM: Fast Model-based Iterative Reconstruction via GPU Acceleration and Non-Uniform Fast Fourier Transforms [Tag-3,8]
Journal of Synchrotron Radiation
D. Kumar, D. Parkinson, J.J. Donatelli
2023
Deploying machine learning based segmentation for scientific imaging analysis at synchrotron facilities [Tag-6, Tag-7]
2023, IS&T International Symposium on Electronic Imaging
Hao, Guanhua, Roberts, Eric J, Chavez, Tanny, Zhao, Zhuowen, Holman, Elizabeth A, Yanxon, Howard, Green, Adam, Krishnan, Harinarayan, Ushizima, Daniela, McReynolds, Dylan
Inter-Bragg crystallographic phase retrieval from shape transforms, stacking faults and substitutional disorder [Tag-1]
Ultramicroscopy
J.P.J. Chen, K. Pande, J.J. Donatelli, A.V. Martin, K. Ayyer, H.N. Chapman, R. Bean, K.E. Schmidt, R.A. Kirian
Autonomous x-ray scattering [Tag-7, Tag-14]
Nanotechnology
K.G. Yager, P.W. Majewski, M.M. Noack, M. Fukuto
Exact Gaussian processes for massive datasets via non-stationary sparsity-discovering kernels [Tag-7]
Scientific reports
M.M. Noack, H. Krishnan, M.D. Risser, K.G. Reyes
Mathematical nuances of Gaussian process-driven autonomous experimentation [Tag-14]
MRS Bulletin
M.M. Noack, K.G. Reyes
Autonomous discovery of emergent morphologies in directed self-assembly of block copolymer blends [Tag-14]
Science Advances
G.S. Doerk, A. Stein, S. Bae, M.M. Noack, M. Fukuto, K.G. Yager
Surface enrichment dictates block copolymer orientation [Tag-14]
Nanoscale
S. Bae, M.M. Noack, K.G. Yager
Detecting Lithium Plating Dynamics in a Solid-State Battery with Operando x-Ray Computed Tomography Using Machine Learning [Tag-3,7,12]
Nature Partner Journal
Y. Huang, D. Perlmutter, A. Su, J. Quenum, I. Zenyuk, D. Ushizima
Advancing the capabilities of polymer blend directed self-assembly [Tag-14]
Novel Patterning Technologies
G.S. Doerk, A. Stein, S. Bae, M. Noack, M. Fukuto, A.A. Kulkarni, K. Toth, C. Osuji, K. Yager
Improve neutron measurement performance with AI and machine learning [Tag-14]
Acta Crystallographica Section A: Foundations of Crystallography
P. Mutti, M. Boehm, Y. Le Goc, T. Weber, M. Noack, J. Sethian
Artificial Intelligence (AI) and Machine Learning (ML) at Experimental Facilities [Tag-7,14]
Artificial Intelligence for Science: A Deep Learning Revolution
J. A. Sethian, J. J. Donatelli, A. Hexemer, M. M. Noack, D. M. Pelt, D. M. Ushizima, P. H. Zwart.
Iterative projection algorithms for phasing diffraction from crystals with conformational disorder [Tag-1]
in preparation
K. Pande, J. P. Chen, J. J. Donatelli, and R. A. Kirian
Image segmentation using u-net architecture for powder x-ray diffraction images [Tag-6,7]
Proceedings of the IEEE/CVF international conference on computer vision
H. Yanxon, E.J. Roberts, H. Parraga, J. Weng, W. Xu, U. Ruett, A. Hexemer, P.H. Zwart, N. Schwarz
Deploying machine learning based segmentation for scientific imaging analysis at synchrotron facilities [Tag-7]
Society for Imaging Science and Technology, Electronic Imaging
G. Hao, E.J. Roberts, T. Chavez, Z. Zhao, E. Holman, H. Yanxon, A. Green, H. Krishnan, D. Ushizima, D. McReynolds, N. Schwarz, P.H. Zwart, A. Hexemer, D.Y. Parkinson
Using Machine Learning Algorithms for Water Segmentation in Gas Diffusion Layers of Polymer Electrolyte Fuel Cells [Tag-6,7]
Transport in Porous Media
A.D. Shum, C.P. Liu, W.H. Lim, D.Y. Parkinson, I.V. Zenyuk
tomoCAM: Fast Model-based Iterative Reconstruction via GPU Acceleration and Non-Uniform Fast Fourier Transforms [Tag-3]
arXiv/in review
D. Kumar, D. Parkinson, J.J. Donatelli
2022
Advanced stationary and nonstationary kernel designs for domain-aware Gaussian processes [Tag-7]
Communications in Applied Mathematics and Computational Science
M.M. Noack, J.A. Sethian
Autonomous scanning probe microscopy investigations over WS2 and Au{111} [Tag-14]
npj Computational Materials
J.C. Thomas, A. Rossi, D. Smalley, L. Francaviglia, Z. Yu, T. Zhang, S. Kumari, J.A. Robinson, M. Terrones, M. Ishigami, E. Rotenberg, E.S. Barnard, A. Raja, E. Wong, D.F. Ogletree, M.M. Noack, A. Weber-Bargioni
Machine-learning for designing nanoarchitectured materials by dealloying [Tag-14]
Communications Materials
C Zhao, CC Chung, S Jiang, MM Noack, JH Chen, K Manandhar, J Lynch, H. Zhong, W. Zhu, P. Maffettone, D. Olds, M. Fukuto, I. Takeuchi, S. Ghose, T. Caswell, K.G. Yager, Y.K. Chen-Wiegart
Cryo-electron tomography with mixed-scale dense neural networks reveals key steps in deployment of Toxoplasma invasion machinery [Tag-6,7]
Proceedings of the National Academy of Sciences Nexus
L. Segev-Zarko, P.D. Dahlberg, S.Y. Sun, D.M. Pelt, C.Y. Kim, E.S. Egan, J.A. Sethian, W. Chiu, J.C. Boothroyd
Validation of Deep Learning Segmentation of CT Images of Fiber-Reinforced Composites [Tag-6,7]
Journal of Composites Science
A. Badran, D. Parkinson, D. Ushizima, D. Marshall, E. Maillet
Validation of Deep Learning Segmentation of CT Images of Fiber-Reinforced Composites [Tag-6,7]
Journal of Composites Science
A. Badran, D. Parkinson, D. Ushizima, D. Marshall, E. Maillet
Unraveling the effect of collagen damage on bone fracture using in situ synchrotron microtomography with deep learning [Tag-7]
Communications Materials
M. Sieverts, Y. Obata, J. L. Rosenberg, W. Woolley, D. Y. Parkinson, H. S. Barnard, D. M. Pelt, C. Acevedo
Structure Determination from Multiple-Scattering Electron Crystallography [Tag-15]
Microscopy and Microanalysis
J.J. Donatelli, J.C.H. Spence
Deep learning-based identification of sub-nuclear structures in FIB-SEM images [Tag-7]
arXiv
N. Gupta, E. J. Roberts, S. Pang, C. S. Xu, H. F. Hess, F. Wu, A. Dernburg, D. Jorgens, P. H. Zwart, V. Kasinath
The case for data science in experimental chemistry: examples and recommendations [Tag-12]
Nature Reviews, Chemistry
Y. Yano, K. J. Gaffney, J. Gregoire, L. Hung, A. Ourmazd, J. Schrier, J. A. Sethian, F. M. Toma
A comparison of deep-learning-based inpainting techniques for experimental X-ray scattering [Tag-7]
Proceedings of the IEEE/CVF International Conference on Computer Vision
T. Chavez, E. Roberts, P.H. Zwart, A. Hexemer
MLExchange: A web-based platform enabling exchangeable machine learning workflows for scientific studies [Tag-7]
IEEE, 2022, 4th Annual Workshop on Extreme-scale Experiment-in-the-Loop Computing (XLOOP)
Z. Zhao, T. Chavez, E. A. Holman, G. Hao, A. Green, H. Krishnan, D. McReynolds, R. Pandolfi, E. J. Roberts, P. H. Zwart, H. Yanxon, N. Schwarz, S. Sankaranarayanan, S. V. Kalinin, A. Mehta, S. Campbell, A. Hexemer
Benchmarking autonomous scattering experiments illustrated on TAS [Tag-14]
Frontiers in Materials
M.T. Parente, A. Schneidewind, G. Brandl, C. Franz, M. Noack, M. Boehm, M. Ganeva
Unveiling characteristic proteins for the structural development of beetle elytra [Tag-3]
Acta Biomaterialia
S. Murata, J. Rivera, M.Y. Noh, N. Hiyoshi, W. Yang, D.Y. Parkinson, H.S. Barnard, Y. Arakane, D. Kisailus, A. Arakaki
Comparing the Purity of Rolled versus Evaporated Lithium Metal Films Using X-ray Microtomography [Tag-3]
ACS Energy Letters
A.S. Ho, A.S. Westover, K. Browning, J.A. Maslyn, D.Y. Parkinson, R. Sahore, N. Dudney, N.P. Balsara
Elucidating effects of catalyst loadings and porous transport layer morphologies on operation of proton exchange membrane water electrolyzers [Tag-3]
Applied Catalysis B: Environmental
D. Kulkarni, A. Huynh, P. Satjaritanun, M. O’Brien, S. Shimpalee, D. Parkinson, P. Shevchenko, F. DeCarlo, N. Danilovic, K.E. Ayers, C. Capuano, I.V. Zenyuk
Towards Data-Informed Motion Artifact Reduction in Quantitative CT Using Piecewise Linear Interpolation [Tag-3]
IEEE Transactions on Computational Imaging
E. Boigné, D.Y. Parkinson, M. Ihme
Failure Mechanisms at the Interfaces between Lithium Metal Electrodes and a Single-Ion Conducting Polymer Gel Electrolyte [Tag-3]
ACS Applied Materials & Interfaces
L. Frenck, P. Lennartz, D.Y. Parkinson, M. Winter, N.P. Balsara, G. Brunklaus
A workflow for segmenting soil and plant X-ray CT images with deep learning in Googles Colaboratory [Tag-3,5]
arXiv
D.A. Rippner, P. Raja, J.M. Earles, A. Buchko, M. Momayyezi, F. Duong, D. Parkinson, E. Forrestel, K. Shackel, J. Neyhart, A.J. McElrone
Failure Mechanisms at the Interfaces between Lithium Metal Electrodes and a Single-Ion Conducting Polymer Gel Electrolyte [Tag-3]
IEEE Transactions on Computational Imaging
E. Boigné, D.Y. Parkinson, M. Ihme
Nano-faceted stabilization of polar-oxide thin films: The case of MgO(111) and NiO(111) surfaces [Tag-2,12]
Applied Surface Science
A. Kerrigan, K. Pande, D. Pingstone, D.A. Cavill, M. Gajdardziska-Josifovska, K.P. McKenna, M. Weinert, V. Lazarov
Joint Iterative Reconstruction and 3D Rigid Alignment for X-ray Tomography [Tag-3]
Optics Express
K. Pande, J. J. Donatelli, D. Y. Parkinson, H. Yan, J. A. Sethian
2021
Cross-correlation Analysis of X-ray Photon Correlation Spectroscopy to Extract Rotational Diffusion Coefficients [Tag-13]
Proceedings of the National Academy of Sciences
Zixi Hu, J.J. Donatelli, and J.A. Sethian
Scaling and Acceleration of Three-dimensional Structure Determination for Single-Particle Imaging Experiments with SpiniFEL [Tag,1,8]
In Parallel Application Workshop, Alternatives to MPI+X (PAW-ATM)
H.Y. Chang, E. Slaughter, S. Mirchandaney, J. Donatelli, C.H. Yoon
Gaussian Processes for Autonomous Data Acquisition at Large-Scale Synchrotron and Neutron Scattering Facilities [Tag-14]
Nature Review Physics, July, 2021 [read the paper here]
Marcus M. Noack, Petrus H. Zwart, Daniela M. Ushizima, Masafumi Fukuto, Kevin G. Yager, Katherine C. Elbert, Christopher B. Murray, Aaron Stein, Gregory S. Doerk, Esther H. R. Tsai, Ruipeng Li, Guillaume Freychet, Mikhail Zhernenkov, Hoi-Ying N. Holman, Steven Lee, Liang Chen, Eli Rotenberg, Tobias Weber, Yannick Le Goc, Martin Bohm, Paul Steffens, Paolo Mutti, and James A. Sethian
Cric searchable image database as a public platform for conventional pap smear cytology data [Tag-6]
Nature Scientific Data, June, 2021
M. Rezende, R. Silva, F. Bernardo, A. Tobias, P. Oliveira, T. Machado, C. Costa, F. Medeiros, D. Ushizima, C. Carneiro, A. Bianchi
Inversion of dynamical Bragg intensities to complex structure factors by iterated projections [TAG-15]
Ultramicroscopy, 222, 113214, 2021
John C.H. Spence and Jeffrey J. Donatelli
GPU-accelerated multitiered iterative phasing algorithm for fluctuation X-ray scattering [TAG-1, TAG-8]
J. Appl. Cryst. 54, 2021
Pranay Reddy Kommera, Vinay Ramakrishnaiah, Christine Sweeney, Jeffrey Donatelli, and Petrus H. Zwart
Microstructure and Water Absorption of Ancient Concrete from Pompeii: An Integrated Synchrotron Microtomography and Neutron Radiography Characterization [Tag-6]
Cement and Concrete Research, January, 2021
K. Xu, A. Tremsin, J. Li, D. Ushizima, C. Davy, A. Bouterf, Y. Su, M. Marroccoli, A. Mauro, M. Osanna, A. Telesca, P. Monteiro
Deep Density: circumventing the Kohn-Sham equations via symmetry preserving neural networks [Tag-2, Tag-7]
J. Comput. Phys. 443, 110523, 2021
L. Zepeda-Nunez, Y. Chen, J. Zhang, W. Jia, L. Zhang, L. Lin
Numerical solution of large scale Hartree-Fock-Bogoliubov equations [TAG-2]
ESIAM: Math. Model. Numer. Anal. (M2AN), 55, 763, 2021
L. Lin and X. Wu
Time-dependent unbounded Hamiltonian simulation with vector norm scaling [TAG-11]
Quantum 5, 459, 2021
D. An, D. Fang, L. Lin
Hierarchical Median Narrow Band for Level Set Segmentation of Cervical Cell Nuclei [TAG-6]
Applied Sciences
A. Braga, R.C.P. Marques, F.N.S. Medeiros, J.F.S. Rocha Neto, A.G.C. Bianchi, C.M. Carneiro, D.M. Ushizima
A Hierarchical Feature-Based Methodology to Perform Cervical Cancer Classification [TAG-6]
Applied Sciences
D.N. Diniz, M.T. Rezende, A.G.C. Bianchi, C.M. Carneiro, D.M. Ushizima, F.N.S. de Medeiros, M.J.F. Souza
Active Contours for Overlapping Cervical Cell Segmentation [TAG-6]
International Journal of Biomedical Engineering and Technology
F.H.D. Araújo, R.R.V. Silva, F.N.S. Medeiros, J.F. Rocha Neto, P.H.C. Oliveira, A.G.C. Bianchi, D. Ushizima
Cric searchable image database as a public platform for conventional pap smear cytology data [TAG-6]
Nature Scientific Data
M.T. Rezende, R. Silva, F.O. Bernardo, A.H.G. Tobias, P.H.C. Oliveira, T.M. Machado, C.S. Costa, F.N.S. Medeiros, D.M. Ushizima, C.M. Carneiro, A.G.C. Bianchi
Microstructure and Water Absorption of Ancient Concrete from Pompeii: An Integrated Synchrotron Microtomography and Neutron Radiography Characterization [TAG-3,6]
Cement and Concrete Research
K. Xu, A.S. Tremsin, J. Li, D.M. Ushizima, C.A. Davy, A. Bouterf, Y.T. Su, M. Marroccoli, A.M. Mauro, M. Osanna, A. Telesca
3D Nanotomography of Calcium Silicate Hydrates by Transmission Electron Microscopy [TAG-3]
Journal of the American Ceramic Society
P. Viseshchitra, P. Panod, P. Ercius, P. J. M. Monteiro, M. Scott, D. Ushizima, J. Li, K. Xu, H.R. Wenk
Persistent and partially mobile oxygen vacancies in Li-rich layered oxides [TAG-4]
Nature Energy 6, pages 642–652 (2021) doi.org/10.1038/s41560-021-00832-7
Peter M. Csernica, Samanbir S. Kalirai, William E. Gent, Kipil Lim, Young-Sang Yu, Yunzhi Liu1, Sung-Jin Ahn, Emma Kaeli, Xin Xu, Kevin H. Stone, Ann F. Marshall, Robert Sinclair, David A. Shapiro, Michael F. Toney and William C. Chueh
2020
Autonomous materials discovery driven by Gaussian process regression with inhomogeneous measurement noise and anisotropic kernels [TAG-14]
Scientific Reports,10, 17663, 2020
Marcus M. Noack, Gregory S. Doerk, Ruipeng Li, Jason K. Streit, Richard A. Vaia, Kevin G. Yager, Masafumi Fukuto
Workflows are the New Applications: Challenges in Performance, Portability, and Productivity [TAG-5]
2020 IEEE/ACM International Workshop on Performance, Portability and Productivity in HPC (P3HPC), doi:10.1109/P3HPC51967.2020.00011.
T. Ben-Nun, T. Gamblin, D. S. Hollman, H. Krishnan and C. J. Newburn
Towards a BES Light Source Wide Event-triggered Tomography Data Analysis Pipeline Using a Sustainable Software Stack [TAG-5]
Microscopy and Microanalysis, doi:10.1017/S143192762002379X
H. Krishnan, T. Caswell, D. Allan, 2020
3D Nanotomography of Calcium Silicate Hydrates by Transmission Electron Microscopy [Tag-6]
Journal of the American Ceramic Society, November, 2020
P. Viseshchitra, P. Ercius, P. Monteiro, M. Scott, D. Ushizima, Y. Li, K. Xu, H. Wenk
Sparse matrix-based hpc tomography [Tag-3, Tag-8]
International Conference on Computational Science (pp. 248-261)
Marchesini, S., Trivedi, A., Enfedaque, P., Perciano, T., & Parkinson, D.
Iterative X-ray spectroscopic ptychography [Tag-4, Tag-8]
Journal of Applied Crystallography
Huibin Chang, Ziqin Rong, Pablo Enfedaque, Stefano Marchesini
AI-enabled high-resolution scanning coherent diffraction imaging [Tag-4, Tag-7]
Applied Physics Letters
Mathew J Cherukara, Tao Zhou, Youssef Nashed, Pablo Enfedaque, Alex Hexemer, Ross J Harder, Martin V Holt
An ultrahigh-resolution soft x-ray microscope for quantitative analysis of chemically heterogeneous nanomaterials [Tag-4]
Science advances
David A Shapiro, Sergey Babin, Richard S Celestre, Weilun Chao, Raymond P Conley, Peter Denes, Bjoern Enders, Pablo Enfedaque, Susan James, John M Joseph, Harinarayan Krishnan, Stefano Marchesini, Krishna Muriki, Kasra Nowrouzi, Sharon R Oh, Howard Padmore, Tony Warwick, Lee Yang, Valeriy V Yashchuk, Young-Sang Yu, Jiangtao Zhao
Scientific Reports,10, 1325, 2020
Advances in Kriging-Based Autonomous X-Ray Scattering Experiments
Marcus M Noack, Gregory S Doerk, Ruipeng Li, Masafumi Fukuto, Kevin G Yager
Inversion of many-beam bragg intensities for phasing by iterated projections: Removal of multiple scattering artifacts from diffraction data [TAG-15]
Physical Review Letters 125.6, 065502, 2020
Jeffrey J. Donatelli and John C.H. Spence
Interactive parallel workflows for synchrotron tomography [TAG-3, TAG-5, TAG-6, TAG-7]
SC20, 2020 IEEE/ACM 2nd Annual Workshop on Extreme-scale Experiment-in-the-Loop Computing (XLOOP), 2020
Dilworth Y Parkinson, Harinarayan Krishnan, Daniela Ushizima, Matthew Henderson, Shreyas Cholia
Accelerating Microstructural Analytics with Dask for Volumetric X-ray Images [TAG-3,TAG-5,TAG-6,TAF-7]
SC20, 2020 IEEE/ACM 9th Workshop on Python for High-Performance and Scientific Computing (PyHPC) , 2020
Daniela Ushizima, Matthew McCormick, Dilworth Parkinson
Evaluating crystallographic likelihood functions using numerical quadratures [TAG-1]
Acta Cryst. D76, 736–750, 2020
Petrus H. Zwart, Elliott D. Perryman
Randomized Algorithms for Scientific Computing (RASC) [TAG-14]
Workshop Report - U.S. Department of Energy, Office of Science, Advanced Scientific Computing Research Program
Aydin Buluc, Tamara G. Kolda, Stefan M. Wild, Mihai Anitescu, Anthony DeGennaro, John Jakeman, Chandrika Kamath, Ramakrishnan (Ramki)Kannan, Miles E. Lopes, Per-Gunnar Martinsson, Kary Myers, Jelani Nelson, Juan M. Restrepo, C. Seshadhri, Draguna Vrabie, Brendt Wohlberg, Stephen J. Wright, Chao Yang, Peter Zwart
Fluctuation X-ray Scattering real-time app [TAG-1, TAG-8]
Proc. of the 19th PYTHON in Science Conf. (SCIPY 2020)
Dujardin, Antoine, Elliott Slaugther, Jeffrey Donatelli, Peter Zwart, Amedeo Perazzo, and Chun Hong Yoon
Materials Data Science for Microstructural Characterization of Archaeological Concrete [Tag-6]
MRS Advances, February 2020.
D. Ushizima, K. Xu, P. Monteiro
Learning the mapping $\mathbf{x}\mapsto \sum_{i=1}^d x_i^2$: the cost of finding the needle in a haystack [Tag-7]
Commun. Appl. Math. Comput. 2020
J. Zhang, L. Zepeda-Nunez, Y. Yao and L. Lin
Enhancing robustness and efficiency of density matrix embedding theory via semidefinite programming and local correlation potential fitting [Tag-2]
Phys. Rev. B, 102, 085123, 2020 (Editor's Suggestion)
X. Wu, M. Lindsey, T. Zhou, Y. Tong and L. Lin
Near-optimal ground state preparation [Tag-11]
Quantum, 4, 372, 2020
L. Lin and Y. Tong
Using models to improve optimizers for variational quantum algorithms [TAG-7, TAG-11]
Quantum Sci. Tech. 5, 044008, 2020
K. J. Sung, J. Yao, M. P. Harrigan, N. C. Rubin, Z. Jiang, L. Lin, R. Babbush, J. R. McClean
An ultra-high resolution soft x-ray microscope for quantitative analysis of chemically heterogeneous nano-materials [TAG-None]
Science Advances, 6 (51), eabc4904 (2020)
David A. Shapiro, Sergey Babin, Richard Celestre, Weilun Chao, Raymond P. Conley, Peter Denes, Bjoern Enders, Pablo Enfedaque, Susan James, John Joseph, Harinarayan Krishnan, Stefano Marchesini, Krishna Muriki, Kasra Nowrouzi, Sharon Oh, Howard Padmore, Tony Warwick, Lee Yang, Valeriy. V. Yashchuk, Young-Sang Yu, and Jiangtao Zhao
2019
Distributed Global Digital Volume Correlation by Optimal Transport [TAG-3,TAG-6,TAG-7]
2019 IEEE/ACM 1st Annual Workshop on Large-scale Experiment-in-the-Loop Computing (XLOOP), 2019
John Michael L MacNeil, Dmitriy Morozov, Francesco Panerai, Dilworth Parkinson, Harold Barnard, Daniela Ushizima
Interactive volumetric segmentation for textile micro‐tomography data using wavelets and nonlocal means [TAG-3,TAG-6,TAG-7]
2019 Statistical Analysis and Data Mining: The ASA Data Science Journal, v12 p338-353, 2019
J Michael L MacNeil, Daniela M Ushizima, Francesco Panerai, Nagi N Mansour, Harold S Barnard, Dilworth Y Parkinson
Evaluating fiber detection models using neural networks [TAG-3,TAG-6,TAG-7]
2019 International Symposium on Visual Computing , 2019
Silvia Miramontes, Daniela M Ushizima, Dilworth Y Parkinson
Reconstructing the three-dimensional latent image of extreme ultraviolet resists with resonant soft x-ray scattering [TAG-10]
J. Micro/Nanolith. MEMS MOEMS 18(2), 024003, Apr–Jun, 2019
Guillaume Freychet, Isvar A. Cordova, Terry McAfee, Dinesh Kumar, Ronald J. Pandolfi, Chris Anderson, Scott D. Dhuey, Patrick Naulleau, Cheng Wang, and Alexander Hexemer
Estimation of Line Cross Sections Using Critical-Dimension Grazing-Incidence Small-Angle X-Ray Scattering [TAG-10]
Phys. Rev. Applied 12, 044026 – Published 11 October 2019
Guillaume Freychet, Dinesh Kumar, Ron J. Pandolfi, Patrick Naulleau, Isvar Cordova, Peter Ercius, Chengyu Song, Joseph Strzalka, and Alexander Hexemer
An Efficient Algorithm for Automatic Structure Optimization in X ray Standing-Wave Experiments [TAG-7]
Journal of Electron Spectrocopy and Related Phenomena, Oct., 2019
Karslioglu, O., Gehlmann, M., Muller, J., Nemsak, S., Sethian, J.A., Kaduwela, A., Bluhm, H., Fadley, C.
Blind Ptychographic Phase Retrieval via Convergent Alternating Direction Method of Multipliers [TAG-4]
SIAM J. Imaging Sci., 12, 1, 2019
Huibin Chang, Pablo Enfedaque, and Stefano Marchesini
Advanced denoising for X-ray ptychography [TAG-4]
Optics express 27, no. 8 (2019): 10395-10418
Chang, H., Enfedaque, P., Zhang, J., Reinhardt, J., Enders, B., Yu, Y.S., Shapiro, D., Schroer, C.G., Zeng, T. and Marchesini, S.
High performance partial coherent x-ray ptychography [TAG-4, TAG-8]
International Conference on Computational Science (pp. 46-59)
Enfedaque, P., Chang, H., Enders, B., Shapiro, D., & Marchesini, S.
Iterative Joint Ptychography-Tomography with Total Variation Regularization [TAG-3, TAG-4, TAG-8]
IEEE International Conference on Image Processing (ICIP)
Chang, H., Enfedaque, P., & Marchesini, S.
Shape transform phasing of edgy nanocrystals [TAG-1]
Acta Crystallographica A. A75, 239-259, January 2019
Chen J.P., Donatelli J.J., Schmidt K.E., and Kirian R.A.
Reconstruction of Objects from Their Averaged Finite Crystal Diffraction Intensity [TAG-1]
2019 IEEE International Conference on Image Processing (ICIP). IEEE, 2019
Chen, J. P., Schmidt, K. E., Kirian, R. A., & Donatelli, J. J.
A multiscale neural network based on hierarchical matrices [Tag-2, Tag-7]
SIAM Multiscale Model. Simul. 17, 1189, 2019
Y. Fan, L. Lin, L. Ying and L. Zepeda-Nunez
Correlative conventional scanning and ptychographic soft x-ray microscopy [TAG-None]
SPIE: X-Ray Nanoimaging: Instruments and Methods IV, 11112 (2019)
Jiangtao Zhao, Kasra Nowrouzi, Richard Celestre, Matthew Marcus, Young-Sang Yu, David A Shapiro
2018
Accelerating Optical Absorption Spectra and Exciton Energy Computation via Interpolative Separable Density Fitting [TAG-2]
Intern. Conf. Computational Science, 2018
W. Hu, M. Shao, A. Cepellotti, F. H. da Jornada, L. Lin, K. ?icke, C. Yang and S. G. Louie
PSelInv: A distributed memory parallel algorithm for selected inversion: the non-symmetric case [TAG-2, TAG-8]
Parallel Comput. 74, 84, 2018
M. Jacquelin, L. Lin and C. Yang
Gradient Boosting Decision Trees for Echocardiogram Images [TAG-6, TAG-7]
2018 International Joint Conference on Neural Networks (IJCNN), 2018
V. V. de Melo, D. M. Ushizima, S. F. Baracho and R. C. Coelho
Computational Analysis of Grazing Incidence Small Angle X-Ray Scattering Data [TAG-10]
Submitted to J. Applied Crystallography, 2018 (in revision).
A. Sarje, S. Chourou, D. Kumar, S. Venkatakrishnan, X. Li, and A. Hexemer
Pursuing the critical dimension using Grazing Incidence Small Angle X-ray Scattering [TAG-10]
Proc. Vol. 10585, Metrology, Inspection, and Process Control for Microlithography XXXII, SPIE Advanced Lithography 2018.
G. Freychet, D. Kumar, R. Pandol?, P. Naulleau, I. Cordova, J. Strzalka, M. Fukuto, and A. Hexemer
Programmed LWR metrology by multi-techniques approach [TAG-10]
Proceeding SPIE Advanced Lithography, Vol. 10585, pp. 105850F, 2018.
J. Reche, M. Besacier, P. Gergaud, Y. Blancquaert, G. Freychet and T. Labbaye
Pursuing the critical dimension in etched patterns using x-ray scattering [TAG-10]
Proceedings SPIE Advanced Lithography, Vol. 10585, pp. 10585-7, 2018.
G. Freychet, D. Kumar, R. Pandol, D. Staacks, P. Naulleau, R. J. Kline, D. Sunday, M. Fukuto, J. Strzalka and A. Hexemer
Ring artifact reduction in synchrotron X-ray tomography through helical acquisition [TAG-6, TAG-7]
Measurement Science and Technology, Volume 29, Number 3, 2018,
D.M. Pelt, and D. Y. Parkinson
Improving Tomographic Reconstruction from Limited Data Using Mixed-Scale Dense Convolutional Neural Networks [TAG-6, TAG-7]
Journal of Imaging, 4(11), 128, 2018
Pelt, D. M., Batenburg, K. J., & Sethian, J. A.
DPP-PMRF: Rethinking Optimization for a Probabilistic Graphical Model Using Data-Parallel Primitives [TAG-6]
8th IEEE Symposium on Large Data Analysis and Visualization in conjunction with IEEE VIS 2018, Berlin, Germany, October 21, 2018.
Brenton Lessley, Talita Perciano, Colleen Heinemann, David Camp, Hank Childs, E. Wes Bethel
A mixed-scale dense convolutional neural network for image analysis [TAG-6,TAG-7]
Proceedings of the National Academy of Sciences, 2018
D.M. Pelt and J.A. Sethian
Xi-cam: A versatile interface for data visualization and analysis [TAG-5,TAG-9]
J. Synchrotron Radiation, Jan., 2018.
Ronald J Pandolfi, Daniel B Allan, Elke Arenholz, Luis Barroso-Luque, Stuart I Campbell, Thomas A Caswell, Austin Blair, Francesco De Carlo, Sean Fackler, Amanda P Fournier, Guillaume Freychet, Masafumi Fukuto, Doga Gürsoy, Zhang Jiang, Harinarayan Krishnan, Dinesh Kumar, R Joseph Kline, Ruipeng Li, Christopher Liman, Stefano Marchesini, Apurva Mehta, Alpha T N'Diaye, Dilworth Y Parkinson, Holden Parks, Lenson A Pellouchoud, Talita Perciano, Fang Ren, Shreya Sahoo, Joseph Strzalka, Daniel Sunday, Christopher J Tassone, Daniela Ushizima, Singanallur Venkatakrishnan, Kevin G Yager, Peter Zwart, James A Sethian, Alexander Hexemer
Dataflow at the COSMIC Beamline-Stream Processing and Supercomputing [TAG-4, TAG-5]
Microscopy and Microanalysis, 24(S2), 58-59, 2018
Enders, B., Nowrouzi, K., Krishnan, H., Marchesini, S., Park, J., Yu, Y. S., & Shapiro, D. A
GPU-Based Implementation of Ptycho-ADMM for High Performance X-Ray Imaging [TAG-4, TAG-8]
International Conference on Computational Science, 540-553. 2018
Enfedaque, P., Chang, H., Krishnan, H. and Marchesini, S.
Partially coherent ptychography by gradient decomposition of the probe [TAG-4]
Acta Crystallographica Section A: Foundations and Advances, 74(3), 157-169, 2018)
Chang, H., Enfedaque, P., Lou, Y., & Marchesini, S
Three-dimensional localization of nanoscale battery reactions using soft X-ray tomography [TAG-4]
Nature communications, 9(1), 921, 2018
Yu, Y. S., Farmand, M., Kim, C., Liu, Y., Grey, C. P., Strobridge, F. C., Krishnan, H., Maia FRNC., Kilcoyne ALD., Marchesini S., Perciano Costa Leite T, Warwick T, Padmore H., Cabana J. & Shapiro, DA.
Variational Phase Retrieval with Globally Convergent Preconditioned Proximal Algorithm [TAG-4]
SIAM Journal on Imaging Sciences, 11(1), 2018
Huibin Chang, Stefano Marchesini, Yifei Lou, and Tieyong Zeng
Mathematics in Pattern Recognition for Scientific Investigations [TAG-6]
DOE Scientific Machine Learning Workshop, 2018.
T. Perciano, B. Loring, H. Krishnan, J. Michael L. MacNeil, D. Ushizima,
Total variation based phase retrieval for Poisson noise removal [TAG-4]
SIAM Journal on Imaging Sciences, 11(1), 2018
Huibin Chang, Yifei Lou, Yuping Duan, and Stefano Marchesini
Denoising Poisson Phaseless Measurements via Orthogonal Dictionary Learning [TAG-4]
Optics Express, 26, 16, 2018
Huibin Chang and Stefano Marchesini
Free-electron laser data for multiple-particle fluctuation scattering analysis [TAG-1]
Nature Scientific Data, 5, 180201, October 2018
Pande K., Donatelli J.J., Malmerberg E., Foucar L.M., Poon B.K., Sutter M., Botha, S., Basu S., Doak R.B., Dorner K., Epp S.W., Englert L., Fromme R., Hartmann E., Hartmann R., Hauser G., Hattne J., Hosseinizadeh A., Kassemeyer S., Lomb L., Montero S.F.C., Menzel A., Rolles D., Rudenko A., Seibert M.M., Sierra R.G., Schwander P., Ourmazd A., Fromme P., Sauter N.K., Bogan M., Bozek J., Bostedt C., Schlichting I., Kerfeld C.A., and Zwart P.H.
Structure determination from experimental fluctuation X-ray scattering [TAG-1]
PNAS, 115(45), 11772-11777, November 2018
Pande K., Donatelli J.J., Malmerberg E., Foucar L., Bostedt C., Schlichting I., and Zwart P.H.,
Nanoscale Visualization of Magnetic Contrasts with Soft X-ray Spectro-Ptychography at the Advanced Light Source [TAG-None]
Microscopy and Microanalysis 24 (S2), 530-531 (2018)
Young-Sang Yu, Richard Celestre, Bjoern Enders, Kasra Nowrouzi, Howard Padmore, Tony Warwick, Jong-Ryul Jeong, David A Shapiro
Three dimensional localization of nanoscale battery reactions using soft X-ray tomography [TAG-None]
Nature Communications, 9, 921 (2018)
Young-Sang Yu, Maryam Farmand, Chunjoong Kim, Yijin Liu, Clare P Grey, Fiona C Strobridge, Tolek Tyliszczak, Rich Celestre, Peter Denes, John Joseph, Harinarayan Krishnan, Filipe RNC Maia, AL David Kilcoyne, Stefano Marchesini, Talita Perciano Costa Leite, Tony Warwick, Howard Padmore, Jordi Cabana, David A Shapiro
Dataflow at the COSMIC Beamline-Stream Processing and Supercomputing [TAG-None]
Microscopy and Microanalysis 24 (S2), 58-59 (2018)
Bjoern Enders, Kasra Nowrouzi, Harinarayan Krishnan, Stefano Marchesini, Jungjin Park, Young-Sang Yu, David A Shapiro
The COSMIC Imaging Beamline at the Advanced Light Source: a new facility for spectro microscopy of nano-materials [TAG-None]
Microscopy and Microanalysis 24 (S2), 8-11 (2018)
David A Shapiro, Richard Celestre, Bjoern Enders, John Joseph, Harinarayan Krishnan, Matthew A Marcus, Kasra Nowrouzi, Howard Padmore, Jungjin Park, Anthony Warwick, Young-Sang Yu
Nanosurveyor 2: A Compact Instrument for Nano-Ptychography at the Advanced Light Source [TAG-None]
Proceeedings MEDSI, DOI: 10.18429/JACoW-MEDSI2018-THPH07 (2018)
Richard Celestre, Kasra Nowrouzi, Howard Padmore, David Shapiro
2017
Correlations in Scattered X-Ray Laser Pulses Reveal Nanoscale Structural Features of Viruses [TAG-1]
Phys. Rev. Letters, 119, 158102, 2017
Ruslan P. Kurta, Jeffrey J. Donatelli, Chun Hong Yoon, Peter Berntsen, Johan Bielecki, Benedikt J. Daurer, Hasan DeMirci, Petra Fromme, Max Felix Hantke, Filipe R.N.C. Maia, Anna Munke, Carl Ne?elblad, Kanupriya Pande, Hemanth K.N. Reddy, Jonas A. Sellberg, Raymond G. Sierra, Martin Svenda, Gijs van der Schot, Ivan A. Vartanyants, Garth J. Williams, P. Lourdu Xavier, Andrew Aquila, Peter H. Zwart, and Adrian P. Mancuso
Reconstruction from limited single-particle diffraction data via simultaneous determination of state, orientation, intensity, and phase [TAG-1]
Proc. National Acad. Sciences, 114(28), 7222-7227, 2017
Jeffrey J. Donatelli, James A. Sethian and Peter H. Zwart
Structural enzymology using X-ray free electron lasers [TAG-1]
Structural Dynamics, 4, 044003
Christopher Kupitz, Jose L. Olmos Jr., Mark Holl, Lee Tremblay, Kanupriya Pande, Suraj Pandey, Dominik Oberthr, Mark Hunter, Mengning Liang, Andrew Aquila, Jason Tenboer, George Calvey, Andrea Katz, Yujie Chen, Max O. Wiedorn, Juraj Knoska, Alke Meents, Valerio Majriani, Tyler Norwood, Ishwor Poudyal, Thomas Grant, Mitchell D. Miller, Weijun Xu, Aleksandra Tolstikova, Andrew Morgan, Markus Metz, Jose M. Martin- Garcia, James D. Zook, Shatabdi Roy-Chowdhury, Jesse Coe, Nirupa Nagaratnam, Domingo Meza, Raimund Fromme, Shibom Basu, Matthias Frank, Tomas White, Anton Barty, Sasa Bajt, Oleksandr Yefanov, Henry N. Chapman, Nadia Zatsepin, Garrett Nelson, Uwe Weierstall, John Spence, Peter Schwander, Lois Pollack, Petra Fromme, Abbas Ourmazd, George N. Phillips Jr., and Marius Schmidt
Highly efficient photocatalytic water splitting over edge-modified phosphorene nanoribbons [TAG-2]
J. Amer. Chem. Soc. 139, 15429, 2017
W. Hu, L. Lin, R. Zhang, C. Yang and J. Yang
Interpolative separable density fitting decomposition for accelerating hybrid density functional calculations with applications to defects in silicon [TAG-2]
J. Chem. Theory Comput. 13, 5420, 2017
W. Hu, L. Lin and C. Yang
Projected Commutator DIIS Method for Accelerating Hybrid Functional Electronic Structure Calculations [TAG-2]
J. Chem. Theory Comput. 13, 5458, 2017
W. Hu, L. Lin and C. Yang
Accelerating selected columns of the density matrix computations via approximate column selection [TAG-2]
SIAM J. Sci. Comput. 39, 1178, 2017
A. Damle, L. Lin and L. Ying
Robust Determination of the Chemical Potential in the Pole Expansion and Selected Inversion Method for Solving Kohn-Sham density functional theory [TAG-2]
J. Chem. Phys. 147, 144107, 2017
W. Jia and L. Lin
A posteriori error estimates for discontinuous Galerkin methods using non-polynomial basis functions, Part II: Eigenvalue problems [TAG-2]
Math. Model. Numer. Anal. 51, 1733, 2017 L. Lin and B. Stamm
Localized spectrum slicing [TAG-2]
Math. Comp. 86, 2345, 2017
L. Lin
Randomized estimation of spectral densities of large matrices made accurate [TAG-2]
Numer. Math. 136, 183, 2017
L. Lin
Adaptively compressed polarizability operator for accelerating large scale ab initio phonon calculations [TAG-2]
Multiscale Model. Simul. 15, 29, 2017
W. Hu, L. Lin, A. Banerjee, E. Vecharynski and C. Yang
SCDM-k: Localized orbitals for solids via selected columns of the density matrix [TAG-2]
J. Comput. Phys. 334, 1, 2017
A. Damle, L. Lin and L. Ying
Adaptive local basis set for Kohn-Sham density functional theory in a discontinuous Galerkin framework II: Force, vibration, and molecular dynamics calculations [TAG-2]
J. Comput. Phys. 335, 426 2017
G. Zhang, L. Lin,W. Hu, C. Yang and J.E. Pask
The Influence of Intrinsic Framework Flexibility on Adsorption in Nanoporous Materials [TAG-12]
Journal of the American Chemical Society 139,5547-5557, 2017
M. Witman, S. Ling, S. Jawahery, P. Boyd, M. Haranczyk, B. Slater, B. Smit
Accurate Characterization of the Pore Volume in Microporous Crystalline Materials [TAG-12]
Langmuir 33, 14529-14538, 2017
D. Ongari, P. Boyd, S. Barthel, M. Witman, M. Haranczyk, B. Smit
Computationally-Guided Synthetic Control over Pore Size in Isostructural Porous Organic Cages [TAG-12]
ACS Central Science 3, 734-742, 2017
A. Slater, P. Reiss, A. Pulido, M. Little, D. Holden, L. Chen, Linjiang, S. Chong, B. Alston, R. Clowes, M. Haranczyk, M. Briggs, T. Hasell, G. Day, A. Cooper
Scanning electron microscopy as a source of morphological data on nanoparticles: image representativeness [TAG-12]
Journal of Microscopy 265, 34-50, 2017
K. Odziomek, D. Ushizima, P. Oberbek, K. Kurzydlowski, T. Puzyn, M. Haranczyk
Machine learning for micro-tomography [TAG-3,TAG-6,TAG-7]
Dev. X-Ray Tomogr. XI 18 (2017).
Parkinson, D. Y., Ushizima, D. M., Perciano, T., Krishnan, H., Barnard, H. S., MacDowell, A. A., Pelt, D., Sethian, J.A.
Insight into 3D micro-CT data: convergence of segmentation algorithms through evaluation metrics [TAG-3,TAG-6]
Journal of Synchrotron Radiation, 24(5): 1065-1077, Sept. 2017
T. Perciano, D. Ushizima, H. Krishnan, D. Parkinson, N. M. Larson, Daniel M. Pelt and F. W. Zok
Maximal clique enumeration with data-parallel primitives [TAG-6]
IEEE 7th Symposium on Large Data Analysis and Visualization (LDAV), Phoenix, AZ, 2017, pp. 16-25, 2017
B. Lessley, T. Perciano, M. Mathai, H. Childs and E. W. Bethel
Data Efficient X-ray Phase Tomography with Self-calibrated Sandpaper Analyzer [TAG-3]
Computational Optical Sensing and Imaging CW2B, 2, 2017
Chen, M., Parkinson, D., Venkatakrishnan, S., Marchesini, S. & Waller, L
Nearest-Neighbour Nanocrystal Bonding Dictates Framework Stability or Collapse in Colloidal Nanocrystal Frameworks [TAG-6]
Chemical Communications, Royal Society of Chemistry, 2017.
Williams, Ushizima, Zhu, Anders, Milliron, Helms
Machine learning for micro-tomography [TAG-3,TAG-7]
Dev. X-Ray Tomogr. XI 18, 2017
Parkinson, D. Y.; Ushizima, D. M.; Perciano, T.; Krishnan, H.; Barnard, H. S.; MacDowell, A. A.; Pelt, D.; Sethian, J. A
Detection and Classification of Cervical Cells [TAG-6]
The Practice of Reproducible Research: Case Studies and Lessons from the Data-Intensive Sciences, Kitzes, J., Turek, D., & Deniz, F. (Eds.), Oakland, CA: Univ. Calif. Press 2017. [book chapter]
Ushizima, D.M.
Detection and Classification of Cervical Cells [TAG-6]
The Practice of Reproducible Research: Case Studies and Lessons from the Data-Intensive Sciences, Kitzes, J., Turek, D., & Deniz, F. (Eds.), Oakland, CA: Univ. Calif. Press 2017. [book chapter]
Ushizima, D.M.
Automating Cell Detection and Classification in Human Brain Fluorescent Microscopy Images Using Dictionary Learning and Sparse Coding [TAG-6]
Journal of Neuroscience Methods, 2017.
Alegro, Theolas, Nguy, Castruita, Seeley, Ushizima, Grinberg
Convolutional Neural Networks with Tensor Flow: theory and practice [TAG-6, TAG-7]
Brazilian Society of Computation Press 2017. [book chapter]
Araujo, Carneiro, Silva, Medeiros, Ushizima
Computer Vision in python with libraries scikit-image and scikit-learn [TAG-6]
Brazilian Society of Computation Press 2017. [book chapter]
Silva, Lopes, Araujo, Medeiros, Ushizima
A multi-objective approach for calibration and detection of cells nuclei [TAG-6]
IEEE Congress on Evolutionary Computation, 2017.
Oliveira, P., Moreira, G., Ushizima, D.M., , C.M. Carneiro, F.M. Medeiros, F. Arujo, R. Silva, A Bianchi
Portable Learning Environments for Hands-On Computational Instruction Using Container- and Cloud- Based Technology to Teach Data Science [TAG-5, TAG-6]
Practice and Experience in Advanced Research Computing Conference, PEARC’17.
Holdgraf, C., Culich, A., Rokem, A., Deniz, F., Alegro, M., Ushizima , D.M.
Distributed Memory Parallel Markov Random Fields using Graph Partitioning [TAG-6]
Fourth International Workshop on High Performance Big Graph Data Management, Analysis, and Mining (BigGraphs 2017): IEEE BigData 2017
C. Heinemann, T. Perciano, D. Ushizima, and E. Wes Bethel
Insight into 3D micro-CT data: convergence of segmentation algorithms through evaluation metrics [TAG-4]
Journal of Synchrotron Radiation, 24(5): 1065-1077, September 2017
T. Perciano, D. Ushizima, H. Krishnan, D. Parkinson, N. M. Larson, Daniel M. Pelt and F. W. Zok
On-the-Fly data assessment for high throughput X-ray diffraction measurement [TAG-5]
ICS Comb. Sci. 19, 377-385, 2017
Ren, F., Pandolfi R., Van Campen, D., Hexemer, A., and Mehta, A.
Data Efficient X-ray Phase Tomography with Self-calibrated Sandpaper Analyzer [TAG-4]
Imaging and Applied Optics, 2017
Michael Chen, Dilworth Parkinson, Singanallur Venkatakrishnan, Stefano Marchesini, and Laura Waller
Nanometer-resolved spectroscopic study reveals the conversion mechanism at an elevated temperature [TAG-4]
Crystal Growth & Design, 17,8, 2017
Guoqing Geng, Jiaqi Li, Young-Sang Yu, David A. Shapiro, David A. L. Kilcoyne, and Paulo J. M. Monteiro
Ptychographic imaging of nano-materials at the Advanced Light Source with the Nanosurveyor Instrument [TAG-4]
IOP Conference Series: Journal of Physics 849 012028, 2017
D.A. Shapiro, R. Celestre, Peter Denes, Maryam Farmand, John Joseph, A.L.D. Kilcoyne, Stefano Marchesini, Howard Padmore, Singanallur V. Venkatakrishnan, Tony Warwick and Young-Sang Yuet
Correlative cellular ptychography with functionalized nanoparticles at the Fe L-edge [TAG-4]
Scientific Reports, 7, 4757 (2017)
Marcus Gallagher-Jones, Carlos Sato Baraldi Dias, Alan Pryor Jr, Karim Bouchmella, Lingrong Zhao, Yuan Hung Lo, Mateus Borba Cardoso, David Shapiro, Jose Rodriguez, and Jianwei Miao
Near-edge X-ray refraction fine structure microscopy [TAG-4]
Appl. Phys. Lett. 110, 063101, 2017
Maryam Farmand, Richard Celestre, Peter Denes, A. L. David Kilcoyne, Stefano Marchesini, Howard Padmore, Tolek Tyliszczak, Tony Warwick, Xiaowen Shi, James Lee2, Young-Sang Yu, Jordi Cabana, John Joseph, Harinarayan Krishnan, Talita Perciano, Filipe R. N. C. Maia, and David A. Shapiro
Nanosurveyor: a framework for real-time data processing [TAG-4, TAG-5]
Advanced Structural and Chemical Imaging 20173:7, 2017
B.J. Daurer, H. Krishnan, T. Perciano, F. R.N.C. Maia, D.A. Shapiro, J.A. Sethian, and Stefano Marchesini
Scanning electron microscopy image representativeness: morphological data on nanoparticles [TAG-6]
Jour. of Microscopy, 265(1), 2017
Odziomek, K., , Ushizima, D., Oberbek, P., Kurzydlowski, K., Puzyn, T., and Haranczyk, M
2016
Chebyshev polynomial filtered subspace iteration in the Discontinuous Galerkin method for large-scale electronic structure calculations [TAG-2]
J. Chem. Phys. 145, 154101, 2016
A. S. Banerjee, L. Lin, W. Hu, C. Yang, J. E. Pask
PSelInv: A distributed memory parallel algorithm for selected inversion: the symmetric case [TAG-2, TAG-8]
ACM Trans. Math. Software 43, 21, 2016
M. Jacquelin, L. Lin and C. Yang
Adaptively compressed exchange operators [TAG-2]
J. Chem. Theory Comput. 12, 2242, 2016
L. Lin
Low rank approximation in G0W0 calculations [TAG-2]
Sci. China Math., 59 1593, 2016
M. Shao, L. Lin, C. Yang, F. Liu, F. Jornada, J. Deslippe and S. G. Louie
Decay estimates of discretized Green’s functions for Schrodinger type operators [TAG-2]
China Math., 59, 1561, 2016
L. Lin and J. Lu
Approximating spectral densities of large matrices [TAG-2]
SIAM Rev. 58, 34, 2016
L. Lin, Y. Saad and C. Yang
Edge-modified phosphorene nanoflake heterojunctions as highly efficient solar cells [TAG-2]
Nano Letters 16 1675, 2016
W. Hu, L. Lin, C. Yang, J. Dai and J. Yang
Enhancing the scalability and load balancing of the parallel selected inversion algorithm via tree-based asynchronous communication [TAG-2]
IEEE IPDPS, 192, 2016
M. Jacquelin, L. Lin, N. Wichmann and C. Yang
A posteriori error estimates for discontinuous Galerkin methods using non-polynomial basis functions. Part I: Second order linear PDE [TAG-2]
Math. Model. Numer. Anal. (M2AN) 50, 1193, 2016
L. Lin and B. Stamm
Large-scale ab initio simulations based on systematically improvable atomic basis [TAG-2]
Mater. Sci. 112 503, 2016
P. Li, X. Liu, M. Chen, P. Lin, X. Ren, L. Lin, C. Yang and L. He
Femtosecond structural dynamics drives the trans/cis isomerization in photoactive yellow protein [TAG-1]
Science, 352(6286), 725-729, 2016
Kanupriya Pande, Christopher D. M. Hutchison, Gerrit Groenhof, Andy Aquila, Josef S. Robinson, Jason Tenboer, Shibom Basu, Sbastien Boutet, Daniel P. DePonte, Mengning Liang, Thomas A. White, Nadia A. Zatsepin, Oleksandr Yefanov, Dmitry Morozov, Dominik Oberthuer, Cornelius Gati, Ganesh Subramanian, Daniel James, Yun Zhao, Jake Koralek, Jennifer Brayshaw, Christopher Kupitz, Chelsie Conrad, Shatabdi Roy-Chowdhury, Jesse D. Coe, Markus Metz, Paulraj Lourdu Xavier, Thomas D. Grant, Jason E. Koglin, Gihan Ketawala, Raimund Fromme, Vukica rajer, Robert Henning, John C. H. Spence, Abbas Ourmazd, Peter Schwander, Uwe Weierstall, Ma?hias Frank, Petra Fromme, Anton Barty, Henry N. Chapman, Keith Moffat, Jasper J. van Thor, Marius Schmidt
Metal-Organic Framework with Optimal Adsorption, Separation, and Selectivity towards Xenon [TAG-12]
Nature Communications 7, 2016
D. Banerjee, A.M. Plonka, C.M. Simon, R.K. Motkuri, J. Liu, X. Chen, B.Smit, J.B. Parise, M. Haranczyk, P.K. Thallapally
A multi-slice simulation algorithm for grazing-incidence small-angle X-ray scattering [TAG-8,TAG-10]
J. Applied Crystallography, Vol.49, Part 6, December 2016.
Singanallur Venkatakrishnan, Jeffrey Donatelli, Dinesh Kumar, Abhinav Sarje, Sunil K. Sinha, Xiaoye S. Li, Alexander Hexemer
Improved tomographic reconstruction of large-scale real-world data by filter optimization [TAG-3]
Advanced Structural and Chemical Imaging, 2:17, 2016
D. M. Pelt and V. De Andrade
Robust model-based phase ptycho-tomography [TAG-3, TAG-4]
IEEE Signal Processing Letters, Vol. 23, no. 7, pp. 944-948, 2016
S. V. Venkatakrishnan, M. Farmand, Y.S. Yu, H. Majidi, K. Van Benthem, S. Marchesini, D. Shapiro, and A. Hexemer
Ammonia gas sensor based on the frequency-dependent impedance characteristics of ultrathin polyaniline films [TAG-6]
Sensors and Actuators A: Physical, 2016
Santos, M.C., Bianchi, A., Ushizima, D., Pavinatto, F.J., Bianchi, R.F.,
Evaluation of Three Algorithms for the Segmentation of Overlapping Cervical Cells [TAG-6]
IEEE Journal of Biomedical and Health Informatics, 99, pp. 2168-2194, 2016.
Lu, Z., Carneiro, G., Bradley, A., and Ushizima, D.M.
Scaling Analytics for Scientific Images from Experimental Instruments [TAG-6]
IEEE Applied Imagery Pattern Recognition October, 2016
Ushizima, D.M., Hexemer, A., Parkinson, D., and Yang , C.
Searchable datasets in Python: images across domains, experiments, algorithms and learning [TAG-6]
PyData, San Francisco 2016
Araujo, F., Silva, R., Ushizima, S.M., and Medeiros, F.
Pathway toward diagnosing and monitoring prodromal Alzheimer’s Disease using novel imaging biomarkers [TAG-6]
California Initiative for the Advancement of Precision Medicine Workshop 2016
Ushizima, D.M. and Grinberg, L.,
Making advanced scientific algorithms and big scientific data management more accessible [TAG-6, TAG-7]
Electronic Imaging, 2016(19):1-7, February 2016
S.V. Venkatakrishnan, K. Aditya Mohan, K. Beattie, J. Correa, E. Dart, J.R. Deslippe, A. Hexemer, H. Krishnan, A. A MacDowell, S. Marchesini, S.J Patton, T. Perciano, J.A Sethian, R. Stromsness, B.L Tierney, C.E. Tull, D. Ushizima, and D.Y. Parkinson
A two-level Markov random field for road network extraction and its application with optical, SAR, and multitemporal data [TAG-6]
International Journal of Remote Sensing, 37(16):3584-3610, July 2016
T. Perciano, F. Tupin, R. Hirata Jr., and R. M. Cesar Jr.
IDEAL: Images Across Domains, Experiments, Algorithms and Learning [TAG-6]
Journal of Minerals, Metals & Materials Society (TMS), pages 1-10 2016
D.M. Ushizima, H. A. Bale, E. W. Bethel, P. Ercius, B. A. Helms, H. Krishnan, L. T. Grinberg, M. Haranczyk, A. A. Macdowell, K. Odziomek, D. Y. Parkinson, T. Perciano, R. O. Ritchie, and C. Yang
Reduced-complexity Image Segmentation under Parallel Markov Random Field Formulation using Graph Partitioning [TAG-6]
IEEE ICIP, 2016
T. Perciano, D. M. Ushizima, Y. Mizrahi, E. W. Bethel, J. A. Sethian
A general framework for denoising phaseless diffraction measurements [TAG-4]
arXiv:1611.01417, 2016
Huibin Chang, Stefano Marchesin
Robust X-ray Phase Ptycho-Tomography [TAG-4]
IEEE Signal Processing Letters, Volume: 23, Issue: 7, July 2016
Singanallur V. Venkatakrishnan; Maryam Farmand; Young-Sang Yu; Hasti Majidi; Klaus van Benthem; Stefano Marchesini; David Shapiro, and Alexander Hexemer
Measuring spectroscopy and magnetism of extracted and intracellular magnetosomes using soft X-ray ptychography [TAG-4]
Proceedings National Academy of Sciences, 113(51), 2016
Xiaohui Zhu, Adam P. Hitchcock, Dennis A. Bazylinski, Peter Denes, John Joseph, Ulysses Lins, Stefano Marchesini, Hung-Wei Shiu, Tolek Tyliszczak, and David A. Shapiro
SHARP: a distributed GPU-based ptychographic solver [TAG-4]
J. Appl. Cryst. ,49, 2016
Marchesini, H. Krishnan, B. J. Daurer, D. A. Shapiro, T. Perciano, J. A. Sethian and F. R. N. C. Maia
ALS User Meeting Highlights Accomplishments and Challenges [TAG-4]
Synchrotron Radiation News 29 (1), 7-11, 2016
K Troutman, E Arenholz, S Marchesini, D Shapiro, C Zhu, A Lanzara
Imaging nanoscale magnetic and structural correlations in thin SmCo5 films using soft x-ray ptychography [TAG-4]
Applied Physics Letters, 2016
SP. Fischer, X. Shi, V. Neu, D. Elefant, J.C.T. Lee, D.A. Shapiro, M. Farmand (ALS LBNL Berkeley CA 94720), W. Shiu, S. Marchesini, S. Roy, S.D. Kevan X. Shi
Alternating Projection, Ptychographic Imaging and Phase Synchronization [TAG-4]
Applied and Computational Harmonic Analysis, 41, pp. 815-85, 2016
Stefano Marchesini, Yu-Chao Tu, Hau-tiengWu
Alternating Projection, Ptychographic Imaging and Phase Synchronization [TAG-4]
Applied and Computational Harmonic Analysis, 41, pp. 815-85, 2016
Stefano Marchesini, Yu-Chao Tu, Hau-tiengWu
Magnetic studies of magnetotactic bacteria by soft X-ray STXM and ptychography [TAG-4]
AIP Conf. Series, AIP 1696, 020002, 2016
X. H. Zhu, T. Tyliszczak, H.-W. Shiu, D. Shapiro, D. A. Bazylinski, U. Lins and A. P. Hitchcock
Nanoscale Chemical Imaging of an Individual Catalyst Particle with Ptychography [TAG-4]
ACS Catalysis, 2016.
Anna M. Wise, Johanna Nelson Weker, Sam Kalirai, Maryam Farmand, David A. Shapiro, Florian Meirer, and Bert M. Weckhuysen
2015
CAMERA: Center for Advanced Mathematics for Energy Research Applications [TAG-6, TAG-7, TAG-9]
Synchrotron Radiation News 28 2 9-Apr 2015
Donatelli, J; Haranczyk, M; Hexemer, A; Krishnan, H; Li, X; Lin, L; Maia, F; Marchesini, S; Parkinson, D; Perciano, T, Sethian, J.A
Iterative phasing for fluctuation X-ray scattering [TAG-1]
Proc. National Acad. Sciences, 112(33), 10286-10291, 2015
J. Donatelli, P.H. Zwart, and J.A. Sethian
Operational properties fluctuation X-ray scattering data [TAG-1]
UCrJ, 2(3), 309-316, May 2015
E. Malmerberg, C.A. Kerfeld, and P.H. Zwart
A proximal gradient method for ensemble density functional theory [TAG-2]
SIAM J. Sci. Comp., June 20, 2015
M. Ulbrich, Z. Wen, C. Yang, D. Klockner, Z. Lu
Fast algorithms for estimating the absorption spectrum within linear response time-dependent density functional theory" [TAG-2]
J. Chem. Theory Comput. 11, 5197, 2015
J. Brabec, L. Lin, M. Shao, N. Govind, C. Yang, Y. Saad, E. Ng
A massively parallel method for large scale density functional theory calculation [TAG-2, TAG-8]
Chem. Phys. 143, 124110, 2015
W. Hu, L. Lin and C. Yang
Edge reconstruction in armchair phosphorene nanoribbons revealed by discontinuous Galerkin density functional theory [TAG-2]
Phys. Chem. Chem. Phys. 17, 31397, 2015
W. Hu, L. Lin and C. Yang
Compressed representation of Kohn-Sham orbitals via selected columns of the density matrix [TAG-2]
Chem. Theory Comput. 11, 1463, 2015
A. Damle, L. Lin and L. Ying
A posteriori error estimator for adaptive local basis functions to solve Kohn-Sham density functional theory [TAG-2]
Commun. Math. Sci. 13, 1741, 2015
J. Kaye, L. Lin and C. Yang
Understanding Small-Molecule Interactions in Metal Organic Frameworks: Coupling Experiment with Theory [TAG-12]
Advanced Materials, 2015
J.S. Lee, B. Vlaisavljevich, D. K. Britt, C. M. Brown, M. Haranczyk, J.B. Neaton, B. Smit, J.R. Long, W.L. Queen
Tunable porosity through cooperative diffusion in a multicomponent porous molecular crystal [TAG-12]
Journal of Physical Chemistry C 119, 22577-22586, 2015
R. Manurung, M. Miklitz, D. Holden, L. Chen, T. Hasell, S.Y. Chong, M. Haranczyk, A.I. Cooper, K.E. Jelfs
HIPGISAXS for Fast Analysis [TAG-8, TAG-10]
canSAS 8 meeting in Tokai, Japan. 2015.
A. Hexemer
Real-Time Data Pipeline and analysis using SPOT and HIPGISAXS [TAG-5, TAG-8, TAG-10]
OLCF Users meeting June 24, 2015.
A. Hexemer and C.E.Tull
HIPGISAXS [TAG-8, TAG-10]
Kyoto Institute of Technology, Japan, May 2015.
A. Hexemer
Fast Analysis for Scattering [TAG-8, TAG-10]
ISPAC, Houston, May 2015.
A. Hexemer
Fast Analysis of Time-Resolved Scattering Data [TAG-8, TAG-10]
APS March Meeting 2015
A. Hexemer
Inverse Modeling Nanostructures from X-ray Scattering Data through Massive Parallelism [TAG-8, TAG-10]
SC15 conference, Nov. 2015.
A. Sarje, X.S. Li, D. Kumar, S. Venkatakrishnan, A. Hexemer
Recovering Nanostructures from X-ray Scattering Data [TAG-8, TAG-10]
NVIDIA GPU Technology Conference, San Jose, Calif., May 2015.
A. Sarje, X.S. Li, D. Kumar, A. Hexemer
Scalable Particle Swarm Optimization for Nanostructure Discovery [TAG-8, TAG-10]
Euro-Par 2015 Conference, Aug. 24-28, 2015, Vienna, 2015
A. Sarje, X. Li and A. Hexemer
Fast Detection of Material Deformation through Structural Dissimilarity [TAG-6]
IEEE Big Data 2015
D. M. Ushizima, T. Perciano, D. Y. Parkinson
Cell reconstruction under Voronoi and enclosing ellipses from 3d microscopy [TAG-6]
IEEE Intern. Symp. Biomedical Imaging (ISBI) 2015.
GLB Ramalho, DS Ferreira, AGC Bianchi, CM Carneiro, FNS Medeiros
Investigating Pill Recognition Methods for a New National Library of Medicine Image Dataset [TAG-6]
Advances in Visual Computing, 410-419, 2015
D Ushizima, A Carneiro, M Souza, F Medeiros
Block Copolymer Packing Limits and Interfacial Reconfigurability in the Assembly of Periodic Mesoporous Organosilicas [TAG-6]
Advanced Functional Materials, 25 (26), pp 4120-4128, 2015
Andrew W. Wills, David J. Michalak, Peter Ercius, Ethan L. Rosenberg, Rory Runser, Talita Perciano, Daniela Ushizima, Brett Helms
Real-time Data Intensive Computing [TAG-5]
Synchrotron Radiation Instrumentation 2015
D.Y. Parkinson, K. Beattie, X. Chen, J. Correa, E. Dart, B. J. Daurer, J.R. Deslippe, A. Hexemer, H. Krishnan, A. MacDowell, F.R.N.C. Maia, S. Marchesini, H.A. Padmore, S.J. Patton, T. Perciano, J.A. Sethian, D.A. Shapiro, R. Stromsness, N. Tamura, B.L. Tierney, C.E. Tull, D. Ushizima
Dependence on crystal size of the nanoscale chemical phase distribution and fracture in LixFePO4 [TAG-4]
Nano Letters, 15 (7), pp 4282-4288 (2015)
Young-Sang Yu, Chunjoong Kim, David A. Shapiro, Maryam Farmand, Danna Qian, Tolek Tyliszczak, A. L. David Kilcoyne, Rich Celestre, Stefano Marchesini, John Joseph, Peter Denes, Tony Warwick, Fiona C. Strobridge, Clare P. Grey, Howard Padmore, Ying Shirley Meng, Robert Kostecki, and Jordi Cabana
Effect of Particle Size, Electronic Connectivity, and Incoherent Nanoscale Domains on the Sequence of Lithiation in LiFePO4 Porous Electrodes [TAG-4]
Advanced Materials 27 (42), 6591-6597, 2015
Yiyang Li, Sophie Meyer, Jongwoo Lim, Sang Chul Lee, William E Gent, Stefano Marchesini, Harinarayan Krishnan, Tolek Tyliszczak, David Shapiro, Arthur L David Kilcoyne, William C Chueh
Soft X-ray Ptychographic Imaging and Morphological Quantification of Calcium Silicate Hydrates [TAG-4]
Journal of the American Ceramic Society 98 (12), 4090-4095, 2015
Sungchul Bae, Rae Taylor, David Shapiro, Peter Denes, John Joseph
2014
Algorithmic framework for X-ray nanocrystallographic reconstruction in the presence of the indexing ambiguity [TAG-1]
Proc. National Acad. Sciences, 111, 2, pp. 593-598, 2014
Electronic structure of large-scale graphene nanoflakes [TAG-2]
J. Chem. Phys. 141, 214704, 2014
W. Hu, L. Lin, C. Yang and J. Yang
SIESTA-PEXSI: Massively parallel method for efficient and accurate ab initio materials simulation without matrix diagonalization [TAG-2]
J. Phys. Condens. Matter 26, 305503, 2014
L. Lin, A. Garcia, G. Huhs and C. Yang
Design of Three-Dimensional Porous Covalent Organic Frameworks via Known Synthesis Routes and Commercially Available Species [TAG-12]
Journal of Physical Chemistry C 118, pp. 23790-23802, 2014
R.L. Martin, C. Simon, B. Medasani, D. Britt, B. Smit, M. Haranczyk
High-Performance Inverse Modeling with Reverse Monte Carlo Simulations [TAG-8, TAG-10]
2014 Intern. Conf. on Parallel Processing (ICPP-2014), Sept 9-14, 2014, Minneapolis, Minn. 2014
A. Sarje, X. Li and A. Hexemer
An In Situ Grazing Incidence X-Ray Scattering Study of Block Copolymer Thin Films During Solvent Vapor Annealing [TAG-10]
Advanced Materials, Volume 26, Issue 2, pp. 273-281. January 15, 2014.
Xiaodan Gu, Ilja Gunkel, Alexander Hexemer, Weiyin Gu and Thomas P. Russell
PbS Nanoparticles Capped with Tetrathiafulvalenetetracarboxylate: Utilizing Energy Level Alignment for Efficient Carrier Transport" [TAG-10]
ACS Nano, ACS Nano, 8 (3), pp. 2532-2540, 2014
M. Scheele, D. Hanifi, D. Zherebetskyy, S.T. Chourou, S. Axnanda, B.J. Rancatore, K. Thorkelsson, T. Xu, Z. Liu, L.-W. Wang, Y. Liu, and A. P. Alivisatos
Model-Based Iterative Reconstruction for Synchrotron X:Ray Tomography [TAG-3]
International Conference on Acoustics, Speech, & Signal Processing, 2014
Mohan, K. A., Venkatakrishnan, S. V, Drummy, L. F., Simmons, J., Parkinson, D. Y., and Bouman, C. A.
Scientific data exchange: a schema for HDF5:based storage of raw and analyzed data [TAG-5, TAG-7]
Journal of Synchrotron Radiation, 2014
De Carlo, F., Gursoy, D., Marone, F., Rivers, M., Parkinson, D. Y., Khan, F., Jacobsen, C
High performance data management and analysis for tomography [TAG-3, TAG-7]
SPIE Optical Engineering Applications , 2014
Parkinson D. Y., Blair, J., Canon, R. S., Deslippe, J., Essiari, A., Hexemer, A., MacDowell, A. A., D.Y. Parkinson, S.J. Patton, L, Ramakrishnan, N, B.L. Tierney, and C.E. Tull
Segmentation of subcellular compartments combining superpixel representation with voronoi diagrams [TAG-6]
IEEE International Symposium on Biomedical Imaging (ISBI) - 1st place in Code Competition, April 2014.
D.M. Ushizima, A.G.C. Bianchi, and C. Carneiro
Structure recognition from high resolution images of ceramic composites [TAG-6]
IEEE International Conference on Big Data, October 2014
D.M. Ushizima, T. Perciano, H. Krishnan, B. Loring, H. Bale, D. Parkinson, and J.A. Sethian
Aperture imaging for Fluorescent X-ray [TAG-4]
Rev. Sci. Instrum. 85, 063704, 2014.
A. Haboub, A. A. MacDowell, S. Marchesini, D. Y. Parkinson
Toward quantitative structure activity relationship (qsar) models for nanoparticles [TAG-6]
American Chemical Society National Meeting - August 2014.
K. Odziomek, D.M. Ushizima, M. Haranczyk, and T. Puzyn
Efficient algorithms for Ptychographic Phase Retrieval [TAG-4]
Inverse Problems and Applications, Contemporary Mathematics, 615, 261 2014
Jianliang Qian, Chao Yang, A. Schirotzek, F. Maia, and S. Marchesini
Rank-1 accelerated illumination recovery in scanning diffractive imaging by transparency estimation [TAG-4]
Technical report LBNL-6734E 2014
Stefano Marchesini, Hau-tieng Wu
Chemical composition mapping with nanometre resolution by soft X-ray microscopy [TAG-4]
Nature Photonics, Sept. 2014
David A. Shapiro, Young-Sang Yu, Tolek Tyliszczak, Jordi Cabana, Rich Celestre, Weilun Chao, Konstantin Kaznatcheev, A. L. David Kilcoyne, Filipe Maia, Stefano Marchesini, Y. Shirley Meng, TonyWarwick, Lee Lisheng Yang & Howard A. Padmore
An algorithmic framework for X-ray nanocrystallographic reconstruction in the presence of the indexing ambiguity [TAG-1]
PNAS, 111(2), January 2014
Jeffrey J. Donatelli and James A. Sethian
2013
Component Particle Structure in Heterogeneous Disordered Ensembles Extracted from High-Throughput Fluctuation X-Ray Scattering [TAG-1]
Phys. Rev. Letters, 110(19), May 2013
G. Chen, P.H. Zwart, and D. Li
Three-dimensional single-particle imaging using angular correlations from X-ray laser data [TAG-1]
Acta Cryst. A, 69(4), 365-373, July 2013
H. Liu, B.K. Poon, D.K. Saldin, J.C.H. Spence, and P.H. Zwart
High accuracy geometric analysis of crystalline porous materials [TAG-12]
Cryst. Eng. Comm 15, pp. 7531-7538, 2013
M. Pinheiro, R.L. Martin, C.H. Rycroft, M. Haranczyk
Elliptic preconditioner for accelerating the selfconsistent field iteration in Kohn-Sham Density Functional Theory [TAG-2]
J. Phys., Condens. Matter, 25, pp. 295501, 2013
L. Lin, M. Chen, C. Yang and L. He
Accelerating Atomic Orbital-based Electronic Structure Calculation via Pole Expansion and Selected Inversion [TAG-2]
J. Phys., Condens. Matter, 25, pp. 295501, 2013
L. Lin, M. Chen, C. Yang and L. He
Exploring frontiers of high surface area metal-organic frameworks [TAG-12]
Chemical Science 4, pp. 1781-1785, 2013
R.L. Martin, M. Haranczyk
Insights into Multi-Objective Design of Metal-Organic Frameworks [TAG-12]
Crystal Growth and Design 13, pp. 4208-4212, 2013.
R.L. Martin, M. Haranczyk
Tuning HipGISAXS on Multi and Many Core Supercomputers [TAG-8, TAG-10]
Proc. of 4th International Workshop on Performance Modeling, Benchmarking and Simulation of High Performance Computer Systems (PMBS13), SC13, Denver, Colorado, November 2013.
A. Sarje and X.S. Li
Synchrotron Light-Source Data Analysis through Massively-Parallel GPU Computing [TAG-8,TAG-10]
NVIDIA GPU Technology Conference, San Jose, Calif., May 2013.
A. Sarje, X.S. Li, S. Chourou, A. Hexemer
HipGISAXS: A High-Performance Software for Simulating GISAXS Data [TAG-8, TAG-10]
J. Applied Crystallography, Vol. 46, Part 6, Dec. 2013
S. T. Chourou, A. Sarje, X. Li, E. Chan, and A. Hexemer
Challenges and New Developments in Imaging with Large Data Sets [TAG-6]
Joint Statistical Meeting (JSM2013), Montreal, Aug 2013
Ushizima, D.M., Bianchi, A.G.C., Krishnam, H
Multiscale Corner Detection in Planar Shape [TAG-6]
Journal of Mathematical Imaging and Vision, March 2013
Paula Jr., I.C., Medeiros, F.N.S, Bezerra, F.N. and Ushizima, D.M
Augmented projections for ptychographic imaging [TAG-4]
Inverse Problems 29, 115009 2013
Stefano Marchesini, Andre Schirotzek, Chao Yang, Hau-tieng Wu, Filipe Maia
Reconstruction algorithms for x-ray nanocrystallography via solution of the twinning problem [TAG-1]
PhD Thesis (University of California, Berkeley), May 2013
Jeffrey J. Donatelli
2012
Computation of fluctuation scattering profile via three-dimensional Zernike polynomials [TAG-1]
Acta. Cryst. A, 68(5), September 2012
H. Liu, B.K. Poon, A.J.E.M. Janssen, and P.H. Zwart
Structure determination of Pt-coated Au dumbbells via fluctuation X-ray scattering [TAG-1]
J.Synchrotron Radiation, 19(5), 695- 700, September 2012
G. Chen, M.A. Modestino, B.K. Poon, A. Schirotzek, S. Marchesini, R.A. Segalman, A. Hexemer, and P.H. Zwart
Element orbitals for Kohn-Sham density functional theory [TAG-2]
Phys. Rev. B, 85:235144, 2012
L. Lin and L. Ying
Optimized local basis set for Kohn-Sham density functional theory [TAG-2]
J. Comput. Phys., 231:4515, 2012
L. Lin, J. Lu, L. Ying and W. E
Adaptive local basis set for Kohn-Sham density functional theory in a discontinuous Galerkin framework I: Total energy calculation [TAG-2]
J. Comput. Phys., 231:2140, 2012
L. Lin, J. Lu, L. Ying and W. E
Algorithms and tools for high-throughput geometry based analysis of crystalline porous materials [TAG-12]
Microporous and Mesoporous Materials, 149, pp. 134-141, 2012.
T.F. Willems, C.H. Rycroft, M. Kazi, J.C. Meza, M. Haranczyk
Addressing challenges of identifying geometrically diverse sets of crystalline porous materials [TAG-12]
Jour. Chem. Information and Modeling 52, pp. 308-318, 2012
R.L. Martin, B. Smit, M. Haranczyk
Accelerating analysis of void space in porous materials on multicore and GPU platforms [TAG-8, TAG-12]
International Journal of High Performance Computing, Feb., 2012
R.L. Martin, Prabhat, Donofrio, J.A. Sethian, M, Haranczyk
Material science image analysis using quant-CT in ImageJ [TAG-6]
ImageJ User and Developer Conference 2012, Oct, Luxembourg, LX.
Ushizima, D.M., Bianchi, A.G.C., deBianchi, C. and Bethel E.W
Massively Parallel X-ray Scattering Simulations [TAG-8, TAG-10]
Proc. of the International Conference for High Performance Computing, Networking, Storage and Analysis (SC12), Salt Lake City, Nov. 10-16, 2012
A. Sarje, X.S. Li, S. Chourou, E. Chan, and A. Hexemer
Augmented topological descriptors of pore network [TAG-6]
Carbon Cycle 2.0 Symposium, LBNL, Feb. 2012.
Ushizima, D.M., Morozov, D, Weber, G.H., Bianchi, A.G.C. and Bethel E.W., in: VisWeek 2012, Oct, Seattle, WA, USA. Algorithms for Microstructure Description applied to Microtomography, Ushizima, D.M., Weber, G., Morozov, D., Bethel, W., Sethian, J.A
Alternating Direction Methods for Classical and Ptychographic Phase Retrieval [TAG-4]
Inverse Problems 28 115010, 2012.
Zaiwen Wen, Chao Yang, Xin Liu, S. Marchesini
2011
Phasing of coherent femtosecond X-ray diffraction from size-varying nanocrystal [TAG-1]
Optics Express 19(4), pp. 2866-2873, 2011
F. C. H. Spence, R. A. Kirian, X. Wang, U. Weierstall, K. E. Schmidt, T. White, A. Barty, H. N. Chapman, S. Marchesini, and J. Holton
Compressive auto-indexing in femtosecond nanocrystallography [TAG-1]
Ultramicroscopy 111(7), 807-811. 2011
F. R. N. C. Maia, C. Yang, and S. Marchesini
Iterative Algorithms for Ptychographic Phase Retrieval [TAG-4]
Technical report LBNL-4598E, 2011
C. Yang, J. Qian, A. Schirotzek, F. Maia, S. Marchesini
2010
Automatic Structure Analysis in High-Throughput Characterization of Porous Material [TAG-12]
J. Chem. Theory Comput., 6 (11), pp 3472-3480, 2010
Haranczyk, M. and Sethian, J.A
2009
Navigating molecular worms inside chemical labyrinths [TAG-12]
Proc. National Acad. Sciences, 106, pp. 1472-21477, 2009.
Haranczyk, M. and Sethian, J.A