A mathematical study of finite-amplitude rock-folding

The problem of the finite-amplitude folding of an isolated, linearly viscous layer under compression and imbedded in a medium of lower viscosity is treated theoretically by using a variational method to derive finite difference equations which are solved on a digital computer. The problem depends on a single physical parameter, the ratio of the fold wavelength, L, to the "dominant wavelength" of the infinitesimal-amplitude treatment, L_d. Therefore, the natural range of physical parameters is covered by the computation of three folds, with L/L_d = 0, 1, and 4.6, up to a maximum dip of 90°.

Significant differences in fold shape are found among the three folds; folds with higher L/L_d have sharper crests. Folds with L/L_d = 0 and L/L_d = 1 become fan folds at high amplitude. A description of the shape in terms of a harmonic analysis of inclination as a function of arc length shows this systematic variation with L/L_d and is relatively insensitive to the initial shape of the layer. This method of shape description is proposed as a convenient way of measuring the shape of natural folds.

The infinitesimal-amplitude treatment does not predict fold-shape development satisfactorily beyond a limb-dip of 5°. A proposed extension of the treatment continues the wavelength-selection mechanism of the infinitesimal treatment up to a limb-dip of 15°; after this stage the wavelength-selection mechanism no longer operates and fold shape is mainly determined by L/L_d and limb-dip.

Strain-rates and finite strains in the medium are calculated f or all stages of the L/L_d = 1 and L/L_d = 4.6 folds. At limb-dips greater than 45° the planes of maximum flattening and maximum flattening rat e show the characteristic orientation and fanning of axial-plane cleavage.

A biochemical and structural characterization of Drosophila neuroglian

A number of cell-cell interactions in the nervous system are mediated by immunoglobulin gene superfamily members. For example, neuroglian, a homophilic neural cell adhesion molecule in Drosophila, has an extracellular portion comprising six C- 2 type immunoglobulin-like domains followed by five fibronectin type III (FnIII) repeats. Neuroglian shares this domain organization and significant sequence identity with Ll, a murine neural adhesion molecule that could be a functional homologue. Here I report the crystal structure of a proteolytic fragment containing the first two FnIII repeats of neuroglian (NgFn 1,2) at 2.0Å. The interpretation of photomicrographs of rotary shadowed Ng, the entire extracellular portion of neuroglian, and NgFnl-5, the five neuroglian Fn III domains, is also discussed.

The structure of NgFn 1,2 consists of two roughly cylindrical β-barrel structural motifs arranged in a head-to-tail fashion with the domains meeting at an angle of ~120, as defined by the cylinder axes. The folding topology of each domain is identical to that previously observed for single FnIII domains from tenascin and fibronectin. The domains of NgFn1,2 are related by an approximate two fold screw axis that is nearly parallel to the longest dimension of the fragment. Assuming this relative orientation is a general property of tandem FnIII repeats, the multiple tandem FnIII domains in neuroglian and other proteins are modeled as thin straight rods with two domain zig-zag repeats. When combined with the dimensions of pairs of tandem immunoglobulin-like domains from CD4 and CD2, this model suggests that neuroglian is a long narrow molecule (20 - 30 Å in diameter) that extends up to 370Å from the cell surface.

In photomicrographs, rotary shadowed Ng and NgFn1-5 appear to be highly flexible rod-like molecules. NgFn 1-5 is observed to bend in at least two positions and has a mean total length consistent with models generated from the NgFn1,2 structure. Ng molecules have up to four bends and a mean total length of 392 Å, consistent with a head-to-tail packing of neuroglian's C2-type domains.

Preparation, characterization and intramolecular electron-transfer studies of ruthenium-modified cytochromes c

Redox-active ruthenium complexes have been covalently attached to the surface of a series of natural, semisynthetic and recombinant cytochromes c. The protein derivatives were characterized by a variety of spectroscopic techniques. Distant Fe^(2+) - Ru^(3+) electronic couplings were extracted from intramolecular electron-transfer rates in Ru(bpy)_2(im)HisX (where X= 33, 39, 62, and 72) derivatives of cyt c. The couplings increase according to 62 (0.0060) < 72 (0.057) < 33 (0.097) < 39 (0.11 cm^(-1)); however, this order is incongruent with histidine to heme edge-edge distances [62 (14.8) > 39 (12.3) > 33 (11.1) > =72 (8.4 Å)]. These results suggest the chemical nature of the intervening medium needs to be considered for a more precise evaluation of couplings. The rates (and couplings) correlate with the lengths of a-tunneling pathways comprised of covalent bonds, hydrogen bonds and through-space jumps from the histidines to the heme group. Space jumps greatly decrease couplings: one from Pro71 to Met80 extends the σ-tunneling length of the His72 pathway by roughly 10 covalent bond units. Experimental couplings also correlate well with those calculated using extended Hiickel theory to evaluate the contribution of the intervening protein medium.

Two horse heart cyt c variants incorporating the unnatural amino acids (S)-2- amino-3-(2,2'-bipyrid-6-yl)-propanoic acid (6Bpa) and (S)-2-amino-3-(2,2'-bipyrid-4-yl)propanoic acid ( 4Bpa) at position 72 have been prepared using semisynthetic protocols. Negligible perturbation of the protein structure results from this introduction of unnatural amino acids. Redox-active Ru(2,2'-bipyridine)_2^(2+) binds to 4Bpa72 cyt c but not to the 6Bpa protein. Enhanced ET rates were observed in the Ru(bpy)_2^(2+)-modified 4Bpa72 cyt c relative to the analogous His72 derivative. The rapid (< 60 nanosecond) photogeneration of ferrous Ru-modified 4Bpa72 cyt c in the conformationally altered alkaline state demonstrates that laser-induced ET can be employed to study submicrosecond protein-folding events.

Capturing protein dynamics with time-resolved luminescence spectroscopy

The presented doctoral research utilizes time-resolved spectroscopy to characterize protein dynamics and folding mechanisms. We resolve millisecond-timescale folding by coupling time-resolved fluorescence energy transfer (trFRET) to a continuous flow microfluidic mixer to obtain intramolecular distance distributions throughout the folding process. We have elucidated the folding mechanisms of two cytochromes---one that exhibits two-state folding (cytochrome cb₅₆₂) and one that has both a kinetic refolding intermediate ensemble and a distinct equilibrium unfolding intermediate (cytochrome c₅₅₂). Our data reveal that the distinct structural features of cytochrome c₅₅₂ contribute to its thermostability.

We have also investigated intrachain contact dynamics in unfolded cytochrome cb₅₆₂ by monitoring electron transfer, which occurs as the heme collides with a ruthenium photosensitizer, covalently bound to residues along the polypeptide. Intrachain diffusion for chemically denatured proteins proceeds on the microsecond timescale with an upper limit of 0.1 microseconds. The power-law dependence (slope = -1.5) of the rate constants on the number of peptide bonds between the heme and Ru complex indicate that cytochrome cb₅₆₂ is minimally frustrated.

In addition, we have explored the pathway dependence of electron tunneling rates between metal sites in proteins. Our research group has converted cytochrome b₅₆₂ to a c-type cytochrome with the porphyrin covalently bound to cysteine sidechains. We have investigated the effects of the changes to the protein structure (i.e., increased rigidity and potential new equatorial tunneling pathways) on the electron transfer rates, measured by transient absorption, in a series of ruthenium photosensitizer-modified proteins.

High-strain composites and dual-matrix composite structures

Most space applications require deployable structures due to the limiting size of current launch vehicles. Specifically, payloads in nanosatellites such as CubeSats require very high compaction ratios due to the very limited space available in this typo of platform. Strain-energy-storing deployable structures can be suitable for these applications, but the curvature to which these structures can be folded is limited to the elastic range. Thanks to fiber microbuckling, high-strain composite materials can be folded into much higher curvatures without showing significant damage, which makes them suitable for very high compaction deployable structure applications. However, in applications that require carrying loads in compression, fiber microbuckling also dominates the strength of the material. A good understanding of the strength in compression of high-strain composites is then needed to determine how suitable they are for this type of application.

The goal of this thesis is to investigate, experimentally and numerically, the microbuckling in compression of high-strain composites. Particularly, the behavior in compression of unidirectional carbon fiber reinforced silicone rods (CFRS) is studied. Experimental testing of the compression failure of CFRS rods showed a higher strength in compression than the strength estimated by analytical models, which is unusual in standard polymer composites. This effect, first discovered in the present research, was attributed to the variation in random carbon fiber angles respect to the nominal direction. This is an important effect, as it implies that microbuckling strength might be increased by controlling the fiber angles. With a higher microbuckling strength, high-strain materials could carry loads in compression without reaching microbuckling and therefore be suitable for several space applications.

A finite element model was developed to predict the homogenized stiffness of the CFRS, and the homogenization results were used in another finite element model that simulated a homogenized rod under axial compression. A statistical representation of the fiber angles was implemented in the model. The presence of fiber angles increased the longitudinal shear stiffness of the material, resulting in a higher strength in compression. The simulations showed a large increase of the strength in compression for lower values of the standard deviation of the fiber angle, and a slight decrease of strength in compression for lower values of the mean fiber angle. The strength observed in the experiments was achieved with the minimum local angle standard deviation observed in the CFRS rods, whereas the shear stiffness measured in torsion tests was achieved with the overall fiber angle distribution observed in the CFRS rods.

High strain composites exhibit good bending capabilities, but they tend to be soft out-of-plane. To achieve a higher out-of-plane stiffness, the concept of dual-matrix composites is introduced. Dual-matrix composites are foldable composites which are soft in the crease regions and stiff elsewhere. Previous attempts to fabricate continuous dual-matrix fiber composite shells had limited performance due to excessive resin flow and matrix mixing. An alternative method, presented in this thesis uses UV-cure silicone and fiberglass to avoid these problems. Preliminary experiments on the effect of folding on the out-of-plane stiffness are presented. An application to a conical log-periodic antenna for CubeSats is proposed, using origami-inspired stowing schemes, that allow a conical dual-matrix composite shell to reach very high compaction ratios.

The Pacoima Area

The Pacoima area consists of Miocene (sediments and basalts) rocks underlain by a quartz diorite basement complex of Jurassic age. The stratigranhic units range from 25 feet to more than 600 feet in thickness. The lower sediments are arkosic land- laid deposits while the Modelo formation, shallow marine in origin, consists of thinly bedded sandstones, shales, volcanic ash and calcareous members. An andesitic mass, possibly a volcanic plug, outcrops near the summit of one of the hills.

An anticline, and possibly an associated syncline, has been developed by compressional folding. Small scale contortion is locally exposed. Regional dip is northward, decreasing from south to north in the area. Faulting is common, most faults trending nearly north-south. Movement along these faults ranges from a few feet to several hundred feet.

There are no important mineral deposits in the area. Quarrying of the basement rocks has been abandoned.