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Publications

Toward unsupervised single-shot diffractive imaging of heterogeneous particles using X-ray free-electron lasers

Cornell Affiliated Author(s)
Author
H.J. Park
N.D. Loh
R.G. Sierra
C.Y. Hampton
D. Starodub
A.V. Martin
A. Barty
A. Aquila
J. Schulz
J. Steinbrener
R.L. Shoeman
L. Lomb
S. Kassemeyer
C. Bostedt
J. Bozek
S.W. Epp
B. Erk
R. Hartmann
D. Rolles
A. Rudenko
B. Rudek
L. Foucar
N. Kimmel
G. Weidenspointner
G. Hauser
P. Holl
E. Pedersoli
M. Liang
M.S. Hunter
L. Gumprecht
N. Coppola
C. Wunderer
H. Graafsma
F.R.N.C. Maia
T. Ekeberg
M. Hantke
H. Fleckenstein
H. Hirsemann
K. Nass
H.J. Tobias
G.R. Farquar
W.H. Benner
S.P. Hau-Riege
C. Reich
A. Hartmann
H. Soltau
S. Marchesini
S. Bajt
M. Barthelmess
L. Strueder
J. Ullrich
P. Bucksbaum
M. Frank
I. Schlichting
H.N. Chapman
M.J. Bogan
V. Elser
Abstract

Single shot diffraction imaging experiments via X-ray freeelectron lasers can generate as many as hundreds of thousands of diffraction patterns of scattering objects. Recovering the real space contrast of a scattering object from these patterns currently requires a reconstruction process with user guidance in a number of steps, introducing severe bottlenecks in data processing. We present a series of measures that replace user guidance with algorithms that reconstruct contrasts in an unsupervised fashion.

Journal
Optics Express
Date Published
Group (Lab)
Veit Elser Group

Direct phasing of nanocrystal diffraction

Cornell Affiliated Author(s)
Author
V. Elser
Abstract

Recent experiments at free-electron laser X-ray sources have been able to resolve the intensity distributions about Bragg peaks in nanocrystals of large biomolecules. Information derived from small shifts in the peak positions augment the Bragg samples of the particle intensity with samples of its gradients. Working on the assumption that the nanocrystal is entirely generated by lattice translations of a particle, an algorithm is developed that reconstructs the particle from intensities and intensity gradients.

Journal
Acta Crystallographica Section A: Foundations of Crystallography
Date Published
Funding Source
DE-FG02-11ER16210
Group (Lab)
Veit Elser Group

Hierarchical porous polymer scaffolds from block copolymers

Cornell Affiliated Author(s)
Author
H. Sai
K.W. Tan
K. Hur
E. Asenath-Smith
R. Hovden
Y. Jiang
M. Riccio
D.A. Muller
V. Elser
L.A. Estroff
Sol Gruner
U. Wiesner
Abstract

Hierarchical porous polymer materials are of increasing importance because of their potential application in catalysis, separation technology, or bioengineering. Examples for their synthesis exist, but there is a need for a facile yet versatile conceptual approach to such hierarchical scaffolds and quantitative characterization of their nonperiodic pore systems.

Journal
Science
Date Published
Research Area
Group (Lab)
Sol M. Gruner Group
Veit Elser Group

Magnetic polarons in two-component hard-core bosons

Cornell Affiliated Author(s)
Author
Y. Yanay
E.J. Mueller
V. Elser
Abstract

We use a high-temperature expansion to explore spin correlations around a single hole in a two-dimensional lattice filled with a hard-core two-component bose gas. We find that the spins around the hole develop ferromagnetic order and quantify the degree of polarization at temperatures of the order of the hopping energy, finding a measurably nonzero polarization. We also discuss the effect of fixing the overall magnetization of the system for finite-sized systems. © 2013 American Physical Society.

Journal
Physical Review A - Atomic, Molecular, and Optical Physics
Date Published
Group (Lab)
Veit Elser Group

Recovering structure from many low-information 2-D images of randomly-oriented samples

Cornell Affiliated Author(s)
Author
H.T. Philipp
K. Ayyer
M.W. Tate
V. Elser
Sol Gruner
Abstract

New sources and detectors are allowing scientists to look at matter with finer spatial and temporal resolutions. These experiments can produce data that are a series of severely Poisson limited snap-shots of randomly oriented samples. An extreme case of this is destructive imaging of single particles with an X-ray free-electron laser-many frames are needed for a reconstruction, but there is no a priori information associated with the frames about particle orientation.

Conference Name
Conference
Date Published
Group (Lab)
Sol M. Gruner Group
Veit Elser Group

Solving structure with sparse, randomly-oriented x-ray data

Cornell Affiliated Author(s)
Author
H.T. Philipp
K. Ayyer
M.W. Tate
V. Elser
Sol Gruner
Abstract

Single-particle imaging experiments of biomolecules at x-ray free-electron lasers (XFELs) require processing hundreds of thousands of images that contain very few x-rays. Each low-fluence image of the diffraction pattern is produced by a single, randomly oriented particle, such as a protein. We demonstrate the feasibility of recovering structural information at these extremes using low-fluence images of a randomly oriented 2D x-ray mask.

Journal
Optics Express
Date Published
Group (Lab)
Sol M. Gruner Group
Veit Elser Group

Time-resolved protein nanocrystallography using an X-ray free-electron laser

Cornell Affiliated Author(s)
Author
A. Aquila
M.S. Hunter
R.B. Doak
R.A. Kirian
P. Fromme
T.A. White
J. Andreasson
D. Arnlund
S. Bajt
T.R.M. Barends
M. Barthelmess
M.J. Bogan
C. Bostedt
H. Bottin
J.D. Bozek
C. Caleman
N. Coppola
J. Davidsson
D.P. DePonte
V. Elser
S.W. Epp
B. Erk
H. Fleckenstein
L. Foucar
M. Frank
R. Fromme
H. Graafsma
I. Grotjohann
L. Gumprecht
J. Hajdu
C.Y. Hampton
A. Hartmann
R. Hartmann
S.P. Hau-Riege
G. Hauser
H. Hirsemann
P. Holl
J.M. Holton
A. Hömke
L. Johansson
N. Kimmel
S. Kassemeyer
F. Krasniqi
K.-U. Kühnel
M. Liang
L. Lomb
E. Malmerberg
S. Marchesini
A.V. Martin
F.R.N.C. Maia
M. Messerschmidt
K. Nass
C. Reich
R. Neutze
D. Rolles
B. Rudek
A. Rudenko
I. Schlichting
C. Schmidt
K.E. Schmidt
J. Schulz
Marvin Seibert
R.L. Shoeman
R. Sierra
H. Soltau
D. Starodub
F. Stellato
S. Stern
L. Strüder
N. Timneanu
J. Ullrich
X. Wang
G.J. Williams
G. Weidenspointner
U. Weierstall
C. Wunderer
A. Barty
J.C.H. Spence
H.N. Chapman
Abstract

We demonstrate the use of an X-ray free electron laser synchronized with an optical pump laser to obtain X-ray diffraction snapshots from the photoactivated states of large membrane protein complexes in the form of nanocrystals flowing in a liquid jet. Light-induced changes of Photosystem I-Ferredoxin co-crystals were observed at time delays of 5 to 10 μs after excitation. The result correlates with the microsecond kinetics of electron transfer from Photosystem I to ferredoxin.

Journal
Optics Express
Date Published
Group (Lab)
Veit Elser Group

Self-terminating diffraction gates femtosecond X-ray nanocrystallography measurements

Cornell Affiliated Author(s)
Author
A. Barty
C. Caleman
A. Aquila
N. Timneanu
L. Lomb
T.A. White
J. Andreasson
D. Arnlund
S. Bajt
T.R.M. Barends
M. Barthelmess
M.J. Bogan
C. Bostedt
J.D. Bozek
R. Coffee
N. Coppola
J. Davidsson
D.P. DePonte
R.B. Doak
T. Ekeberg
V. Elser
S.W. Epp
B. Erk
H. Fleckenstein
L. Foucar
P. Fromme
H. Graafsma
L. Gumprecht
J. Hajdu
C.Y. Hampton
R. Hartmann
A. Hartmann
G. Hauser
H. Hirsemann
P. Holl
M.S. Hunter
L. Johansson
S. Kassemeyer
N. Kimmel
R.A. Kirian
M. Liang
F.R.N.C. Maia
E. Malmerberg
S. Marchesini
A.V. Martin
K. Nass
R. Neutze
C. Reich
D. Rolles
B. Rudek
A. Rudenko
H. Scott
I. Schlichting
J. Schulz
Marvin Seibert
R.L. Shoeman
R.G. Sierra
H. Soltau
J.C.H. Spence
F. Stellato
S. Stern
L. Strüder
J. Ullrich
X. Wang
G. Weidenspointner
U. Weierstall
C.B. Wunderer
H.N. Chapman
Abstract

X-ray free-electron lasers have enabled new approaches to the structural determination of protein crystals that are too small or radiation-sensitive for conventional analysis. For sufficiently short pulses, diffraction is collected before significant changes occur to the sample, and it has been predicted that pulses as short as 10 fs may be required to acquire atomic-resolution structural information.

Journal
Nature Photonics
Date Published
Funding Source
0417142
MCB-1021557
1R01GM095583-01
1U54GM094625-01
DE-AC52-07NA27344
Group (Lab)
Veit Elser Group

Three-dimensional structure from intensity correlations

Cornell Affiliated Author(s)
Author
V. Elser
Abstract

We develop the analysis of x-ray intensity correlations from dilute ensembles of identical particles in a number of ways. Firstly, we show that the three-dimensional (3D) particle structure can be determined if the particles can be aligned with respect to a single axis having a known angle with respect to the incident beam. Secondly, we clarify the phase problem in this setting and introduce a data reduction scheme that assesses the integrity of the data even before particle reconstruction is attempted.

Journal
New Journal of Physics
Date Published
Group (Lab)
Veit Elser Group

Upper Bound on the Packing Density of Regular Tetrahedra and Octahedra

Cornell Affiliated Author(s)
Author
S. Gravel
V. Elser
Y. Kallus
Abstract

Aristotle contended that (regular) tetrahedra tile space, an opinion that remained widespread until it was observed that non-overlapping tetrahedra cannot subtend a solid angle of 4π around a point if this point lies on a tetrahedron edge. From this 15th century argument, we can deduce that tetrahedra do not tile space but, more than 500 years later, we are unaware of any known non-trivial upper bound to the packing density of tetrahedra. In this article, we calculate such a bound.

Journal
Discrete and Computational Geometry
Date Published
Group (Lab)
Veit Elser Group