Person: Dimiduk, Thomas G.
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Dimiduk
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Thomas G.
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Dimiduk, Thomas G.
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Publication Holographic Microscopy for Soft Matter and Biophysics(2016-09-14) Dimiduk, Thomas G.; Manoharan, Vinothan N.; Needleman, Daniel; Rycroft, ChrisI discuss a series of advancements I have made towards making digital holographic microscopy into a useful tool for experimental scientists in soft-matter physics and biophysics. Digital holograms can be recorded with simple hardware at high speed to capture three-dimensional information about the dynamics of aqueous suspensions of colloidal particles, cells, viruses or other microscopic objects. The challenge of working with holograms is that they map information about the objects non-locally onto an interference pattern. Therefore, post processing is needed to extract the information from a hologram. Traditionally this has been done by reconstructions, effectively shining light back through the hologram to obtain a representation of the recorded objects. More recently Ovryn and Izen (JOSA A 2000) and Lee, Grier and coworkers (Opt. Express 2012) have shown that more precise information can be recovered by physically modelling the light scattering that creates the hologram and solving a constrained inverse-scattering problem to obtain information about the scatterers such as their position or size. This technique gives precise results but requires a scattering model for the objects under observation. It therefore requires significant expertise to set up and implement. In this dissertation I present several advances that improve upon this state-of-the art. First, I present a simple, inexpensive, portable, battery-powered holographic microscope that is suitable for imaging biological samples inside an incubator. Next, I describe a method using a general scattering model called the discrete dipole approximation to analyze holograms of non-spherical particles. Because this analysis is computationally expensive, I present a new method based on analyzing a random subset of the pixels of a hologram. This method, which significantly speeds up computation, is the basis for a framework based on Bayesian inference that gives a more intuitive and rigorous way of specifying prior information and presenting uncertainty in results, which I present at the end. The motivating thread through this thesis is building tools to enable new experiments using holography and making it easier for scientists who are not experts in holography and light scattering to use holography as a tool to do the science that interests them. In support of these goals, I have implemented all of the computational techniques and physical models in an open source library, HoloPy, to make it as easy as possible for other scientists to use them.Publication Random-subset fitting of digital holograms for fast three-dimensional particle tracking(Optical Society of America, 2014) Dimiduk, Thomas G.; Perry, Rebecca Wood; Fung, Jerome; Manoharan, VinothanFitting scattering solutions to time series of digital holograms is a precise way to measure three-dimensional dynamics of microscale objects such as colloidal particles. However, this inverse-problem approach is computationally expensive. We show that the computational time can be reduced by an order of magnitude or more by fitting to a random subset of the pixels in a hologram. We demonstrate our algorithm on experimentally measured holograms of micrometer-scale colloidal particles, and we show that 20-fold increases in speed, relative to fitting full frames, can be attained while introducing errors in the particle positions of 10 nm or less. The method is straightforward to implement and works for any scattering model. It also enables a parallelization strategy wherein random-subset fitting is used to quickly determine initial guesses that are subsequently used to fit full frames in parallel. This approach may prove particularly useful for studying rare events, such as nucleation, that can only be captured with high frame rates over long times.Publication Using the discrete dipole approximation and holographic microscopy to measure rotational dynamics of non-spherical colloidal particles(Elsevier BV, 2014) Wang, Anna; Dimiduk, Thomas G.; Fung, Jerome; Razavi, Sepideh; Kretzschmar, Ilona; Chaudhary, Kundan; Manoharan, VinothanWe present a new, high-speed technique to track the three-dimensional translation and rotation of non-spherical colloidal particles. We capture digital holograms of micrometer-scale silica rods and sub-micrometer-scale Janus particles freely diffusing in water, and then fit numerical scattering models based on the discrete dipole approximation to the measured holograms. This inverse-scattering approach allows us to extract the position and orientation of the particles as a function of time, along with static parameters including the size, shape, and refractive index. The best-fit sizes and refractive indices of both particles agree well with expected values. The technique is able to track the center of mass of the rod to a precision of 35 nm and its orientation to a precision of 1.5°, comparable to or better than the precision of other 3D diffusion measurements on non-spherical particles. Furthermore, the measured translational and rotational diffusion coefficients for the silica rods agree with hydrodynamic predictions for a spherocylinder to within 0.3%. We also show that although the Janus particles have only weak optical asymmetry, the technique can track their 2D translation and azimuthal rotation over a depth of field of several micrometers, yielding independent measurements of the effective hydrodynamic radius that agree to within 0.2%. The internal and external consistency of these measurements validate the technique. Because the discrete dipole approximation can model scattering from arbitrarily shaped particles, our technique could be used in a range of applications, including particle tracking, microrheology, and fundamental studies of colloidal self-assembly or microbial motion.Publication Real-space studies of the structure and dynamics of self-assembled colloidal clusters(Royal Society of Chemistry (RSC), 2012) Perry, Rebecca Wood; Meng, Guangnan; Dimiduk, Thomas G.; Fung, Jerome; Manoharan, VinothanThe energetics and assembly pathways of small clusters may yield insights into processes occurring at the earliest stages of nucleation. We use a model system consisting of micrometer-sized, spherical colloidal particles to study the structure and dynamics of small clusters, where the number of particles is small (N ≤ 10). The particles interact through a short-range depletion attraction with a depth of a few kBT. We describe two methods to form colloidal clusters, one based on isolating the particles in microwells and another based on directly assembling clusters in the gas phase using optical tweezers. We use the first technique to obtain ensemble-averaged probabilities of cluster structures as a function of N. These experiments show that clusters with symmetries compatible with crystalline order are rarely formed under equilibrium conditions. We use the second technique to study the dynamics of the clusters, and in particular how they transition between free-energy minima. To monitor the clusters we use a fast three-dimensional imaging technique, digital holographic microscopy, that can resolve the positions of each particle in the cluster with 30–45 nm precision on millisecond timescales. The real-space measurements allow us to obtain estimates for the lifetimes of the energy minima and the transition states. It is not yet clear whether the observed dynamics are relevant for small nuclei, which may not have sufficient time to transition between states before other particles or clusters attach to them. However, the measurements do provide some glimpses into how systems containing a small number of particles traverse their free-energy landscape.Publication Imaging Multiple Colloidal Particles by Fitting Electromagnetic Scattering Solutions to Digital Holograms(Elsevier BV, 2012) Fung, Jerome; Perry, Rebecca Wood; Dimiduk, Thomas G.; Manoharan, VinothanDigital holographic microscopy is a fast three-dimensional (3D) imaging tool with many applications in soft matter physics. Recent studies have shown that electromagnetic scattering solutions can be fit to digital holograms to obtain the 3D positions of isolated colloidal spheres with nanometer precision and millisecond temporal resolution. Here we describe the results of new techniques that extend the range of systems that can be studied with fitting. We show that an exact multisphere superposition scattering solution can fit holograms of colloidal clusters containing up to six spheres. We also introduce an approximate and computationally simpler solution, Mie superposition, that is valid for multiple spheres spaced several wavelengths or more from one another. We show that this method can be used to analyze holograms of several spheres on an emulsion droplet, and we give a quantitative criterion for assessing its validity.Publication A Simple, Inexpensive Holographic Microscope(2010) Dimiduk, Thomas G.; Kosheleva, Ekaterina Alexeevna; Kaz, David; McGorty, Ryan; Gardel, Emily Jeanette; Manoharan, VinothanWe have built a simple holographic microscope completely out of consumer components. We obtain at least 2.8 micrometer resolution and depth of field greater than 200 micrometers from an instrument costing less than $1000.