Designing folding rings using polynomial continuation

© 2014 by ASME. Two types of foldable rings are designed using polynomial continuation. The first type of ring, when deployed, forms regular polygons with an even number of sides and is designed by specifying a sequence of orientations which each bar must attain at various stages throughout deployment. A design criterion is that these foldable rings must fold with all bars parallel in the stowed position. At first, all three Euler angles are used to specify bar orientations, but elimination is also used to reduce the number of specified Euler angles to two, allowing greater freedom in the design process. The second type of ring, when deployed, forms doubly plane-symmetric (irregular) polygons. The doubly symmetric rings are designed using polynomial continuation, but in this example a series of bar end locations (in the stowed position) is used as the design criterion with focus restricted to those rings possessing eight bars.

Integrated folding 4x4 optical matrix switch with total internal reflection mirrors on SOI by anisotropic chemical etching

A folding rearrangeable nonblocking 4 x 4 optical matrix switch was designed and fabricated on silicon-on-insulator wafer. To compress chip size, switch elements (SEs) were interconnected by total internal reflection (TIR) mirrors instead of conventional S-bends. For obtaining smooth interfaces, potassium hydroxide anisotropic chemical etching of silicon was utilized to make the matrix switch for the first time. The device has a compact size of 20 x 1.6 mm(2) and a fast response of 7.5 mu s. The power consumption of each 2 x 2 SE and the average excess loss per mirror were 145 mW and -1.1 dB, respectively. Low path dependence of +/- 0.7 dB in total excess loss was obtained because of the symmetry of propagation paths in this novel matrix switch.

Novel folding large-scale optical switch matrix with total internal reflection mirrors on silicon-on-insulator by anisotropy chemical etching

A compact optical switch matrix was designed, in which light circuits were folded by total internal reflective (TIR) mirrors. Two key elements, 2 x 2 switch and TIR mirror, have been fabricated on silicon-on-insulator wafer by anisotropy chemical etching. The 2 x 2 switch showed very low power consumption of 140 mW and a very high speed of 8 +/- 1 mus. An improved design for the TIR mirror was developed, and the fabricated mirror with smooth and vertical reflective facet showed low excess loss of 0.7 +/- 0.3 dB at 1.55 mum.

Novel folding 8x8 silicon-based optical matrix switch with tapered waveguides and self-aligned corner mirrors

Novel folding 8 x 8 matrix switches based on silicon on insulator were demonstrated. In the design, single-mode rib waveguides and multimode interferences are connected by optimized tapered waveguides to reduce the mode coupling loss between the two types of waveguides. The self-aligned method was applied to the key integrated turning mirrors for perfect positions and low loss of them. A mixed etching process including inductively coupled plasma and chemical etching was employed to etch waveguides and mirrors, respectively. The compact size of the device is only 20 x 3.2 mm(2). The switch element with high switching speed and low power consumption is presented in the matrix. The average insertion loss of the matrix is about -21 dB, and the excess loss of one mirror is measured of -1.4 dB. The worst crosstalk is larger than 21 dB. Experimental results illuminate that some of the main characteristics of optical matrix switches are. developed in the modified design, which is in accord with theoretic analyses.

An 8-b 1-GSmaples/s CMOS cascaded folding and interpolating ADC

This paper presents an 8-bit low power cascaded folding and interpolating analog-to-digital converter (ADC). A reduction in the number of comparators, equal to the number of times the signal is folded, is obtained. The interleaved architecture is used to improve the sampling rate of the ADC. The circuit including a bandgap is implemented in a 0.18-mu m CMOS technology, and measures 1.47 mm X 1.47 mm (including pads). The simulation results illustrate a conversion rate of 1-GSamples/s and a power dissipation of less than 290mW.

Self-assembly morphology effects on the crystallization of semicrystalline block copolymer thin film

Self-assembly morphology effects on the crystalline behavior of asymmetric semicrystalline block copolymer polystyrene-block-poly(L-lactic acid) thin film were investigated. Firstly, a series of distinctive self-assembly aggregates, from spherical to ellipsoid and rhombic lamellar micelles (two different kinds of rhombic micelles, defined as rhomb 1 and rhomb 2) was prepared by means of promoting the solvent selectivity. Then, the effects of these self-assembly aggregates on crystallization at the early stage of film evolution were investigated by in situ hot stage atomic force microscopy. Heterogeneous nucleation initiated from the spherical micelles and dendrites with flat on crystals appeared with increasing temperature. At high temperature, protruding structures were observed due to the thickening of the flat-on crystals and finally more thermodynamically stable crystallization formed. Annealing the rhombic lamellar micelles resulted in different phenomena. Turtle-shell-like crystalline structure initiated from the periphery of the rhombic micelle 1 and spread over the whole film surface in the presence of mostly noncrystalline domain interior. Erosion and small hole appeared at the surface of the rhombic lamellar micelle 2; no crystallization like that in rhomb 1 occurred. It indicated that the chain-folding degree was different in these two micelles, which resulted in different annealing behaviors.

Dominant kinetic paths on biomolecular binding-folding energy landscape

The identification of kinetic pathways is a central issue in understanding the nature of flexible binding. A new approach is proposed here to study the dynamics of this binding-folding process through the establishment of a path integral framework on the underlying energy landscape. The dominant kinetic paths of binding and folding can be determined and quantified. In this case, the corresponding kinetic paths of binding are shown to be intimately correlated with those of folding and the dynamics becomes quite cooperative. The kinetic time can be obtained through the contributions from the dominant paths and has a U-shape dependence on temperature.

Quantifying the kinetic paths of flexible biomolecular recognition

Biomolecular recognition often involves large conformational changes, sometimes even local unfolding. The identification of kinetic pathways has become a central issue in understanding the nature of binding. A new approach is proposed here to study the dynamics of this binding-folding process through the establishment of a path-integral framework on the underlying energy landscape. The dominant kinetic paths of binding and folding can be determined and quantified. The significant coupling between the binding and folding of biomolecules often exists in many important cellular processes. In this case, the corresponding kinetic paths of binding are shown to be intimately correlated with those of folding and the dynamics becomes quite cooperative. This implies that binding and folding happen concurrently. When the coupling between binding and folding is weak (strong), the kinetic process usually starts with significant folding (binding) first, with the binding (folding) later proceeding to the end. The kinetic rate can be obtained through the contributions from the dominant paths. The rate is shown to have a bell-shaped dependence on temperature in the concentration-saturated regime consistent with experiment. The changes of the kinetics that occur upon changing the parameters of the underlying binding-folding energy landscape are studied.

Effect of crystallization on the lamellar orientation in thin films of symmetric poly(styrene)-b-poly(L-lactide) diblock copolymer

The effect of crystallization on the lamellar orientation of poly( styrene)-b-poly(L-lactide) (PS-PLLA) semicrystalline diblock copolymer in thin films has been investigated by atomic force microscopy (AFM), transmission electronic microscopy (TEM), and X-ray photoelectron spectroscopy (XPS). In the melt state, microphase separation leads to a symmetric wetting structure with PLLA blocks located at both polymer/substrate and polymer/air interfaces. The lamellar period is equal to the long period L in bulk determined by small-angle X-ray scattering (SAXS). Symmetric wetting structure formed in the melt state provides a model structure to study the crystallization of PLLA monolayer tethered on glassy (T-c < T-g,T-PS) or rubber (T-c > T-g,T-PS) PS substrate. In both cases, it is found that the crystallization of PLLA results in a "sandwich" structure with amorphous PS layer located at both folding surfaces. For T-c <= T-g,T- PS, the crystallization induces a transition of the lamellar orientation from parallel to perpendicular to substrate in between and front of the crystals. In addition, the depletion of materials around the crystals leads to the formation of holes of 1/2 L, leaving the adsorbed monolayer exposure at the bottom of the holes.

Single-molecule dynamics reveals cooperative binding-folding in protein recognition

The study of associations between two biomolecules is the key to understanding molecular function and recognition. Molecular function is often thought to be determined by underlying structures. Here, combining a single-molecule study of protein binding with an energy-landscape-inspired microscopic model, we found strong evidence that biomolecular recognition is determined by flexibilities in addition to structures. Our model is based on coarse-grained molecular dynamics on the residue level with the energy function biased toward the native binding structure ( the Go model). With our model, the underlying free-energy landscape of the binding can be explored. There are two distinct conformational states at the free-energy minimum, one with partial folding of CBD itself and significant interface binding of CBD to Cdc42, and the other with native folding of CBD itself and native interface binding of CBD to Cdc42. This shows that the binding process proceeds with a significant interface binding of CBD with Cdc42 first, without a complete folding of CBD itself, and that binding and folding are then coupled to reach the native binding state.

Jesus, the Resurrection: A Sermon

Memorial Sermon

Protein Docking by the Underestimation of Free Energy Funnels in the Space of Encounter Complexes

Similarly to protein folding, the association of two proteins is driven by a free energy funnel, determined by favorable interactions in some neighborhood of the native state. We describe a docking method based on stochastic global minimization of funnel-shaped energy functions in the space of rigid body motions (SE(3)) while accounting for flexibility of the interface side chains. The method, called semi-definite programming-based underestimation (SDU), employs a general quadratic function to underestimate a set of local energy minima and uses the resulting underestimator to bias further sampling. While SDU effectively minimizes functions with funnel-shaped basins, its application to docking in the rotational and translational space SE(3) is not straightforward due to the geometry of that space. We introduce a strategy that uses separate independent variables for side-chain optimization, center-to-center distance of the two proteins, and five angular descriptors of the relative orientations of the molecules. The removal of the center-to-center distance turns out to vastly improve the efficiency of the search, because the five-dimensional space now exhibits a well-behaved energy surface suitable for underestimation. This algorithm explores the free energy surface spanned by encounter complexes that correspond to local free energy minima and shows similarity to the model of macromolecular association that proceeds through a series of collisions. Results for standard protein docking benchmarks establish that in this space the free energy landscape is a funnel in a reasonably broad neighborhood of the native state and that the SDU strategy can generate docking predictions with less than 5 � ligand interface Ca root-mean-square deviation while achieving an approximately 20-fold efficiency gain compared to Monte Carlo methods.

Improving the Performance of Overlay Routing and P2P File Sharing using Selfish Neighbor Selection

A foundational issue underlying many overlay network applications ranging from routing to P2P file sharing is that of connectivity management, i.e., folding new arrivals into the existing mesh and re-wiring to cope with changing network conditions. Previous work has considered the problem from two perspectives: devising practical heuristics for specific applications designed to work well in real deployments, and providing abstractions for the underlying problem that are tractable to address via theoretical analyses, especially game-theoretic analysis. Our work unifies these two thrusts first by distilling insights gleaned from clean theoretical models, notably that under natural resource constraints, selfish players can select neighbors so as to efficiently reach near-equilibria that also provide high global performance. Using Egoist, a prototype overlay routing system we implemented on PlanetLab, we demonstrate that our neighbor selection primitives significantly outperform existing heuristics on a variety of performance metrics; that Egoist is competitive with an optimal, but unscalable full-mesh approach; and that it remains highly effective under significant churn. We also describe variants of Egoist's current design that would enable it to scale to overlays of much larger scale and allow it to cater effectively to applications, such as P2P file sharing in unstructured overlays, based on the use of primitives such as scoped-flooding rather than routing.

The EGOIST Overlay Routing System

A foundational issue underlying many overlay network applications ranging from routing to peer-to-peer file sharing is that of connectivity management, i.e., folding new arrivals into an existing overlay, and rewiring to cope with changing network conditions. Previous work has considered the problem from two perspectives: devising practical heuristics for specific applications designed to work well in real deployments, and providing abstractions for the underlying problem that are analytically tractable, especially via game-theoretic analysis. In this paper, we unify these two thrusts by using insights gleaned from novel, realistic theoretic models in the design of Egoist – a distributed overlay routing system that we implemented, deployed, and evaluated on PlanetLab. Using extensive measurements of paths between nodes, we demonstrate that Egoist’s neighbor selection primitives significantly outperform existing heuristics on a variety of performance metrics, including delay, available bandwidth, and node utilization. Moreover, we demonstrate that Egoist is competitive with an optimal, but unscalable full-mesh approach, remains highly effective under significant churn, is robust to cheating, and incurs minimal overhead. Finally, we use a multiplayer peer-to-peer game to demonstrate the value of Egoist to end-user applications. This technical report supersedes BUCS-TR-2007-013.

Home, family and society: women of the Irish landed class, 1860-1914. A Munster case study

The thesis analyses the roles and experiences of female members of the Irish landed class (wives, sisters and daughters of gentry and aristocratic landlords with estates over 1,000 acres) using primary personal material generated by twelve sample families over an important period of decline for the class, and growing rights for women. Notably, it analyses the experiences of relatively unknown married and unmarried women, something previously untried in Irish historiography. It demonstrates that women’s roles were more significant than has been assumed in the existing literature, and leads to a more rounded understanding of the entire class. Four chapters focus on themes which emerge from the sources used and which deal with their roles both inside and outside the home. These chapters argue that: Married and unmarried women were more closely bound to the priorities of their class than their sex, and prioritised male-centred values of family and estate. Male and female duties on the property overlapped, as marriage relationships were more equal than the legislation of the time would suggest. London was the cultural centre for this class. Due to close familial links with Britain (60% of sample daughters married English men) their self-perception was British or English, as well as Irish. With the self-confidence of their class, these women enjoyed cultural and political activities and movements outside the home (sport, travel, fashion, art, writing, philanthropy, (anti-)suffrage, and politics). Far from being pawns in arranged marriages, women were deeply conscious of their marriage decisions and chose socially, financially and personally compatible husbands; they also looked for sexual satisfaction. Childbirth sometimes caused lasting health problems, but pregnancy did not confine wealthy women to an invalid state. In opposition to the stereotypical distant aristocratic mother, these women breastfed their children, and were involved mothers. However, motherhood was not permitted to impinge on the more pressing role of wife