Computation, prediction, and experimental tests of fitness for bacteriophage T7 mutants with permuted genomes

We created a simulation based on experimental data from bacteriophage T7 that computes the developmental cycle of the wild-type phage and also of mutants that have an altered genome order. We used the simulation to compute the fitness of more than 105 mutants. We tested these computations by constructing and experimentally characterizing T7 mutants in which we repositioned gene 1, coding for T7 RNA polymerase. Computed protein synthesis rates for ectopic gene 1 strains were in moderate agreement with observed rates. Computed phage-doubling rates were close to observations for two of four strains, but significantly overestimated those of the other two. Computations indicate that the genome organization of wild-type T7 is nearly optimal for growth: only 2.8% of random genome permutations were computed to grow faster, the highest 31% faster, than wild type. Specific discrepancies between computations and observations suggest that a better understanding of the translation efficiency of individual mRNAs and the functions of qualitatively “nonessential” genes will be needed to improve the T7 simulation. In silico representations of biological systems can serve to assess and advance our understanding of the underlying biology. Iteration between computation, prediction, and observation should increase the rate at which biological hypotheses are formulated and tested.

Molecular computation: RNA solutions to chess problems

We have expanded the field of “DNA computers” to RNA and present a general approach for the solution of satisfiability problems. As an example, we consider a variant of the “Knight problem,” which asks generally what configurations of knights can one place on an n × n chess board such that no knight is attacking any other knight on the board. Using specific ribonuclease digestion to manipulate strands of a 10-bit binary RNA library, we developed a molecular algorithm and applied it to a 3 × 3 chessboard as a 9-bit instance of this problem. Here, the nine spaces on the board correspond to nine “bits” or placeholders in a combinatorial RNA library. We recovered a set of “winning” molecules that describe solutions to this problem.

Computation of Surface Electrical Potentials of Plant Cell Membranes : Correspondence to Published Zeta Potentials from Diverse Plant Sources

A Gouy-Chapman-Stern model has been developed for the computation of surface electrical potential (ψ0) of plant cell membranes in response to ionic solutes. The present model is a modification of an earlier version developed to compute the sorption of ions by wheat (Triticum aestivum L. cv Scout 66) root plasma membranes. A single set of model parameters generates values for ψ0 that correlate highly with published ζ potentials of protoplasts and plasma membrane vesicles from diverse plant sources. The model assumes ion binding to a negatively charged site (R− = 0.3074 μmol m−2) and to a neutral site (P0 = 2.4 μmol m−2) according to the reactions R− + IΖ ⇌ RIΖ−1 and P0 + IΖ ⇌ PIΖ, where IΖ represents an ion of charge Ζ. Binding constants for the negative site are 21,500 m−1 for H+, 20,000 m−1 for Al3+, 2,200 m−1 for La3+, 30 m−1 for Ca2+ and Mg2+, and 1 m−1 for Na+ and K+. Binding constants for the neutral site are 1/180 the value for binding to the negative site. Ion activities at the membrane surface, computed on the basis of ψ0, appear to determine many aspects of plant-mineral interactions, including mineral nutrition and the induction and alleviation of mineral toxicities, according to previous and ongoing studies. A computer program with instructions for the computation of ψ0, ion binding, ion concentrations, and ion activities at membrane surfaces may be requested from the authors.

The evolution of emergent computation.

A simple evolutionary process can discover sophisticated methods for emergent information processing in decentralized spatially extended systems. The mechanisms underlying the resulting emergent computation are explicated by a technique for analyzing particle-based logic embedded in pattern-forming systems. Understanding how globally coordinated computation can emerge in evolution is relevant both for the scientific understanding of natural information processing and for engineering new forms of parallel computing systems.

Rapid local synchronization of action potentials: toward computation with coupled integrate-and-fire neurons.

The collective behavior of interconnected spiking nerve cells is investigated. It is shown that a variety of model systems exhibit the same short-time behavior and rapidly converge to (approximately) periodic firing patterns with locally synchronized action potentials. The dynamics of one model can be described by a downhill motion on an abstract energy landscape. Since an energy landscape makes it possible to understand and program computation done by an attractor network, the results will extend our understanding of collective computation from models based on a firing-rate description to biologically more realistic systems with integrate-and-fire neurons.

Estudio y mejora de métodos de registro 3D: aceleración sobre unidades de procesamiento gráfico y caracterización del espacio de transformaciones iniciales

Durante los últimos años ha sido creciente el uso de las unidades de procesamiento gráfico, más conocidas como GPU (Graphic Processing Unit), en aplicaciones de propósito general, dejando a un lado el objetivo para el que fueron creadas y que no era otro que el renderizado de gráficos por computador. Este crecimiento se debe en parte a la evolución que han experimentado estos dispositivos durante este tiempo y que les ha dotado de gran potencia de cálculo, consiguiendo que su uso se extienda desde ordenadores personales a grandes cluster. Este hecho unido a la proliferación de sensores RGB-D de bajo coste ha hecho que crezca el número de aplicaciones de visión que hacen uso de esta tecnología para la resolución de problemas, así como también para el desarrollo de nuevas aplicaciones. Todas estas mejoras no solamente se han realizado en la parte hardware, es decir en los dispositivos, sino también en la parte software con la aparición de nuevas herramientas de desarrollo que facilitan la programación de estos dispositivos GPU. Este nuevo paradigma se acuñó como Computación de Propósito General sobre Unidades de Proceso Gráfico (General-Purpose computation on Graphics Processing Units, GPGPU). Los dispositivos GPU se clasifican en diferentes familias, en función de las distintas características hardware que poseen. Cada nueva familia que aparece incorpora nuevas mejoras tecnológicas que le permite conseguir mejor rendimiento que las anteriores. No obstante, para sacar un rendimiento óptimo a un dispositivo GPU es necesario configurarlo correctamente antes de usarlo. Esta configuración viene determinada por los valores asignados a una serie de parámetros del dispositivo. Por tanto, muchas de las implementaciones que hoy en día hacen uso de los dispositivos GPU para el registro denso de nubes de puntos 3D, podrían ver mejorado su rendimiento con una configuración óptima de dichos parámetros, en función del dispositivo utilizado. Es por ello que, ante la falta de un estudio detallado del grado de afectación de los parámetros GPU sobre el rendimiento final de una implementación, se consideró muy conveniente la realización de este estudio. Este estudio no sólo se realizó con distintas configuraciones de parámetros GPU, sino también con diferentes arquitecturas de dispositivos GPU. El objetivo de este estudio es proporcionar una herramienta de decisión que ayude a los desarrolladores a la hora implementar aplicaciones para dispositivos GPU. Uno de los campos de investigación en los que más prolifera el uso de estas tecnologías es el campo de la robótica ya que tradicionalmente en robótica, sobre todo en la robótica móvil, se utilizaban combinaciones de sensores de distinta naturaleza con un alto coste económico, como el láser, el sónar o el sensor de contacto, para obtener datos del entorno. Más tarde, estos datos eran utilizados en aplicaciones de visión por computador con un coste computacional muy alto. Todo este coste, tanto el económico de los sensores utilizados como el coste computacional, se ha visto reducido notablemente gracias a estas nuevas tecnologías. Dentro de las aplicaciones de visión por computador más utilizadas está el registro de nubes de puntos. Este proceso es, en general, la transformación de diferentes nubes de puntos a un sistema de coordenadas conocido. Los datos pueden proceder de fotografías, de diferentes sensores, etc. Se utiliza en diferentes campos como son la visión artificial, la imagen médica, el reconocimiento de objetos y el análisis de imágenes y datos de satélites. El registro se utiliza para poder comparar o integrar los datos obtenidos en diferentes mediciones. En este trabajo se realiza un repaso del estado del arte de los métodos de registro 3D. Al mismo tiempo, se presenta un profundo estudio sobre el método de registro 3D más utilizado, Iterative Closest Point (ICP), y una de sus variantes más conocidas, Expectation-Maximization ICP (EMICP). Este estudio contempla tanto su implementación secuencial como su implementación paralela en dispositivos GPU, centrándose en cómo afectan a su rendimiento las distintas configuraciones de parámetros GPU. Como consecuencia de este estudio, también se presenta una propuesta para mejorar el aprovechamiento de la memoria de los dispositivos GPU, permitiendo el trabajo con nubes de puntos más grandes, reduciendo el problema de la limitación de memoria impuesta por el dispositivo. El funcionamiento de los métodos de registro 3D utilizados en este trabajo depende en gran medida de la inicialización del problema. En este caso, esa inicialización del problema consiste en la correcta elección de la matriz de transformación con la que se iniciará el algoritmo. Debido a que este aspecto es muy importante en este tipo de algoritmos, ya que de él depende llegar antes o no a la solución o, incluso, no llegar nunca a la solución, en este trabajo se presenta un estudio sobre el espacio de transformaciones con el objetivo de caracterizarlo y facilitar la elección de la transformación inicial a utilizar en estos algoritmos.

Japanese virtual communication survey : a brief analysis of contemporary graphic designers from Japan

To research graphic design in a globalized context it is primordial to consider cultural, social, historical and even anthropological studies to fully understand the aesthetics’ choices made by the designer’s. Being the “Japanese graphic design” a topic still to be better understand in the West, it is mandatory to gather information from primary sources. These data will be analyzed with support of secondary sources of information about Japanese visual communication, social and cultural studies. This paper presents comments about the result of a survey applied to 105 Japanese graphic designers. The survey was designed with 44 questions. The original survey, to better follow this report can be found in www.studiohobo.com/CONVERGENCIAS/Flavio_Hobo_Survey.pdf

Mr. Monis's computation about printing his Hebrew Grammar, [ca. 1734]

A one-page handwritten computation by Judah Monis for printing the Hebrew Grammar and binding it in sheep and calf skins. The document was written on one folio-sized leaf that is torn in two pieces.

Barnstable, Massachusetts 15 Minute Digital Raster Graphic

This layer is a digital raster graphic of the historic 15-minute USGS topographic quadrangle map of Barnstable, Massachusetts. The edition date is 1893 and the map was reprinted in 1907. A digital raster graphic (DRG) is a scanned image of a U.S. Geological Survey (USGS) standard series topographic map, including all map collar information. The image inside the map neatline is geo-referenced to the surface of the earth and fit to the Universal Transverse Mercator projection. The horizontal positional accuracy and datum of the DRG matches the accuracy and datum of the source map. The names of quadrangles which border this one appear on the map collar in their respective positions (N,S,E,W) in relation to this map.

Barre, Massachusetts 15 Minute Digital Raster Graphic

This layer is a digital raster graphic of the historic 15-minute USGS topographic quadrangle map of Barre, Massachusetts. The suvery (ground condition) date is 1887, the edition date is March, 1894 and the map was reprinted in 1942. A digital raster graphic (DRG) is a scanned image of a U.S. Geological Survey (USGS) standard series topographic map, including all map collar information. The image inside the map neatline is geo-referenced to the surface of the earth and fit to the Universal Transverse Mercator projection. The horizontal positional accuracy and datum of the DRG matches the accuracy and datum of the source map. The names of quadrangles which border this one appear on the map collar in their respective positions (N,S,E,W) in relation to this map.

Becket, Massachusetts 15 Minute Digital Raster Graphic

This layer is a digital raster graphic of the historic 15-minute USGS topographic quadrangle map of Becket, Massachusetts. The survey (ground condition) date is 1886. A digital raster graphic (DRG) is a scanned image of a U.S. Geological Survey (USGS) standard series topographic map, including all map collar information. The image inside the map neatline is geo-referenced to the surface of the earth and fit to the Universal Transverse Mercator projection. The horizontal positional accuracy and datum of the DRG matches the accuracy and datum of the source map. The names of quadrangles which border this one appear on the map collar in their respective positions (N,S,E,W) in relation to this map.

Belchertown, Massachusetts 15 Minute Digital Raster Graphic

This layer is a digital raster graphic of the historic 15-minute USGS topographic map of the Belchertown, Massachusetts quadrangle. The suvey (ground condition) dates are 1885 and 1887; the edition date is November, 1893. A digital raster graphic (DRG) is a scanned image of a U.S. Geological Survey (USGS) standard series topographic map, including all map collar information. The image inside the map neatline is geo-referenced to the surface of the earth and fit to the Universal Transverse Mercator projection. The horizontal positional accuracy and datum of the DRG matches the accuracy and datum of the source map. The names of quadrangles which border this one appear on the map collar in their respective positions (N,S,E,W) in relation to this map.

Berlin (N.Y.) Massachusetts 15 Minute Digital Raster Graphic

This layer is a digital raster graphic of the historic 15-minute USGS topographic quadrangle map entitled Berlin, (N.Y.) which also shows towns and features in Massachusetts. The survey dates (ground condition) for this map are 1885-88, and the edition date is 1890. A digital raster graphic (DRG) is a scanned image of a U.S. Geological Survey (USGS) standard series topographic map, including all map collar information. The image inside the map neatline is geo-referenced to the surface of the earth and fit to the Universal Transverse Mercator projection. The horizontal positional accuracy and datum of the DRG matches the accuracy and datum of the source map. The names of quadrangles which border this one appear on the map collar in their respective positions (N,S,E,W) in relation to this map.