Publications

X-ray Free-Electron Lasers

"Structure Determination from Experimental Fluctuation X-ray Scattering Data", Pande K. et al., 2018 (In preparation).

"Free Electron Laser based Multiple Particle Fluctuation Scattering Data", Pande K. et al., 2018 (In preparation).

"Filtering techniques for small/wide-angle and Fluctuation X-ray scattering", Donatelli J.J., Pande K., and Zwart P.H., 2018 (In preparation).

"Interparticle coherence effects in fluctuation X-ray scattering", Donatelli J.J., Pande K., and Zwart P.H., 2018 (In preparation).

"Correlations in Scattered X-Ray Laser Pulses Reveal Nanoscale Structural Features of Viruses", 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, Phys. Rev. Letters, 119, 158102, 2017.

"Reconstruction from limited single-particle diffraction data via simultaneous determination of state, orientation, intensity, and phase", Jeffrey J. Donatelli, James A. Sethian and Peter H. Zwart, Proc. National Acad. Sciences, 114(28), 7222-7227, 2017.

"Structural enzymology using X-ray free electron lasers", 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, Ma?hias Frank, ?omas White, Anton Barty, Sasa Bajt, Oleksandr Yefanov, Henry N. Chapman, Nadia Zatsepin, Garre ? Nelson, Uwe Weierstall, John Spence, Peter Schwander, Lois Pollack, Petra Fromme, Abbas Ourmazd, George N. Phillips Jr., and Marius Schmidt, Structural Dynamics, 4, 044003, 2017,

"Femtosecond structural dynamics drives the trans/cis isomerization in photoactive yellow protein", Kanupriya Pande, Christopher D. M. Hutchison, Gerrit Groenhof, Andy Aquila, Josef S. Robinson, Jason Tenboer, Shibom Basu, Sbastien Boutet, Daniel P. DePonte, Mengning Liang, ?omas A. White, Nadia A. Zatsepin, Oleksandr Yefanov, Dmitry Morozov, Dominik Oberthuer2, 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, ?omas 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 Mo?at, Jasper J. van Thor, Marius Schmidt, Science, 352(6286), 725-729, 2016.

"The Linac linac coherent light source single particle imaging road map, Andrew Aquila, Anton Barty, Christoph Bostedt, Sebastien Boutet, Gabriella Carini, P Drell, S Doniach, KH Downing, T Earnest, H Elmlund, V Elser, M Ghr, J Hajdu, J Hastings, SP Hau-Riege, Z Huang, EE La?man, FRNC Maia, S Marchesini, A Ourmazd, C Pellegrini, R, Santra, I Schlichting, C Schroer, JCH Spence, IA Vartanyants, S Wakatsuki, WI Weis, GJ Williams, Structural Dynamics 2 Issue 4, Pages 041701, 2015/7/1

"Iterative phasing for fluctuation X-ray scattering J.J.  Donatelli, P.H. Zwart, and J.A. Sethian, Proc. National Acad. Sciences, 112(33), 10286-10291, 2015.

"Operational properties of ?uctuation X-ray scattering data", E. Malmerberg, C.A. Kerfeld, and P.H. Zwart, IUCrJ, 2(3), 309-316, May 2015.

"Simulations on time-resolved structure determination of uncrystallized biomolecules in the presence of shot noise", K. Pande, M. Schmidt, P. Schwander, and D.K. Saldin,
Struct Dyn, 2(2), 024103, 2015.  42

"Deducing fast electron density changes in randomly oriented uncrystallized biomolecules in a pump-probe experiment", K. Pande, P. Schwander, M. Schmidt, and D.K. Saldin, Philos Trans R Soc Lond B Biol Sci, 369(1647), 20130332, 2014.

"Time-resolved serial crystallography captures high resolution intermediates of photoactive yellow protein", Jason Tenboer, Shibom Basu, Nadia Zatsepin, Kanupriya Pande, Despina Milathianaki, Ma?hias Frank, Mark Hunter, Sbastien Boutet, Garth J.  Williams, Jason E. Koglin, Dominik Oberthuer, Michael Heymann, Christopher Kupitz, Chelsie Conrad, Jesse Coe, Shatabdi Roy-Chowdhury, Uwe Weierstall, Daniel James, Dingjie Wang, Thomas Grant, Anton Barty, Oleksandr Yefanov, Jennifer Scales, Cornelius Gati, Carolin Seuring, Vukica Srajer, Robert Henning, Peter Schwander, Raimund Fromme, Abbas Ourmazd, Keith Mo?at, Jasper J.  Van ?or, John C. H. Spence, Petra Fromme, Henry N. Chapman, Marius Schmidt, Science, 346(6214), 1242-1246, 2014.

"New Light on Disordered Ensembles: Ab-Initio Structure Determination of One Particle From Scattering Fluctuations of many copies", D. K. Saldin, H. C. Poon, M. J. Bogan, S. Marchesini, D. A. Shapiro, R. A.  Kirian, U. Weierstall, and J. C. H. Spence, Phys. Rev.  Letters 106, 115501 (2011). (viewpoint in Physics).

"Structure of a single particle from scattering by many particles randomly oriented about an axis: toward structure solution without crystallization?", D. K.  Saldin, V. L. Shneerson, M. R. Howells, S. Marchesini, H. N. Chapman, M. Bogan, D. Shapiro, R. A. Kirian, U.Weierstall, K. E. Schmidt and J. C. H. Spence, New J. Phys. 12, 035014, (2010).

"Algorithmic framework for X-ray nanocrystallographic reconstruction in the presence of the indexing ambiguity", Donatelli, J.J. and Sethian, J.A., Proc.  National Acad. Sciences, 111, 2, pp. 593-598, 2014.

"Component Particle Structure in Heterogeneous Disordered Ensembles Extracted from High-Throughput Fluctuation X-Ray Scattering", G. Chen, P.H. Zwart, and D. Li, Phys. Rev. Le?., 110(19), May 2013
.
"Free-dimensional single-particle imaging using angular correlations from X-ray laser data", H. Liu, B.K. Poon, D.K. Saldin, J.C.H. Spence, and P.H.  Zwart, Acta Cryst. A, 69(4), 365-373, July 2013.

"Computation of fluctuation scattering profile via three-dimensional Zernike polynomials", H. Liu, B.K.  Poon, A.J.E.M. Janssen, and P.H. Zwart, Acta. Cryst.  A, 68(5), September 2012.

"Structure determination of Pt-coated Au dumbbells via fluctuation X-ray scattering", G. Chen, M.A. Modestino, B.K. Poon, A. Schirotzek, S. Marchesini, R.A.  Segalman, A. Hexemer, and P.H. Zwart, 19(5), 695- 700, September 2012.

"Phasing of coherent femtosecond X-ray diffraction from size-varying nanocrystal", J. 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, Optics Express 19(4), pp. 2866-2873, 2011.  

"Compressive auto-indexing in femtosecond nanocrystallography", F. R. N. C. Maia, C. Yang, and S.  Marchesini, Ultramicroscopy 111(7), 807-811. 2011.  

"Orientation determination for 3D single molecule diffraction imaging", Chao Yang, Zhen Wang, and Stefano Marchesini, Proc. SPIE Vol. 7800, 78000P (2010).

 

Electronic Structure

"Accelerating Optical Absorption Spectra and Exciton Energy Computation via Interpolative Separable Density Fitting", W. Hu, M. Shao, A. Cepellotti, F. H. da Jornada, L. Lin, K. ?icke, C. Yang and S. G. Louie, accepted, Intern. Conf. Computational Science, 2018.

"PSelInv: A distributed memory parallel algorithm for selected inversion: the non-symmetric case", M.  Jacquelin, L. Lin and C. Yang, Parallel Comput. 74, 84, 2018

"Highly efficient photocatalytic water splitting over edge-modified phosphorene nanoribbons", W. Hu, L.  Lin, R. Zhang, C. Yang and J. Yang, J. Amer. Chem.  Soc. 139, 15429, 2017

"Interpolative separable density fitting decomposition for accelerating hybrid density functional calculations with applications to defects in silicon", W. Hu, L. Lin and C. Yang, J. Chem. Theory Comput. 13, 5420, 2017

"Projected Commutator DIIS Method for Accelerating Hybrid Functional Electronic Structure Calculations", 43 W. Hu, L. Lin and C. Yang, J. Chem. Theory Comput.  13, 5458, 2017

"Accelerating selected columns of the density matrix computations via approximate column selection", A.  Damle, L. Lin and L. Ying, SIAM J. Sci. Comput. 39, 1178, 2017

"Robust Determination of the Chemical Potential in the Pole Expansion and Selected Inversion Method for Solving Kohn-Sham density functional theory, W. Jia and L. Lin, J. Chem. Phys. 147, 144107, 2017

"A posteriori error estimates for discontinuous Galerkin methods using non-polynomial basis functions", Part II: Eigenvalue problems, L. Lin and B. Stamm, Math. Model. Numer. Anal. 51, 1733, 2017

"Localized spectrum slicing", L. Lin, Math. Comp. 86, 2345, 2017

"Randomized estimation of spectral densities of large matrices made accurate", L. Lin, Numer. Math. 136, 183, 2017

"Adaptively compressed exchange operator for large scale hybrid density functional calculations with applications to the adsorption of water on silicene", W.  Hu, L. Lin, A. Banerjee, E. Vecharynski and C. Yang, J. Chem. Theory Comput. 13, 1188, 2017

"Adaptively compressed polarizability operator for accelerating large scale ab initio phonon calculations", L.  Lin, Z. Xu and L. Ying, Multiscale Model. Simul. 15, 29, 2017

"SCDM-k: Localized orbitals for solids via selected columns of the density matrix", A. Damle, L. Lin and L. Ying, J. Comput. Phys. 334, 1, 2017

"Adaptive local basis set for Kohn-Sham density functional theory in a discontinuous Galerkin framework II: Force, vibration, and molecular dynamics calculations",
G. Zhang, L. Lin,W. Hu, C. Yang and J.E. Pask, J. Comput. Phys. 335, 426 2017

"PSelInv: A distributed memory parallel algorithm for selected inversion: the symmetric case", M. Jacquelin, L. Lin and C. Yang, ACM Trans. Math. So?ware 43, 21, 2016

"Chebyshev polynomial ?ltered subspace iteration in the Discontinuous Galerkin method for large-scale electronic structure calculations", A. S. Banerjee, L.  Lin, W. Hu, C. Yang, J. E. Pask, J. Chem. Phys. 145, 154101, 2016

"Adaptively compressed exchange operators", L. Lin, J.  Chem. Theory Comput. 12, 2242, 2016

"Low rank approximation in G0W0 calculations", M.  Shao, L. Lin, C. Yang, F. Liu, F. Jornada, J. Deslippe and S. G. Louie, Sci. China Math., 59 1593, 2016

"Decay estimates of discretized Green’s functions for Schrodinger type operators", L. Lin and J. Lu, Sci.  China Math., 59, 1561, 2016

"Approximating spectral densities of large matrices", L.  Lin, Y. Saad and C. Yang, SIAM Rev. 58, 34, 2016

"A proximal gradient method for ensemble density functional theory", M. Ulbrich, Z. Wen, C. Yang, D.  Klockner, Z. Lu,, SIAM J. Sci. Comp., June 20, 2015,

"Edge-modified phosphorene nanoflake heterojunctions as highly efficient solar cells", W. Hu, L. Lin, C. Yang, J. Dai and J. Yang, Nano Le?. 16 1675, 2016

"Enhancing the scalability and load balancing of the parallel selected inversion algorithm via tree-based asynchronous communication", M. Jacquelin, L. Lin, N. Wichmann and C. Yang, IEEE IPDPS, 192, 2016

"A posteriori error estimates for discontinuous Galerkin methods using non-polynomial basis functions. Part I: Second order linear PDE", L. Lin and B. Stamm, Math.  Model. Numer. Anal. (M2AN) 50, 1193, 2016

"Large-scale ab initio simulations based on systematically improvable atomic basis", P. Li, X. Liu, M. Chen, P. Lin, X. Ren, L. Lin, C. Yang and L. He, Comput.  Mater. Sci. 112 503, 2016

"Fast algorithms for estimating the absorption spectrum within linear response time-dependent density functional theory", J. Brabec, L. Lin, M. Shao, N.  Govind, C. Yang, Y. Saad, E. Ng, J. Chem. Theory Comput. 11, 5197, 2015

"A massively parallel method for large scale density functional theory calculation", W. Hu, L. Lin and C.  Yang, DGDFT. Chem. Phys. 143, 124110, 2015

"Edge reconstruction in armchair phosphorene nanoribbons revealed by discontinuous Galerkin density functional theory", W. Hu, L. Lin and C. Yang, Phys. Chem.  Chem. Phys. 17, 31397, 2015

"Compressed representation of Kohn-Sham orbitals via selected columns of the density matrix", A. Damle, L.  Lin and L. Ying, .Chem. Theory Comput. 11, 1463, 2015

"Electronic structure of large-scale graphene nanoflakes", W. Hu, L. Lin, C. Yang and J. Yang, J.  Chem. Phys. 141, 214704, 2014

"SIESTA-PEXSI: Massively parallel method for efficient and accurate ab initio materials simulation without matrix diagonalization", L. Lin, A. Garcia, G. Huhs and C. Yang, J. Phys. Condens. Matter 26, 305503, 2014

"A posteriori error estimator for adaptive local basis functions to solve Kohn-Sham density functional theory", J. Kaye, L. Lin and C. Yang, Commun. Math. Sci.  13, 1741, 2015

"Elliptic preconditioner for accelerating the selfconsistent field iteration in Kohn-Sham Density Functional Theory", L. Lin and C. Yang, SIAM J. Sci. Comp., 35(5), S277-S298, 2013.

"Accelerating Atomic Orbital-based Electronic Structure Calculation via Pole Expansion and Selected Inversion", L. Lin, M. Chen, C. Yang and L. He,J. Phys., Condens. Matter, 25, pp. 295501, 2013.

"Element orbitals for Kohn-Sham density functional theory", L. Lin and L. Ying, Phys. Rev. B, 85:235144, 2012.

"Optimized local basis set for Kohn-Sham density functional theory", L. Lin, J. Lu, L. Ying and W. E, J. Comput.  Phys., 231:4515, 2012,

"Adaptive local basis set for Kohn-Sham density functional theory in a discontinuous Galerkin framework I: Total energy calculation", L. Lin, J. Lu, L. Ying and W. E, J. Comput. Phys., 231:2140, 2012.

Material Informatics

"A Surrogate Model Approach to Autonomous Experimentation and Applications to X-Ray Imaging", Noack, M., Fukuto, M., Yager, K., Hexemer, A., 2018 (In preparation).

"A High-Performance QED Ray Tracer for X-Ray Scattering Computations", Noack, M., Fukuto, M., Yager, K., Sethian, J., 2018 (In preparation).

"Accurate Characterization of the Pore Volume in Microporous Crystalline Materials", D. Ongari, P. Boyd, S. Barthel, M. Witman, M. Haranczyk, B. Smit, Langmuir 33 (2017), 14529-14538. (featured on cover)

"Computationally-Guided Synthetic Control over Pore Size in Isostructural Porous Organic Cages", 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, ACS Central Science 3 (2017) 734-742.

"The Influence of Intrinsic Framework Flexibility on Adsorption in Nanoporous Materials", M. Witman, S.  Ling, S. Jawahery, P. Boyd, M. Haranczyk, B. Slater, B. Smit, Journal of the American Chemical Society 139 (2017) 5547-5557.

"Scanning electron microscopy as a source of morphological data on nanoparticles: image representativeness", K. Odziomek, D. Ushizima, P. Oberbek, K.  Kurzydlowski, T. Puzyn, M. Haranczyk, Journal of Microscopy 265 (2017) 34-50

"Metal-Organic Framework with Optimal Adsorption, Separation, and Selectivity towards Xenon", 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, Nature Communications 7 (2016)

"Tunable porosity through cooperative di?usion in a multicomponent porous molecular crystal", R. Manurung, M. Miklitz, D. Holden, L. Chen, T. Hasell, S.Y.  Chong, M. Haranczyk, A.I. Cooper, K.E. Jelfs, Journal of Physical Chemistry C 119 (2015) 22577-22586

"Understanding Small-Molecule Interactions in Metal Organic Frameworks: Coupling Experiment with Theory", J.S. Lee, B. Vlaisavljevich, D. K. Britt, C. M. Brown, M. Haranczyk, J.B. Neaton, B. Smit, J.R.  Long, W.L. Queen, Advanced Materials (2015)

"Design of Tree-Dimensional Porous Covalent Organic Frameworks via Known Synthesis Routes and Commercially Available Species", R.L. Martin, C. Simon, B.  Medasani, D. Britt, B. Smit, M. Haranczyk, Journal of Physical Chemistry C 118, pp. 23790-23802, 2014,

"Exploring frontiers of high surface area metal-organic frameworks", R.L. Martin, M. Haranczyk, Chemical Science 4, pp. 1781-1785, 2013,

"High accuracy geometric analysis of crystalline porous materials, M. Pinheiro, R.L. Martin, C.H.  Rycroft, M. Haranczyk, Cryst. Eng. Comm 15, pp.  7531-7538, 2013.

"Insights into Multi-Objective Design of Metal-Organic Frameworks", R.L. Martin, M. Haranczyk , Crystal Growth and Design 13, pp. 4208-4212, 2013.

"Algorithms and tools for high-throughput geometry based analysis of crystalline porous materials", T.F.  Willems, C.H. Rycroft, M. Kazi, J.C. Meza, M. Haranczyk, Microporous and Mesoporous Materials, 149, pp. 134-141, 2012.

"Addressing challenges of identifying geometrically diverse sets of crystalline porous materials", R.L. Martin, B. Smit, M. Haranczyk. Jour. Chem. Information and Modeling 52, pp. 308-318, 2012,

"Accelerating analysis of void space in porous materials on multicore and GPU platforms", R.L. Martin, Prabhat, Donofrio, J.A. Sethian, M, Haranczyk, International Journal of High Performance Computing, Feb., 2012

"Automatic Structure Analysis in High-Throughput Characterization of Porous Material", M. Haranczyk and Sethian, J.A., J. Chem. Theory Comput., 2010, 6 (11), pp 3472-3480,

"Navigating molecular worms inside chemical labyrinths", Haranczyk, M. and Sethian, J.A., Proc.  National Acad. Sciences, 106, pp. 1472-21477, 2009.

GISAXS

"Computational Analysis of Grazing Incidence Small Angle X-Ray Scattering Data", A. Sarje, S. Chourou, D. Kumar, S. Venkatakrishnan, X. Li, and A. Hexemer, submitted to J. Applied Crystallography, 2018 (in revision).

"Accurate Multi-slice Grazing-Incidence X-ray Simulation", S.V. Venkatakrishnan, Je?rey Donatelli, Dinesh Kumar, Abhinav Sarje, Sunil K. Sinha, Xiaoye S.  Li, Alexander Hexemer, J. Applied Crystallography, Vol.49, Part 6, December 2016.

"Pursuing the critical dimension using Grazing Incidence Small Angle X-ray Scattering", G. Freychet, D.  Kumar, R. Pandol?, P. Naulleau, I. Cordova, J. Strzalka, M. Fukuto, and A. Hexemer, Proc. Vol. 10585, Metrology, Inspection, and Process Control for Microlithography XXXII, SPIE Advanced Lithography 2018.

"DOE Scientists Team up to Demonstrate Scientific Potential of Big Data Infrastructure", LBNL News Feb. 3, 2015.

"Organic Photovoltaics Experiments Showcase "Superfacility" Concept, LBNL News March 17, 2015.

"Real-Time Data Pipeline and analysis using SPOT and HIPGISAXS", A. Hexemer and C.E.Tull, OLCF Users meeting June 24, 2015.

"HIPGISAXS for fast analysis", A. Hexemer, canSAS 8 meeting in Tokai, Japan. 2015.

"HIPGISAXS", A. Hexemer, Kyoto Institute of Technology, Japan, May 2015.

"Fast Analysis for Scattering", A. Hexemer, ISPAC, Houston, May 2015.

"Fast Analysis of Time-Resolved Scattering Data", A.  Hexemer APS March Meeting 2015.

"Inverse Modeling Nanostructures from X-ray Scattering Data through Massive Parallelism", A. Sarje, X.S.  Li, D. Kumar, S. Venkatakrishnan, A. Hexemer, SC15 conference, Nov. 2015.

"Recovering Nanostructures from X-ray Scattering Data", A. Sarje, X.S. Li, D. Kumar, A. Hexemer, NVIDIA GPU Technology Conference, San Jose, Calif., May 2015.

"Scalable Particle Swarm Optimization for Nanostructure Discovery", A. Sarje, X. Li and A. Hexemer, Euro-Par 2015 Conference, Aug. 24-28, 2015, Vienna.


"High-Performance Inverse Modeling with Reverse Monte Carlo Simulations", A. Sarje, X. Li and A. Hexemer, 2014 Intern. Conf. on Parallel Processing (ICPP-2014), Sept 9-14, 2014, Minneapolis, Minn.

"PbS Nanoparticles Capped with Tetrathiafulvalenetetracarboxylate: Utilizing Energy Level Alignment for Efficient Carrier Transport", 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, ACS Nano, ACS Nano, 2014, 8 (3), pp. 2532-2540.

"An In Situ Grazing Incidence X-Ray Sca?ering Study of Block Copolymer Thin Films During Solvent Vapor Annealing", Xiaodan Gu, Ilja Gunkel, Alexander Hexemer, Weiyin Gu and ?omas P. Russell, Advanced Materials, Volume 26, Issue 2, pp. 273-281. January 15, 2014.

"HipGISAXS: A High-Performance Software for Simulating GISAXS Data", S. T. Chourou, A. Sarje, X. Li, E. Chan, and A. Hexemer, J. Applied Crystallography, Vol. 46, Part 6, Dec. 2013.

"Tuning HipGISAXS on Multi and Many Core Supercomputers", A. Sarje and X.S. Li, Proc. of 4th International Workshop on Performance Modeling, Benchmarking and Simulation of High Performance Computer Systems (PMBS13), SC13, Denver, Colorado, November 2013.

"Synchrotron Light-Source Data Analysis through Massively-Parallel GPU Computing", A. Sarje, X.S. Li, S. Chourou, A. Hexemer, NVIDIA GPU Technology Conference, San Jose, Calif., May 2013.

"Massively Parallel X-ray Scattering Simulations", A. Sarje, X.S. Li, S. Chourou, E. Chan, and A. Hexemer, Proc. of ?e International Conference for High Performance Computing, Networking, Storage and Analysis (SC12), Salt Lake City, Nov. 10-16, 2012.

"Pursuing the critical dimension in etched patterns using x-ray scattering", G. Freychet, D. Kumar, R. Pandol, D. Staacks, P. Naulleau, R. J. Kline, D. Sunday, M. Fukuto, J. Strzalka and A. Hexemer, Proceeding SPIE Advanced Lithography, Vol. 10585, pp. 10585-7, 2018.

"Programmed LWR metrology by multi-techniques approach", J. Reche, M. Besacier, P. Gergaud, Y. Blancquaert, G. Freychet and T. Labbaye, Proceeding SPIE Advanced Lithography, Vol. 10585, pp. 105850F, 2018.

Tomography

"Improving Tomographic Reconstruction from Limited Data Using Mixed-Scale Dense Convolutional Neural Networks", Pelt, D. M., Batenburg, K. J., & Sethian, J. A  Journal of Imaging, 4(11), 128, 2018

"Achieving fast high-resolution 3D imaging by combining synchrotron x-ray microCT, advanced algorithms, and high performance data management". Dilworth Y. Parkinson, Joseph I. Pacold, Miela Gross, Tristan D. McDougall, Chandler Jones, John Bows, Ian Hamilton, Danil E. Smiles, Stefano De Santis, Alessandro Ratti, Daniël M. Pelt, James Sethian, Harold Barnard, Joshua Peterson, Alvaro Ramirez-Hong, Alastair MacDowell, David K. Shuh, (Conference Presentation:) In Image Sensing Technologies: Materials, Devices, Systems, and Applications V (Vol. 10656, p. 106560S). International Society for Optics and Photonics, 2018
 

"TomoBank: a tomographic data repository for computational x-ray science", De Carlo, F., Gürsoy, D., Ching, D. J., Batenburg, K. J., Ludwig, W., Mancini, L., Marone, F., Mokso, R., Pelt, D. M., Sijbers, J., & Rivers, M. (2018).  Measurement Science and Technology, 29(3), 034004.


"Ring artifact reduction in synchrotron X-ray tomography through helical acquisition", D.M. Pelt, and D. Y.  Parkinson, Measurement Science and Technology, Volume 29, Number 3 (2018).

"Machine learning for micro-tomography", Parkinson, D. Y., Ushizima, D. M., Perciano, T., Krishnan, H., Barnard, H. S., MacDowell, A. A., Pelt, D., Sethian,
J. A. , Dev. X-Ray Tomogr. XI 18 (2017).

"Insight into 3D micro-CT data: convergence of segmentation algorithms through evaluation metrics", T. Perciano, D. Ushizima, H. Krishnan, D. Parkinson, N. M. Larson, Daniel M. Pelt and F. W. Zok, Journal of Synchrotron Radiation, 24(5): 1065-1077, Sept. 2017

"Improved tomographic reconstruction of large-scale real-world data by filter optimization", D. M. Pelt and V. De Andrade. Advanced Structural and Chemical Imaging 2016 2:17.

"Insight into 3D micro-CT data: convergence of segmentation algorithms through evaluation metrics", T.  Perciano, D. Ushizima, H. Krishnan, D. Parkinson, N.  M. Larson, Daniel M. Pelt and F. W. Zok, Journal of Synchrotron Radiation, 24(5): 1065-1077, Sept. 2017

"Model:Based Iterative Reconstruction for Synchrotron X:Ray Tomography", Mohan, K. A., Venkatakrishnan, S. V, Drummy, L. F., Simmons, J., Parkinson, D. Y., and Bouman, C. A,, ICASSP, 2014.

"Scientific data exchange: a schema for HDF5:based storage of raw and analyzed data", De Carlo, F., Gursoy, D., Marone, F., Rivers, M., Parkinson, D. Y., Khan, F., Jacobsen, C, Journal of Synchrotron Radiation, 21(Pt 6), 1224-30.

"High performance data management and analysis for tomography", Parkinson D. Y., Blair, J., Canon, R. S., Deslippe, J., Essiari, A., Hexemer, A., MacDowell, A. A., and others, In SPIE Optical Engineering and Applications (p. 92121G - 92121G

 

Image Analysis

"Gradient Boosting Decision Trees for Echo Images", Melo, Ushizima, Barachio, Coelho, IEEE World Congress on Computational Intelligence, International Joint Conference on Neural Networks (IJCNN) 2018 (accepted).

"Active contours for overlapping cell segmentation", Araujo, Silva, Medeiros, Farias, Calaes, Bianchi, Ushizima, International Journal of Biomedical Engineering and Technology 2018 (accepted).

"DPP-PMRF: Rethinking Optimization for a Probabilistic Graphical Model Using Data-Parallel Primitives. ", Brenton Lessley, Talita Perciano, Colleen Heinemann, David Camp, Hank Childs, E. Wes Bethel (2018). DPP-PMRF,  In The 8th IEEE Symposium on Large Data Analysis and Visualization in conjunction with IEEE VIS 2018, Berlin, Germany, October 21, 2018.
 


A mixed-scale dense convolutional neural network for image analysis", D.M. Pelt and J.A. Sethian, Proceedings of the National Academy of Sciences, 115(2), 254-259, 2018

"Xi-cam: A versatile interface for data visualization and analysis", Pandolfi, Allan, Arenholz, Barroso-Luque, Campbell, Caswell, Blair, Carlo, Fackler, Fournier, Freychet, Fukuto, Gursoy, Jiang, Krishnan, Kumar, Kline, Li, Liman, Marchesini, Mehta, N’Diaye, Parkinson, Parks, Pellouchoud, Perciano, Ren, Sahoo, Strzalka, Sunday, Tassone, Ushizima, Venkatakrishnan, Yager, Zwart, Sethian, Hexemer, Journal of Synchrotron Radiation 2018 (accepted).

"Mathematics in Pattern Recognition for Scientific Investigations", T. Perciano, B. Loring, H. Krishnan, J.  Michael L. MacNeil, D. Ushizima, position paper in the DOE Scientific Machine Learning Workshop, 2018.

"Maximal clique enumeration with data-parallel primitives", B. Lessley, T. Perciano, M. Mathai, H. Childs and E. W. Bethel, IEEE 7th Symposium on Large Data Analysis and Visualization (LDAV), Phoenix, AZ, 2017, pp. 16-25, 2017

"Data Efficient X-ray Phase Tomography with Self-calibrated Sandpaper Analyzer", Chen, M., Parkinson, D., Venkatakrishnan, S., Marchesini, S. & Waller, L., Computational Optical Sensing and Imaging CW2B, 2 (2017).

"Machine learning for micro-tomography", Parkinson, D. Y.; Ushizima, D. M.; Perciano, T.; Krishnan, H.; Barnard, H. S.; MacDowell, A. A.; Pelt, D.; Sethian, J. A. , Dev. X-Ray Tomogr. XI 18 (2017).  Nearest-Neighbour Nanocrystal Bonding Dictates

"Framework Stability or Collapse in Colloidal Nanocrystal Frameworks", Williams, Ushizima, Zhu, Anders, Milliron, Helms, Chemical Communications, Royal Society of Chemistry, 2017.

"Automating Cell Detection and Classification in Human Brain Fluorescent Microscopy Images Using Dictionary Learning and Sparse Coding", Alegro, Theolas, Nguy, Castruita, Seeley, Ushizima, Grinberg, Journal of Neuroscience Methods, 2017.

"Detection and Classi?cation of Cervical Cells", Ushizima, D. in 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]

"Convolutional Neural Networks with Tensor Flow: theory and practice", Araujo, Carneiro, Silva, Medeiros, Ushizima, p. 382-406. Brazilian Society of Computation Press 2017. [book chapter]

"Computer Vision in python with libraries scikit-image and scikit-learn", Silva, Lopes, Araujo, Medeiros, Ushizima, p. 407-428. Brazilian Society of Computation Press 2017. [book chapter]

"A multi-objective approach for calibration and detection of cells nuclei", Oliveira, Moreira, Ushizima, Carneiro, Medeiros, Araujo, Silva, Bianchi, IEEE Congress on Evolutionary Computation, 2017.

"Portable Learning Environments for Hands-On Computational Instruction Using Container- and Cloud- Based Technology to Teach Data Science", Holdgraf, Rokem, Culich, Alegro, Deniz, Ushizima, Practice and Experience in Advanced Research Computing Conference, PEARC’17.

"Distributed Memory Parallel Markov Random Fields using Graph Partitioning", C. Heinemann, T. Perciano, D. Ushizima, and E. Wes Bethel, Fourth International Workshop on High Performance Big Graph Data Management, Analysis, and Mining (BigGraphs 2017), in conjunction with IEEE BigData 2017, December 11-14, 2017, Boston MA, USA.

"Insight into 3D micro-CT data: convergence of segmentation algorithms through evaluation metrics", T.  Perciano, D. Ushizima, H. Krishnan, D. Parkinson, N.  M. Larson, Daniel M. Pelt and F. W. Zok, Journal of Synchrotron Radiation, 24(5): 1065-1077, September 2017

"Improved tomographic reconstruction of large-scale real-world data by filter optimization", D. M. Pelt and V. De Andrade, Advanced Structural and Chemical Imaging 2016 2:17.

"Robust model-based phase ptycho-tomography", Singanallur V. Venkatakrishnan, Maryam Farmand, Young-Sang Yu, Hasti Majidi, Klaus Van Benthem, Stefano Marchesini, David Shapiro, and Alexander
Hexemer, IEEE Signal Processing Letters, Vol. 23, no. 7, pp. 944-948, July 2016

"Scanning electron microscopy image representativeness: morphological data on nanoparticles", Odziomek, K., , Ushizima, D., Oberbek, P., Kurzydlowski, K., Puzyn, T., and Haranczyk, M., Jour. of Microscopy, 265(1), 2017

"Ammonia gas sensor based on the frequencydependent impedance characteristics of ultrathin polyaniline films", Santos, Bianchi, A., Ushizima, D., Pavinatto, Bianchi, Sensors and Actuators A: Physical, 2016

"Evaluation of Tree Algorithms for the Segmentation of Overlapping Cervical Cells", Lu, Carneiro, Bradley, Ushizima, Nosrati, Bianchi, Carneiro, Hamarneh, IEEE Journal of Biomedical and Health Informatics, 99, pp. 2168-2194, 2016.

"Scaling Analytics for Scientific Images from Experimental Instruments", Ushizima, Hexemer, Parkinson, Yang, IEEE Applied Imagery Pa?ern Recognition October, 2016

"Searchable datasets in Python: images across domains, experiments, algorithms and learning", Araujo, Silva, Ushizima, Medeiros, PyData, San Francisco 2016;

"Pathway toward diagnosing and monitoring prodromal Alzheimer’s Disease using novel imaging biomarkers", Ushizima, Grinberg, California Initiative for the Advancement of Precision Medicine Workshop 2016

"A two-level Markov random field for road network extraction and its application with optical, SAR, and multitemporal data", T. Perciano, F. Tupin, R. Hirata Jr., and R. M. Cesar Jr., International Journal of Remote Sensing, 37(16):3584-3610, July 2016

"Making advanced scientific algorithms and big scientific data management more accessible", S.V. Venkatakrishnan, K. Aditya Mohan, K. Bea?ie, J. Correa, E. Dart, J.R. Deslippe, A. Hexemer, H. Krishnan, A. A MacDowell, S. Marchesini, S.J Pa?on, T.  Perciano, J.A Sethian, R. Stromsness, B.L Tierney, C.E. Tull, D. Ushizima, and D.Y. Parkinson. Electronic Imaging, 2016(19):1-7, February 2016

"IDEAL: Images Across Domains, Experiments, Algorithms and Learning", 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. Journal of Minerals, Metals & Materials Society (TMS), pages 1-10 2016

"Model-Based Iterative Reconstruction for Synchrotron X:Ray Tomography", Mohan, K. A., Venkatakrishnan, S. V, Drummy, L. F., Simmons, J., Parkinson, D. Y., & Bouman, C. A,, ICASSP, 2014.

"Scientific data exchange: a schema for HDF5:based storage of raw and analyzed data", De Carlo, F., Gursoy, D., Marone, F., Rivers, M., Parkinson, D. Y., Khan, F., Jacobsen, C, Journal of Synchrotron Radiation, 21(Pt 6), 1224-30.

"High performance data management and analysis for tomography", Parkinson D. Y., Blair, J., Canon, R. S., Deslippe, J., Essiari, A., Hexemer, A., MacDowell, A. A., and others, In SPIE Optical Engineering Applications

"CAMERA: Center for Advanced Mathematics for Energy Research Applications", Donatelli, J; Haranczyk, M; Hexemer, A; Krishnan, H; Li, X; Lin, L; Maia, F; Marchesini, S; Parkinson, D; Perciano, T, Sethian, J.A., Synchrotron Radiation News 28 2 9-Apr 2015

"Evaluation of Algorithms for the Segmentation of Overlapping Cervical Cells", Z Lu, G Carneiro, A Bradley, D Ushizima, MS Nosrati, A Bianchi, IEEE Journal of Biomedical and Health Informatics 2016.

"Fast Detection of Material Deformation through Structural Dissimilarity", D. M. Ushizima, T. Perciano, D. Y. Parkinson, IEEE Big Data 2015.

"Cell reconstruction under Voronoi and enclosing ellipses from 3d microscopy", GLB Ramalho, DS Ferreira, AGC Bianchi, CM Carneiro, FNS Medeiros, IEEE Intern.  Symp. Biomedical Imaging (ISBI) 2015.

"Investigating Pill Recognition Methods for a New National Library of Medicine Image Dataset", D Ushizima, A Carneiro, M Souza, F Medeiros, Advances in Visual Computing, 410-419.

"Reduced-complexity Image Segmentation under Parallel Markov Random Field Formulation using Graph Partitioning", T. Perciano, D. M. Ushizima, Y. Mizrahi, E. W. Bethel, J. A. Sethian, IEEE ICIP, 2016

"Block Copolymer Packing Limits and Interfacial Reconfigurability in the Assembly of Periodic Mesoporous Organosilicas", Andrew W. Wills, David J.  Michalak, Peter Ercius, Ethan L. Rosenberg, Rory Runser, Talita Perciano, Daniela Ushizima, Brett Helms, Advanced Functional Materials, 25 (26), pp 4120-4128, 2015,

"Real-time Data Intensive Computing", 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.  Pa?on, T. Perciano, J.A. Sethian, D.A. Shapiro, R.  Stromsness, N. Tamura, B.L. Tierney, C.E. Tull2, D.  Ushizima, Synchrotron Radiation Instrumentation 2015.

"Aperture imaging for Fluorescent X-ray", A. Haboub, A. A. MacDowell, S. Marchesini, D. Y. Parkinson, Rev. Sci. Instrum. 85, 063704, 2014.

"Structure recognition from high resolution images of ceramic composites", D.M. Ushizima, T. Perciano, H. Krishnan, B. Loring, H. Bale, D. Parkinson, and J.  Sethian., IEEE International Conference on Big Data, October 2014.

"Toward quantitative structure activity relationship (qsar) models for nanoparticles", K. Odziomek, D.M. Ushizima, M. Haranczyk, and T. Puzyn. American Chemical Society National Meeting - Scienti?c Excellence Award, August 2014.

"Segmentation of subcellular compartments combining superpixel representation with voronoi diagrams", D.M.  Ushizima, A.G.C. Bianchi, and C. Carneiro. IEEE International Symposium on Biomedical Imaging (ISBI) - 1st place in Code Competition, April 2014.  Corner Detection in Planar Shapes, Paula Jr., I.C., Medeiros, F.N.S., Bezerra, F.N. and Ushizima, D.M., Journal of Mathematical Imaging and Vision, March 2013.

"Challenges and New Developments in Imaging with Large Data Sets", Ushizima, D.M., Bianchi, A.G.C., Krishnam, H., Joint Statistical Meeting (JSM2013), Montreal, Aug 2013 (oral presentation).

"Multiscale Corner Detection in Planar Shape", Paula Jr., I.C., Medeiros, F.N.S, Bezerra, F.N. and Ushizima, D.M., Journal of Mathematical Imaging and Vision, March 2013.

"Material science image analysis using quant-CT in ImageJ", Ushizima, D.M., Bianchi, A.G.C., deBianchi, C. and Bethel E.W.,in: ImageJ User and Developer Conference 2012, Oct, Luxembourg, LX.

"Augmented topological descriptors of pore network", 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., Carbon Cycle 2.0 Symposium, LBNL, Feb. 2012.

"Compressive phase contrast tomography", F. Maia, A.  MacDowell, S. Marchesini, H. A. Padmore, D. Y. Parkinson, J. Pien, A. Schirotzek, and C. Yang, Proc. SPIE Vol. 7800, 78000F, 2010

 

Ptychography

“Blind Ptychographic Phase Retrieval via Convergent Alternating Direction Method of Multipliers” Chang, H., Enfedaque, P., & Marchesini, S. SIAM Journal Imaging Science (2018) accepted (arXiv preprint arXiv:1808.05802).

 

“Denoising Poisson phaseless measurements via orthogonal dictionary learning”,  Chang, H., & Marchesini, S. Optics express, 26(16), 19773-19796 (2018).

 

“Dataflow at the COSMIC Beamline-Stream Processing and Supercomputing.” Enders, B., Nowrouzi, K., Krishnan, H., Marchesini, S., Park, J., Yu, Y. S., & Shapiro, D. A. Microscopy and Microanalysis, 24(S2), 58-59 (2018).

 

“GPU-Based Implementation of Ptycho-ADMM for High Performance X-Ray Imaging”, Enfedaque, P., Chang, H., Krishnan, H., & Marchesini, S.  In International Conference on Computational Science, 540-553. 2018.  

 

“Partially coherent ptychography by gradient decomposition of the probe”, Chang, H., Enfedaque, P., Lou, Y., & Marchesini, S. Acta Crystallographica Section A: Foundations and Advances, 74(3), 157-169 (2018).

Three-dimensional localization of nanoscale battery reactions using soft X-ray tomography", 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., Nature communications, 9(1), 921. (2018).

"Variational Phase Retrieval with Globally Convergent Preconditioned Proximal Algorithm", Huibin Chang, Stefano Marchesini, Yifei Lou, and Tieyong Zeng, SIAM Journal on Imaging Sciences, 11(1), 2018

"Total variation based phase retrieval for Poisson noise removal", Huibin Chang, Yifei Lou, Yuping Duan, and Stefano Marchesini, SIAM Journal on Imaging Sciences, 11(1), 2018

"Data Efficient X-ray Phase Tomography with Self-calibrated Sandpaper Analyzer", Chen, Michael, et al.  Computational Optical Sensing and Imaging. Optical Society of America, 2017.

"Nanometer-resolved spectroscopic study reveals the conversion mechanism at an elevated temperature", G. Geng, et al, Crystal Growth and Design, 17 (8), 4246-4253, 2017

"Ptychographic imaging of nano-materials at the Advanced Light Source with the Nanosurveyor Instrument", Shapiro, D.A., Celestre, R., Peter Denes, Maryam Farmand, John Joseph, A.L.D. Kilcoyne, Stefano Marchesini, Howard Padmore, Singanallur V.  Venkatakrishnan, Tony Warwick and Young-Sang Yuet al, IOP Conference Series: Journal of Physics 849 012028 (2017)

"Correlative cellular ptychography with functionalized nanoparticles at the Fe L-edge", M. Gallagher-Jones, et al, Scientific Reports, 7, 4757 (2017)

"Near-edge X-ray refraction ?ne structure microscopy", M Farmand, R Celestre, P Denes, ALD Kilcoyne, S Marchesini, et al, Applied Physics Le?ers 110 (6), 063101 (2017)


"A general framework for denoising phaseless diffraction measurements", Huibin Chang, Stefano Marchesini, arXiv preprint arXiv:1611.01417, 2016

"Denoising Poisson Phaseless Measurements via Orthogonal Dictionary Learning", Huibin Chang, Stefano Marchesini, arXiv:1612.08656, 2016

"Robust X-ray Phase Ptycho-Tomography", Venkatakrishnan, V., et. al., IEEE Signal Processing Letters, 10.1109/LSP.2016.2562504 (2016)

"Measuring spectroscopy and magnetism of extracted and intracellular magnetosomes using soft X-ray ptychography", X. Ahu, et. al., PNAS, 2016, 113(51), E8219-E8227.

"Nanosurveyor: a framework for real-time data processing", B.J. Daurer, H. Krishnan, T. Perciano, F. R.N.C. Maia, D.A. Shapiro, J.A. Sethian, Stefano Marchesini, Advanced Structural and Chemical Imaging 20173:7,

"SHARP: a distributed GPU-based ptychographic solver", S. Marchesini, H. Krishnan, B. J. Daurer, D. A. Shapiro, T. Perciano, J. A. Sethian and F. R. N. C.  Maia, J. Appl. Cryst. (2016). 49

"ALS User Meeting Highlights Accomplishments and Challenges", K Troutman, E Arenholz, S Marchesini, D Shapiro, C Zhu, A Lanzara, Synchrotron Radiation News 29 (1), 7-11, 2016

"Imaging nanoscale magnetic and structural correlations in thin SmCo5 films using soft x-ray ptychography", P. 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, Applied Physics Letters, 2016

"Nanoscale Chemical Imaging of an Individual Catalyst Particle with Ptychography", Anna M. Wise, Johanna Nelson Weker, Sam Kalirai, Maryam Farmand, David A. Shapiro, Florian Meirer, and Bert M.
Weckhuysen, ACS Catalysis, 2016.

"Soft X-ray Ptychographic Imaging and Morphological Quantification of Calcium Silicate Hydrates", Sungchul Bae, Rae Taylor, David Shapiro, Peter Denes, John Joseph, Journal of the American Ceramic Society 98 (12), 4090-4095

"Effect of Particle Size, Electronic Connectivity, and Incoherent Nanoscale Domains on the Sequence of Lithiation in LiFePO4 Porous Electrodes", 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, Advanced Materials 27 (42), 6591-6597

"Magnetic studies of magnetotactic bacteria by soft X-ray STXM and ptychography", X. H. Zhu, T.  Tyliszczak, H.-W. Shiu, D. Shapiro, D. A. Bazylinski, U. Lins and A. P. Hitchcock, AIP Conf. Series, AIP 1696, 020002, 2016

"Dependence on crystal size of the nanoscale chemical phase distribution and fracture in LixFePO4", Y.-S. Yu et al, Nano Letters, 15 (7), pp 4282-4288 (2015)


"Alternating Projection, Ptychographic Imaging and Phase Synchronization", Stefano Marchesini, Yu-Chao Tu, Hau-tiengWu, Applied and Computational Harmonic Analysis, 41 (2016), pp. 815-851, technical report LBNL-6583E (2014)

"Chemical composition mapping with nanometre resolution by soft X-ray microscopy", 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, Nature Photonics, Sept. 2014.

"Rank-1 accelerated illumination recovery in scanning diffractive imaging by transparency estimation", Stefano Marchesini, Hau-tieng Wu, Technical report LBNL-6734E 2014.

"Efficient algorithms for Ptychographic Phase Retrieval", Jianliang Qian, Chao Yang, A. Schirotzek, F. Maia, and S. Marchesini, Inverse Problems and Applications, Contemporary Mathematics, 615, 261 2014.

"Augmented projections for ptychographic imaging", Stefano Marchesini, Andre Schirotzek, Chao Yang, Hau-tieng Wu, Filipe Maia, Inverse Problems 29, 115009 2013.

"Alternating Direction Methods for Classical and Ptychographic Phase Retrieval", Zaiwen Wen, Chao Yang, Xin Liu, S. Marchesini, Inverse Problems 28 115010, 2012.

"Iterative Algorithms for Ptychographic Phase Retrieval", C. Yang, J. Qian, A. Schirotzek, F. Maia, S. Marchesini, 2011. technical report LBNL-4598E

"Massively parallel X-ray holography", S. Marchesini, S. Boutet, A. E. Sakdinawat, M. J. Bogan, S. Bajt, A.  Barty, H. N. Chapman, M. Frank, S. P. Hau-Riege, A. Szoke, C. Cui, M. R. Howells, D. A. Shapiro, J. C.  H. Spence, J. W. Shaevitz, J. Y. Lee, J. Hajdu, M. M.  Seibert, Nature Phot. 2, 560 - 563 (2008),

"Phase Retrieval and Saddle-Point Optimization", S.  Marchesini, J. Opt. Soc. Am. A 24,32890-3296 (2007)

"A unified evaluation of iterative projection algorithms for phase retrieval", S. Marchesini, Rev. Sci, Inst. 78, 011301 (2007),

"Phase Aberrations in Diffraction Microscopy", S.  Marchesini, H. N. Chapman, A. Barty, C. Cui, M. R. Howells, J. C. H. Spence, U. Weierstall, A. M. Minor, IPAP Conf. Series 7 pp.380-382, 2006,

"Coherent X-ray Diffractive Imaging; applications and limitations", S. Marchesini, H. N. Chapman, S. P. HauRiege, R. A. London, A. Szoke, H. He, M. R. Howells, H. Padmore, R. Rosen, J. C. H. Spence, U. Weierstall, Optics Express 11(19), 2344 (2003),

"X-ray Fluorescence holography: beyond the diffraction limit", S. Marchesini, C. S. Fadley, PRB 67, 024115 (2003),

"X-ray image reconstruction from a di?raction pattern alone", S. Marchesini, H. He, H. N. Chapman, S. P. Hau-Riege, A. Noy, M. R. Howells, U.  Weierstall, J.C.H. Spence, PRB 68, 140101(R) (2003),

"X-ray microscopy by phase-retrieval methods at the advanced light source", M.R. Howells, H. Chapman, S. Hau-Riege, H. He, S. Marchesini, J. Spence and U.  Weierstall, J. Phys. IV 104 Pr2-557 (2003)

 

 

User Interfaces, Workflows, and Remote Execution

"Xi-cam: A versatile interface for data visualization and analysis", Pandolfi R., et al, submitted to J. Synchrotron Radiation, Jan., 2018.

"On-the-Fly data assessment for high throughput X-ray diffraction measurement", Ren, F., Pandolfi R., Van Campen, D., Hexemer, A., and Mehta, A.: ACS Comb. Sci. 19, 377-385, 2017.

"Nanosurveyor: a framework for real-time data processing", B.J. Daurer, H. Krishnan, T. Perciano, F.  R.N.C. Maia, D.A. Shapiro, J.A. Sethian, S. Marchesini, arXiv:1609.02831. Advanced Structural and 51 Chemical Imaging 20173:7.