Margreet W. Docter

Measuring the wavelength-dependent divergence of transmission through sub-wavelength hole-arrays by spectral imaging

We present a study on the far-field patterns of light transmitted through sub-wavelength metallic hole-arrays. Spectral imaging measurements are used here on hole arrays for the first time. It provides both spatial and spectral information of the transmission in far-field. The visibility of the images, measured in two illumination modes: Köhler and collimated, is calculated for different planes in and out of focus. The transmission under collimated illumination reveals that 75% of the beam if non-divergent. The results are in agreement with the low divergence measured by Lezec [Science 297, 820 (2002)].

Structured illumination microscopy using extraordinary transmission through sub-wavelength hole-arrays

A new microscopy method for multi diffraction-limited spot illumination is based on extraordinary light transmission through a periodic metal grid (typical period of 600 nm) of sub-wavelength holes (150 nm). Multiple spots illuminate a fluorescently labeled sample and the emission is collected by far-field optics. Theoretical comparison with a confocal microscope reveals equivalent spot sizes and a scanning method with the advantage of multiple illumination spots. The system is used to measure the actual transmitted field with a fluorescent sample in far-field. The obtained results are consistent with the theoretical prediction and provide a proof of concept of the midfield microscope.

Toward the development of a Three-Dimensional Mid–Field Microscope

Recently, an extraordinary transmission of light through small holes (<200 nm) in a thin metallic film has been described. This phenomenon has been shown to be the result of the photon-plasmon interaction in thin films where a periodic structure (such as a set of holes) is embedded in the film. One of the extraordinary results is that the beam that passes through a hole has a very small diffraction in extreme contrast to the wide angle predicted by diffraction theory. Based on this effect, we propose here a new type of microscopy that we term mid-field microscopy. It combines an illumination of the sample through a metallic hole-array with far-field collection optics, a scanning mechanism and a CCD. When compared to other high resolution methods, what we suggest here is relatively simple because it is based on a thin metallic film with an array of nano-sized holes. Such a method can be widely used in high-resolution microscopy and provide a novel simple-to-use tool in many life-sciences laboratories. When compared to near-field scanning optical microscopy (NSOM), the suggested mid-field method provides a significant improvement. This is chiefly for three reasons: 1. The penetration depth of the microscope increases from a few nanometers to a few micrometers, hence the name mid-field microscope. 2. It allows one to measure an image faster because the image is measured through many holes in parallel rather then through a single fiber tip used in conventional near-field microscopy, and 3. It enables one to perform three-dimensional reconstruction of images due to a semi-confocal effect. We describe the physical basics of the photon-plasmon interaction that allows the coupling of light to the surface plasmons and determines the main spectral characteristics of the device. This mechanism can be ascribed due to the super-periodicity of the electron oscillations on the metallic surface engendered by the grating-like structure of the hole-array.

Hysteresis in DNA compaction by Dps is described by an Ising model

Significance Cooperativity has been a fundamental concept in our understanding of biological systems for over a century. Here, we describe the observation of cooperative binding that exhibits long-lived hysteresis and cannot be described by a standard Hill model. Inspired by the Ising model of ferromagnetism, we describe this hysteresis as a consequence of cooperative binding in the limit of large complexes. We provide a method to relate the amount of hysteresis to the strength of the neighboring interactions between bound proteins and DNA. This novel kinetic feature of macromolecular complexes allows cells to create a binary response to small changes in external conditions and causes complexes to retain a memory of past conditions over long timescales. In all organisms, DNA molecules are tightly compacted into a dynamic 3D nucleoprotein complex. In bacteria, this compaction is governed by the family of nucleoid-associated proteins (NAPs). Under conditions of stress and starvation, an NAP called Dps (DNA-binding protein from starved cells) becomes highly up-regulated and can massively reorganize the bacterial chromosome. Although static structures of Dps–DNA complexes have been documented, little is known about the dynamics of their assembly. Here, we use fluorescence microscopy and magnetic-tweezers measurements to resolve the process of DNA compaction by Dps. Real-time in vitro studies demonstrated a highly cooperative process of Dps binding characterized by an abrupt collapse of the DNA extension, even under applied tension. Surprisingly, we also discovered a reproducible hysteresis in the process of compaction and decompaction of the Dps–DNA complex. This hysteresis is extremely stable over hour-long timescales despite the rapid binding and dissociation rates of Dps. A modified Ising model is successfully applied to fit these kinetic features. We find that long-lived hysteresis arises naturally as a consequence of protein cooperativity in large complexes and provides a useful mechanism for cells to adopt unique epigenetic states.

Measuring the near-field of extraordinary transmission through a periodic hole-array

The knowledge of the near-field of extraordinary transmission through hole-arrays is mostly theoretical; there is less experimental validation of the theory. We study the near-field properties by measuring fluorescent molecules that are immersed in a solution and their Brownian motion. The measurements are performed by filling the space above the hole-array with fluorescent solution and exciting these molecules through the hole-array. By measuring both the fluorescence and the direct exciting light, it is possible to learn about the near-field properties.

Uniform ion beam milling of a non-flat surface at off-normal incidence and four azimuths

Atom removal from surfaces via bombardment by ion beams –ion beam sputtering or ion milling– is a widely employed technique to form geometric structures in materials. In this work we present and test a new method to achieving uniform material removal from an irregular surface. The method is based on ion milling at off‐normal incidence under four consecutive perpendicular azimuthal specimen orientations. Mathematical analysis shows that uniform ion milling of an uneven surface is achieved at the polar angle of incidence θ where the quantity has its maximum [Y(θ) is the number of removed atoms per incident ion].

Small influence of surface plasmons on the near-field transmission intensity spatial distribution

We developed an analytical model which calculates the near- & far-field intensity distribution for transmission through sub-wavelength hole-arrays. We modeled with and without plasmons; interference dominates the near-field spatial distribution, plasmons only influence the intensity.

Field pattern of metal hole-arrays opens the way for a new near- and mid-field high resolution microscopy

We calculated the field pattern above hole-arrays with an analytical model that we developed. Spectral imaging measurements strongly confirm the model. Such a pattern can be used for high resolution fluorescence measurements of biological samples.