Building Proteins in a Day: Efficient 3D Molecular Reconstruction

Discovering the 3D atomic structure of molecules such as proteins and viruses is a fundamental research problem in biology and medicine. Electron Cryomicroscopy (Cryo-EM) is a promising vision-based technique for structure estimation which attempts to reconstruct 3D structures from 2D images. This paper addresses the challenging problem of 3D reconstruction from 2D Cryo-EM images. A new framework for estimation is introduced which relies on modern stochastic optimization techniques to scale to large datasets. We also introduce a novel technique which reduces the cost of evaluating the objective function during optimization by over five orders or magnitude. The net result is an approach capable of estimating 3D molecular structure from large scale datasets in about a day on a single workstation.Comment: To be presented at IEEE Conference on Computer Vision and Pattern Recognition (CVPR) 201

Multiple Time Scales in Diffraction Measurements of Diffusive Surface Relaxation

We grew SrTiO3 on SrTiO3 (001) by pulsed laser deposition, using x-ray scattering to monitor the growth in real time. The time-resolved small angle scattering exhibits a well-defined length scale associated with the spacing between unit cell high surface features. This length scale imposes a discrete spectrum of Fourier components and rate constants upon the diffusion equation solution, evident in multiple exponential relaxation of the "anti-Bragg" diffracted intensity. An Arrhenius analysis of measured rate constants confirms that they originate from a single activation energy.Comment: 4 pages, 3 figure

Spatial oscillations in the spontaneous emission rate of an atom inside a metallic wedge

A method of images is applied to study the spontaneous emission of an atom inside a metallic wedge with an opening angle of $\pi/N$, where N is an arbitrary positive integer. We show the method of images gives a rate formula consistent with that from Quantum Electrodynamics. Using the method of images, we show the correspondence between the oscillations in the spontaneous emission rate and the closed-orbits of emitted photon going away and returning to the atom inside the wedge. The closed-orbits can be readily constructed using the method of images and they are also extracted from the spontaneous emission rate.Comment: 8 figure

Observed Effects of a Changing Step-Edge Density on Thin-Film Growth Dynamics

We grew SrTiO3 on SrTiO3 [001] by pulsed laser deposition, while observing x-ray diffraction at the (0 0 .5) position. The drop dI in the x-ray intensity following a laser pulse contains information about plume-surface interactions. Kinematic theory predicts dI/I = -4sigma(1-sigma), so that dI/I depends only on the amount of deposited material sigma. In contrast, we observed experimentally that |dI/I| < 4sigma(1-sigma), and that dI/I depends on the phase of x-ray growth oscillations. The combined results suggest a fast smoothing mechanism that depends on surface step-edge density.Comment: 4 figure

X-ray scattering from surfaces: discrete and continuous components of roughness

Incoherent surface scattering yields a statistical description of the surface, due to the ensemble averaging over many independently sampled volumes. Depending on the state of the surface and direction of the scattering vector relative to the surface normal, the height distribution is discrete, continuous, or a combination of the two. We present a treatment for the influence of multimodal surface height distributions on Crystal Truncation Rod scattering. The effects of a multimodal height distribution are especially evident during in situ monitoring of layer-by-layer thin-film growth via Pulsed Laser Deposition. We model the total height distribution as a convolution of discrete and continuous components, resulting in a broadly applicable parameterization of surface roughness which can be applied to other scattering probes, such as electrons and neutrons. Convolution of such distributions could potentially be applied to interface or chemical scattering. Here we find that this analysis describes accurately our experimental studies of SrTiO3 annealing and homoepitaxial growth.Comment: 15 pages, 7 figure

Seeking children's perspectives: a respectful layered research approach

This article discusses why researchers and educators might choose to seek children's perspectives. It also highlights some of the key considerations when seeing children as having the right to contribute to decisions that affect them. The article draws on findings from a study that used pedagogically oriented methods for researching three- and four-year-old children's perspectives about outdoor spaces in the early childhood setting they attended. The article discusses the possibilities and practicalities of this research approach for both research and pedagogy. Examples are provided for others who may be considering working/researching in these ways