Minkowski Tensors of Anisotropic Spatial Structure

This article describes the theoretical foundation of and explicit algorithms for a novel approach to morphology and anisotropy analysis of complex spatial structure using tensor-valued Minkowski functionals, the so-called Minkowski tensors. Minkowski tensors are generalisations of the well-known scalar Minkowski functionals and are explicitly sensitive to anisotropic aspects of morphology, relevant for example for elastic moduli or permeability of microstructured materials. Here we derive explicit linear-time algorithms to compute these tensorial measures for three-dimensional shapes. These apply to representations of any object that can be represented by a triangulation of its bounding surface; their application is illustrated for the polyhedral Voronoi cellular complexes of jammed sphere configurations, and for triangulations of a biopolymer fibre network obtained by confocal microscopy. The article further bridges the substantial notational and conceptual gap between the different but equivalent approaches to scalar or tensorial Minkowski functionals in mathematics and in physics, hence making the mathematical measure theoretic method more readily accessible for future application in the physical sciences

Introduction to relational programming

A new method of programming, called relational programming, is introduced. This is a style of programming in which entire relations are manipulated rather than individual data. This is analogous to functional programming, wherein entire functions are the value manipulated by the operators. Because of its ability to manipulate complex data structures other than lists, relational programming seems to have distinct advantages over other very high level languages. This paper introduces the basic concepts of relational programming and a preliminary notation for expressing them; it does not define a programming language, per se. (Author)Prepared for: Naval Postgraduate School, Monterey, California 93940. -- Cover.http://archive.org/details/introductiontore00maclN0001481WR10034N

Two Refinements of the Template-Guided DNA Recombination Model of Ciliate Computing

To solve the mystery of the intricate gene unscrambling mechanism in ciliates, various theoretical models for this process have been proposed from the point of view of computation. Two main models are the reversible guided recombination system by Kari and Landweber and the template-guided recombination (TGR) system by Prescott, Ehrenfeucht and Rozenberg, based on two categories of DNA recombination: the pointer guided and the template directed recombination respectively. The latter model has been generalized by Daley and McQuillan. In this thesis, we propose a new approach to generate regular languages using the iterated TGR system with a finite initial language and a finite set of templates, that reduces the size of the template language and the alphabet compared to that of the Daley-McQuillan model. To achieve computational completeness using only finite components we also propose an extension of the contextual template-guided recombination system (CTGR system) by Daley and McQuillan, by adding an extra control called permitting contexts on the usage of templates. Then we prove that our proposed system, the CTGR system using permitting contexts, has the capability to characterize the family of recursively enumerable languages using a finite initial language and a finite set of templates. Lastly, we present a comparison and analysis of the computational power of the reversible guided recombination system and the TGR system. Keywords: ciliates, gene unscrambling, in vivo computing, DNA computing, cellular computing, reversible guided recombination, template-guided recombination

NASA SBIR abstracts of 1990 phase 1 projects

The research objectives of the 280 projects placed under contract in the National Aeronautics and Space Administration (NASA) 1990 Small Business Innovation Research (SBIR) Phase 1 program are described. The basic document consists of edited, non-proprietary abstracts of the winning proposals submitted by small businesses in response to NASA's 1990 SBIR Phase 1 Program Solicitation. The abstracts are presented under the 15 technical topics within which Phase 1 proposals were solicited. Each project was assigned a sequential identifying number from 001 to 280, in order of its appearance in the body of the report. The document also includes Appendixes to provide additional information about the SBIR program and permit cross-reference in the 1990 Phase 1 projects by company name, location by state, principal investigator, NASA field center responsible for management of each project, and NASA contract number

Working Notes from the 1992 AAAI Spring Symposium on Practical Approaches to Scheduling and Planning

The symposium presented issues involved in the development of scheduling systems that can deal with resource and time limitations. To qualify, a system must be implemented and tested to some degree on non-trivial problems (ideally, on real-world problems). However, a system need not be fully deployed to qualify. Systems that schedule actions in terms of metric time constraints typically represent and reason about an external numeric clock or calendar and can be contrasted with those systems that represent time purely symbolically. The following topics are discussed: integrating planning and scheduling; integrating symbolic goals and numerical utilities; managing uncertainty; incremental rescheduling; managing limited computation time; anytime scheduling and planning algorithms, systems; dependency analysis and schedule reuse; management of schedule and plan execution; and incorporation of discrete event techniques

Economic Activity and Institutions

This paper is one of two working papers concerning the waste management sector transition project run from MERIT under the direction of René Kemp. This paper examines some of the numerous meanings and interpretations associated with the words “institution” and “institutions” and the different levels at which the two notions are employed. Institutionalism, institutionalization, institutional change and related terms are discussed followed by an examination of the links between “institutionalism” and the discipline of economics. The analytical, policy and political implications of the institutionalist approach are discussed and ways in which the institutionalist approach may be applied to changes in the economy during transitions are explored.Institutions, Institutional Analysis, Scale, Policy

Energetics of Biological Mechanics and Dynamics

Living matter is a class of soft matter systems that maintains itself away from thermodynamic equilibrium by the continual consumption of chemical energy. Indi- vidual proteins consume energy and break detailed balance to drive active force generation by molecular motors, force-dependent binding kinetics, and chemically driven (dis)assembly. These non-equilibrium dynamics propagate across heterogeneous structures to drive essential life processes such as replication, migration, and shape change at the scale of both single cells and multicellular tissues. While much work has been done to understand the molecular processes underlying each individual non-equilibrium behaviors, we lack a general understanding of how the microscopic breaking of detailed balance translates to large-scale cellular behaviors and materials properties.Using the tools of non-equilibrium thermodynamics, this thesis examines this question by measuring energy dissipation during dynamical and mechanical phase transitions seen in experiments, simulations, and theoretical models of biological materials. We choose the actomyosin cytoskeleton, a network composed of polymeric proteins (actin) that are driven away from thermodynamic equilibrium by the activity of molecular motors (myosin), as our model system. Actomyosin contains the three types of non-equilibrium driving we will focus on: force generation, non-equilibrium binding kinetics, and active (dis)assembly. At the subcellular level, analysis of actin filament motions in experiments shows that energy dissipated through bending controls the transition between stable and contractile steady states. Using simulations, we show that non-equilibrium binding kinetics of molecular motors controls a fluid-solid phase transition characterized by thermodynamic quantities with opposite symmetries under time-reversal. At the cellular level, we develop new tools for measuring irreversibility in spatiotemporal dynamics to analyze the energetic costs of oscillations and synchronization of a model biochemical oscillator inspired by (dis)assembly driven actomyosin dynamics. Throughout this thesis, we show that a cell’s distance from equilibrium, quantified by energy dissipation, tunes its mechanical properties and dynamics. This provides a framework to unify disparate biological function through the lens of non-equilibrium thermodynamics

Social Investment for Sustainability of Groundwater: A Revealed Preference Approach

Groundwater is a form of natural capital that is valued for the goods it provides, including ecosystem health, water quality, and water consumption. Degradation of groundwater could be alleviated through social investment such as for water reuse and desalination to reduce the need for withdrawals from groundwater. This paper develops a participatory planning process—based on combining revealed preference with economic optimization—to choose a desired future for sustaining groundwater. Generation of potential groundwater futures is based on an optimal control model with investment and withdrawal from groundwater as control variables. In this model, groundwater stock and aquatic health are included as inter-temporal public goods. The social discount rate expressing time preference—an important parameter that drives optimization—is revealed through the participatory planning process. To implement the chosen future, a new method of inter-temporal pricing is presented to finance investment and supply costs. Furthermore, it is shown that the desired social outcome could be achieved by a form of privatization in which the pricing method, the appropriate discount rate, and the planning period are contractually specifie