The genetics of parallel evolution: a case study using thermal and non-thermal ecotypes of Mimulus guttatus from Yellowstone National Park

Understanding the genetic mechanisms of adaptation has long been a goal of evolutionary biologists. However, the predictability of genetic change across adaptive events and the patterns observed during adaptive transitions across species remain poorly understood. Numerous parallel evolutionary transitions within the model plant genus Mimulus (monkeyflowers) provide a wonderful comparative context for investigating the predictability of the underlying mechanisms. Because multiple traits, with inherent differences in the underlying molecular pathways and potentially different vulnerabilities to negative pleiotropy, are often involved in parallel adaptation to harsh edaphic conditions, the diversity in Mimulus provides an opportunity to compare genetic architecture among traits as well as among transitions. Here, I use the yellow monkeyflower (Mimulus guttatus) to investigate the genetic basis of edaphic adaptive divergence along a thermal soil gradient in Yellowstone National Park (YNP). Thermal and non-thermal M. guttatus are differentiated for annuality/perenniality, flowering time, mating system, and two more putatively adaptive traits; trichome production and pigment patterning. I employ a targeted comparative quantitative trait loci (QTL) analysis to ask whether the genetics underlying the transitions I observe in YNP are the same or different compared to parallel phenotypic transitions previously characterized within the M. guttatus species complex. I found a parallel genetic basis for some traits and a disparate basis for others. The evolution of annuality (and associated traits) in thermal M. guttatus is accomplished through novel genetic mechanisms as compared to parallel phenotypic transitions in Mimulus. While the genetic architecture of early flowering, reproductive output, and allocation to vegetative growth is not highly conserved, a striking number of target regions implicated in other transitions are involved in this system. I found reduced complexity in the architecture underlying early trichome production. Finally, the genetic architecture involved in anthocyanin production in YNP is highly conserved and predictable based on previous work in Mimulus and other flowering plants. My research elucidates the genetic basis of thermal/non-thermal divergence of M. guttatus in YNP. It also provides an important comparative context for evolutionary trajectories within the M. guttatus species complex and amongst other parallel, adaptive evolutionary transitions

PRAIS: Distributed, real-time knowledge-based systems made easy

This paper discusses an architecture for real-time, distributed (parallel) knowledge-based systems called the Parallel Real-time Artificial Intelligence System (PRAIS). PRAIS strives for transparently parallelizing production (rule-based) systems, even when under real-time constraints. PRAIS accomplishes these goals by incorporating a dynamic task scheduler, operating system extensions for fact handling, and message-passing among multiple copies of CLIPS executing on a virtual blackboard. This distributed knowledge-based system tool uses the portability of CLIPS and common message-passing protocols to operate over a heterogeneous network of processors

Extensible Component Based Architecture for FLASH, A Massively Parallel, Multiphysics Simulation Code

FLASH is a publicly available high performance application code which has evolved into a modular, extensible software system from a collection of unconnected legacy codes. FLASH has been successful because its capabilities have been driven by the needs of scientific applications, without compromising maintainability, performance, and usability. In its newest incarnation, FLASH3 consists of inter-operable modules that can be combined to generate different applications. The FLASH architecture allows arbitrarily many alternative implementations of its components to co-exist and interchange with each other, resulting in greater flexibility. Further, a simple and elegant mechanism exists for customization of code functionality without the need to modify the core implementation of the source. A built-in unit test framework providing verifiability, combined with a rigorous software maintenance process, allow the code to operate simultaneously in the dual mode of production and development. In this paper we describe the FLASH3 architecture, with emphasis on solutions to the more challenging conflicts arising from solver complexity, portable performance requirements, and legacy codes. We also include results from user surveys conducted in 2005 and 2007, which highlight the success of the code.Comment: 33 pages, 7 figures; revised paper submitted to Parallel Computin

Integration of a parallel-architecture delta robot into a virtualized production system

ilustraciones, diagramas, fotografíasEl propósito de este trabajo final de maestría es diseñar, desarrollar, construir y validar un prototipo de robot de arquitectura paralela tipo delta de tres grados de libertad con tres actuadores rotacionales e integrarlo a una fábrica virtual con el fin de ejecutar operaciones de pick and place haciendo uso de un gemelo digital y funcionalidades ciberfísicas. En la parte inicial de este documento se presentan las bases matemáticas y geométricas para desarrollar un robot delta. Se muestran de manera numérica y gráfica ejemplos de cinemática directa e inversa. Para la etapa de diseño se parte de una lista de requerimientos, posteriormente se plantea una arquitectura de hardware, de software y de control, se construyen las bases de los sistemas mecánico, eléctrico y electrónico y se desarrolla un algoritmo para la generación de trayectorias lineales en el espacio. Adicionalmente, se genera un gemelo digital del robot que permita comprobar movimientos, posibles colisiones y el espacio de trabajo del robot. En la etapa de implementación se procede a la construcción mecánica, eléctrica y electrónica, se realizan rutinas de control, se desarrolla una interfaz gráfica para el control y monitoreo del robot y se implementan dentro del controlador de movimiento los modelos matemáticos de cinemática directa, cinemática inversa y el algoritmo para la generación de trayectorias lineales en el espacio. Haciendo uso del robot construido se realizan ejercicios de movimientos lineales con el fin de determinar el desempeño del prototipo. Posteriormente, haciendo uso de funcionalidades ciberfísicas, se integra el prototipo de robot delta construido, con un modelo de fábrica virtual para ejecutar tareas de pick and place. Finalmente, se describen los resultados obtenidos y las recomendaciones para el desarrollo de un robot delta y su integración con un modelo de fábrica virtual haciendo uso de funcionalidades ciberfísicas. (Texto tomado de la fuente)This master’s degree final project aims to design, develop, build, and validate a prototype of a robot of a three-degree of freedom delta type parallel architecture using three rotary actuators and its integration to a virtual factory model in order to execute pick and place operations by using a digital twin and cyber-physical functionalities. The initial part of this document presents the mathematical and geometrical basic concepts to develop a delta robot. It provides examples of forward and inverse kinematics, along with numeric and graphic representations. The design phase begins with a list of requirements and then proposes an architecture of hardware, software and control, establishes the bases for the mechanical, electrical and electronic systems and develops an algorithm for linear trajectory generation in space. Additionally, a digital twin of the robot is created to test its movements, possible collisions, and workspace. The implementation stage carries out the mechanical, electric, and electronic construction, the execution of control routines, the development of a graphical user interface to control and monitor the robot as well as the implementation of forward and inverse mathematical models of kinematics and the algorithm for linear trajectory generation in space into the motion controller. The built robot permits us to practice lineal movement exercises to determine the prototype performance. Then, applying cyber-physical functionalities, the built delta robot prototype is integrated with a virtual factory model to execute pick and place tasks. Finally, the achieved results and the recommendations to develop a delta robot and its integration to a virtual factory model by using cyber-physical functionalities are fully described.MaestríaMagíster en Ingeniería - Automatización IndustrialAutomatización en la industria colombian

Consequences of Proportional Systems in Architecture

The system of architecture inscribed by Vitruvius in De Architectura and famously drawn by Leonardo da Vinci in 1490, as well as Cesar Cesariano after him in 1521, has provided modern architecture and art historians with argumentation for placing the architectural object at the centre of a system of relations between symmetry, geometry and proportion. When one looks at the last 100 years, this system of relations can be seen to have regulated, in varying ways, architectural design methodology since its ‘rediscovery’ and re-inscription into architectural discourse in the middle of the 20th century by the architecture and art historians, such as Rudolf Wittkower in his book Architectural Principles in the Age of Humanism (1949) and the essays by Colin Rowe titled “The Mathematics of the Ideal Villa” (Architectural Review, 1947) and “Mannerism and Modernism” (Architectural Review, 1950). This paper, which is a work-in-progress excerpt from PhD research by the author, argues that these works established a dominant fiction(1) in the discipline of architecture, or a way for architects to perceive and interpret the built environment. However, with advances in the technology of production in the last twenty years, and, in parallel, the development of contemporary discourses of computation and digital design in relationship to the natural sciences, this system can be questioned and the dialogue between forms of production, systems of proportion and architecture re-opened.1 – The term ‘dominant fiction’ was outlined in Silverman, Kaja. Male Subjectivities at the Margin, Psychology Press (1992)

The BaBar Prompt Reconstruction manager: A real life example of a constructive approach to software development

The need for a working system to automate the Online Prompt Reconstruction (OPR) subsystem has led the members of the OPR group to develop their system using the software cycles development model. Starting with a complete design, they have implemented the system in each cycle using multi-paradigm methods, combining different techniques and languages and enhancing the working system gradually while using it in the production phase. The OPR software has evolved from a set of shell scripts, which were run manually, into a set of partially automated Perl/shell scripts. These will be transformed into a completely automated system based on Perl/C++/Java code with a CORBA distributed architecture, able to execute parallel/multiple PR jobs on a farm of Unix machines