Non-equilibrium Anisotropic Phases, Nucleation and Critical Behavior in a Driven Lennard-Jones Fluid

We describe short-time kinetic and steady-state properties of the non--equilibrium phases, namely, solid, liquid and gas anisotropic phases in a driven Lennard-Jones fluid. This is a computationally-convenient two-dimensional model which exhibits a net current and striped structures at low temperature, thus resembling many situations in nature. We here focus on both critical behavior and details of the nucleation process. In spite of the anisotropy of the late--time spinodal decomposition process, earlier nucleation seems to proceed by Smoluchowski coagulation and Ostwald ripening, which are known to account for nucleation in equilibrium, isotropic lattice systems and actual fluids. On the other hand, a detailed analysis of the system critical behavior rises some intriguing questions on the role of symmetries; this concerns the computer and field-theoretical modeling of non-equilibrium fluids.Comment: 7 pages, 9 ps figures, to appear in PR

Functionally heterogeneous porous scaffold design for tissue engineering

Most of the current tissue scaffolds are mainly designed with homogeneous porosity which does not represent the spatial heterogeneity found in actual tissues. Therefore engineering a realistic tissue scaffolds with properly graded properties to facilitate the mimicry of the complex elegance of native tissues are critical for the successful tissue regeneration. In this work, novel bio-mimetic heterogeneous porous scaffolds have been modeled. First, the geometry of the scaffold is extracted along with its internal regional heterogeneity. Then the model has been discretized with planner slices suitable for layer based fabrication. An optimum filament deposition angle has been determined for each slice based on the contour geometry and the internal heterogeneity. The internal region has been discritized considering the homogeneity factor along the deposition direction. Finally, an area weight based approach has been used to generate the spatial porosity function that determines the filament deposition location for desired biomimetic porosity. The proposed methodology has been implemented and illustrative examples are provided. The effective porosity has been compared between the proposed design and the conventional homogeneous scaffolds. The result shows a significant error reduction towards achieving the biomimetic porosity in the scaffold design and provides better control over the desired porosity level. Moreover, sample designed structures have also been fabricated with a NC motion controlled micro-nozzle biomaterial deposition system

Structure and phase behavior of colloidal dumbbells with tunable attractive interactions

We investigate thermodynamic and structural properties of colloidal dumbbells in the framework provided by the Reference Interaction Site Model (RISM) theory of molecular fluids and Monte Carlo simulations. We consider two different models: in the first one we set identical square-well attractions on the two tangent spheres composing the molecule (SW-SW model); in the second scheme, one of square-well interactions is switched off (HS-SW model). Appreciable differences emerge between the physical properties of the two models. Specifically, the $k \to 0$ behavior of SW-SW structure factors $S(k)$ points to the presence of a gas-liquid coexistence, as confirmed by subsequent fluid phase equilibria calculations. Conversely, the HS-SW $S(k)$ develops a low-$k$ peak, signaling the presence of aggregates; such a process destabilizes the gas-liquid phase separation, promoting at low temperatures the formation of a cluster phase, whose structure depends on the system density. We further investigate such differences by studying the phase behavior of a series of intermediate models, obtained from the original SW-SW by progressively reducing the depth of one square-well interaction. RISM structural predictions positively reproduce the simulation data, including the rise of $S(k \to 0$) in the SW-SW model and the low-$k$ peak in the HS-SW structure factor. As for the phase behavior, RISM agrees with Monte Carlo simulations in predicting a gas-liquid coexistence for the SW-SW model (though the critical parameters appears overestimated by the theory) and its progressive disappearance moving toward the HS-SW model.Comment: 12 pages, 13 figures, 1 table, 78 reference

Three-dimensional entanglement: knots, knits and nets

Three-dimensional entanglement, including knots, periodic arrays of woven filaments (weavings) and periodic arrays of interpenetrating networks (nets), forms an integral part of the analysis of structure within the natural sciences. This thesis constructs a catalogue of 3-periodic entanglements via a scaffold of Triply-Periodic Minimal Surfaces (TPMS). The two-dimensional Hyperbolic plane can be wrapped over a TPMS in much the same way as the two-dimensional Euclidean plane can be wrapped over a cylinder. Thus vertices and edges of free tilings of the Hyperbolic plane, which are tilings by tiles of infinite size, can be wrapped over a TPMS to represent vertices and edges of an array in three-dimensional Euclidean space. In doing this, we harness the simplicity of a two-dimensional surface as compared with 3D space to build our catalogue. We numerically tighten these entangled flexible knits and nets to an ideal conformation that minimises the ratio of edge (or filament) length to diameter. To enable the tightening of periodic entanglements which may contain vertices, we extend the Shrink-On-No-Overlaps algorithm, a simple and fast algorithm for tightening finite knots and links. The ideal geometry of 3-periodic weavings found through the tightening process exposes an interesting physical property: Dilatancy. The cooperative straightening of the filaments with a fixed diameter induces an expansion of the material accompanied with an increase in the free volume of the material. Further, we predict a dilatant rod packing as the structure of the keratin matrix in the corneocytes of mammalian skin, where the dilatant property of the matrix allows the skin to maintain structural integrity while experiencing a large expansion during the uptake of water

Stable Frank-Kasper phases of self-assembled, soft matter spheres

Single molecular species can self-assemble into Frank Kasper (FK) phases, finite approximants of dodecagonal quasicrystals, defying intuitive notions that thermodynamic ground states are maximally symmetric. FK phases are speculated to emerge as the minimal-distortional packings of space-filling spherical domains, but a precise quantitation of this distortion and how it affects assembly thermodynamics remains ambiguous. We use two complementary approaches to demonstrate that the principles driving FK lattice formation in diblock copolymers emerge directly from the strong-stretching theory of spherical domains, in which minimal inter-block area competes with minimal stretching of space-filling chains. The relative stability of FK lattices is studied first using a diblock foam model with unconstrained particle volumes and shapes, which correctly predicts not only the equilibrium {\sigma} lattice, but also the unequal volumes of the equilibrium domains. We then provide a molecular interpretation for these results via self-consistent field theory, illuminating how molecular stiffness regulates the coupling between intra-domain chain configurations and the asymmetry of local packing. These findings shed new light on the role of volume exchange on the formation of distinct FK phases in copolymers, and suggest a paradigm for formation of FK phases in soft matter systems in which unequal domain volumes are selected by the thermodynamic competition between distinct measures of shape asymmetry.Comment: 40 pages, 22 figure

VLSI Routing for Advanced Technology

Routing is a major step in VLSI design, the design process of complex integrated circuits (commonly known as chips). The basic task in routing is to connect predetermined locations on a chip (pins) with wires which serve as electrical connections. One main challenge in routing for advanced chip technology is the increasing complexity of design rules which reflect manufacturing requirements. In this thesis we investigate various aspects of this challenge. First, we consider polygon decomposition problems in the context of VLSI design rules. We introduce different width notions for polygons which are important for width-dependent design rules in VLSI routing, and we present efficient algorithms for computing width-preserving decompositions of rectilinear polygons into rectangles. Such decompositions are used in routing to allow for fast design rule checking. A main contribution of this thesis is an O(n) time algorithm for computing a decomposition of a simple rectilinear polygon with n vertices into O(n) rectangles, preseverving two-dimensional width. Here the two-dimensional width at a point of the polygon is defined as the edge length of a largest square that contains the point and is contained in the polygon. In order to obtain these results we establish a connection between such decompositions and Voronoi diagrams. Furthermore, we consider implications of multiple patterning and other advanced design rules for VLSI routing. The main contribution in this context is the detailed description of a routing approach which is able to manage such advanced design rules. As a main algorithmic concept we use multi-label shortest paths where certain path properties (which model design rules) can be enforced by defining labels assigned to path vertices and allowing only certain label transitions. The described approach has been implemented in BonnRoute, a VLSI routing tool developed at the Research Institute for Discrete Mathematics, University of Bonn, in cooperation with IBM. We present experimental results confirming that a flow combining BonnRoute and an external cleanup step produces far superior results compared to an industry standard router. In particular, our proposed flow runs more than twice as fast, reduces the via count by more than 20%, the wiring length by more than 10%, and the number of remaining design rule errors by more than 60%. These results obtained by applying our multiple patterning approach to real-world chip instances provided by IBM are another main contribution of this thesis. We note that IBM uses our proposed combined BonnRoute flow as the default tool for signal routing