Kyle DouglassÉcole Polytechnique Fédérale de Lausanne | EPFL · Institute of Physics of Biological Systems
Kyle Douglass
PhD Optics
About
31
Publications
5,313
Reads
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620
Citations
Introduction
I develop microscopy and other optical methodologies for sensing applications in soft matter.
Currently, this involves developing new superresolution fluorescence microscopy techniques for understanding the structure of chromatin and other organelles.
Skills and Expertise
Additional affiliations
November 2013 - present
Position
- PostDoc Position
Description
- I develop new optical and computational methods for super-resolution fluorescence microscopy. My specialization is in chromatin imaging and conformational studies.
August 2007 - September 2013
Position
- Research Assistant
Description
- I developed several optics-based diagnostic tools for sensing in biological, soft matter, and other complex systems. This included the development of a fiber optic catheter for sensing blood coagulation in vivo.
June 2006 - August 2006
Position
- Student
Description
- I created a visible-light spectrometer to work in a vacuum system. The spectrometer aided the alignment of a Ti-Sapphire laser beam for creating high harmonically generated X-rays from plasmas.
Education
August 2007 - September 2013
CREOL, The College of Optics & Photonics
Field of study
- Optics
August 2003 - May 2007
Publications
Publications (31)
Self-assembling complex systems exhibit properties that involve a broad spectrum of thermal, structural, morphological, and optical transitions. Various techniques have been used to assess different aspects of the phase transitions in these complex systems. However, because inherent technical constraints, structural information is usually provided...
We demonstrate that a non-vanishing interaction force exists between pairs of
induced dipoles in random, statistically stationary electromagnetic field. This
new type of optical binding force leads to long-range interaction between
dipolar particles even when placed in spatially incoherent fields. We also
discuss several unique features of dipole-d...
Active media are complex systems driven by both thermal fluctuations and
additional energy sources and are encountered in a variety of phenomena
including mobile bacteria, protein diffusion or turbulent flows.
However, studying the non-equilibrium dynamics of active media is often
difficult because of their size and complexity. Here, we demonstrate...
Super-resolution microscopies have become an established tool in biological research. However, imaging throughput remains a main bottleneck in acquiring large datasets required for quantitative biology. Here we describe multifocal flat illumination for field-independent imaging (mfFIFI). By integrating mfFIFI into an instant structured illumination...
Super-resolution microscopies, which allow features below the diffraction limit to be resolved, have become an established tool in biological research. However, imaging throughput remains a major bottleneck in using them for quantitative biology, which requires large datasets to overcome the noise of the imaging itself and to capture the variabilit...
Chromatin is organized into topologically associating domains (TADs) enriched in distinct histone marks. In cancer, gain-of-function mutations in the gene encoding the enhancer of zeste homolog 2 protein (EZH2) lead to a genome-wide increase in histone-3 Lys27 trimethylation (H3K27me3) associated with transcriptional repression. However, the effect...
Super-resolution fluorescence microscopy improves spatial resolution, but this comes at a loss of image throughput and presents unique challenges in identifying optimal acquisition parameters. Microscope automation routines can offset these drawbacks, but thus far have required user inputs that presume a priori knowledge about the sample. Here, we...
Single-particle reconstruction (SPR) from electron microscopy (EM) images is widely used in structural biology, but it lacks direct information on protein identity. To address this limitation, we developed a computational and analytical framework that reconstructs and coaligns multiple proteins from 2D super-resolution fluorescence images. To demon...
Super-resolution fluorescence microscopy improves spatial resolution, but this comes at a loss of image throughput and presents unique challenges in identifying optimal acquisition parameters. Microscope automation routines can offset these drawbacks, but thus far have required user inputs that presume a priori knowledge about the sample. Here, we...
Super-resolution fluorescence microscopy (SRM) is increasingly being applied as a complementary method to resolve the organization of large biomolecular assemblies. One of its main advantages is that it provides information on protein organization and identity simultaneously, within the native cellular milieu. It also extends the accessible range o...
Single-particle reconstruction (SPR) from electron microscopy images is widely used in structural biology, but lacks direct information on protein identity. To address this limitation, we developed a computational and analytical framework that reconstructs and co-aligns multiple proteins from 2D super-resolution fluorescence images. We demonstrate...
Telomeres are specialized nucleoprotein structures that protect chromosome ends from DNA damage response (DDR) and DNA rearrangements. The telomeric shelterin protein TRF2 suppresses the DDR, and this function has been attributed to its abilities to trigger t-loop formation or prevent massive decompaction and loss of density of telomeric chromatin....
Biological processes are inherently multi-scale, and supramolecular complexes at the nanoscale determine changes at the cellular scale and beyond. Single-molecule localization microscopy (SMLM) techniques have been established as important tools for studying cellular features with resolutions of the order of around 10 nm. However, in their current...
Three-dimensional (3D) localization-based super-resolution microscopy (SR) requires correction of aberrations to accurately represent 3D structure. Here we show how a depth-dependent lateral shift in the apparent position of a fluorescent point source, which we term `wobble`, results in warped 3D SR images and provide a software tool to correct thi...
We explore the nature of forces induced by random electromagnetic fields on microscopic polarizable matter. Particle-field coupling is considered for a single and multiple interacting particles. We also discuss new experiments for controlling disordered systems.
Schwann cell motility was observed on laminin-coated quartz cylinders with different curvatures over an 18 hour period. A new analysis based on difference images helped to determine the minimal radius of curvature, 46 μm, which restricted motility along the cylinder axis. The migration speed, measured by calculating differences between successive i...
The light-matter interaction in complex media allows for selective excitation into nonequilibrium states. We experimentally observe controllable superdiffusion of particles in strong, dynamic volume speckle fields and demonstrate models for coupled, active media.
In the Spring Semester of 2011, Univ. of Central Florida's CREOL
introduced an elective course in Optomechanical Design. In addition to
homework assignments and exams, one component of the course grade was a
design project. Rather than the traditional "assigned" project, the
instructor experimented with a novel research-centric approach.
Specifical...
Two different transport regimes of light are observed in reflection from the same disordered photonic crystal. A model based on the scaling theory of localization explains the behavior of the path length-resolved reflection at two different probing wavelengths. Our results demonstrate the continuous renormalization of the photon diffusion coefficie...
We introduce and demonstrate a method for expanding the field of view of a typical imaging system by multiplexing images encoded onto different polarization states and recovering them from a limited number of measurements.
We demonstrate the concept of stochastic resonance in optically induced rotations and discuss its applications for optimizing the effects of optical torques on small anisotropic particles and optically bound systems of particles.
Two different transport regimes of light are observed in the same medium and are explained by the scaling theory of localization. Our results constitute the first demonstration of continuous renormalization of the optical diffusion coefficient.
Based on optical-path-length spectroscopy, we present a method for determining optical diffusion coefficients that does not require a priori knowledge about the physical properties of inherent interfaces. Comparisons are made with both standard theoretical estimates for bulk diffusion and with traditional approaches relying on surface corrections.
We introduce and demonstrate experimentally a method for expanding the field of view of an imaging system by multiplexing polarimetrically encoded images and decoding them with a limited a number of measurements.
The interaction between coherent waves and random media is a complicated, deterministic process that is usually examined upon ensemble averaging. The result of one realization of the interaction process depends on the specific disorder present in an experimentally controllable interaction volume. We show that this randomness can be quantified and s...
Random media with identical averaged properties may differ greatly in their detailed structure. These differences manifest in fluctuations between realizations. We examine fluctuations in path length and polarimetric quantities as a means of structural differentiation.
Questions
Question (1)
I have found an analytical expression for the radius of gyration for a wormlike chain that ignores excluded volume effects in Zhao, Sun, and Zhang, "Statistics of wormlike chains. I. Properties of a single chain", J. Chem. Phys. 106, 2520 (1997). In this work, they demonstrated that the radius of gyration (squared) and the mean-squared end-to-end distance scale with the contour length of the polymer.
I also know that with excluded volume effects included in the model, the scaling exponent for the mean-squared end-to-end distance changes from 1 to 6/5 in the limit of 0 persistence length.
Would someone be able to provide a citation to an analytical expression for the radius of gyration of the worm-like chain with excluded volume effects? I suspect it will also scale like 6/5 with the contour length of the chain, but I may be wrong.
Thanks!
