Publications
A network that learns Strassen multiplication
We study neural networks whose only non-linear components are multipliers, to test a new training rule in a context where the precise representation of data is paramount. These networks are challenged to discover the rules of matrix multiplication, given many examples. By limiting the number of multipliers, the network is forced to discover the Strassen multiplication rules. This is the mathematical equivalent of finding low rank decompositions of the n x n matrix multiplication tensor, Mn.
Protein crystal structure from non-oriented, single-axis sparse X-ray data
X-ray free-electron lasers (XFELs) have inspired the development of serial femtosecond crystallography (SFX) as a method to solve the structure of proteins. SFX datasets are collected from a sequence of protein microcrystals injected across ultrashort X-ray pulses. The idea behind SFX is that diffraction from the intense, ultrashort X-ray pulses leaves the crystal before the crystal is obliterated by the effects of the X-ray pulse.
Exotic Self-trapped States of an Electron in Superfluid Helium
We explore the possibility that the fast and exotic negative ions in superfluid helium are electrons bound to quantized vortex structures, the simplest being a ring. In the states we consider, the electron energy is only slightly below the conduction band minimum of bulk helium. To support our proposal, we present two calculations. In the first, we show that the electron pressure on the vortex core is insufficient to cavitate the helium and form an electron bubble.
The linac coherent light source single particle imaging road map
Intense femtosecond x-ray pulses from free-electron laser sources allow the imaging of individual particles in a single shot. Early experiments at the Linac Coherent Light Source (LCLS) have led to rapid progress in the field and, so far, coherent diffractive images have been recorded from biological specimens, aerosols, and quantum systems with a few-tens-of-nanometers resolution. In March 2014, LCLS held a workshop to discuss the scientific and technical challenges for reaching the ultimate goal of atomic resolution with single-shot coherent diffractive imaging.
Erratum to: Indivisibility of Electron Bubbles in Helium [Journal of Low Temperature Physics, 123, 1, 2, (2001), DOI:10.1023/A:1017534129860]
Determination of crystallographic intensities from sparse data
X-ray serial microcrystallography involves the collection and merging of frames of diffraction data from randomly oriented protein microcrystals. The number of diffracted X-rays in each frame is limited by radiation damage, and this number decreases with crystal size. The data in the frame are said to be sparse if too few X-rays are collected to determine the orientation of the microcrystal. It is commonly assumed that sparse crystal diffraction frames cannot be merged, thereby setting a lower limit to the size of microcrystals that may be merged with a given source fluence.
Compressed sensing, sparsity, and the reliability of tomographic reconstructions
Phonon contribution to the entropy of hard-sphere crystals
Comparing the entropies of hard spheres in the limit of close packing, for different stacking sequences of the hexagonal layers, has been a challenge because the differences are so small. Here we present a method based on a "sticky-sphere" model by which the system interpolates between hard spheres in one limit and a harmonic crystal in the other. For the fcc and hcp stackings we have calculated the entropy difference in the harmonic (sticky) limit, as well as the differences in the free energy change upon removing the stickiness in the model.
Breaking the Crowther limit: Combining depth-sectioning and tilt tomography for high-resolution, wide-field 3D reconstructions
To date, high-resolution (<1. nm) imaging of extended objects in three-dimensions (3D) has not been possible. A restriction known as the Crowther criterion forces a tradeoff between object size and resolution for 3D reconstructions by tomography. Further, the sub-Angstrom resolution of aberration-corrected electron microscopes is accompanied by a greatly diminished depth of field, causing regions of larger specimens (>6. nm) to appear blurred or missing.
Real-Space x-ray tomographic reconstruction of randomly oriented objects with sparse data frames
Schemes for X-ray imaging single protein molecules using new x-ray sources, like x-ray free electron lasers (XFELs), require processing many frames of data that are obtained by taking temporally short snapshots of identical molecules, each with a random and unknown orientation. Due to the small size of the molecules and short exposure times, average signal levels of much less than 1 photon/pixel/frame are expected, much too low to be processed using standard methods. One approach to process the data is to use statistical methods developed in the EMC algorithm (Loh & Elser, Phys. Rev.