Publications

Electronic Structure

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

 

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

 

"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, submitted, 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, 37:A1975--A20, doi: 10.1137/14098973X

 

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

 

"SCDM-k: Localized orbitals for solids via selected columns of the density matrix", A. Damle, L. Lin and L. Ying, submitted http://arxiv.org/abs/1507.03354

 

"Fast algorithms for estimating the absorption spectrum within linear response time-dependent density functional theory", 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

 

"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

 

​"Localized spectrum slicing", L. Lin, , Math. Comp. in press 2016

 

"Randomized estimation of spectral densities of large matrices made accurate", L. Lin, submitted https://arxiv.org/abs/1504.0769

 

"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

 

"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, submitted http://arxiv.org/abs/1408.4926

 "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

 

"A distributed memory parallel algorithm for selected inversion : the symmetric case",M. Jacquelin, L. Lin and C. Yang, ACM Trans. Math. Software in press 2016

 

"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 http://dx.doi.org/10.1088/0953-8984/26/30/305503

 

"A posteriori error estimator for adaptive local basis functions to solve Kohn-Sham density functional theory", J. Kaye, L. Lin and C. Yang, submitted to Communications in Mathematical Sciences, 2014. http://arxiv.org/abs/1401.0920 

 

"Elliptic preconditioner for accelerating the self-consistent field iteration in Kohn-Sham Density Functional Theory", L. Lin and C. Yang, SIAM J. Sci. Comp., 35(5), S277–S298, 2013.  http://epubs.siam.org/doi/abs/10.1137/120880604

 

"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.  http://iopscience.iop.org/0953-8984/25/29/295501/pdf/0953-8984_25_29_295501.pdf. 

 

"Element orbitals for Kohn-Sham density functional theory", L. Lin and L. Ying, Phys. Rev. B, 85:235144, 2012.  http://prb.aps.org/abstract/PRB/v85/i23/e235144 

 

"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,  http://www.sciencedirect.com/science/article/pii/S0021999112001507

 

"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. http://www.sciencedirect.com/science/article/pii/S0021999111006875

 

GISAXS

”Accurate Multi-slice Grazing-Incidence X-ray Simulation",S.V. Venkatakrishnan, Jeffrey Donatelli, Dinesh Kumar, Abhinav Sarje, SunilK. Sinha, Xiaoye S. Li, Alex ander Hexemer,submitted to J. Applied Crystallography, Feb., 2016

 

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 Metting 2015.

 

 "Inverse Modeling Nanostructures from X-ray Scattering Data through Massive Parallelism", A. Sarje, X.S. Li, D. Kumar, S. Venkatakrishnan, A. Hexemer, submitted to 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, CA, May 2015.

 

Scalable Particle Swarm Optimization for Nanostructure Discovery”, A. Sarje, X. Li and A. Hexemer, submitted to 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 International Conference on Parallel Processing (ICPP-2014), Sept 9-14, 2014, Minneapolis, M 

 

"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. Alivisato, ACS Nano, to appear. http://pubs.acs.org/doi/abs/10.1021/nn406127s  

 

An In Situ Grazing Incidence X-Ray Scattering Study of Block Copolymer Thin Films During Solvent Vapor Annealing, ADVANCED MATERIALS Xiaodan Gu, Ilja Gunkel, Alexander Hexemer, Weiyin Gu and Thomas P. Russell, , 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. http://journals.iucr.org/j/issues/2013/06/00/nb5076/index.html

 

"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. http://www.dcs.warwick.ac.uk/~sdh/pmbs13papers/pmbs1430.pdf

 

“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, CA, May 2013. http://on-demand.gputechconf.com/gtc/2013/presentations/S3282-Synchrotron-Light-Source-Analysis.pdf

 

"Massively Parallel X-ray Scattering Simulations'', A. Sarje, X.S. Li, S. Chourou, E. Chan, and A. Hexemer,  Proc. of The International Conference for High Performance Computing, Networking, Storage and Analysis (SC12), Salt Lake City, Nov. 10-16, 2012. http://dl.acm.org/citation.cfm?id=2389059

 

"A SAXS/WAXS/GISAXS Beamline with Multilayer Monochromator", A. Hexemer, W. Bras, J. Glossinger,  E. Schaible, E.Gann, R.Kirian, A.MacDowell, M.Church, B.Rude, H.Padmore, J. Phys. Conf. Ser. 2010, 247, 012007. http://iopscience.iop.org/1742-6596/247/1/012007/pdf/1742-6596_247_1_012007.pdf

Image Analysis and Tomography

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.,  Journal of Microscopy, 2016 (accepted)

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

"Evaluation of Three 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 Pattern 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, Keith Beattie, Joaquin Correa, Eli Dart, Jack R Deslippe, Alexander Hexemer, Harinarayan Krishnan, Alastair A MacDowell, Stefano Marchesini, Simon J Patton, Talita Perciano, James A Sethian, Rune Stromsness, Brian L Tierney,

Craig E Tull, Daniela Ushizima, and Dilworth 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. JOM - The Journal of The Minerals, Metals & Materials Society (TMS), pages 1-10 2016

"Automated Image Segmentation Algorithms for Analysis of 3D Micro-Tomography Data", T. Perciano, D. Ushizima, H. Krishnan, D. Parkinson, N. M. Larson, and F. W. Zok. Submitted to Statistical Analysis and Data Mining, 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., Gürsoy, D., Marone, F., Rivers, M., Parkinson, D. Y., Khan, F., Jacobsen, C, Journal of Synchrotron Radiation, 21(Pt 6), 1224–30. doi:10.1107/S160057751401604X

 

"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., ... others,   In SPIE Optical Engineering+ Applications (p. 92121G–92121G).

 

"CAMERA: The 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 International Symposium on 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

"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, DOI: 10.1002/adfm.201501059.

 

"Real-time Data Intensive Computing", Dilworth Y. Parkinson, Keith Beattie, Xian Chen, Joaquin Correa, Eli Dart, Benedikt J. Daurer, Jack R. Deslippe, Alexander Hexemer, Harinarayan Krishnan, Alastair MacDowell, Filipe R.N.C. Maia, Stefano Marchesini, Howard A. Padmore, Simon J. Patton, Talita Perciano, James A. Sethian, David Shapiro, Rune Stromsness, Nobumichi Tamura, Brian L. Tierney, Craig E. Tull2, Daniela Ushizima, Synchrotron Radiation Instrumentation 2015.  

 

Coded aperture imaging for fluorescent x-rays, 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 - Scientific 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.

 

"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. http://www.springerlink.com/content/l207405uq71u3521/fulltext.pdf 

 

"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. http://www.springerlink.com/content/l207405uq71u3521/fulltext.pdf 

 

"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. http://vis.lbl.gov/~daniela/pubs/C2symposium2012.pdf  

 

"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). http://arxiv.org/abs/1009.1380

 

Material Informatics

"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 diffusion 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, link

 

"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), DOI: 10.1002/adma.201500966

 

"Design of Three-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, http://pubs.acs.org/doi/abs

/10.1021/jp507152j

 

“Exploring frontiers of high surface area metal-organic frameworks“,    R.L. Martin, M. Haranczyk,  Chemical Science 4, pp. 1781-1785, 2013, http://pubs.rsc.org/en/Content/ArticleLanding/2013/SC/C3SC00033H

 

“High accuracy geometric analysis of crystalline porous materials”, M. Pinheiro, R.L. Martin, C.H. Rycroft, M. Haranczyk,  CrystEngComm 15, pp. 7531-7538, 2013.  http://pubs.rsc.org/en/content/articlelanding/2013/ce/c3ce41057a

 

“Insights into Multi-Objective Design of Metal-Organic Frameworks”, R.L. Martin, M. Haranczyk , Crystal Growth and Design 13, pp. 4208-4212,  2013. http://pubs.acs.org/doi/abs/10.1021/cg401240f.

 

 “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.  http://www.sciencedirect.com/science/article/pii/S1387181111003738.

 

“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,  http://pubs.acs.org/doi/abs/10.1021/ci200386x.

 

"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, 1094342011431591

 

"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, http://pubs.acs.org/doi/abs/10.1021/ct100433z

 

 “Navigating molecular worms inside chemical labyrinths”, Haranczyk, M. and Sethian, J.A., Proc. National Acad. Sciences, 106,  pp. 1472-21477, 2009.   http://www.pnas.org/content/106/51/2147

Nanocrystallography, Fluctuation Scattering, and Single Particle Imaging

 "Three-dimensional structure determination from membrane-embedded proteins via multi-wavelength
fluctuation X-ray scattering"Donatelli J.J., Saldin D.K., and Zwart P.H., 2016,(In preparation)


"Angular cross-correlation analysis of x-ray scattering measured from single viruses with an x-ray free-electron laser",Kurta R.P. et al.,,  (In preparation)


"Simultaneous determination of state, orientation, intensity, and phase from a sparse set of single-particle diffraction images" ,Donatelli J.J., Sethian J.A., and Zwart P.H, (Submitted, Proc. Nat. Acad. Sciences)

 

"Macromolecular fluctuation X-ray scattering with a free electron laser", Malbmerberg, et. al.,  2016, (In preparation)

 

"Signatures of coherence in fluctuation X-ray scattering data" (In preparation), Malmerberg E.L., Poon B.K., Donatelli J.J., and Zwart P.H

"The 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 Gühr, J Hajdu, J Hastings, SP Hau-Riege, Z Huang,
EE Lattman, 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, 201513738, 2015. http://www.pnas.org/content/early/2015/07/30/1513738112.full.pdf?sid=3c462e7b-ae59-491e-9d6f-3ea2c25c4597.

 

"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. Lett. 106, 115501 (2011). (viewpoint in Physics). (ALS highlight) link

 

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). link

 

“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. http://www.pnas.org/content/111/2/593.full.pdf+html

 

 “Phasing of coherent femtosecond X-ray diffraction from size-varying nanocrystals, 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. http://dx.doi.org/10.1364/OE.19.002866 .

 

 “Compressive auto-indexing in femtosecond nanocrystallography”, F. R. N. C. Maia, C. Yang, and S. Marchesini, Ultramicroscopy 111(7), 807-811. 2011.  http://arxiv.org/abs/1011.3072

 

 "Orientation determination for 3D single molecule diffraction imaging", Chao Yang, Zhen Wang, and Stefano Marchesini, Proc. SPIE Vol. 7800, 78000P (2010). http://dx.doi.org/10.1117/12.860810

Ptychography

"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., submitted to PNAS, 2016.

"Nanosurveyor: a framework for real-time data processing", Benedikt J. Daurer, Hari Krishnan, Talita Perciano, Filipe R.N.C., Maia, David A. Shapiro, James A. Sethian, Stefano Marchesini, arXiv:1609.02831 , submitted for publication

"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

 

"Near-edge X-ray Refraction Fine Structure Microscopy of Nano-materials", Farmand, M., et al, submitted to Nature Communications, 2016

 

"Three dimensional localization of battery reactions using soft X-ray tomography", Y.-S. Yu, et al, submitted to Nature Materials, 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, in press, 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, in press, 2016, link

 

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

 

"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, link

 

"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, doi: 10.1063/1.4937496, link

 

 

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-tieng Wu, Applied and Computational Harmonic Analysis, 41 (2016), pp. 815-851, technical report LBNL-6583E (2014)  http://arxiv.org/abs/1402.0550

 

"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, Tony Warwick, Lee Lisheng Yang & Howard A. Padmore, Nature Photonics, Sept. 2014.   http://dx.doi.org/10.1038/nphoton.2014.207. math.lbl.gov/~sethian/shapiro.nphoton.2014.207.pdf 

 

"Rank-1 accelerated illumination recovery in scanning diffractive imaging by transparency estimation"  Stefano Marchesini, Hau-tieng Wu, Technical report LBNL-6734E 2014. http://arxiv.org/abs/1408.1922 

 

“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. link

 

Augmented projections for ptychographic imaging”, Stefano Marchesini, Andre Schirotzek, Chao Yang, Hau-tieng Wu, Filipe Maia, Inverse Problems 29, 115009 2013.  http://dx.doi.org/10.1088/0266-5611/29/11/115009 

 

“Alternating Direction Methods for Classical and Ptychographic Phase Retrieval”, Zaiwen Wen, Chao Yang, Xin Liu, S. Marchesini, Inverse Problems 28 115010, 2012. http://dx.doi.org/10.1088/0266-5611/28/11/115010

 

Iterative Algorithms for Ptychographic Phase Retrieval”, C. Yang, J. Qian, A. Schirotzek, F. Maia, S. Marchesini, 2011. technical report LBNL-4598E http://arxiv.org/abs/1105.5628 

 

Ab initio compressive phase retrieval, S. Marchesini,  [doi:10.1017/S1431927609099620]. [arxiv:0809.2006]. 

 

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), [arXiv:0801.4969].

 

"Phase Retrieval and Saddle-Point Optimization", S. Marchesini, J. Opt. Soc. Am. A 24,32890-3296 (2007), [arXiv:physics/0611233].

 

A unified evaluation of iterative projection algorithms for phase retrieval, S. Marchesini, Rev. Sci, Inst. 78, 011301 (2007), [arXiv:physics/0603201].

 

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, [arXiv:physics/0510033].

 

Coherent X-ray Diffractive Imaging; applications and limitations, S. Marchesini, H. N. Chapman, S. P. Hau-Riege, 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), [arXiv:physics/0308064]. 

 

X-ray fluorescence holography: beyond the diffraction limit, S. Marchesini, C. S. Fadley, PRB 67, 024115 (2003), arXiv:cond-mat/0202064

 

X-ray image reconstruction from a diffraction 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), [arXiv:physics/0306174]. -see e.g.  US7672430 patent AREA X-RAY OR UV CAMERA SYSTEM FOR  HIGH'INTENSITY BEAMS for applications.

 

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)  link