Simulating Three-Dimensional Hydrodynamics on a Cellular-Automata Machine

We demonstrate how three-dimensional fluid flow simulations can be carried out on the Cellular Automata Machine 8 (CAM-8), a special-purpose computer for cellular-automata computations. The principal algorithmic innovation is the use of a lattice-gas model with a 16-bit collision operator that is specially adapted to the machine architecture. It is shown how the collision rules can be optimized to obtain a low viscosity of the fluid. Predictions of the viscosity based on a Boltzmann approximation agree well with measurements of the viscosity made on CAM-8. Several test simulations of flows in simple geometries -- channels, pipes, and a cubic array of spheres -- are carried out. Measurements of average flux in these geometries compare well with theoretical predictions.Comment: 19 pages, REVTeX and epsf macros require

Unravelling cell migration: defining movement from the cell surface

Cell motility is essential for life and development. Unfortunately, cell migration is also linked to several pathological processes, such as cancer metastasis. Cells’ ability to migrate relies on many actors. Cells change their migratory strategy based on their phenotype and the properties of the surrounding microenvironment. Cell migration is, therefore, an extremely complex phenomenon. Researchers have investigated cell motility for more than a century. Recent discoveries have uncovered some of the mysteries associated with the mechanisms involved in cell migration, such as intracellular signaling and cell mechanics. These findings involve different players, including transmembrane receptors, adhesive complexes, cytoskeletal components , the nucleus, and the extracellular matrix. This review aims to give a global overview of our current understanding of cell migration

Unconventional programming: non-programmable systems

Die Forschung aus dem Bereich der unkonventionellen und natürlichen Informationsverarbeitungssysteme verspricht kontrollierbare Rechenprozesse in ungewöhnlichen Medien zu realisieren, zum Beispiel auf der molekularen Ebene oder in Bakterienkolonien. Vielversprechende Eigenschaften dieser Systeme sind das nichtlineare Verhalten und der hohe Verknüpfungsgrad der beteiligten Komponenten in Analogie zu Neuronen im Gehirn. Da aber Programmierung meist auf Prinzipien wie Modularisierung, Kapselung und Vorhersagbarkeit beruht sind diese Systeme oft schwer- bzw. unprogrammierbar. Im Gegensatz zu vielen Arbeiten über unkonventionelle Rechensysteme soll in dieser Arbeit aber nicht hauptsächlich nach neuen rechnenden Systemen und Anwendungen dieser gesucht werden. Stattdessen konzentriert sich diese Dissertation auf unkonventionelle Programmieransätze, die sowohl für unkonventionelle Computer als auch für herkommliche digitale Rechner neue Perspektiven eröffnen sollen. Hauptsächlich in Bezug auf ein Modell künstlicher chemischer Neuronen werden Ansätze für unkonventionelle Programmierverfahren, basierend auf Evolutionären Algorithmen, Informationstheorie und Selbstorganisation bis hin zur Selbstassemblierung untersucht. Ein spezielles Augenmerk liegt dabei auf dem Problem der Symbolkodierung: Oft gibt es mehrere oder sogar unendlich viele Möglichkeiten, Informationen in den Zuständen eines komplexen dynamischen Systems zu kodieren. In Neuronalen Netzen gibt es unter anderem die Spikefrequenz aber auch Populationskodes. In Abhängigkeit von den weiteren Eigenschaften des Systems, beispielsweise von der Informationsverarbeitungsaufgabe und dem gewünschten Eingabe-Ausgabeverhalten dürften sich verschiedene Kodierungen als unterschiedlich nützlich erweisen. Daher werden hier Methoden betrachtet um die verschiedene Symbolkodierungmethoden zu evaluieren, zu analysieren und um nach neuen, geeigneten Kodierungen zu suchen.Unconventional and natural computing research offers controlled information modification processes in uncommon media, for example on the molecular scale or in bacteria colonies. Promising aspects of such systems are often the non-linear behavior and the high connectivity of the involved information processing components in analogy to neurons in the nervous system. Unfortunately, such properties make the system behavior hard to understand, hard to predict and thus also hard to program with common engineering principles like modularization and composition, leading to the term of non-programmable systems. In contrast to many unconventional computing works that are often focused on finding novel computing substrates and potential applications, unconventional programming approaches for such systems are the theme of this thesis: How can new programming concepts open up new perspectives for unconventional but hopefully also for traditional, digital computing systems? Mostly based on a model of artificial wet chemical neurons, different unconventional programming approaches from evolutionary algorithms, information theory, self-organization and self-assembly are explored. A particular emphasis is given on the problem of symbol encodings: Often there are multiple or even an unlimited number of possibilities to encode information in the phase space of dynamical systems, e.g. spike frequencies or population coding in neural networks. But different encodings will probably be differently useful, dependent on the system properties, the information transformation task and the desired connectivity to other systems. Hence methods are investigated that can evaluate, analyse as well as identify suitable symbol encoding schemes

Cell Migration within 3D Microenvironments: an Integrative Perspective from the Membrane to the Nucleus

La migración celular es fundamental para la vida y el desarrollo. Desafortunadamente, la movilidad celular también está asociada con algunas de las principales causas de morbilidad y mortalidad, incluidos los trastornos inmunitarios, esqueléticos y cardiovasculares, así como la metástasis del cáncer. Las células dependen en su capacidad para percibir y responder a estímulos externos en muchos procesos fisiológicos y patológicos (p. ej., desarrollo embrionario, angiogénesis, reparación de tejidos y progresión tumoral). El objetivo global de esta tesis doctoral fue investigar la respuesta migratoria de células individuales a señales bioquímicas y biofísicas. En particular, el enfoque de esta investigación se centró en los mecanismos que permiten a las células percibir e internalizar señales bioquímicas y biofísicas y la influencia de estos estímulos en la respuesta migratoria de las células individuales.El primer estudio tuvo como objetivo establecer una metodología para facilitar la integración de estudios teóricos con datos experimentales. Al minimizar la intervención del usuario, el sistema propuesto basado en técnicas de optimización Bayesiana gestionó de manera eficiente la calibración de los modelos in silico, que de otro modo sería tediosa y propensa a errores. Posteriormente, se construyó un modelo in silico para investigar cómo los estímulos bioquímicos y biofísicos influyen en el movimiento celular en tres dimensiones. Este modelo computacional integró algunos de los principales actores que permiten a las células percibir y responder a señales externas, que pueden actuar a diferentes escalas e interactuar entre sí. Los resultados mostraron, por un lado, que las células cambian su comportamiento migratorio en función de la pendiente de los gradientes químicos y la concentración absoluta de factores químicos (por ejemplo, factores de crecimiento) a su alrededor. Por otro lado, estos resultados revelaron que la respuesta migratoria de las células a la rigidez y densidad de la matriz depende de su fenotipo. En general, la tesis destaca la dependencia de la migración celular tridimensional al fenotipo de las células (es decir, el tamaño de su núcleo, la deformabilidad del mismo) y las propiedades del microambiente circundante (por ejemplo, el perfil químico, la rigidez de la matriz, el confinamiento).Cell migration is fundamental for life and development. Unfortunately, cell motility is also associated with some of the leading causes of morbidity and mortality, including immune, skeletal, and cardiovascular disorders as well as cancer metastasis. Cells rely on their ability to perceive and respond to external stimuli in many physiological and pathological processes (e.g., embryonic development, angiogenesis, tissue repair, and tumor progression). The global objective of this doctoral thesis was to investigate the migratory response of individual cells to biochemical and biophysical cues. In particular, the focus of this research was on the mechanisms enabling cells to perceive and internalize biochemical and biophysical cues and the influence of these stimuli on the migratory response of individual cells. The first study aimed at establishing a methodology to facilitate the integration of theoretical studies with experimental data. By minimizing user intervention, the proposed framework based on Bayesian optimization techniques efficiently handled the otherwise tedious and error-prone calibration of in silico models. Afterward, an in silico model was built to investigate how biochemical and biophysical stimuli influence three-dimensional cell motion. This computational model integrated some of the main actors enabling cells to probe and respond to external cues, which may act at different scales and interact with each other. The results showed, on the one hand, that cells change their migratory behavior based on the slope of chemical gradients and the absolute concentration of chemical factors (e.g., growth factors) around them. On the other hand, these results revealed that cells’ migratory response to matrix stiffness and density depends on their phenotype. Overall, this thesis highlights the dependence of three-dimensional cell migration on both cells’ phenotype (i.e., nucleus size, deformability) and the properties of the surrounding microenvironment (e.g., chemical profile, matrix rigidity, confinement).<br /

The 1991 3rd NASA Symposium on VLSI Design

Papers from the symposium are presented from the following sessions: (1) featured presentations 1; (2) very large scale integration (VLSI) circuit design; (3) VLSI architecture 1; (4) featured presentations 2; (5) neural networks; (6) VLSI architectures 2; (7) featured presentations 3; (8) verification 1; (9) analog design; (10) verification 2; (11) design innovations 1; (12) asynchronous design; and (13) design innovations 2

Aerospace Medicine and Biology - A cumulative index to a continuing bibliography

Cumulative index for abstracts of NASA documents on aerospace medicine and biolog

Three-dimensional lattice gas with minimal interactions

Proceedings of the Conference ``Euromech 287: Discrete Models in Fluid-Dynamics'', 1992, Ed. P. NelsonInternational audienceAn interaction has been added to the classical lattice gas model that exchanges momentum between sites. The hydrodynamic limit of the model can be obtained from a Chapman-Enskog expansion and all the coefficients can be expressed explicitly. The interaction contributions to viscous terms are independent of the initial interaction-free model and grow like r2. When the interaction range r is large enough, the pressure acquires a negative slope for certain densities. The model then has a phase transition, observed in simulations. Some examples of a three-dimensional phase separation are shown. Whatever the dimension of space, the model can be represented by a cellular automaton with only nearest neighbor communications, using messenger particles or photons. In 2 dimensions of space, this allows fitting the model into a 16 bit table adequate for a special purpose cellular automaton machine like the RAP1