Search

Your search keyword '"Burnham, Daniel R."' showing total 40 results
Start Over Author "Burnham, Daniel R."
40 results on '"Burnham, Daniel R."'

3. Microscopic applications of holographic beam shaping and studies of optically trapped aerosols

Author

Burnham, Daniel R. and McGloin, David

Subjects
530.0724, Optical manipulation, Aerosols
Abstract

This thesis has two themes. Firstly, it concerns the original application of holographic beam shaping, employed through the methods associated with optical manipulation, to three microscopic fields of research. Secondly, it studies the optical trapping of aerosol droplets through experimentation and computational modelling. The aims are to not only provide an account of the work carried out but also a base for future researchers and students. Chapter 1 provides an introduction to the field of optical manipulation and the relevance of my studies. Chapter 2 outlines the construction of an optical tweezers which is the basis of advanced experimental work described in later chapters. It also overviews how optical tweezers operate and are quantified. In chapter 3 I describe how beam shaping is implemented for my investigations with a spatial light modulator and phase-only holograms. I detail the algorithms and software written before discussing their performance and finally the optimisation of the apparatus. Chapter 4 describes three original applications of beam shaping, including the trapping and coagulation of multiple aerosols, the manipulation of filamentous fungi hyphal tips and novel digital microfluidic operations using thermocapillary forces. I also lay down preliminary results for observing orbital angular acceleration using beams carrying orbital angular momentum. To study single optically trapped aerosols I use two methods. Firstly, their Brownian motion is investigated through sub diffraction limit position detection. Unique results in optical tweezers are shown with liquid droplets behaving as under-damped Brownian oscillators. Through these studies I demonstrate a new technique for sizing trapped aerosols, with significant advantages over current methods. I also show that the droplets can be be parametrically excited which can result in trap failure. Secondly, in chapter 6, I use a theoretical model to describe the forces imparted to a trapped droplet. I extend current theories to include the effects of a three medium focal region to accurately describe airborne optical traps. The work qualitatively explains the phenomena observed experimentally. The work contained here leaves much scope for future investigations, for which I provide an overview in chapter 7.

Published
2009

9. Bioconjugation of ultrabright semiconducting polymer dots for specific cellular targeting

Author

Changfeng Wu, Schneider, Thomas, Zeigler, Maxwell, Jiangbo Yu, Schiro, Perry G., Burnham, Daniel R., McNeill, Jason D., and Chiu, Daniel T.

Subjects
Fluorescence -- Measurement, Polymers -- Structure, Polymers -- Chemical properties, Polymers -- Electric properties, Semiconductors -- Chemical properties, Semiconductors -- Electric properties, Semiconductors -- Optical properties, Surface chemistry -- Analysis, Chemistry
Abstract

A powerful conjugation method is described for overcoming the challenge of controlling the surface chemistry and bioconjugation of semiconducting polymer dots (Pdots). The successful bioconjugation of the ultrabright nanoparticles have provided an opportunity to apply versatile semiconducting polymers to various fluorescence measurements in modern biology and biomedicine.

Published
2010

18. Highly Parallel Magnetic Tweezers for the Study of DNA-Protein Interactions

Author

Burnham, Daniel R., primary, De Vlaminck, Iwijn, additional, Henighan, Thomas, additional, van Loenhout, Marijn T.J., additional, Pfeiffer, Indriati, additional, Huijts, Julius, additional, Kerssemakers, Jacob, additional, van Langen-Suurling, Anja, additional, van der Drift, Emil, additional, Wyman, Claire, additional, and Dekker, Cees, additional

Published
2012
Full Text
View/download PDF

36. Annealing helicase HARP closes RPA-stabilized DNA bubbles non-processively

Author

Burnham, Daniel R., Nijholt, Bas, De Vlaminck, Iwijn, Quan, Jinhua, Yusufzai, Timur, and Dekker, Cees

Abstract

We investigate the mechanistic nature of the Snf2 family protein HARP, mutations of which are responsible for Schimke immuno-osseous dysplasia. Using a single-molecule magnetic tweezers assay, we construct RPA-stabilized DNA bubbles within torsionally constrained DNA to investigate the annealing action of HARP on a physiologically relevant substrate. We find that HARP closes RPA-stabilized bubbles in a slow reaction, taking on the order of tens of minutes for ∼600 bp of DNA to be re-annealed. The data indicate that DNA re-anneals through the removal of RPA, which is observed as clear steps in the bubble-closing traces. The dependence of the closing rate on both ionic strength and HARP concentration indicates that removal of RPA occurs via an association-dissociation mechanism where HARP does not remain associated with the DNA. The enzyme exhibits classical Michaelis–Menten kinetics and acts cooperatively with a Hill coefficient of 3 ± 1. Our work also allows the determination of some important features of RPA-bubble structures at low supercoiling, including the existence of multiple bubbles and that RPA molecules are mis-registered on the two strands.

Published
2017
Full Text
View/download PDF

37. Enhanced Signal-to-Noise and Fast Calibration of Optical Tweezers Using Single Trapping Events.

Author

Stilgoe, Alexander B., Armstrong, Declan J., Rubinsztein-Dunlop, Halina, Jones, Philip, and Burnham, Daniel R.

Subjects
OPTICAL tweezers, CALIBRATION, NANOPOSITIONING systems, TRANSDUCERS, OPTICAL properties, BROWNIAN motion, MICROFLUIDICS, NANOFLUIDICS
Abstract

The trap stiffness us the key property in using optical tweezers as a force transducer. Force reconstruction via maximum-likelihood-estimator analysis (FORMA) determines the optical trap stiffness based on estimation of the particle velocity from statistical trajectories. Using a modification of this technique, we determine the trap stiffness for a two micron particle within 2 ms to a precision of ∼10% using camera measurements at 10 kfps with the contribution of pixel noise to the signal being larger the level Brownian motion. This is done by observing a particle fall into an optical trap once at a high stiffness. This type of calibration is attractive, as it avoids the use of a nanopositioning stage, which makes it ideal for systems of large numbers of particles, e.g., micro-fluidics or active matter systems. [ABSTRACT FROM AUTHOR]

Published
2021
Full Text
View/download PDF

38. The mechanism of DNA unwinding by the eukaryotic replicative helicase

Author

Burnham, Daniel R, Kose, Hazal B, Hoyle, Rebecca B, and Yardimci, Hasan

Subjects
Genome Integrity & Repair, Cell Cycle & Chromosomes, Biochemistry & Proteomics, 3. Good health, Structural Biology & Biophysics, Imaging
Abstract

Accurate DNA replication is tightly regulated in eukaryotes to ensure genome stability during cell division and is performed by the multi-protein replisome. At the core an AAA+ hetero-hexameric complex, Mcm2-7, together with GINS and Cdc45 form the active replicative helicase Cdc45/Mcm2-7/GINS (CMG). It is not clear how this replicative ring helicase translocates on, and unwinds, DNA. We measure real-time dynamics of purified recombinant Drosophila melanogaster CMG unwinding DNA with single-molecule magnetic tweezers. Our data demonstrates that CMG exhibits a biased random walk, not the expected unidirectional motion. Through building a kinetic model we find CMG may enter up to three paused states rather than unwinding, and should these be prevented, in vivo fork rates would be recovered in vitro. We propose a mechanism in which CMG couples ATP hydrolysis to unwinding by acting as a lazy Brownian ratchet, thus providing quantitative understanding of the central process in eukaryotic DNA replication.

39. The mechanism of DNA unwinding by the eukaryotic replicative helicase

Author

Burnham, Daniel R, Kose, Hazal B, Hoyle, Rebecca B, and Yardimci, Hasan

Subjects
Genome Integrity & Repair, Cell Cycle & Chromosomes, Biochemistry & Proteomics, 3. Good health, Structural Biology & Biophysics, Imaging
Abstract

Accurate DNA replication is tightly regulated in eukaryotes to ensure genome stability during cell division and is performed by the multi-protein replisome. At the core an AAA+ hetero-hexameric complex, Mcm2-7, together with GINS and Cdc45 form the active replicative helicase Cdc45/Mcm2-7/GINS (CMG). It is not clear how this replicative ring helicase translocates on, and unwinds, DNA. We measure real-time dynamics of purified recombinant Drosophila melanogaster CMG unwinding DNA with single-molecule magnetic tweezers. Our data demonstrates that CMG exhibits a biased random walk, not the expected unidirectional motion. Through building a kinetic model we find CMG may enter up to three paused states rather than unwinding, and should these be prevented, in vivo fork rates would be recovered in vitro. We propose a mechanism in which CMG couples ATP hydrolysis to unwinding by acting as a lazy Brownian ratchet, thus providing quantitative understanding of the central process in eukaryotic DNA replication.

40. Optical Trapping Enabled Parallel Delivery of Biological Stimuli with High Spatial and Temporal Resolution.

Author

Burnham DR, Schneider T, and Chiu DT

Abstract

We have developed a method that employs nanocapsules, optical trapping, and single-pulse laser photolysis for delivering bioactive molecules to cells with both high spatial and temporal resolutions. This method is particularly suitable for a cell-culture setting, in which a single nanocapsule can be optically trapped and positioned at a pre-defined location next to the cell, followed by single-pulse laser photolysis to release the contents of the nanocapsule onto the cell. To parallelize this method such that a large array of nanocapsules can be manipulated, positioned, and photolyzed simultaneously, we have turned to the use of spatial light modulators and holographic beam shaping techniques. This paper outlines the progress we have made so far and details the issues we had to address in order to achieve efficient parallel optical manipulations of nanocapsules and particles.

Published
2010
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results