Publications

The publications are organized by year and tag. Please use the search 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

2021

Joint Iterative Reconstruction and 3D Rigid Alignment for X-ray Tomography [Tag-3]

to be submitted to Journal of the Optical Society of America A

K. Pande, J. J. Donatelli, D. Y. Parkinson, H. Yan, J. A. Sethian


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

Cross-correlation Analysis of X-ray Photon Correlation Spectroscopy to Extract Rotational Diffusion Coefficients [Tag-13]

Proceedings of the National Academy of Sciences, to appear

Zixi Hu, J.J. Donatelli, and J.A. Sethian

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

Persistent and partially mobile oxygen vacancies in Li-rich layered oxides

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

Advances in Kriging-Based Autonomous X-Ray Scattering Experiments [TAG-14]

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,TAF-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

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

SPIE: X-Ray Nanoimaging: Instruments and Methods IV, 11112 (2019)

Jiangtao Zhao, Kasra Nowrouzi, Richard Celestre, Matthew Marcus, Young-Sang Yu, David A Shapiro


Advanced Denoising for X-ray Ptychography

Optics Express, 27 (8), 10395-10418 (2019)

Huibin Chang, Pablo Enfedaque, Stefano Marchesini, Juliane Reinhardt, Bjoern Enders, Young-Sang Yu, David Shapiro, Christian G Schroer, Tieyong Zeng


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

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

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

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

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

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