Simon Mochrie - Academia.edu (original) (raw)

Papers by Simon Mochrie

Advanced Materials, Jan 1, 2010

A tunable, double multilayer x-ray monochromator has recently been implemented on the National Sy... more A tunable, double multilayer x-ray monochromator has recently been implemented on the National Synchrotron Light Source (NSLS) X25 wiggler beam line. It is based on a parallel pair of tungsten-boron-carbide multilayer films grown on silicon substrates and purchased from Osmic, Inc. of Troy, Michigan, USA. It acts as an optional alternative to the conventional double silicon crystal monochromator, and uses

We investigate the physical mechanism for color production by isotropic nanostructures with short... more We investigate the physical mechanism for color production by isotropic nanostructures with short-range order in bird feather barbs. While the primary peak in optical scattering spectra results from constructive interference of singly-scattered light, many species exhibit secondary peaks with distinct characteristic. Our experimental and numerical studies show that these secondary peaks result from double scattering of light by the correlated

We have implemented the newly-introduced, coherence-based technique of x-ray near-field speckle (... more We have implemented the newly-introduced, coherence-based technique of x-ray near-field speckle (XNFS) at 8-ID-I at the Advanced Photon Source. In the near field regime of high-brilliance synchrotron x-rays scattered from a sample of interest, it turns out, that, when the scattered radiation and the main beam both impinge upon an x-ray area detector, the measured intensity shows low-contrast speckles, resulting

Nature communications, 2015

The nuclear lamina is thought to be the primary mechanical defence of the nucleus. However, the l... more The nuclear lamina is thought to be the primary mechanical defence of the nucleus. However, the lamina is integrated within a network of lipids, proteins and chromatin; the interdependence of this network poses a challenge to defining the individual mechanical contributions of these components. Here, we isolate the role of chromatin in nuclear mechanics by using a system lacking lamins. Using novel imaging analyses, we observe that untethering chromatin from the inner nuclear membrane results in highly deformable nuclei in vivo, particularly in response to cytoskeletal forces. Using optical tweezers, we find that isolated nuclei lacking inner nuclear membrane tethers are less stiff than wild-type nuclei and exhibit increased chromatin flow, particularly in frequency ranges that recapitulate the kinetics of cytoskeletal dynamics. We suggest that modulating chromatin flow can define both transient and long-lived changes in nuclear shape that are biologically important and may be alter...

Optics Express, 2010

$Research paper thumbnail of Measuring the nematic order of suspensions of colloidal fd virus by x-ray diffraction and optical birefringence$

Physical Review E, 2003

The orientational distribution function of the nematic phase of suspensions of the semiflexible r... more The orientational distribution function of the nematic phase of suspensions of the semiflexible rodlike virus fd is measured by x-ray diffraction as a function of concentration and ionic strength. X-ray diffraction from a single-domain nematic phase of fd is influenced by interparticle correlations at low angle, while only intraparticle scatter contributes at high angle. Consequently, the angular distribution of the scattered intensity arises from only the single-particle orientational distribution function at high angle but it also includes spatial and orientational correlations at low angle. Experimental measurements of the orientational distribution function from both the interparticle ͑structure factor͒ and intraparticle ͑form factor͒ scattering were made to test whether the correlations present in interparticle scatter influence the measurement of the single-particle orientational distribution function. It was found that the two types of scatter yield consistent values for the nematic order parameter. It was also found that x-ray diffraction is insensitive to the orientational distribution function's precise form, and the measured angular intensity distribution is described equally well by both Onsager's trial function and a Gaussian. At high ionic strength, the order parameter S of the nematic phase coexisting with the isotropic phase approaches theoretical predictions for long semiflexible rods Sϭ0.55, but deviations from theory increase with decreasing ionic strength. The concentration dependence of the nematic order parameter also better agrees with theoretical predictions at high ionic strength indicating that electrostatic interactions have a measurable effect on the nematic order parameter. The x-ray order parameters are shown to be proportional to the measured birefringence, and the saturation birefringence of fd is determined enabling a simple, inexpensive way to measure the order parameter. Additionally, the spatial ordering of nematic fd was probed. Measurements of the nematic structure factor revealed a single large peak in contrast to nematics of rigid rods.

Physical Review Letters, 1999

Herein we establish a relationship between controlled nanoscale surface interactions and subseque... more Herein we establish a relationship between controlled nanoscale surface interactions and subsequent macromolecular ordering. Striped surfaces of oxide and metal are generated over large areas, where the stripe width is comparable to the size of a polymer molecule. Homopolymers are found to anisotropically dewet such surfaces, while incompatible polymer mixtures phase separate at the substrate/polymer interface on a molecular level.

CLEO: 2013, 2013

ABSTRACT We studied how the short-range-ordered nanostructures in bird feather barbs create angle... more ABSTRACT We studied how the short-range-ordered nanostructures in bird feather barbs create angle-invariant colors. By manipulating the interplay between light scattering and absorption, we fabricated biomimetic nanostructures that produce isotropic color.

Intensity fluctuation spectroscopy with coherent x-rays offers a unique tool to observe the dynam... more Intensity fluctuation spectroscopy with coherent x-rays offers a unique tool to observe the dynamics of equilibrium fluctuations at small length scales. We have performed small-angle scattering using a coherent x-ray beam from the MIT-McGill-IBM beamline at the Advanced Photon Source to study equilibrium fluctuations at the critical point of the miscibility gap in the Al-Zn system. Analysis of the data

Physical Review Letters, 2003

The dynamics of supported polymer films were studied by probing the surface height fluctuations a... more The dynamics of supported polymer films were studied by probing the surface height fluctuations as a function of lateral length scale using x-ray photon correlation spectroscopy. Measurements were performed on polystyrene (PS) films of thicknesses varying from 84 to 333nm at temperatures above the PS glass transition temperature. Within a range of wave vectors spanning 10-3 to 10-2 nm-1, good

Macromolecules, 2006

X-ray photon correlation spectroscopy experiments were conducted on bicontinuous microemulsion an... more X-ray photon correlation spectroscopy experiments were conducted on bicontinuous microemulsion and lamellar phases in polystyrene/polyisoprene/poly (styrene-b-isoprene) blends. Regardless of the microstructure, the scattering intensity autocorrelation function ...

Macromolecules, 2005

The phase behavior of a poly (styrene-block-isoprene) copolymer (SI) with styrene volume fraction... more The phase behavior of a poly (styrene-block-isoprene) copolymer (SI) with styrene volume fraction f= 0.18 was studied by small-angle X-ray scattering (SAXS), optical birefringence, and rheology conducted under quiescent conditions and under the influence of shear flow ...

Soft Matter, 2009

Some of the most vivid colors in the animal kingdom are created not by pigments, but by wavelengt... more Some of the most vivid colors in the animal kingdom are created not by pigments, but by wavelength-selective scattering of light from nanostructures. Here we investigate quasi-ordered nanostructures of avian feather barbs which produce vivid non-iridescent colors. These b-keratin and air nanostructures are found in two basic morphologies: tortuous channels and amorphous packings of spheres. Each class of nanostructure is isotropic and has a pronounced characteristic length scale of variation in composition. These local structural correlations lead to strong backscattering over a narrow range of optical frequencies and little variation with angle of incidence. Such optical properties play important roles in social and sexual communication. To be effective, birds need to precisely control the development of these nanoscale structures, yet little is known about how they grow. We hypothesize that multiple lineages of birds have convergently evolved to exploit phase separation and kinetic arrest to self-assemble spongy color-producing nanostructures in feather barbs. Observed avian nanostructures are strikingly similar to those self-assembled during the phase separation of fluid mixtures; the channel and sphere morphologies are characteristic of phase separation by spinodal decomposition and nucleation and growth, respectively. These unstable structures are locked-in by the kinetic arrest of the b-keratin matrix, likely through the entanglement or cross-linking of supermolecular bkeratin fibers. Using the power of self-assembly, birds can robustly realize a diverse range of nanoscopic morphologies with relatively small physical and chemical changes during feather development.

Proceedings of the National Academy of Sciences, 2002

We have used small angle x-ray scattering and computer simulations with a coarse-grained model to... more We have used small angle x-ray scattering and computer simulations with a coarse-grained model to provide a time-resolved picture of the global folding process of the Tetrahymena group I RNA over a time window of more than five orders of magnitude. A substantial phase of compaction is observed on the low millisecond timescale, and the overall compaction and global shape changes are largely complete within one second, earlier than any known tertiary contacts are formed. This finding indicates that the RNA forms a nonspecifically collapsed intermediate and then searches for its tertiary contacts within a highly restricted subset of conformational space. The collapsed intermediate early in folding of this RNA is grossly akin to molten globule intermediates in protein folding.

Physical Review Letters, 2004

Multispeckle x-ray photon correlation spectroscopy was employed to characterize the slow dynamics... more Multispeckle x-ray photon correlation spectroscopy was employed to characterize the slow dynamics of a colloidal suspension formed by highly-charged, nanometer-sized disks. At scattering wave vectors q corresponding to interparticle length scales, the dynamic structure factor follows a form f (q, t) ∼ exp[−(t/τ ) β ], where β ≈ 1.5. The characteristic relaxation time τ increases with the sample age ta approximately as τ ∼ t 1.8 a and decreases with q approximately as τ ∼ q −1 . Such a compressed exponential decay with relaxation time that varies inversely with q is consistent with recent models that describe the dynamics in disordered elastic media in terms of strain from random, local structural rearrangements. The amplitude of the measured decay in f (q, t) varies with q in a manner that implies caged particle motion at short times. The decrease in the range of this motion and an increase in suspension conductivity with increasing ta indicate a growth in the interparticle repulsion as the mechanism for internal stress development implied by the models. PACS numbers: 82.70.Dd, 62.25.+g, 61.10.Eq

Physical Review Letters, 1997

We study the morphology of symmetric diblock copolymer films with thicknesses below the bulk equi... more We study the morphology of symmetric diblock copolymer films with thicknesses below the bulk equilibrium period supported by both flat and corrugated substrates. In this thickness regime, the film morphology is characterized by the formation of uniformly sized lateral domains. On flat substrates, these domains are randomly arranged. In contrast, on corrugated substrates, similar films exhibit domains which decorate the peaks of the substrate corrugations. Our observations suggest a novel and simple scheme for the lateral nanometer scale patterning of diblock copolymer films.

Physical Review Letters, 2006

The relationship between structural relaxation on molecular length scales and macroscopic stress ... more The relationship between structural relaxation on molecular length scales and macroscopic stress relaxation was explored in a disordered block-copolymer melt. Experiments show that the structural relaxation time, measured by x-ray photon correlation spectroscopy is larger than the terminal stress relaxation time, measured by rheology, by factors as large as 100. We demonstrate that the structural relaxation data are dominated by the diffusion of intact micelles while the stress relaxation data are dominated by contributions due to disordered concentration fluctuations.

Physical Review E, 2006

The theory for surface dynamics of the thermally excited fluctuations on a homogenous single-laye... more The theory for surface dynamics of the thermally excited fluctuations on a homogenous single-layer film of arbitrary depth is generalized to describe surface and interfacial dynamics of polymeric liquid bilayer films in terms of susceptibilities, power spectra, and characteristic relaxation time constants. The effects on surface dynamics originating from viscosity inhomogeneities close to the surface and interfacial regions are investigated by the bilayer theory and compared with the surface dynamics of homogeneous single-layer films under nonslip and slip boundary conditions. Our bilayer theory can also be extended to study interfacial dynamics of more generalized multilayer systems. The effects of viscoelasticity and van der Waals interactions on surface and interfacial dynamics are also briefly discussed.