Timothy Senden

Geometrical structure of disordered sphere packings

The three-dimensional structure of large packings of monosized spheres with volume fractions ranging between 0.58 and 0.64 has been studied with x-ray computed tomography. We search for signatures of organization, classifying local arrangements and exploring the effects of local geometrical constrains on the global packing. This study is the largest and the most accurate empirical analysis of disordered packings at the grain-scale to date, mapping over 380,000 sphere coordinates with precision within 0.1% of the sphere diameters. We discuss topological and geometrical methods to characterize and classify these systems emphasizing the implications that local geometry can have on the mechanisms of formation of these amorphous structures. Some of the main results are (1) the observation that the average number of contacts increases with the volume fraction; (2) the discovery that these systems have a very compact contact network; (3) the finding that disordered packing can be locally more efficient than crystalline packings; (4) the observation that the peaks of the radial distribution function follow power law divergences; (5) the discovery that geometrical frustration plays no role in the formation of such amorphous packings.

Surface chemistry and tip-sample interactions in atomic force microscopy

Abstract Microfabricated silicon nitride cantilevers with integral tips are commonly employed in atomic force microscopy. The link between surface chemistry, including surface group acid-base dissociation and counterion complexation, and tip-sample interaction in aqueous electrolyte solution is examined. Silicon nitride tip interaction with “flat plate” samples of both muscovite mica and silicon nitride as a function of aqueous solution pH and electrolyte concentration is investigated. The long-range component of the interaction is normalized with respect to an effective tip radius, and as a result electrical double layer and van der Waals interactions can be discussed quantitatively. Microfracture and tribochemical tip wear is also discussed with reference to atomic force microscope contact mode imaging. Non-retarded Hamaker constants are reported for a range of silicon nitride, silica, silicon and muscovite mica systems.

Force microscopy and surface interactions

The force microscope provides the most flexible of surface force measurement techniques for probing the richness and complexity of surface interactions. The technique is reviewed over the past 3 years for developments in instrumentation, colloidal force measurement, and nano-mechanical measurements on single molecules.

Investigating the geometrical structure of disordered sphere packings

Bead packs of up to 150,000 mono-sized spheres with packing densities ranging from 0.58 to 0.64 have been studied by means of X-ray computed tomography. These studies represent the largest and the most accurate description of the structure of disordered packings at the grain-scale ever attempted. We investigate the geometrical structure of such packings looking for signatures of disorder. We discuss ways to characterize and classify these systems and the implications that local geometry can have on densification dynamics.

An exceptional Devonian fish from Australia sheds light on tetrapod origins

The transition from fishes to tetrapods was one of the most dramatic events in the evolution of vertebrates, but many pivotal fossils are incomplete, resulting in gaps in the data that are used for phylogenetic reconstruction. Here we present new observations from the most complete, acid-prepared Devonian tetrapodomorph fish yet discovered, Gogonasus, which was previously placed just crownward of Kenichthys and rhizodontids, the most primitive taxa on the tetrapod lineage. Unexpectedly, Gogonasus shows a mosaic of plesiomorphic and derived tetrapod-like features. Whereas the braincase and dermal cranial skeleton exhibit generalized morphologies with respect to Eusthenopteron or Panderichthys, taxa that are traditionally considered to be phyletically close to tetrapods, the presence of a deeply invaginated, wide spiracle, advanced internal spiracular architecture and near-horizontal hyomandibula are specialized features that are absent from Eusthenopteron. Furthermore, the pectoral fin skeleton of Gogonasus shares several features with that of Tiktaalik, the most tetrapod-like fish. A new phylogenetic analysis places Gogonasus crownward of Eusthenopteron as the sister taxon to the Elpistostegalia. Aspects of the basic tetrapod limb skeleton and middle ear architecture can now be traced further back within the tetrapodomorph radiation.

Onset of mechanical stability in random packings of frictional spheres

Using sedimentation to obtain precisely controlled packings of noncohesive spheres, we find that the volume fraction phiRLP of the loosest mechanically stable packing is in an operational sense well defined by a limit process. This random loose packing volume fraction decreases with decreasing pressure p and increasing interparticle friction coefficient mu. Using x-ray tomography to correct for a container boundary effect that depends on particle size, we find for rough particles in the limit p-->0 a new lower bound, phiRLP=0.550+/-0.001.

Live birth in the Devonian period

The extinct placoderm fishes were the dominant group of vertebrates throughout the Middle Palaeozoic era, yet controversy about their relationships within the gnathostomes (jawed vertebrates) is partly due to different interpretations of their reproductive biology. Here we document the oldest record of a live-bearing vertebrate in a new ptyctodontid placoderm, Materpiscis attenboroughi gen. et sp. nov., from the Late Devonian Gogo Formation of Australia (approximately 380 million years ago). The new specimen, remarkably preserved in three dimensions, contains a single, intra-uterine embryo connected by a permineralized umbilical cord. An amorphous crystalline mass near the umbilical cord possibly represents the recrystallized yolk sac. Another ptyctodont from the Gogo Formation, Austroptyctodus gardineri, also shows three small embryos inside it in the same position. Ptyctodontids have already provided the oldest definite evidence for vertebrate copulation, and the new specimens confirm that some placoderms had a remarkably advanced reproductive biology, comparable to that of some modern sharks and rays. The new discovery points to internal fertilization and viviparity in vertebrates as originating earliest within placoderms.

Digital Core Laboratory: Properties of reservoir core derived from 3D images

A facility for digital imaging, visualizing and calculation of reservoir rock properties in three dimensions (3D) is described. The facility includes a high resolution X-ray micro-computed tomography system capable of acquiring 3D images made up of 2000 voxels on core plugs up to 5 cm diameter with resolutions down to 2 μm. Subsets of four sandstone reservoir core plugs (5 mm in diameter) from a single well of a producing gas field are imaged in this study. The four cores exhibit a broad range of pore and grain sizes, porosity, permeability and mineralogy. Computational results made directly on the digitized tomographic images are presented for the pore size distribution, permeability, formation factor, NMR response and drainage capillary pressure. We show that data across a range of porosity can be computed from the suite of 5 mm plugs. Computations of permeability, formation factor and drainage capillary pressure are compared to data from a comprehensive SCAL laboratory study on 70 cores from the same well. The results are in good agreement. Empirical correlations between permeability and other petrophysical parameters are made and compared to common correlations. The results demonstrate the potential to predict petrophysical properties from core material not suited for laboratory testing (e.g., drill cuttings, sidewall core or damaged core) and the feasibility of combining digitized images with numerical calculations to predict properties and derive correlations for individual reservoir rock lithologies.

Supramolecular structure and nuclear targeting efficiency determine the enhancement of transfection by modified polylysines

Polylysine (pLy) has been used as a DNA carrier in nonviral gene delivery systems because it forms complexes with plasmid DNA via charge interaction, and condenses it into a compact structure. We have recently shown that cross-linking nuclear localization sequences (NLSs) to pLy can enhance transfection by conferring specific recognition by the cellular nuclear import ‘receptor’, the NLS-binding importin α/β heterodimer. The present study examines and correlates for the first time the effect of the lysine/nucleotide (Ly/Nu) ratio on transfection, recognition by importin α/β, and structure as determined using electron microscopy (EM) and atomic force microscopy (AFM), for pLy–DNA complexes with and without NLSs or mutant versions thereof. Intriguingly, we observed two distinct peaks of transfection enhancement at Ly/Nu ratios of 0.4 and 4.0, attributable to specific NLS recognition by importins and DNA compaction, respectively. The results indicate a clear correlation between the pLy–DNA structure, importin α/β recognition, and gene transfer efficiency, thus underlining the importance of using pLy–DNA at the optimal Ly/Nu ratio.

Examination of the geometry of long-range tip—sample interaction in atomic force microscopy

A simple method for the in situ determination of the effective large-scale curvature of the atomic force microscope (AFM) imaging tip is presented. In the method, the interaction between a spherical particle of known radius and a planar surface, both coated with an adsorbed surfactant bilayer, in aqueous solution is measured. This standard interaction is then compared with the measurements of the force of interaction between AFM tips and planar surfaces possessing the same adsorbed surfactant bilayers in aqueous solution. The probable effects of both geometrical simplifications and surface roughness are considered in the discussion of the method. The range from 100 to 400 nm is found to cover most of the effective radii (Reff) for the commonly used microfabricated silicon nitride tips.