From Cnn Dynamics to Cellular Wave Computers
NASA Astrophysics Data System (ADS)
Roska, Tamas
2013-01-01
Embedded in a historical overview, the development of the Cellular Wave Computing paradigm is presented, starting from the standard CNN dynamics. The theoretical aspects, the physical implementation, the innovation process, as well as the biological relevance are discussed in details. Finally, the latest developments, the physical versus virtual cellular machines, as well as some open questions are presented.
Computer-Automated Static, Dynamic and Cellular Bone Histomorphometry
Hong, Seung-Hyun; Jiang, Xi; Chen, Li; Josh, Pujan; Shin, Dong-Guk; Rowe, David
2013-01-01
Dynamic and cellular histomorphometry of trabeculae is the most biologically relevant way of assessing steady state bone health. Traditional measurement involves manual visual feature identification by a trained and qualified professional. Inherent with this methodology is the time and cost expenditure, as well as the subjectivity that naturally arises under human visual inspection. In this work, we propose a rapidly deployable, automated, and objective method for dynamic histomorphometry. We demonstrate that our method is highly effective in assessing cellular activities in distal femur and vertebra of mice which are injected with calcein and alizarin complexone 7 and 2 days prior to sacrifice. The mineralized bone tissues of mice are cryosectioned using a tape transfer protocol. A sequential workflow is implemented in which endogenous fluorescent signals (bone mineral, green and red mineralization lines), tartrate resistant acid phosphatase identified by ELF-97 and alkaline phosphatase identified by Fast Red are captured as individual tiled images of the section for each fluorescent color. All the images are then submitted to an image analysis pipeline that automates identification of the mineralized regions of bone and selection of a region of interest. The TRAP and AP stained images are aligned to the mineralized image using strategically placed fluorescent registration beads. Fluorescent signals are identified and are related to the trabecular surface within the ROI. Subsequently, the pipelined method computes static measurements, dynamic measurements, and cellular activities of osteoclast and osteoblast related to the trabecular surface. Our method has been applied to the distal femurs and vertebrae of 8 and 16 week old male and female C57Bl/6J mice. The histomorphometric results reveal a significantly greater bone turnover rate in female in contrast to male irrespective of age, validating similar outcomes reported by other studies. PMID:25019033
A full computation-relevant topological dynamics classification of elementary cellular automata
NASA Astrophysics Data System (ADS)
Schüle, Martin; Stoop, Ruedi
2012-12-01
Cellular automata are both computational and dynamical systems. We give a complete classification of the dynamic behaviour of elementary cellular automata (ECA) in terms of fundamental dynamic system notions such as sensitivity and chaoticity. The "complex" ECA emerge to be sensitive, but not chaotic and not eventually weakly periodic. Based on this classification, we conjecture that elementary cellular automata capable of carrying out complex computations, such as needed for Turing-universality, are at the "edge of chaos."
Naudé, Jérémie; Cessac, Bruno; Berry, Hugues; Delord, Bruno
2013-09-18
Homeostatic intrinsic plasticity (HIP) is a ubiquitous cellular mechanism regulating neuronal activity, cardinal for the proper functioning of nervous systems. In invertebrates, HIP is critical for orchestrating stereotyped activity patterns. The functional impact of HIP remains more obscure in vertebrate networks, where higher order cognitive processes rely on complex neural dynamics. The hypothesis has emerged that HIP might control the complexity of activity dynamics in recurrent networks, with important computational consequences. However, conflicting results about the causal relationships between cellular HIP, network dynamics, and computational performance have arisen from machine-learning studies. Here, we assess how cellular HIP effects translate into collective dynamics and computational properties in biological recurrent networks. We develop a realistic multiscale model including a generic HIP rule regulating the neuronal threshold with actual molecular signaling pathways kinetics, Dale's principle, sparse connectivity, synaptic balance, and Hebbian synaptic plasticity (SP). Dynamic mean-field analysis and simulations unravel that HIP sets a working point at which inputs are transduced by large derivative ranges of the transfer function. This cellular mechanism ensures increased network dynamics complexity, robust balance with SP at the edge of chaos, and improved input separability. Although critically dependent upon balanced excitatory and inhibitory drives, these effects display striking robustness to changes in network architecture, learning rates, and input features. Thus, the mechanism we unveil might represent a ubiquitous cellular basis for complex dynamics in neural networks. Understanding this robustness is an important challenge to unraveling principles underlying self-organization around criticality in biological recurrent neural networks. PMID:24048833
Luitel, Bipul; Venayagamoorthy, Ganesh Kumar
2014-02-01
Neural networks for implementing large networked systems such as smart electric power grids consist of multiple inputs and outputs. Many outputs lead to a greater number of parameters to be adapted. Each additional variable increases the dimensionality of the problem and hence learning becomes a challenge. Cellular computational networks (CCNs) are a class of sparsely connected dynamic recurrent networks (DRNs). By proper selection of a set of input elements for each output variable in a given application, a DRN can be modified into a CCN which significantly reduces the complexity of the neural network and allows use of simple training methods for independent learning in each cell thus making it scalable. This article demonstrates this concept of developing a CCN using dimensionality reduction in a DRN for scalability and better performance. The concept has been analytically explained and empirically verified through application. PMID:24300549
Papadimitriou, Konstantinos I.; Stan, Guy-Bart V.; Drakakis, Emmanuel M.
2013-01-01
This paper presents a novel method for the systematic implementation of low-power microelectronic circuits aimed at computing nonlinear cellular and molecular dynamics. The method proposed is based on the Nonlinear Bernoulli Cell Formalism (NBCF), an advanced mathematical framework stemming from the Bernoulli Cell Formalism (BCF) originally exploited for the modular synthesis and analysis of linear, time-invariant, high dynamic range, logarithmic filters. Our approach identifies and exploits the striking similarities existing between the NBCF and coupled nonlinear ordinary differential equations (ODEs) typically appearing in models of naturally encountered biochemical systems. The resulting continuous-time, continuous-value, low-power CytoMimetic electronic circuits succeed in simulating fast and with good accuracy cellular and molecular dynamics. The application of the method is illustrated by synthesising for the first time microelectronic CytoMimetic topologies which simulate successfully: 1) a nonlinear intracellular calcium oscillations model for several Hill coefficient values and 2) a gene-protein regulatory system model. The dynamic behaviours generated by the proposed CytoMimetic circuits are compared and found to be in very good agreement with their biological counterparts. The circuits exploit the exponential law codifying the low-power subthreshold operation regime and have been simulated with realistic parameters from a commercially available CMOS process. They occupy an area of a fraction of a square-millimetre, while consuming between 1 and 12 microwatts of power. Simulations of fabrication-related variability results are also presented. PMID:23393550
Li, Yanjun; Solomon, Thomas P. J.; Haus, Jacob M.; Saidel, Gerald M.; Cabrera, Marco E.
2010-01-01
Identifying the mechanisms by which insulin regulates glucose metabolism in skeletal muscle is critical to understanding the etiology of insulin resistance and type 2 diabetes. Our knowledge of these mechanisms is limited by the difficulty of obtaining in vivo intracellular data. To quantitatively distinguish significant transport and metabolic mechanisms from limited experimental data, we developed a physiologically based, multiscale mathematical model of cellular metabolic dynamics in skeletal muscle. The model describes mass transport and metabolic processes including distinctive processes of the cytosol and mitochondria. The model simulated skeletal muscle metabolic responses to insulin corresponding to human hyperinsulinemic-euglycemic clamp studies. Insulin-mediated rate of glucose disposal was the primary model input. For model validation, simulations were compared with experimental data: intracellular metabolite concentrations and patterns of glucose disposal. Model variations were simulated to investigate three alternative mechanisms to explain insulin enhancements: Model 1 (M.1), simple mass action; M.2, insulin-mediated activation of key metabolic enzymes (i.e., hexokinase, glycogen synthase, pyruvate dehydrogenase); or M.3, parallel activation by a phenomenological insulin-mediated intracellular signal that modifies reaction rate coefficients. These simulations indicated that models M.1 and M.2 were not sufficient to explain the experimentally measured metabolic responses. However, by application of mechanism M.3, the model predicts metabolite concentration changes and glucose partitioning patterns consistent with experimental data. The reaction rate fluxes quantified by this detailed model of insulin/glucose metabolism provide information that can be used to evaluate the development of type 2 diabetes. PMID:20332360
Amorphous and Cellular Computing
NASA Astrophysics Data System (ADS)
Abelson, Harold; Sussman, Gerald J.; Knight, Thomas F., Jr
2001-08-01
The objective of this research is to create the architectural, algorithmic, and technological foundations for exploiting programmable materials. These are materials that incorporate vast numbers of programmable elements that react to each other and to their environment. Such materials can be fabricated economically, provided that the computing elements are amassed in bulk without arranging for precision interconnect and testing. In order to exploit programmable materials we must identify engineering principles for organizing and instructing myriad programmable entities to cooperate to robustly achieve pre-established goals, even though the individual entities are unreliable and interconnected in unknown, irregular, and time-varying ways. Progress in microfabrication and in bioengineering will make it possible to assemble such amorphous systems at almost no cost, provided that (1) the units need not all work correctly; (2) the units are identically programmed; and (3) there is no need to manufacture precise geometrical arrangements of the units or precise interconnections among them.
Cellular automatons applied to gas dynamic problems
NASA Astrophysics Data System (ADS)
Long, Lyle N.; Coopersmith, Robert M.; McLachlan, B. G.
1987-06-01
This paper compares the results of a relatively new computational fluid dynamics method, cellular automatons, with experimental data and analytical results. This technique has been shown to qualitatively predict fluidlike behavior; however, there have been few published comparisons with experiment or other theories. Comparisons are made for a one-dimensional supersonic piston problem, Stokes first problem, and the flow past a normal flat plate. These comparisons are used to assess the ability of the method to accurately model fluid dynamic behavior and to point out its limitations. Reasonable results were obtained for all three test cases, but the fundamental limitations of cellular automatons are numerous. It may be misleading, at this time, to say that cellular automatons are a computationally efficient technique. Other methods, based on continuum or kinetic theory, would also be very efficient if as little of the physics were included.
Cellular automatons applied to gas dynamic problems
NASA Technical Reports Server (NTRS)
Long, Lyle N.; Coopersmith, Robert M.; Mclachlan, B. G.
1987-01-01
This paper compares the results of a relatively new computational fluid dynamics method, cellular automatons, with experimental data and analytical results. This technique has been shown to qualitatively predict fluidlike behavior; however, there have been few published comparisons with experiment or other theories. Comparisons are made for a one-dimensional supersonic piston problem, Stokes first problem, and the flow past a normal flat plate. These comparisons are used to assess the ability of the method to accurately model fluid dynamic behavior and to point out its limitations. Reasonable results were obtained for all three test cases, but the fundamental limitations of cellular automatons are numerous. It may be misleading, at this time, to say that cellular automatons are a computationally efficient technique. Other methods, based on continuum or kinetic theory, would also be very efficient if as little of the physics were included.
Symbolic Computation Using Cellular Automata-Based Hyperdimensional Computing.
Yilmaz, Ozgur
2015-12-01
This letter introduces a novel framework of reservoir computing that is capable of both connectionist machine intelligence and symbolic computation. A cellular automaton is used as the reservoir of dynamical systems. Input is randomly projected onto the initial conditions of automaton cells, and nonlinear computation is performed on the input via application of a rule in the automaton for a period of time. The evolution of the automaton creates a space-time volume of the automaton state space, and it is used as the reservoir. The proposed framework is shown to be capable of long-term memory, and it requires orders of magnitude less computation compared to echo state networks. As the focus of the letter, we suggest that binary reservoir feature vectors can be combined using Boolean operations as in hyperdimensional computing, paving a direct way for concept building and symbolic processing. To demonstrate the capability of the proposed system, we make analogies directly on image data by asking, What is the automobile of air? PMID:26496041
Cellular ubiquitin pool dynamics and homeostasis
Ryu, Kwon-Yul
2014-01-01
Ubiquitin (Ub) is a versatile signaling molecule that plays important roles in a variety of cellular processes. Cellular Ub pools, which are composed of free Ub and Ub conjugates, are in dynamic equilibrium inside cells. In particular, increasing evidence suggests that Ub homeostasis, or the maintenance of free Ub above certain threshold levels, is important for cellular function and survival under normal or stress conditions. Accurate determination of various Ub species, including levels of free Ub and specific Ub chain linkages, have become possible in biological specimens as a result of the introduction of the proteomic approach using mass spectrometry. This technology has facilitated research on dynamic properties of cellular Ub pools and has provided tools for in-depth investigation of Ub homeostasis. In this review, we have also discussed the consequences of the disruption of Ub pool dynamics and homeostasis via deletion of polyubiquitin genes or mutations of deubiquitinating enzymes. The common consequence was a reduced availability of free Ub and a significant impact on the function and viability of cells. These observations further indicate that the levels of free Ub are important determinants for cellular protection. [BMB Reports 2014; 47(9): 475-482] PMID:24924398
A hierarchical cellular logic for pyramid computers
Tanimoto, S.L.
1984-11-01
Hierarchical structure occurs in biological vision systems and there is good reason to incorporate it into a model of computation for processing binary images. A mathematical formalism is presented which can describe a wide variety of operations useful in image processing and graphics. The formalism allows for two kinds of simple transformations on the values (called pyramids) of a set of cells called a hierarchical domain: the first are binary operations on boolean values, and the second are neighborhood-matching operations. The implied model of computation is more structured than previously discussed pyramidal models, and is more readily realized in parallel hardware, while it remains sufficiently rich to provide efficient solutions to a wide variety of problems. The model has a simplicity which is due to the restricted nature of the operations and the implied synchronization across the hierarchical domain. A corresponding algebraic simplicity in the logic makes possible the concise representation of many cellular-data operations.
Dynamical Systems Perspective of Wolfram's Cellular Automata
NASA Astrophysics Data System (ADS)
Courbage, M.; Kamiński, B.
2013-01-01
Leon Chua, following Wolfram, devoted a big effort to understand deeply the wealth of complexity of the rules of all elementary one-dimensional cellular automata from the point of view of the nonlinear dynamicist. Here we complete this point of view by a dynamical system perspective, extending them to the limit of infinite number of sites.
NASA Technical Reports Server (NTRS)
1989-01-01
An overview of computational fluid dynamics (CFD) activities at the Langley Research Center is given. The role of supercomputers in CFD research, algorithm development, multigrid approaches to computational fluid flows, aerodynamics computer programs, computational grid generation, turbulence research, and studies of rarefied gas flows are among the topics that are briefly surveyed.
Computer Modeling of the Earliest Cellular Structures and Functions
NASA Technical Reports Server (NTRS)
Pohorille, Andrew; Chipot, Christophe; Schweighofer, Karl
2000-01-01
In the absence of extinct or extant record of protocells (the earliest ancestors of contemporary cells). the most direct way to test our understanding of the origin of cellular life is to construct laboratory models of protocells. Such efforts are currently underway in the NASA Astrobiology Program. They are accompanied by computational studies aimed at explaining self-organization of simple molecules into ordered structures and developing designs for molecules that perform proto-cellular functions. Many of these functions, such as import of nutrients, capture and storage of energy. and response to changes in the environment are carried out by proteins bound to membrane< We will discuss a series of large-scale, molecular-level computer simulations which demonstrate (a) how small proteins (peptides) organize themselves into ordered structures at water-membrane interfaces and insert into membranes, (b) how these peptides aggregate to form membrane-spanning structures (eg. channels), and (c) by what mechanisms such aggregates perform essential proto-cellular functions, such as proton transport of protons across cell walls, a key step in cellular bioenergetics. The simulations were performed using the molecular dynamics method, in which Newton's equations of motion for each item in the system are solved iteratively. The problems of interest required simulations on multi-nanosecond time scales, which corresponded to 10(exp 6)-10(exp 8) time steps.
Evolving cellular automata to perform computations. Final technical report
Crutchfield, J.P.; Mitchell, M.
1998-04-01
The overall goals of the project are to determine the usefulness of genetic algorithms (GAs) in designing spatially extended parallel systems to perform computational tasks and to develop theoretical frameworks both for understanding the computation in the systems evolved by the GA and for understanding the evolutionary process which successful systems are designed. In the original proposal the authors scheduled the first year of the project to be devoted to experimental grounding. During the first year they developed the simulation and graphics software necessary for doing experiments and analysis on one dimensional cellular automata (CAs), and they performed extensive experiments and analysis concerning two computational tasks--density classification and synchronization. Details of these experiments and results, and a list of resulting publications, were given in the 1994--1995 report. The authors scheduled the second year to be devoted to theoretical development. (A third year, to be funded by the National Science Foundation, will be devoted to applications.) Accordingly, most of the effort during the second year was spent on theory, both of GAs and of the CAs that they evolve. A central notion is that of the computational strategy of a CA, which they formalize in terms of domains, particles, and particle interactions. This formalization builds on the computational mechanics framework developed by Crutchfield and Hanson for understanding intrinsic computation in spatially extended dynamical systems. They have made significant progress in the following areas: (1) statistical dynamics of GAs; (2) formalizing particle based computation in cellular automata; and (3) computation in two-dimensional CAs.
NASA Astrophysics Data System (ADS)
McCune, Matthew; Kosztin, Ioan
2013-03-01
Cellular Particle Dynamics (CPD) is a theoretical-computational-experimental framework for describing and predicting the time evolution of biomechanical relaxation processes of multi-cellular systems, such as fusion, sorting and compression. In CPD, cells are modeled as an ensemble of cellular particles (CPs) that interact via short range contact interactions, characterized by an attractive (adhesive interaction) and a repulsive (excluded volume interaction) component. The time evolution of the spatial conformation of the multicellular system is determined by following the trajectories of all CPs through numerical integration of their equations of motion. Here we present CPD simulation results for the fusion of both spherical and cylindrical multi-cellular aggregates. First, we calibrate the relevant CPD model parameters for a given cell type by comparing the CPD simulation results for the fusion of two spherical aggregates to the corresponding experimental results. Next, CPD simulations are used to predict the time evolution of the fusion of cylindrical aggregates. The latter is relevant for the formation of tubular multi-cellular structures (i.e., primitive blood vessels) created by the novel bioprinting technology. Work supported by NSF [PHY-0957914]. Computer time provided by the University of Missouri Bioinformatics Consortium.
Literature Review on Dynamic Cellular Manufacturing System
NASA Astrophysics Data System (ADS)
Nouri Houshyar, A.; Leman, Z.; Pakzad Moghadam, H.; Ariffin, M. K. A. M.; Ismail, N.; Iranmanesh, H.
2014-06-01
In previous decades, manufacturers faced a lot of challenges because of globalization and high competition in markets. These problems arise from shortening product life cycle, rapid variation in demand of products, and also rapid changes in manufcaturing technologies. Nowadays most manufacturing companies expend considerable attention for improving flexibility and responsiveness in order to overcome these kinds of problems and also meet customer's needs. By considering the trend toward the shorter product life cycle, the manufacturing environment is towards manufacturing a wide variety of parts in small batches [1]. One of the major techniques which are applied for improving manufacturing competitiveness is Cellular Manufacturing System (CMS). CMS is type of manufacturing system which tries to combine flexibility of job shop and also productivity of flow shop. In addition, Dynamic cellular manufacturing system which considers different time periods for the manufacturing system becomes an important topic and attracts a lot of attention to itself. Therefore, this paper made attempt to have a brief review on this issue and focused on all published paper on this subject. Although, this topic gains a lot of attention to itself during these years, none of previous researchers focused on reviewing the literature of that which can be helpful and useful for other researchers who intend to do the research on this topic. Therefore, this paper is the first study which has focused and reviewed the literature of dynamic cellular manufacturing system.
Complex dynamics of cellular automata rule 119
NASA Astrophysics Data System (ADS)
Chen, Fang-Fang; Chen, Fang-Yue
2009-03-01
In this paper, the dynamical behaviors of cellular automata rule 119 are studied from the viewpoint of symbolic dynamics in the bi-infinite symbolic sequence space Σ2. It is shown that there exists one Bernoulli-measure global attractor of rule 119, which is also the nonwandering set of the rule. Moreover, it is demonstrated that rule 119 is topologically mixing on the global attractor and possesses the positive topological entropy. Therefore, rule 119 is chaotic in the sense of both Li-Yorke and Devaney on the global attractor. It is interesting that rule 119, a member of Wolfram’s class II which was said to be simple as periodic before, actually possesses a chaotic global attractor in Σ2. Finally, it is noted that the method presented in this work is also applicable to studying the dynamics of other rules, especially the 112 Bernoulli-shift rules therein.
Traffic jam dynamics in stochastic cellular automata
Nagel, K. |; Schreckenberg, M.
1995-09-01
Simple models for particles hopping on a grid (cellular automata) are used to simulate (single lane) traffic flow. Despite their simplicity, these models are astonishingly realistic in reproducing start-stop-waves and realistic fundamental diagrams. One can use these models to investigate traffic phenomena near maximum flow. A so-called phase transition at average maximum flow is visible in the life-times of jams. The resulting dynamic picture is consistent with recent fluid-dynamical results by Kuehne/Kerner/Konhaeuser, and with Treiterer`s hysteresis description. This places CA models between car-following models and fluid-dynamical models for traffic flow. CA models are tested in projects in Los Alamos (USA) and in NRW (Germany) for large scale microsimulations of network traffic.
The Spatiotemporal Cellular Dynamics of Lung Immunity
Lelkes, E.; Headley, M.B.; Thornton, E.E.; Looney, M.R.; Krummel, M.F.
2014-01-01
The lung is a complex structure that is interdigitated with immune cells. Understanding the 4-dimensional process of normal and defective lung function and immunity has been a centuries-old problem. Challenges intrinsic to the lung have limited adequate microscopic evaluation of its cellular dynamics in real time, until recently. Because of emerging technologies, we now recognize alveolar-to-airway transport of inhaled antigen. We understand the nature of neutrophil entry during lung injury and are learning more about cellular interactions during inflammatory states. Insights are also accumulating in lung development and the metatastatic niche of the lung. Here we assess the developing technology of lung imaging, its merits for studies of pathophysiology and areas where further advances are needed. PMID:24974157
Parameter-less approaches for interpreting dynamic cellular response
2014-01-01
Cellular response such as cell signaling is an integral part of information processing in biology. Upon receptor stimulation, numerous intracellular molecules are invoked to trigger the transcription of genes for specific biological purposes, such as growth, differentiation, apoptosis or immune response. How complex are such specialized and sophisticated machinery? Computational modeling is an important tool for investigating dynamic cellular behaviors. Here, I focus on certain types of key signaling pathways that can be interpreted well using simple physical rules based on Boolean logic and linear superposition of response terms. From the examples shown, it is conceivable that for small-scale network modeling, reaction topology, rather than parameter values, is crucial for understanding population-wide cellular behaviors. For large-scale response, non-parametric statistical approaches have proven valuable for revealing emergent properties. PMID:25183996
Rapid Cellular Identification by Dynamic Electromechanical Response
Nikiforov, Maxim; Jesse, Stephen; Kalinin, Sergei V; Reukov, Vladimir V; Vertegel, Alexey; Thompson, Gary L
2009-01-01
Coupling between electrical and mechanical phenomena is ubiquitous in living systems. Here, we demonstrate rapid identification of cellular organisms using difference in electromechanical activity in a broad frequency range. Principal component analysis of the dynamic electromechanical response spectra bundled with neural network based recognition provides a robust identification algorithm based on their electromechanical signature, and allows unambiguous differentiation of model Micrococcus Lysodeikticus and Pseudomonas Fluorescens system. This methodology provides a universal pathway for biological identification obviating the need for well-defined analytical models of Scanning Probe Microscopy response.
Dynamics of active cellular response under stress
NASA Astrophysics Data System (ADS)
de, Rumi; Zemel, Assaf; Safran, Samuel
2008-03-01
Forces exerted by and on adherent cells are important for many physiological processes such as wound healing and tissue formation. In addition, recent experiments have shown that stem cell differentiation is controlled, at least in part, by the elasticity of the surrounding matrix. Using a simple theoretical model that includes the forces due to both the mechanosensitive nature of cells and the elastic response of the matrix, we predict the dynamics of orientation of cells. The model predicts many features observed in measurements of cellular forces and orientation including the increase with time of the forces generated by cells in the absence of applied stress and the consequent decrease of the force in the presence of quasi-static stresses. We also explain the puzzling observation of parallel alignment of cells for static and quasi-static stresses and of nearly perpendicular alignment for dynamically varying stresses. In addition, we predict the response of the cellular orientation to a sinusoidally varying applied stress as a function of frequency. The dependence of the cell orientation angle on the Poisson ratio of the surrounding material can be used to distinguish systems in which cell activity is controlled by stress from those where cell activity is controlled by strain. Reference: Nature Physics, vol. 3, pp 655 (2007).
Javaheri, Narjes; Dries, Roland; Kaandorp, Jaap
2014-01-01
Controlled synthesis of silicon is a major challenge in nanotechnology and material science. Diatoms, the unicellular algae, are an inspiring example of silica biosynthesis, producing complex and delicate nano-structures. This happens in several cell compartments, including cytoplasm and silica deposition vesicle (SDV). Considering the low concentration of silicic acid in oceans, cells have developed silicon transporter proteins (SIT). Moreover, cells change the level of active SITs during one cell cycle, likely as a response to the level of external nutrients and internal deposition rates. Despite this topic being of fundamental interest, the intracellular dynamics of nutrients and cell regulation strategies remain poorly understood. One reason is the difficulties in measurements and manipulation of these mechanisms at such small scales, and even when possible, data often contain large errors. Therefore, using computational techniques seems inevitable. We have constructed a mathematical model for silicon dynamics in the diatom Thalassiosira pseudonana in four compartments: external environment, cytoplasm, SDV and deposited silica. The model builds on mass conservation and Michaelis-Menten kinetics as mass transport equations. In order to find the free parameters of the model from sparse, noisy experimental data, an optimization technique (global and local search), together with enzyme related penalty terms, has been applied. We have connected population-level data to individual-cell-level quantities including the effect of early division of non-synchronized cells. Our model is robust, proven by sensitivity and perturbation analysis, and predicts dynamics of intracellular nutrients and enzymes in different compartments. The model produces different uptake regimes, previously recognized as surge, externally-controlled and internally-controlled uptakes. Finally, we imposed a flux of SITs to the model and compared it with previous classical kinetics. The model
Cellular automata and complex dynamics of driven elastic media
Coppersmith, S.N.; Littlewodd, P.B.; Sibani, P.
1995-12-01
Several systems of importance in condensed matter physics can be modelled as an elastic medium in a disordered environment and driven by an external force. In the simplest cases, the equation of motion involves competition between a local non-linear potential (fluctuating in space) and elastic coupling, as well as relaxational (inertialess) dynamics. Despite a simple mathematical description, the interactions between many degrees of freedom lead to the emergence of time and length scales much longer than those set by the microscopic dynamics. Extensive computations have improved the understanding of the behavior of such models, but full solutions of the equations of motion for very large systems are time-consuming and may obscure important physical principles in a massive volume of output. The development of cellular automata models has been crucial, both in conceptual simplification and in allowing the collection of data on many replicas of very large systems. We will discuss how the marriage of cellular automata models and parallel computation on a MasPar MP-1216 computer has helped to elucidate the dynamical properties of these many-degree-of-freedom systems.
Cellular automata modelling of biomolecular networks dynamics.
Bonchev, D; Thomas, S; Apte, A; Kier, L B
2010-01-01
The modelling of biological systems dynamics is traditionally performed by ordinary differential equations (ODEs). When dealing with intracellular networks of genes, proteins and metabolites, however, this approach is hindered by network complexity and the lack of experimental kinetic parameters. This opened the field for other modelling techniques, such as cellular automata (CA) and agent-based modelling (ABM). This article reviews this emerging field of studies on network dynamics in molecular biology. The basics of the CA technique are discussed along with an extensive list of related software and websites. The application of CA to networks of biochemical reactions is exemplified in detail by the case studies of the mitogen-activated protein kinase (MAPK) signalling pathway, the FAS-ligand (FASL)-induced and Bcl-2-related apoptosis. The potential of the CA method to model basic pathways patterns, to identify ways to control pathway dynamics and to help in generating strategies to fight with cancer is demonstrated. The different line of CA applications presented includes the search for the best-performing network motifs, an analysis of importance for effective intracellular signalling and pathway cross-talk. PMID:20373215
Infinity computations in cellular automaton forest-fire model
NASA Astrophysics Data System (ADS)
Iudin, D. I.; Sergeyev, Ya. D.; Hayakawa, M.
2015-03-01
Recently a number of traditional models related to the percolation theory has been considered by means of a new computational methodology that does not use Cantor's ideas and describes infinite and infinitesimal numbers in accordance with the principle 'The whole is greater than the part' (Euclid's Common Notion 5). Here we apply the new arithmetic to a cellular automaton forest-fire model which is connected with the percolation methodology and in some sense combines the dynamic and the static percolation problems and under certain conditions exhibits critical fluctuations. It is well known that there exist two versions of the model: real forest-fire model where fire catches adjacent trees in the forest in the step by step manner and simplified version with instantaneous combustion. Using new approach we observe that in both situations we deal with the same model but with different time resolution. We show that depending on the "microscope" we use the same cellular automaton forest-fire model reveals either instantaneous forest combustion or step by step firing. By means of the new approach it was also observed that as far as we choose an infinitesimal tree growing rate and infinitesimal ratio between the ignition probability and the growth probability we determine the measure or extent of the system size infinity that provides the criticality of the system dynamics. Correspondent inequalities for grosspowers are derived.
Computer Modeling of the Earliest Cellular Structures and Functions
NASA Astrophysics Data System (ADS)
Pohorille, Andrew
2000-03-01
In the absence of extinct or extant record of protocells (the earliest ancestors of contemporary cells), the most direct way to test ourunderstanding of the origin of cellular life is to construct laboratory models of protocells. Such efforts are currently underway in the NASA Astrobiology Program. They are accompanied by computational studies aimed at explaining self-organization of simple molecules into ordered structures and developing designs for molecules that perform protocellular functions. Many of these functions, such as import of nutrients, capture and storage of energy, and response to changes in the environment are carried out by proteins bound to membranes. We will discuss a series of large-scale, molecular-level computer simulations which demonstrate (a) how small proteins (peptides)organize themselves into ordered structures at water-membrane interfaces and insert into membranes, (b) how these peptides aggregate to form membrane-spanning structures (e.g. channels), and (c) by what mechanisms such aggregates perform essential protocellular functions, such as proton transport of protons across cell walls, a key step in cellular bioenergetics. The simulations were performed using the molecular dynamics method, in which Newton's equations of motion for each atom in the system are solved iteratively. The problems of interest required simulations on multi-nanosecond time scales, which corresponded to 10^6-10^8 time steps.
Computational fluid dynamic control
NASA Technical Reports Server (NTRS)
Hartley, Tom T.; Deabreu-Garcia, Alex
1989-01-01
A general technique is presented for modeling fluid, or gas, dynamic systems specifically for the development of control systems. The numerical methods which are generally used in computational fluid dynamics are borrowed to create either continuous-time or discrete-time models of the particular fluid system. The resulting equations can be either left in a nonlinear form, or easily linearized about an operating point. As there are typically very many states in these systems, the usual linear model reduction methods can be used on them to allow a low-order controller to be designed. A simple example is given which typifies many internal flow control problems. The resulting control is termed computational fluid dynamic control.
NASA Astrophysics Data System (ADS)
Chung, T. J.
2002-03-01
Computational fluid dynamics (CFD) techniques are used to study and solve complex fluid flow and heat transfer problems. This comprehensive text ranges from elementary concepts for the beginner to state-of-the-art CFD for the practitioner. It discusses and illustrates the basic principles of finite difference (FD), finite element (FE), and finite volume (FV) methods, with step-by-step hand calculations. Chapters go on to examine structured and unstructured grids, adaptive methods, computing techniques, and parallel processing. Finally, the author describes a variety of practical applications to problems in turbulence, reacting flows and combustion, acoustics, combined mode radiative heat transfer, multiphase flows, electromagnetic fields, and relativistic astrophysical flows. Students and practitioners--particularly in mechanical, aerospace, chemical, and civil engineering--will use this authoritative text to learn about and apply numerical techniques to the solution of fluid dynamics problems.
Computational fluid dynamics research
NASA Technical Reports Server (NTRS)
Chandra, Suresh; Jones, Kenneth; Hassan, Hassan; Mcrae, David Scott
1992-01-01
The focus of research in the computational fluid dynamics (CFD) area is two fold: (1) to develop new approaches for turbulence modeling so that high speed compressible flows can be studied for applications to entry and re-entry flows; and (2) to perform research to improve CFD algorithm accuracy and efficiency for high speed flows. Research activities, faculty and student participation, publications, and financial information are outlined.
Computational reacting gas dynamics
NASA Technical Reports Server (NTRS)
Lam, S. H.
1993-01-01
In the study of high speed flows at high altitudes, such as that encountered by re-entry spacecrafts, the interaction of chemical reactions and other non-equilibrium processes in the flow field with the gas dynamics is crucial. Generally speaking, problems of this level of complexity must resort to numerical methods for solutions, using sophisticated computational fluid dynamics (CFD) codes. The difficulties introduced by reacting gas dynamics can be classified into three distinct headings: (1) the usually inadequate knowledge of the reaction rate coefficients in the non-equilibrium reaction system; (2) the vastly larger number of unknowns involved in the computation and the expected stiffness of the equations; and (3) the interpretation of the detailed reacting CFD numerical results. The research performed accepts the premise that reacting flows of practical interest in the future will in general be too complex or 'untractable' for traditional analytical developments. The power of modern computers must be exploited. However, instead of focusing solely on the construction of numerical solutions of full-model equations, attention is also directed to the 'derivation' of the simplified model from the given full-model. In other words, the present research aims to utilize computations to do tasks which have traditionally been done by skilled theoreticians: to reduce an originally complex full-model system into an approximate but otherwise equivalent simplified model system. The tacit assumption is that once the appropriate simplified model is derived, the interpretation of the detailed numerical reacting CFD numerical results will become much easier. The approach of the research is called computational singular perturbation (CSP).
Congenital limb malformations are among the most frequent malformation occurs in humans, with a frequency of about 1 in 500 to 1 in 1000 human live births. ToxCast is profiling the bioactivity of thousands of chemicals based on high-throughput (HTS) and computational methods that...
Computational fluid dynamic applications
Chang, S.-L.; Lottes, S. A.; Zhou, C. Q.
2000-04-03
The rapid advancement of computational capability including speed and memory size has prompted the wide use of computational fluid dynamics (CFD) codes to simulate complex flow systems. CFD simulations are used to study the operating problems encountered in system, to evaluate the impacts of operation/design parameters on the performance of a system, and to investigate novel design concepts. CFD codes are generally developed based on the conservation laws of mass, momentum, and energy that govern the characteristics of a flow. The governing equations are simplified and discretized for a selected computational grid system. Numerical methods are selected to simplify and calculate approximate flow properties. For turbulent, reacting, and multiphase flow systems the complex processes relating to these aspects of the flow, i.e., turbulent diffusion, combustion kinetics, interfacial drag and heat and mass transfer, etc., are described in mathematical models, based on a combination of fundamental physics and empirical data, that are incorporated into the code. CFD simulation has been applied to a large variety of practical and industrial scale flow systems.
A computational study of liposome logic: towards cellular computing from the bottom up.
Smaldon, James; Romero-Campero, Francisco J; Fernández Trillo, Francisco; Gheorghe, Marian; Alexander, Cameron; Krasnogor, Natalio
2010-09-01
In this paper we propose a new bottom-up approach to cellular computing, in which computational chemical processes are encapsulated within liposomes. This "liposome logic" approach (also called vesicle computing) makes use of supra-molecular chemistry constructs, e.g. protocells, chells, etc. as minimal cellular platforms to which logical functionality can be added. Modeling and simulations feature prominently in "top-down" synthetic biology, particularly in the specification, design and implementation of logic circuits through bacterial genome reengineering. The second contribution in this paper is the demonstration of a novel set of tools for the specification, modelling and analysis of "bottom-up" liposome logic. In particular, simulation and modelling techniques are used to analyse some example liposome logic designs, ranging from relatively simple NOT gates and NAND gates to SR-Latches, D Flip-Flops all the way to 3 bit ripple counters. The approach we propose consists of specifying, by means of P systems, gene regulatory network-like systems operating inside proto-membranes. This P systems specification can be automatically translated and executed through a multiscaled pipeline composed of dissipative particle dynamics (DPD) simulator and Gillespie's stochastic simulation algorithm (SSA). Finally, model selection and analysis can be performed through a model checking phase. This is the first paper we are aware of that brings to bear formal specifications, DPD, SSA and model checking to the problem of modeling target computational functionality in protocells. Potential chemical routes for the laboratory implementation of these simulations are also discussed thus for the first time suggesting a potentially realistic physiochemical implementation for membrane computing from the bottom-up. PMID:21886681
Stochastic cellular automata model for wildland fire spread dynamics
NASA Astrophysics Data System (ADS)
Maduro Almeida, Rodolfo; Macau, Elbert E. N.
2011-03-01
A stochastic cellular automata model for wildland fire spread under flat terrain and no-wind conditions is proposed and its dynamics is characterized and analyzed. One of three possible states characterizes each cell: vegetation cell, burning cell and burnt cell. The dynamics of fire spread is modeled as a stochastic event with an effective fire spread probability S which is a function of three probabilities that characterize: the proportion of vegetation cells across the lattice, the probability of a burning cell becomes burnt, and the probability of the fire spread from a burning cell to a neighboring vegetation cell. A set of simulation experiments is performed to analyze the effects of different values of the three probabilities in the fire pattern. Monte-Carlo simulations indicate that there is a critical line in the model parameter space that separates the set of parameters which a fire can propagate from those for which it cannot propagate. Finally, the relevance of the model is discussed under the light of computational experiments that illustrate the capability of the model catches both the dynamical and static qualitative properties of fire propagation.
Computational Fluid Dynamics Library
Energy Science and Technology Software Center (ESTSC)
2005-03-04
CFDLib05 is the Los Alamos Computational Fluid Dynamics LIBrary. This is a collection of hydrocodes using a common data structure and a common numerical method, for problems ranging from single-field, incompressible flow, to multi-species, multi-field, compressible flow. The data structure is multi-block, with a so-called structured grid in each block. The numerical method is a Finite-Volume scheme employing a state vector that is fully cell-centered. This means that the integral form of the conservation lawsmore » is solved on the physical domain that is represented by a mesh of control volumes. The typical control volume is an arbitrary quadrilateral in 2D and an arbitrary hexahedron in 3D. The Finite-Volume scheme is for time-unsteady flow and remains well coupled by means of time and space centered fluxes; if a steady state solution is required, the problem is integrated forward in time until the user is satisfied that the state is stationary.« less
Daniels, Bryan C.; Nemenman, Ilya
2015-01-01
The nonlinearity of dynamics in systems biology makes it hard to infer them from experimental data. Simple linear models are computationally efficient, but cannot incorporate these important nonlinearities. An adaptive method based on the S-system formalism, which is a sensible representation of nonlinear mass-action kinetics typically found in cellular dynamics, maintains the efficiency of linear regression. We combine this approach with adaptive model selection to obtain efficient and parsimonious representations of cellular dynamics. The approach is tested by inferring the dynamics of yeast glycolysis from simulated data. With little computing time, it produces dynamical models with high predictive power and with structural complexity adapted to the difficulty of the inference problem. PMID:25806510
Quantum-cellular-automata quantum computing with endohedral fullerenes
NASA Astrophysics Data System (ADS)
Twamley, J.
2003-05-01
We present a scheme to perform universal quantum computation using global addressing techniques as applied to a physical system of endohedrally doped fullerenes. The system consists of an ABAB linear array of group-V endohedrally doped fullerenes. Each molecule spin site consists of a nuclear spin coupled via a hyperfine interaction to an electron spin. The electron spin of each molecule is in a quartet ground state S=3/2. Neighboring molecular electron spins are coupled via a magnetic dipole interaction. We find that an all-electron construction of a quantum cellular automaton is frustrated due to the degeneracy of the electronic transitions. However, we can construct a quantum-cellular-automata quantum computing architecture using these molecules by encoding the quantum information on the nuclear spins while using the electron spins as a local bus. We deduce the NMR and ESR pulses required to execute the basic cellular automaton operation and obtain a rough figure of merit for the number of gate operations per decoherence time. We find that this figure of merit compares well with other physical quantum computer proposals. We argue that the proposed architecture meets well the first four DiVincenzo criteria and we outline various routes toward meeting the fifth criterion: qubit readout.
Real-Time Bioluminescent Tracking of Cellular Population Dynamics
Close, Dan; Sayler, Gary Steven; Xu, Tingting; Ripp, Steven Anthony
2014-01-01
Cellular population dynamics are routinely monitored across many diverse fields for a variety of purposes. In general, these dynamics are assayed either through the direct counting of cellular aliquots followed by extrapolation to the total population size, or through the monitoring of signal intensity from any number of externally stimulated reporter proteins. While both viable methods, here we describe a novel technique that allows for the automated, non-destructive tracking of cellular population dynamics in real-time. This method, which relies on the detection of a continuous bioluminescent signal produced through expression of the bacterial luciferase gene cassette, provides a low cost, low time-intensive means for generating additional data compared to alternative methods.
The role of cellular environment in dynamic light scattering
NASA Astrophysics Data System (ADS)
An, Ran; Jeong, Kwan; Turek, John; Nolte, David
2011-03-01
We have developed motility contrast imaging (MCI) as a coherence-domain volumetric imaging approach that uses subcellular dynamics as an endogenous imaging contrast agent of living tissue. Fluctuation spectroscopy analysis of dynamic light scattering (DLS) from 3-D tissue has identified functional frequency bands related to organelle transport, membrane undulations and cell shape change. In this paper, we track the behavior of dynamic light scattering as we bridge the gap between the two extremes of 2-D cell culture on the one hand, and 3-D tissue spheroids on the other. In a light backscattering geometry, we capture speckle from 2-D cell culture consisting of isolated cells or planar rafts of cells on cell-culture surfaces. DLS from that cell culture shows differences and lower sensitivity to intra-cellular dynamics compared with the 3-D tissue. The motility contrast is weak in this limit. As the cellular density increases to cover the surface, the motility contrast increases. As environmental perturbations or pharmaceuticals are applied, the fluctuation spectral response becomes more dramatic as the dimensionality of the cellular aggregations increases. We show that changing optical thickness of the cellular-to-tissue targets usually causes characteristic frequency shifts in the spectrograms, while changing cellular dimensionality causes characteristic frequencies to be enhanced or suppressed.
Inferring biological dynamics in heterogeneous cellular environments
NASA Astrophysics Data System (ADS)
Pressé, Steve
In complex environments, it often appears that biomolecules such as proteins do not diffuse normally. That is, their mean square displacement does not scale linearly with time. This anomalous diffusion happens for multiple reasons: proteins can bind to structures and other proteins; fluorophores used to label proteins may flicker or blink making it appear that the labeled protein is diffusing anomalously; and proteins can diffuse in differently crowded environments. Here we describe methods for learning about such processes from imaging data collected inside the heterogeneous environment of the living cell. Refs.: ''Inferring Diffusional Dynamics from FCS in Heterogeneous Nuclear Environments'' Konstantinos Tsekouras, Amanda Siegel, Richard N. Day, Steve Pressé*, Biophys. J. , 109, 7 (2015). ''A data-driven alternative to the fractional Fokker-Planck equation'' Steve Pressé*, J. Stat. Phys.: Th. and Expmt. , P07009 (2015).
Bimolecular dynamics by computer analysis
Eilbeck, J.C.; Lomdahl, P.S.; Scott, A.C.
1984-01-01
As numerical tools (computers and display equipment) become more powerful and the atomic structures of important biological molecules become known, the importance of detailed computation of nonequilibrium biomolecular dynamics increases. In this manuscript we report results from a well developed study of the hydrogen bonded polypeptide crystal acetanilide, a model protein. Directions for future research are suggested. 9 references, 6 figures.
Computational aspects of multibody dynamics
NASA Technical Reports Server (NTRS)
Park, K. C.
1989-01-01
Computational aspects are addressed which impact the requirements for developing a next generation software system for flexible multibody dynamics simulation which include: criteria for selecting candidate formulation, pairing of formulations with appropriate solution procedures, need for concurrent algorithms to utilize computer hardware advances, and provisions for allowing open-ended yet modular analysis modules.
Computer animation challenges for computational fluid dynamics
NASA Astrophysics Data System (ADS)
Vines, Mauricio; Lee, Won-Sook; Mavriplis, Catherine
2012-07-01
Computer animation requirements differ from those of traditional computational fluid dynamics (CFD) investigations in that visual plausibility and rapid frame update rates trump physical accuracy. We present an overview of the main techniques for fluid simulation in computer animation, starting with Eulerian grid approaches, the Lattice Boltzmann method, Fourier transform techniques and Lagrangian particle introduction. Adaptive grid methods, precomputation of results for model reduction, parallelisation and computation on graphical processing units (GPUs) are reviewed in the context of accelerating simulation computations for animation. A survey of current specific approaches for the application of these techniques to the simulation of smoke, fire, water, bubbles, mixing, phase change and solid-fluid coupling is also included. Adding plausibility to results through particle introduction, turbulence detail and concentration on regions of interest by level set techniques has elevated the degree of accuracy and realism of recent animations. Basic approaches are described here. Techniques to control the simulation to produce a desired visual effect are also discussed. Finally, some references to rendering techniques and haptic applications are mentioned to provide the reader with a complete picture of the challenges of simulating fluids in computer animation.
Computational Workbench for Multibody Dynamics
NASA Technical Reports Server (NTRS)
Edmonds, Karina
2007-01-01
PyCraft is a computer program that provides an interactive, workbenchlike computing environment for developing and testing algorithms for multibody dynamics. Examples of multibody dynamic systems amenable to analysis with the help of PyCraft include land vehicles, spacecraft, robots, and molecular models. PyCraft is based on the Spatial-Operator- Algebra (SOA) formulation for multibody dynamics. The SOA operators enable construction of simple and compact representations of complex multibody dynamical equations. Within the Py-Craft computational workbench, users can, essentially, use the high-level SOA operator notation to represent the variety of dynamical quantities and algorithms and to perform computations interactively. PyCraft provides a Python-language interface to underlying C++ code. Working with SOA concepts, a user can create and manipulate Python-level operator classes in order to implement and evaluate new dynamical quantities and algorithms. During use of PyCraft, virtually all SOA-based algorithms are available for computational experiments.
Incisive Imaging and Computation for Cellular Mysteries: Lessons from Abscission
Elia, Natalie; Ott, Carolyn; Lippincott-Schwartz, Jennifer
2014-01-01
The final cleavage event that terminates cell division, abscission of the small, dense intercellular bridge, has been particularly challenging to resolve. Here, we describe imaging innovations that helped answer long-standing questions about the mechanism of abscission. We further explain how computational modeling of high-resolution data was employed to test hypotheses and generate additional insights. We present the model that emerges from application of these complimentary approaches. Similar experimental strategies will undoubtedly reveal exciting details about other underresolved cellular structures. PMID:24315094
Cellular Dynamic Simulator: An Event Driven Molecular Simulation Environment for Cellular Physiology
Byrne, Michael J.; Waxham, M. Neal; Kubota, Yoshihisa
2010-01-01
In this paper, we present the Cellular Dynamic Simulator (CDS) for simulating diffusion and chemical reactions within crowded molecular environments. CDS is based on a novel event driven algorithm specifically designed for precise calculation of the timing of collisions, reactions and other events for each individual molecule in the environment. Generic mesh based compartments allow the creation / importation of very simple or detailed cellular structures that exist in a 3D environment. Multiple levels of compartments and static obstacles can be used to create a dense environment to mimic cellular boundaries and the intracellular space. The CDS algorithm takes into account volume exclusion and molecular crowding that may impact signaling cascades in small sub-cellular compartments such as dendritic spines. With the CDS, we can simulate simple enzyme reactions; aggregation, channel transport, as well as highly complicated chemical reaction networks of both freely diffusing and membrane bound multi-protein complexes. Components of the CDS are generally defined such that the simulator can be applied to a wide range of environments in terms of scale and level of detail. Through an initialization GUI, a simple simulation environment can be created and populated within minutes yet is powerful enough to design complex 3D cellular architecture. The initialization tool allows visual confirmation of the environment construction prior to execution by the simulator. This paper describes the CDS algorithm, design implementation, and provides an overview of the types of features available and the utility of those features are highlighted in demonstrations. PMID:20361275
Coordination of Cellular Dynamics Contributes to Tooth Epithelium Deformations.
Morita, Ritsuko; Kihira, Miho; Nakatsu, Yousuke; Nomoto, Yohei; Ogawa, Miho; Ohashi, Kazumasa; Mizuno, Kensaku; Tachikawa, Tetsuhiko; Ishimoto, Yukitaka; Morishita, Yoshihiro; Tsuji, Takashi
2016-01-01
The morphologies of ectodermal organs are shaped by appropriate combinations of several deformation modes, such as invagination and anisotropic tissue elongation. However, how multicellular dynamics are coordinated during deformation processes remains to be elucidated. Here, we developed a four-dimensional (4D) analysis system for tracking cell movement and division at a single-cell resolution in developing tooth epithelium. The expression patterns of a Fucci probe clarified the region- and stage-specific cell cycle patterns within the tooth germ, which were in good agreement with the pattern of the volume growth rate estimated from tissue-level deformation analysis. Cellular motility was higher in the regions with higher growth rates, while the mitotic orientation was significantly biased along the direction of tissue elongation in the epithelium. Further, these spatio-temporal patterns of cellular dynamics and tissue-level deformation were highly correlated with that of the activity of cofilin, which is an actin depolymerization factor, suggesting that the coordination of cellular dynamics via actin remodeling plays an important role in tooth epithelial morphogenesis. Our system enhances the understanding of how cellular behaviors are coordinated during ectodermal organogenesis, which cannot be observed from histological analyses. PMID:27588418
Molecular dynamics on vector computers
NASA Astrophysics Data System (ADS)
Sullivan, F.; Mountain, R. D.; Oconnell, J.
1985-10-01
An algorithm called the method of lights (MOL) has been developed for the computerized simulation of molecular dynamics. The MOL, implemented on the CYBER 205 computer, is based on sorting and reformulating the manner in which neighbor lists are compiled, and it uses data structures compatible with specialized vector statements that perform parallel computations. The MOL is found to reduce running time over standard methods in scalar form, and vectorization is shown to produce an order-of-magnitude reduction in execution time.
Analysing Dynamical Behavior of Cellular Networks via Stochastic Bifurcations
Zakharova, Anna; Kurths, Jürgen; Vadivasova, Tatyana; Koseska, Aneta
2011-01-01
The dynamical structure of genetic networks determines the occurrence of various biological mechanisms, such as cellular differentiation. However, the question of how cellular diversity evolves in relation to the inherent stochasticity and intercellular communication remains still to be understood. Here, we define a concept of stochastic bifurcations suitable to investigate the dynamical structure of genetic networks, and show that under stochastic influence, the expression of given proteins of interest is defined via the probability distribution of the phase variable, representing one of the genes constituting the system. Moreover, we show that under changing stochastic conditions, the probabilities of expressing certain concentration values are different, leading to different functionality of the cells, and thus to differentiation of the cells in the various types. PMID:21647432
Application-Aware Dynamic Retransmission Control in Mobile Cellular Networks
NASA Astrophysics Data System (ADS)
Halima, Nadhir Ben; Kliazovich, Dzmitry; Granelli, Fabrizio
This paper proposes an application-aware cross-layer approach between application/transport layers on the mobile terminal and link layer at the wireless base station to enable dynamic control on the strength of per-packet error protection for multimedia and data transfers. Specifically, in the context of cellular networks, the proposed scheme allows to control the desired level of Hybrid ARQ (HARQ) protection by using an in-band control feedback channel. Such protection is dynamically adapted on a per-packet basis and depends on the perceptual importance of different packets as well as on the reception history of the flow.
Analog computation with dynamical systems
NASA Astrophysics Data System (ADS)
Siegelmann, Hava T.; Fishman, Shmuel
1998-09-01
Physical systems exhibit various levels of complexity: their long term dynamics may converge to fixed points or exhibit complex chaotic behavior. This paper presents a theory that enables to interpret natural processes as special purpose analog computers. Since physical systems are naturally described in continuous time, a definition of computational complexity for continuous time systems is required. In analogy with the classical discrete theory we develop fundamentals of computational complexity for dynamical systems, discrete or continuous in time, on the basis of an intrinsic time scale of the system. Dissipative dynamical systems are classified into the computational complexity classes P d, Co-RP d, NP d and EXP d, corresponding to their standard counterparts, according to the complexity of their long term behavior. The complexity of chaotic attractors relative to regular ones leads to the conjecture P d ≠ NP d. Continuous time flows have been proven useful in solving various practical problems. Our theory provides the tools for an algorithmic analysis of such flows. As an example we analyze the continuous Hopfield network.
Changes in single-molecule integrin dynamics linked to local cellular behavior
Jaqaman, Khuloud; Galbraith, James A.; Davidson, Michael W.; Galbraith, Catherine G.
2016-01-01
Recent advances in light microscopy permit visualization of the behavior of individual molecules within dense macromolecular ensembles in live cells. It is now conceptually possible to relate the dynamic organization of molecular machinery to cellular function. However, inherent heterogeneities, as well as disparities between spatial and temporal scales, pose substantial challenges in deriving such a relationship. New approaches are required to link discrete single-molecule behavior with continuous cellular-level processes. Here we combined intercalated molecular and cellular imaging with a computational framework to detect reproducible transient changes in the behavior of individual molecules that are linked to cellular behaviors. Applying our approach to integrin transmembrane receptors revealed a spatial density gradient underlying characteristic molecular density increases and mobility decreases, indicating the subsequent onset of local protrusive activity. Integrin mutants further revealed that these density and mobility transients are separable and depend on different binding domains within the integrin cytoplasmic tail. Our approach provides a generalizable paradigm for dissecting dynamic spatiotemporal molecular behaviors linked to local cellular events. PMID:27009207
Cellular Biotechnology Operations Support System Fluid Dynamics Investigation
NASA Technical Reports Server (NTRS)
2003-01-01
Aboard the International Space Station (ISS), the Tissue Culture Medium (TCM) is the bioreactor vessel in which cell cultures are grown. With its two syringe ports, it is much like a bag used to administer intravenous fluid, except it allows gas exchange needed for life. The TCM contains cell culture medium, and when frozen cells are flown to the ISS, they are thawed and introduced to the TCM through the syringe ports. In the Cellular Biotechnology Operations Support System-Fluid Dynamics Investigation (CBOSS-FDI) experiment, several mixing procedures are being assessed to determine which method achieves the most uniform mixing of growing cells and culture medium.
Dynamic computing random access memory.
Traversa, F L; Bonani, F; Pershin, Y V; Di Ventra, M
2014-07-18
The present von Neumann computing paradigm involves a significant amount of information transfer between a central processing unit and memory, with concomitant limitations in the actual execution speed. However, it has been recently argued that a different form of computation, dubbed memcomputing (Di Ventra and Pershin 2013 Nat. Phys. 9 200-2) and inspired by the operation of our brain, can resolve the intrinsic limitations of present day architectures by allowing for computing and storing of information on the same physical platform. Here we show a simple and practical realization of memcomputing that utilizes easy-to-build memcapacitive systems. We name this architecture dynamic computing random access memory (DCRAM). We show that DCRAM provides massively-parallel and polymorphic digital logic, namely it allows for different logic operations with the same architecture, by varying only the control signals. In addition, by taking into account realistic parameters, its energy expenditures can be as low as a few fJ per operation. DCRAM is fully compatible with CMOS technology, can be realized with current fabrication facilities, and therefore can really serve as an alternative to the present computing technology. PMID:24972387
Dynamic computing random access memory
NASA Astrophysics Data System (ADS)
Traversa, F. L.; Bonani, F.; Pershin, Y. V.; Di Ventra, M.
2014-07-01
The present von Neumann computing paradigm involves a significant amount of information transfer between a central processing unit and memory, with concomitant limitations in the actual execution speed. However, it has been recently argued that a different form of computation, dubbed memcomputing (Di Ventra and Pershin 2013 Nat. Phys. 9 200-2) and inspired by the operation of our brain, can resolve the intrinsic limitations of present day architectures by allowing for computing and storing of information on the same physical platform. Here we show a simple and practical realization of memcomputing that utilizes easy-to-build memcapacitive systems. We name this architecture dynamic computing random access memory (DCRAM). We show that DCRAM provides massively-parallel and polymorphic digital logic, namely it allows for different logic operations with the same architecture, by varying only the control signals. In addition, by taking into account realistic parameters, its energy expenditures can be as low as a few fJ per operation. DCRAM is fully compatible with CMOS technology, can be realized with current fabrication facilities, and therefore can really serve as an alternative to the present computing technology.
Examining the architecture of cellular computing through a comparative study with a computer.
Wang, Degeng; Gribskov, Michael
2005-06-22
The computer and the cell both use information embedded in simple coding, the binary software code and the quadruple genomic code, respectively, to support system operations. A comparative examination of their system architecture as well as their information storage and utilization schemes is performed. On top of the code, both systems display a modular, multi-layered architecture, which, in the case of a computer, arises from human engineering efforts through a combination of hardware implementation and software abstraction. Using the computer as a reference system, a simplistic mapping of the architectural components between the two is easily detected. This comparison also reveals that a cell abolishes the software-hardware barrier through genomic encoding for the constituents of the biochemical network, a cell's "hardware" equivalent to the computer central processing unit (CPU). The information loading (gene expression) process acts as a major determinant of the encoded constituent's abundance, which, in turn, often determines the "bandwidth" of a biochemical pathway. Cellular processes are implemented in biochemical pathways in parallel manners. In a computer, on the other hand, the software provides only instructions and data for the CPU. A process represents just sequentially ordered actions by the CPU and only virtual parallelism can be implemented through CPU time-sharing. Whereas process management in a computer may simply mean job scheduling, coordinating pathway bandwidth through the gene expression machinery represents a major process management scheme in a cell. In summary, a cell can be viewed as a super-parallel computer, which computes through controlled hardware composition. While we have, at best, a very fragmented understanding of cellular operation, we have a thorough understanding of the computer throughout the engineering process. The potential utilization of this knowledge to the benefit of systems biology is discussed. PMID:16849179
Dynamical theory of active cellular response to external stress.
De, Rumi; Safran, Samuel A
2008-09-01
We present a comprehensive, theoretical treatment of the orientational response to external stress of active, contractile cells embedded in a gel-like elastic medium. The theory includes both the forces that arise from the deformation of the matrix as well as forces due to the internal regulation of the stress fibers and focal adhesions of the cell. We calculate the time-dependent response of both the magnitude and the direction of the elastic dipole that characterizes the active forces exerted by the cell, for various situations. For static or quasistatic external stress, cells orient parallel to the stress while for high frequency dynamic external stress, cells orient nearly perpendicular. Both numerical and analytical calculations of these effects are presented. In addition we predict the relaxation time for the cellular response for both slowly and rapidly varying external stresses; several characteristic scaling regimes for the relaxation time as a function of applied frequency are predicted. We also treat the case of cells for which the regulation of the stress fibers and focal adhesions is controlled by strain (instead of stress) and show that the predicted dependence of the cellular orientation on the Poisson ratio of the matrix can differentiate strain vs stress regulation of cellular response. PMID:18851081
Dynamical theory of active cellular response to external stress
NASA Astrophysics Data System (ADS)
de, Rumi; Safran, Samuel A.
2008-09-01
We present a comprehensive, theoretical treatment of the orientational response to external stress of active, contractile cells embedded in a gel-like elastic medium. The theory includes both the forces that arise from the deformation of the matrix as well as forces due to the internal regulation of the stress fibers and focal adhesions of the cell. We calculate the time-dependent response of both the magnitude and the direction of the elastic dipole that characterizes the active forces exerted by the cell, for various situations. For static or quasistatic external stress, cells orient parallel to the stress while for high frequency dynamic external stress, cells orient nearly perpendicular. Both numerical and analytical calculations of these effects are presented. In addition we predict the relaxation time for the cellular response for both slowly and rapidly varying external stresses; several characteristic scaling regimes for the relaxation time as a function of applied frequency are predicted. We also treat the case of cells for which the regulation of the stress fibers and focal adhesions is controlled by strain (instead of stress) and show that the predicted dependence of the cellular orientation on the Poisson ratio of the matrix can differentiate strain vs stress regulation of cellular response.
Mosquito population dynamics from cellular automata-based simulation
NASA Astrophysics Data System (ADS)
Syafarina, Inna; Sadikin, Rifki; Nuraini, Nuning
2016-02-01
In this paper we present an innovative model for simulating mosquito-vector population dynamics. The simulation consist of two stages: demography and dispersal dynamics. For demography simulation, we follow the existing model for modeling a mosquito life cycles. Moreover, we use cellular automata-based model for simulating dispersal of the vector. In simulation, each individual vector is able to move to other grid based on a random walk. Our model is also capable to represent immunity factor for each grid. We simulate the model to evaluate its correctness. Based on the simulations, we can conclude that our model is correct. However, our model need to be improved to find a realistic parameters to match real data.
NASA Astrophysics Data System (ADS)
McCune, Matthew; Shafiee, Ashkan; Forgacs, Gabor; Kosztin, Ioan
2014-03-01
Cellular Particle Dynamics (CPD) is an effective computational method for describing and predicting the time evolution of biomechanical relaxation processes of multicellular systems. A typical example is the fusion of spheroidal bioink particles during post bioprinting structure formation. In CPD cells are modeled as an ensemble of cellular particles (CPs) that interact via short-range contact interactions, characterized by an attractive (adhesive interaction) and a repulsive (excluded volume interaction) component. The time evolution of the spatial conformation of the multicellular system is determined by following the trajectories of all CPs through integration of their equations of motion. CPD was successfully applied to describe and predict the fusion of 3D tissue construct involving identical spherical aggregates. Here, we demonstrate that CPD can also predict tissue formation involving uneven spherical aggregates whose volumes decrease during the fusion process. Work supported by NSF [PHY-0957914]. Computer time provided by the University of Missouri Bioinformatics Consortium.
Multiparametric cytometry for exploration of complex cellular dynamics.
Gondois-Rey, Françoise; Granjeaud, Samuel; Kieu, Suong Le Thi; Herrera, Diana; Hirsch, Ivan; Olive, Daniel
2012-04-01
The development of polychromatic cytometry has contributed to significant progress in the field of human immunology. Although numerous functional studies of rare cell populations have been performed using this technology, here we used polychromatic cytometry to explore the dynamics of complex cellular systems implicated in innate immunity. We used PBMC stimulated with live influenza virus as an experimental model. We studied the time course of activation of PBMC, which contain DC, monocytes, and NK cells, all of which are, in addition to their innate immune properties, susceptible to Flu infection. We developed 12 color panels to investigate intracellular expression of IFN-α, TNF-α, IL-12, IL-6, IFN-γ, CD107, and influenza virus nucleoprotein simultaneously in these cell populations. These panels allowed reproducible determination of activation markers induced in DC after their direct exposure to various stimulations or in NK cells by indirect DC-mediated activation within the complex cellular environment. The ability to use a low number of cells and reduced quantities of reagents permitted us to perform kinetic experiments. The power of polychromatic cytometry associated with bioinformatic tools allowed us to analyze the multiple functional data generated as dynamic clustering maps. These maps present a readily understandable view of activation events induced in different populations of PBMC. In addition, it reveals new information on the coordination of the complex pathways induced and on the cellular interactions that sustained indirect DC-mediated NK cell activation. Our work shows that polychromatic cytometry is a tool for discoveries in unexplored complex cell systems, at the crossroads of immunology and virology. © 2012 International Society for Advancement of Cytometry. PMID:22278900
Computational Methods for Structural Mechanics and Dynamics
NASA Technical Reports Server (NTRS)
Stroud, W. Jefferson (Editor); Housner, Jerrold M. (Editor); Tanner, John A. (Editor); Hayduk, Robert J. (Editor)
1989-01-01
Topics addressed include: transient dynamics; transient finite element method; transient analysis in impact and crash dynamic studies; multibody computer codes; dynamic analysis of space structures; multibody mechanics and manipulators; spatial and coplanar linkage systems; flexible body simulation; multibody dynamics; dynamical systems; and nonlinear characteristics of joints.
Cellular dynamics of neuronal migration in the hippocampus
Hayashi, Kanehiro; Kubo, Ken-ichiro; Kitazawa, Ayako; Nakajima, Kazunori
2015-01-01
A fine structure of the hippocampus is required for proper functions, and disruption of this formation by neuronal migration defects during development may play a role in some psychiatric illnesses. During hippocampal development in rodents, pyramidal neurons in the Ammon's horn are mostly generated in the ventricular zone (VZ), spent as multipolar cells just above the VZ, and then migrate radially toward the pial surface, ultimately settling into the hippocampal plate. Although this process is similar to that of neocortical projection neurons, these are not identical. In addition to numerous histological studies, the development of novel techniques gives a clear picture of the cellular dynamics of hippocampal neurons, as well as neocortical neurons. In this article, we provide an overview of the cellular mechanisms of rodent hippocampal neuronal migration including those of dentate granule cells, especially focusing on the differences of migration modes between hippocampal neurons and neocortical neurons. The unique migration mode of hippocampal pyramidal neurons might enable clonally related cells in the Ammon's horn to distribute in a horizontal fashion. PMID:25964735
Motor Schema-Based Cellular Automaton Model for Pedestrian Dynamics
NASA Astrophysics Data System (ADS)
Weng, Wenguo; Hasemi, Yuji; Fan, Weicheng
A new cellular automaton model for pedestrian dynamics based on motor schema is presented. Each pedestrian is treated as an intelligent mobile robot, and motor schemas including move-to-goal, avoid-away and avoid-around drive pedestrians to interact with their environment. We investigate the phenomenon of many pedestrians with different move velocities escaping from a room. The results show that the pedestrian with high velocity have predominance in competitive evacuation, if we only consider repulsion from or avoiding around other pedestrians, and interaction with each other leads to disordered evacuation, i.e., decreased evacuation efficiency. Extensions of the model using learning algorithms for controlling pedestrians, i.e., reinforcement learning, neural network and genetic algorithms, etc. are noted.
Myosins and cell dynamics in cellular slime molds.
Yumura, Shigehiko; Uyeda, Taro Q P
2003-01-01
Myosin is a mechanochemical transducer and serves as a motor for various motile activities such as cell migration, cytokinesis, maintenance of cell shape, phagocytosis, and morphogenesis. Nonmuscle myosin in vivo does not either stay static at specific subcellular regions or construct highly organized structures, such as sarcomere in skeletal muscle cells. The cellular slime mold Dictyostelium discoideum is an ideal "model organism" for the investigation of cell movement and cytokinesis. The advantages of this organism prompted researchers to carry out pioneering cell biological, biochemical, and molecular genetic studies on myosin II, which resulted in elucidation of many fundamental features of function and regulation of this most abundant molecular motor. Furthermore, recent molecular biological research has revealed that many unconventional myosins play various functions in vivo. In this article, how myosins are organized and regulated in a dynamic manner in Dictyostelium cells is reviewed and discussed. PMID:12722951
Cellular Manufacturing System with Dynamic Lot Size Material Handling
NASA Astrophysics Data System (ADS)
Khannan, M. S. A.; Maruf, A.; Wangsaputra, R.; Sutrisno, S.; Wibawa, T.
2016-02-01
Material Handling take as important role in Cellular Manufacturing System (CMS) design. In several study at CMS design material handling was assumed per pieces or with constant lot size. In real industrial practice, lot size may change during rolling period to cope with demand changes. This study develops CMS Model with Dynamic Lot Size Material Handling. Integer Linear Programming is used to solve the problem. Objective function of this model is minimizing total expected cost consisting machinery depreciation cost, operating costs, inter-cell material handling cost, intra-cell material handling cost, machine relocation costs, setup costs, and production planning cost. This model determines optimum cell formation and optimum lot size. Numerical examples are elaborated in the paper to ilustrate the characterictic of the model.
Etournay, Raphaël; Merkel, Matthias; Popović, Marko; Brandl, Holger; Dye, Natalie A; Aigouy, Benoît; Salbreux, Guillaume; Eaton, Suzanne; Jülicher, Frank
2016-01-01
Segmentation and tracking of cells in long-term time-lapse experiments has emerged as a powerful method to understand how tissue shape changes emerge from the complex choreography of constituent cells. However, methods to store and interrogate the large datasets produced by these experiments are not widely available. Furthermore, recently developed methods for relating tissue shape changes to cell dynamics have not yet been widely applied by biologists because of their technical complexity. We therefore developed a database format that stores cellular connectivity and geometry information of deforming epithelial tissues, and computational tools to interrogate it and perform multi-scale analysis of morphogenesis. We provide tutorials for this computational framework, called TissueMiner, and demonstrate its capabilities by comparing cell and tissue dynamics in vein and inter-vein subregions of the Drosophila pupal wing. These analyses reveal an unexpected role for convergent extension in shaping wing veins. PMID:27228153
Cellular automata-based modelling and simulation of biofilm structure on multi-core computers.
Skoneczny, Szymon
2015-01-01
The article presents a mathematical model of biofilm growth for aerobic biodegradation of a toxic carbonaceous substrate. Modelling of biofilm growth has fundamental significance in numerous processes of biotechnology and mathematical modelling of bioreactors. The process following double-substrate kinetics with substrate inhibition proceeding in a biofilm has not been modelled so far by means of cellular automata. Each process in the model proposed, i.e. diffusion of substrates, uptake of substrates, growth and decay of microorganisms and biofilm detachment, is simulated in a discrete manner. It was shown that for flat biofilm of constant thickness, the results of the presented model agree with those of a continuous model. The primary outcome of the study was to propose a mathematical model of biofilm growth; however a considerable amount of focus was also placed on the development of efficient algorithms for its solution. Two parallel algorithms were created, differing in the way computations are distributed. Computer programs were created using OpenMP Application Programming Interface for C++ programming language. Simulations of biofilm growth were performed on three high-performance computers. Speed-up coefficients of computer programs were compared. Both algorithms enabled a significant reduction of computation time. It is important, inter alia, in modelling and simulation of bioreactor dynamics. PMID:26606102
Visualization of Computational Fluid Dynamics
NASA Technical Reports Server (NTRS)
Gerald-Yamasaki, Michael; Hultquist, Jeff; Bryson, Steve; Kenwright, David; Lane, David; Walatka, Pamela; Clucas, Jean; Watson, Velvin; Lasinski, T. A. (Technical Monitor)
1995-01-01
Scientific visualization serves the dual purpose of exploration and exposition of the results of numerical simulations of fluid flow. Along with the basic visualization process which transforms source data into images, there are four additional components to a complete visualization system: Source Data Processing, User Interface and Control, Presentation, and Information Management. The requirements imposed by the desired mode of operation (i.e. real-time, interactive, or batch) and the source data have their effect on each of these visualization system components. The special requirements imposed by the wide variety and size of the source data provided by the numerical simulation of fluid flow presents an enormous challenge to the visualization system designer. We describe the visualization system components including specific visualization techniques and how the mode of operation and source data requirements effect the construction of computational fluid dynamics visualization systems.
Dynamic Load Balancing for Computational Plasticity on Parallel Computers
NASA Technical Reports Server (NTRS)
Pramono, Eddy; Simon, Horst
1994-01-01
The simulation of the computational plasticity on a complex structure remains a formidable computational task, especially when a highly nonlinear, complex material model was used. It appears that the computational requirements for a such problem can only be satisfied by massively parallel architectures. In order to effectively harness the tremendous computational power provided by such architectures, it is imperative to investigate and to study the algorithmic and implementation issues pertaining to dynamic load balancing for computational plasticity on a highly parallel, distributed-memory, multiple-instruction, multiple-data computers. This paper will measure the effectiveness of the algorithms developed in handling the dynamic load balancing.
Reprint of Infinity computations in cellular automaton forest-fire model
NASA Astrophysics Data System (ADS)
Iudin, D. I.; Sergeyev, Ya. D.; Hayakawa, M.
2015-04-01
Recently a number of traditional models related to the percolation theory has been considered by means of a new computational methodology that does not use Cantor's ideas and describes infinite and infinitesimal numbers in accordance with the principle 'The whole is greater than the part' (Euclid's Common Notion 5). Here we apply the new arithmetic to a cellular automaton forest-fire model which is connected with the percolation methodology and in some sense combines the dynamic and the static percolation problems and under certain conditions exhibits critical fluctuations. It is well known that there exist two versions of the model: real forest-fire model where fire catches adjacent trees in the forest in the step by step manner and simplified version with instantaneous combustion. Using new approach we observe that in both situations we deal with the same model but with different time resolution. We show that depending on the "microscope" we use the same cellular automaton forest-fire model reveals either instantaneous forest combustion or step by step firing. By means of the new approach it was also observed that as far as we choose an infinitesimal tree growing rate and infinitesimal ratio between the ignition probability and the growth probability we determine the measure or extent of the system size infinity that provides the criticality of the system dynamics. Correspondent inequalities for grosspowers are derived.
Modeling dynamics of HIV infected cells using stochastic cellular automaton
NASA Astrophysics Data System (ADS)
Precharattana, Monamorn; Triampo, Wannapong
2014-08-01
Ever since HIV was first diagnosed in human, a great number of scientific works have been undertaken to explore the biological mechanisms involved in the infection and progression of the disease. Several cellular automata (CA) models have been introduced to gain insights into the dynamics of the disease progression but none of them has taken into account effects of certain immune cells such as the dendritic cells (DCs) and the CD8+ T lymphocytes (CD8+ T cells). In this work, we present a CA model, which incorporates effects of the HIV specific immune response focusing on the cell-mediated immunities, and investigate the interaction between the host immune response and the HIV infected cells in the lymph nodes. The aim of our work is to propose a model more realistic than the one in Precharattana et al. (2010) [10], by incorporating roles of the DCs, the CD4+ T cells, and the CD8+ T cells into the model so that it would reproduce the HIV infection dynamics during the primary phase of HIV infection.
Nonlinear dynamics of C-terminal tails in cellular microtubules.
Sekulic, Dalibor L; Sataric, Bogdan M; Zdravkovic, Slobodan; Bugay, Aleksandr N; Sataric, Miljko V
2016-07-01
The mechanical and electrical properties, and information processing capabilities of microtubules are the permanent subject of interest for carrying out experiments in vitro and in silico, as well as for theoretical attempts to elucidate the underlying processes. In this paper, we developed a new model of the mechano-electrical waves elicited in the rows of very flexible C-terminal tails which decorate the outer surface of each microtubule. The fact that C-terminal tails play very diverse roles in many cellular functions, such as recruitment of motor proteins and microtubule-associated proteins, motivated us to consider their collective dynamics as the source of localized waves aimed for communication between microtubule and associated proteins. Our approach is based on the ferroelectric liquid crystal model and it leads to the effective asymmetric double-well potential which brings about the conditions for the appearance of kink-waves conducted by intrinsic electric fields embedded in microtubules. These kinks can serve as the signals for control and regulation of intracellular traffic along microtubules performed by processive motions of motor proteins, primarly from kinesin and dynein families. On the other hand, they can be precursors for initiation of dynamical instability of microtubules by recruiting the proper proteins responsible for the depolymerization process. PMID:27475079
Nonlinear dynamics of C-terminal tails in cellular microtubules
NASA Astrophysics Data System (ADS)
Sekulic, Dalibor L.; Sataric, Bogdan M.; Zdravkovic, Slobodan; Bugay, Aleksandr N.; Sataric, Miljko V.
2016-07-01
The mechanical and electrical properties, and information processing capabilities of microtubules are the permanent subject of interest for carrying out experiments in vitro and in silico, as well as for theoretical attempts to elucidate the underlying processes. In this paper, we developed a new model of the mechano-electrical waves elicited in the rows of very flexible C-terminal tails which decorate the outer surface of each microtubule. The fact that C-terminal tails play very diverse roles in many cellular functions, such as recruitment of motor proteins and microtubule-associated proteins, motivated us to consider their collective dynamics as the source of localized waves aimed for communication between microtubule and associated proteins. Our approach is based on the ferroelectric liquid crystal model and it leads to the effective asymmetric double-well potential which brings about the conditions for the appearance of kink-waves conducted by intrinsic electric fields embedded in microtubules. These kinks can serve as the signals for control and regulation of intracellular traffic along microtubules performed by processive motions of motor proteins, primarly from kinesin and dynein families. On the other hand, they can be precursors for initiation of dynamical instability of microtubules by recruiting the proper proteins responsible for the depolymerization process.
Research on Computational Fluid Dynamics and Turbulence
NASA Technical Reports Server (NTRS)
1986-01-01
Preconditioning matrices for Chebyshev derivative operators in several space dimensions; the Jacobi matrix technique in computational fluid dynamics; and Chebyshev techniques for periodic problems are discussed.
Dynamic involvement of ATG5 in cellular stress responses
Lin, H H; Lin, S-M; Chung, Y; Vonderfecht, S; Camden, J M; Flodby, P; Borok, Z; Limesand, K H; Mizushima, N; Ann, D K
2014-01-01
Autophagy maintains cell and tissue homeostasis through catabolic degradation. To better delineate the in vivo function for autophagy in adaptive responses to tissue injury, we examined the impact of compromised autophagy in mouse submandibular glands (SMGs) subjected to main excretory duct ligation. Blocking outflow from exocrine glands causes glandular atrophy by increased ductal pressure. Atg5f/−;Aqp5-Cre mice with salivary acinar-specific knockout (KO) of autophagy essential gene Atg5 were generated. While duct ligation induced autophagy and the expression of inflammatory mediators, SMGs in Atg5f/−;Aqp5-Cre mice, before ligation, already expressed higher levels of proinflammatory cytokine and Cdkn1a/p21 messages. Extended ligation period resulted in the caspase-3 activation and acinar cell death, which was delayed by Atg5 knockout. Moreover, expression of a set of senescence-associated secretory phenotype (SASP) factors was elevated in the post-ligated glands. Dysregulation of cell-cycle inhibitor CDKN1A/p21 and activation of senescence-associated β-galactosidase were detected in the stressed SMG duct cells. These senescence markers peaked at day 3 after ligation and partially resolved by day 7 in post-ligated SMGs of wild-type (WT) mice, but not in KO mice. The role of autophagy-related 5 (ATG5)-dependent autophagy in regulating the tempo, duration and magnitude of cellular stress responses in vivo was corroborated by in vitro studies using MEFs lacking ATG5 or autophagy-related 7 (ATG7) and autophagy inhibitors. Collectively, our results highlight the role of ATG5 in the dynamic regulation of ligation-induced cellular senescence and apoptosis, and suggest the involvement of autophagy resolution in salivary repair. PMID:25341032
Advances in fluorescence labeling strategies for dynamic cellular imaging
Dean, Kevin M; Palmer, Amy E
2014-01-01
Synergistic advances in optical physics, probe design, molecular biology, labeling techniques and computational analysis have propelled fluorescence imaging into new realms of spatiotemporal resolution and sensitivity. This review aims to discuss advances in fluorescent probes and live-cell labeling strategies, two areas that remain pivotal for future advances in imaging technology. Fluorescent protein– and bio-orthogonal–based methods for protein and RNA imaging are discussed as well as emerging bioengineering techniques that enable their expression at specific genomic loci (for example, CRISPR and TALENs). Important attributes that contribute to the success of each technique are emphasized, providing a guideline for future advances in dynamic live-cell imaging. PMID:24937069
Parallel Computation Of Forward Dynamics Of Manipulators
NASA Technical Reports Server (NTRS)
Fijany, Amir; Bejczy, Antal K.
1993-01-01
Report presents parallel algorithms and special parallel architecture for computation of forward dynamics of robotics manipulators. Products of effort to find best method of parallel computation to achieve required computational efficiency. Significant speedup of computation anticipated as well as cost reduction.
Predictive Dynamic Security Assessment through Advanced Computing
Huang, Zhenyu; Diao, Ruisheng; Jin, Shuangshuang; Chen, Yousu
2014-11-30
Abstract— Traditional dynamic security assessment is limited by several factors and thus falls short in providing real-time information to be predictive for power system operation. These factors include the steady-state assumption of current operating points, static transfer limits, and low computational speed. This addresses these factors and frames predictive dynamic security assessment. The primary objective of predictive dynamic security assessment is to enhance the functionality and computational process of dynamic security assessment through the use of high-speed phasor measurements and the application of advanced computing technologies for faster-than-real-time simulation. This paper presents algorithms, computing platforms, and simulation frameworks that constitute the predictive dynamic security assessment capability. Examples of phasor application and fast computation for dynamic security assessment are included to demonstrate the feasibility and speed enhancement for real-time applications.
Dance Dynamics: Computers and Dance.
ERIC Educational Resources Information Center
Gray, Judith A., Ed.; And Others
1983-01-01
Five articles discuss the use of computers in dance and dance education. They describe: (1) a computerized behavioral profile of a dance teacher; (2) computer-based dance notation; (3) elementary school computer-assisted dance instruction; (4) quantified analysis of dance criticism; and (5) computerized simulation of human body movements in a…
Vectorization of computer programs with applications to computational fluid dynamics
NASA Astrophysics Data System (ADS)
Gentzsch, W.
Techniques for adapting serial computer programs to the architecture of modern vector computers are presented and illustrated with examples, mainly from the field of computational fluid dynamics. The limitations of conventional computers are reviewed; the vector computers CRAY-1S and CDC-CYBER 205 are characterized; and chapters are devoted to vectorization of FORTRAN programs, sample-program vectorization on five different vector and parallel-architecture computers, restructuring of basic linear-algebra algorithms, iterative methods, vectorization of simple numerical algorithms, and fluid-dynamics vectorization on CRAY-1 (including an implicit beam and warming scheme, an implicit finite-difference method for laminar boundary-layer equations, the Galerkin method and a direct Monte Carlo simulation). Diagrams, charts, tables, and photographs are provided.
Cellular Automata Models Applied to the Study of Landslide Dynamics
NASA Astrophysics Data System (ADS)
Liucci, Luisa; Melelli, Laura; Suteanu, Cristian
2015-04-01
Landslides are caused by complex processes controlled by the interaction of numerous factors. Increasing efforts are being made to understand the spatial and temporal evolution of this phenomenon, and the use of remote sensing data is making significant contributions in improving forecast. This paper studies landslides seen as complex dynamic systems, in order to investigate their potential Self Organized Critical (SOC) behavior, and in particular, scale-invariant aspects of processes governing the spatial development of landslides and their temporal evolution, as well as the mechanisms involved in driving the system and keeping it in a critical state. For this purpose, we build Cellular Automata Models, which have been shown to be capable of reproducing the complexity of real world features using a small number of variables and simple rules, thus allowing for the reduction of the number of input parameters commonly used in the study of processes governing landslide evolution, such as those linked to the geomechanical properties of soils. This type of models has already been successfully applied in studying the dynamics of other natural hazards, such as earthquakes and forest fires. The basic structure of the model is composed of three modules: (i) An initialization module, which defines the topographic surface at time zero as a grid of square cells, each described by an altitude value; the surface is acquired from real Digital Elevation Models (DEMs). (ii) A transition function, which defines the rules used by the model to update the state of the system at each iteration. The rules use a stability criterion based on the slope angle and introduce a variable describing the weakening of the material over time, caused for example by rainfall. The weakening brings some sites of the system out of equilibrium thus causing the triggering of landslides, which propagate within the system through local interactions between neighboring cells. By using different rates of
Role of cellular adhesions in tissue dynamics spectroscopy
NASA Astrophysics Data System (ADS)
Merrill, Daniel A.; An, Ran; Turek, John; Nolte, David
2014-02-01
Cellular adhesions play a critical role in cell behavior, and modified expression of cellular adhesion compounds has been linked to various cancers. We tested the role of cellular adhesions in drug response by studying three cellular culture models: three-dimensional tumor spheroids with well-developed cellular adhesions and extracellular matrix (ECM), dense three-dimensional cell pellets with moderate numbers of adhesions, and dilute three-dimensional cell suspensions in agarose having few adhesions. Our technique for measuring the drug response for the spheroids and cell pellets was biodynamic imaging (BDI), and for the suspensions was quasi-elastic light scattering (QELS). We tested several cytoskeletal chemotherapeutic drugs (nocodazole, cytochalasin-D, paclitaxel, and colchicine) on three cancer cell lines chosen from human colorectal adenocarcinoma (HT-29), human pancreatic carcinoma (MIA PaCa-2), and rat osteosarcoma (UMR-106) to exhibit differences in adhesion strength. Comparing tumor spheroid behavior to that of cell suspensions showed shifts in the spectral motion of the cancer tissues that match predictions based on different degrees of cell-cell contacts. The HT-29 cell line, which has the strongest adhesions in the spheroid model, exhibits anomalous behavior in some cases. These results highlight the importance of using three-dimensional tissue models in drug screening with cellular adhesions being a contributory factor in phenotypic differences between the drug responses of tissue and cells.
A Computational Model of Cellular Response to Modulated Radiation Fields
McMahon, Stephen J.; Butterworth, Karl T.; McGarry, Conor K.; Trainor, Colman; O'Sullivan, Joe M.; Hounsell, Alan R.; Prise, Kevin M.
2012-09-01
Purpose: To develop a model to describe the response of cell populations to spatially modulated radiation exposures of relevance to advanced radiotherapies. Materials and Methods: A Monte Carlo model of cellular radiation response was developed. This model incorporated damage from both direct radiation and intercellular communication including bystander signaling. The predictions of this model were compared to previously measured survival curves for a normal human fibroblast line (AGO1522) and prostate tumor cells (DU145) exposed to spatially modulated fields. Results: The model was found to be able to accurately reproduce cell survival both in populations which were directly exposed to radiation and those which were outside the primary treatment field. The model predicts that the bystander effect makes a significant contribution to cell killing even in uniformly irradiated cells. The bystander effect contribution varies strongly with dose, falling from a high of 80% at low doses to 25% and 50% at 4 Gy for AGO1522 and DU145 cells, respectively. This was verified using the inducible nitric oxide synthase inhibitor aminoguanidine to inhibit the bystander effect in cells exposed to different doses, which showed significantly larger reductions in cell killing at lower doses. Conclusions: The model presented in this work accurately reproduces cell survival following modulated radiation exposures, both in and out of the primary treatment field, by incorporating a bystander component. In addition, the model suggests that the bystander effect is responsible for a significant portion of cell killing in uniformly irradiated cells, 50% and 70% at doses of 2 Gy in AGO1522 and DU145 cells, respectively. This description is a significant departure from accepted radiobiological models and may have a significant impact on optimization of treatment planning approaches if proven to be applicable in vivo.
Fluid dynamics computer programs for NERVA turbopump
NASA Technical Reports Server (NTRS)
Brunner, J. J.
1972-01-01
During the design of the NERVA turbopump, numerous computer programs were developed for the analyses of fluid dynamic problems within the machine. Program descriptions, example cases, users instructions, and listings for the majority of these programs are presented.
A Computational Fluid Dynamics Algorithm on a Massively Parallel Computer
NASA Technical Reports Server (NTRS)
Jespersen, Dennis C.; Levit, Creon
1989-01-01
The discipline of computational fluid dynamics is demanding ever-increasing computational power to deal with complex fluid flow problems. We investigate the performance of a finite-difference computational fluid dynamics algorithm on a massively parallel computer, the Connection Machine. Of special interest is an implicit time-stepping algorithm; to obtain maximum performance from the Connection Machine, it is necessary to use a nonstandard algorithm to solve the linear systems that arise in the implicit algorithm. We find that the Connection Machine ran achieve very high computation rates on both explicit and implicit algorithms. The performance of the Connection Machine puts it in the same class as today's most powerful conventional supercomputers.
Takada, Ryu; Munetaka, Daigo; Kobayashi, Shoji; Suemitsu, Yoshikazu; Nara, Shigetoshi
2007-09-01
Chaotic dynamics in a recurrent neural network model and in two-dimensional cellular automata, where both have finite but large degrees of freedom, are investigated from the viewpoint of harnessing chaos and are applied to motion control to indicate that both have potential capabilities for complex function control by simple rule(s). An important point is that chaotic dynamics generated in these two systems give us autonomous complex pattern dynamics itinerating through intermediate state points between embedded patterns (attractors) in high-dimensional state space. An application of these chaotic dynamics to complex controlling is proposed based on an idea that with the use of simple adaptive switching between a weakly chaotic regime and a strongly chaotic regime, complex problems can be solved. As an actual example, a two-dimensional maze, where it should be noted that the spatial structure of the maze is one of typical ill-posed problems, is solved with the use of chaos in both systems. Our computer simulations show that the success rate over 300 trials is much better, at least, than that of a random number generator. Our functional simulations indicate that both systems are almost equivalent from the viewpoint of functional aspects based on our idea, harnessing of chaos. PMID:19003512
COLD-SAT Dynamic Model Computer Code
NASA Technical Reports Server (NTRS)
Bollenbacher, G.; Adams, N. S.
1995-01-01
COLD-SAT Dynamic Model (CSDM) computer code implements six-degree-of-freedom, rigid-body mathematical model for simulation of spacecraft in orbit around Earth. Investigates flow dynamics and thermodynamics of subcritical cryogenic fluids in microgravity. Consists of three parts: translation model, rotation model, and slosh model. Written in FORTRAN 77.
Types or States? Cellular Dynamics and Regenerative Potential.
Adler, Carolyn E; Sánchez Alvarado, Alejandro
2015-11-01
Many of our organs can maintain and repair themselves during homeostasis and injury, as a result of the action of tissue-specific, multipotent stem cells. However, recent evidence from mammalian systems suggests that injury stimulates dramatic plasticity, or transient changes in cell potential, in both stem cells and more differentiated cells. Planarian flatworms possess abundant stem cells, making them an exceptional model for understanding the cellular behavior underlying homeostasis and regeneration. Recent discoveries of cell lineages and regeneration-specific events provide an initial framework for unraveling the complex cellular contributions to regeneration. In this review, we discuss the concept of cellular plasticity in the context of planarian regeneration, and consider the possibility that pluripotency may be a transient, probabilistic state exhibited by stem cells. PMID:26437587
A SAND approach based on cellular computation models for analysis and optimization
NASA Astrophysics Data System (ADS)
Canyurt, O. E.; Hajela, P.
2007-06-01
Genetic algorithms (GAs) have received considerable recent attention in problems of design optimization. The mechanics of population-based search in GAs are highly amenable to implementation on parallel computers. The present article describes a fine-grained model of parallel GA implementation that derives from a cellular-automata-like computation. The central idea behind the cellular genetic algorithm (CGA) approach is to treat the GA population as being distributed over a 2-D grid of cells, with each member of the population occupying a particular cell and defining the state of that cell. Evolution of the cell state is tantamount to updating the design information contained in a cell site and, as in cellular automata computations, takes place on the basis of local interaction with neighbouring cells. A special focus of the article is in the use of cellular automata (CA)-based models for structural analysis in conjunction with the CGA approach to optimization. In such an approach, the analysis and optimization are evolved simultaneously in a unified cellular computational framework. The article describes the implementation of this approach and examines its efficiency in the context of representative structural optimization problems.
Fast Parallel Computation Of Manipulator Inverse Dynamics
NASA Technical Reports Server (NTRS)
Fijany, Amir; Bejczy, Antal K.
1991-01-01
Method for fast parallel computation of inverse dynamics problem, essential for real-time dynamic control and simulation of robot manipulators, undergoing development. Enables exploitation of high degree of parallelism and, achievement of significant computational efficiency, while minimizing various communication and synchronization overheads as well as complexity of required computer architecture. Universal real-time robotic controller and simulator (URRCS) consists of internal host processor and several SIMD processors with ring topology. Architecture modular and expandable: more SIMD processors added to match size of problem. Operate asynchronously and in MIMD fashion.
TissueMiner: A multiscale analysis toolkit to quantify how cellular processes create tissue dynamics
Etournay, Raphaël; Merkel, Matthias; Popović, Marko; Brandl, Holger; Dye, Natalie A; Aigouy, Benoît; Salbreux, Guillaume; Eaton, Suzanne; Jülicher, Frank
2016-01-01
Segmentation and tracking of cells in long-term time-lapse experiments has emerged as a powerful method to understand how tissue shape changes emerge from the complex choreography of constituent cells. However, methods to store and interrogate the large datasets produced by these experiments are not widely available. Furthermore, recently developed methods for relating tissue shape changes to cell dynamics have not yet been widely applied by biologists because of their technical complexity. We therefore developed a database format that stores cellular connectivity and geometry information of deforming epithelial tissues, and computational tools to interrogate it and perform multi-scale analysis of morphogenesis. We provide tutorials for this computational framework, called TissueMiner, and demonstrate its capabilities by comparing cell and tissue dynamics in vein and inter-vein subregions of the Drosophila pupal wing. These analyses reveal an unexpected role for convergent extension in shaping wing veins. DOI: http://dx.doi.org/10.7554/eLife.14334.001 PMID:27228153
Computational Physics and Evolutionary Dynamics
NASA Astrophysics Data System (ADS)
Fontana, Walter
2000-03-01
One aspect of computational physics deals with the characterization of statistical regularities in materials. Computational physics meets biology when these materials can evolve. RNA molecules are a case in point. The folding of RNA sequences into secondary structures (shapes) inspires a simple biophysically grounded genotype-phenotype map that can be explored computationally and in the laboratory. We have identified some statistical regularities of this map and begin to understand their evolutionary consequences. (1) ``typical shapes'': Only a small subset of shapes realized by the RNA folding map is typical, in the sense of containing shapes that are realized significantly more often than others. Consequence: evolutionary histories mostly involve typical shapes, and thus exhibit generic properties. (2) ``neutral networks'': Sequences folding into the same shape are mutationally connected into a network that reaches across sequence space. Consequence: Evolutionary transitions between shapes reflect the fraction of boundary shared by the corresponding neutral networks in sequence space. The notion of a (dis)continuous transition can be made rigorous. (3) ``shape space covering'': Given a random sequence, a modest number of mutations suffices to reach a sequence realizing any typical shape. Consequence: The effective search space for evolutionary optimization is greatly reduced, and adaptive success is less dependent on initial conditions. (4) ``plasticity mirrors variability'': The repertoire of low energy shapes of a sequence is an indicator of how much and in which ways its energetically optimal shape can be altered by a single point mutation. Consequence: (i) Thermodynamic shape stability and mutational robustness are intimately linked. (ii) When natural selection favors the increase of stability, extreme mutational robustness -- to the point of an evolutionary dead-end -- is produced as a side effect. (iii) The hallmark of robust shapes is modularity.
Computational fluid dynamics - The coming revolution
NASA Technical Reports Server (NTRS)
Graves, R. A., Jr.
1982-01-01
The development of aerodynamic theory is traced from the days of Aristotle to the present, with the next stage in computational fluid dynamics dependent on superspeed computers for flow calculations. Additional attention is given to the history of numerical methods inherent in writing computer codes applicable to viscous and inviscid analyses for complex configurations. The advent of the superconducting Josephson junction is noted to place configurational demands on computer design to avoid limitations imposed by the speed of light, and a Japanese projection of a computer capable of several hundred billion operations/sec is mentioned. The NASA Numerical Aerodynamic Simulator is described, showing capabilities of a billion operations/sec with a memory of 240 million words using existing technology. Near-term advances in fluid dynamics are discussed.
Single neuron dynamics and computation.
Brunel, Nicolas; Hakim, Vincent; Richardson, Magnus J E
2014-04-01
At the single neuron level, information processing involves the transformation of input spike trains into an appropriate output spike train. Building upon the classical view of a neuron as a threshold device, models have been developed in recent years that take into account the diverse electrophysiological make-up of neurons and accurately describe their input-output relations. Here, we review these recent advances and survey the computational roles that they have uncovered for various electrophysiological properties, for dendritic arbor anatomy as well as for short-term synaptic plasticity. PMID:24492069
Three-Dimensional Computational Fluid Dynamics
Haworth, D.C.; O'Rourke, P.J.; Ranganathan, R.
1998-09-01
Computational fluid dynamics (CFD) is one discipline falling under the broad heading of computer-aided engineering (CAE). CAE, together with computer-aided design (CAD) and computer-aided manufacturing (CAM), comprise a mathematical-based approach to engineering product and process design, analysis and fabrication. In this overview of CFD for the design engineer, our purposes are three-fold: (1) to define the scope of CFD and motivate its utility for engineering, (2) to provide a basic technical foundation for CFD, and (3) to convey how CFD is incorporated into engineering product and process design.
Kinetic Monte Carlo and cellular particle dynamics simulations of multicellular systems
NASA Astrophysics Data System (ADS)
Flenner, Elijah; Janosi, Lorant; Barz, Bogdan; Neagu, Adrian; Forgacs, Gabor; Kosztin, Ioan
2012-03-01
Computer modeling of multicellular systems has been a valuable tool for interpreting and guiding in vitro experiments relevant to embryonic morphogenesis, tumor growth, angiogenesis and, lately, structure formation following the printing of cell aggregates as bioink particles. Here we formulate two computer simulation methods: (1) a kinetic Monte Carlo (KMC) and (2) a cellular particle dynamics (CPD) method, which are capable of describing and predicting the shape evolution in time of three-dimensional multicellular systems during their biomechanical relaxation. Our work is motivated by the need of developing quantitative methods for optimizing postprinting structure formation in bioprinting-assisted tissue engineering. The KMC and CPD model parameters are determined and calibrated by using an original computational-theoretical-experimental framework applied to the fusion of two spherical cell aggregates. The two methods are used to predict the (1) formation of a toroidal structure through fusion of spherical aggregates and (2) cell sorting within an aggregate formed by two types of cells with different adhesivities.
Adiponectin fine-tuning of liver regeneration dynamics revealed through cellular network modelling.
Correnti, Jason M; Cook, Daniel; Aksamitiene, Edita; Swarup, Aditi; Ogunnaike, Babatunde; Vadigepalli, Rajanikanth; Hoek, Jan B
2015-01-15
Following partial hepatectomy, the liver initiates a regenerative programme involving hepatocyte priming and replication driven by the coordinated actions of cytokine and growth factors. We investigated the mechanisms underlying adiponectin's (Adn) regulation of liver regeneration through modulation of these mediators. Adn(-/-) mice showed delayed onset of hepatocyte replication, but accelerated cell cycle progression relative to wild-type mice, suggesting Adn has multiple effects fine-tuning the kinetics of liver regeneration. We developed a computational model describing the molecular and physiological kinetics of liver regeneration in Adn(-/-) mice. We employed this computational model to evaluate the underlying regulatory mechanisms. Our analysis predicted that Adn is required for an efficient early cytokine response to partial hepatectomy, but is inhibitory to later growth factor actions. Consistent with this prediction, Adn knockout reduced hepatocyte responses to interleukin-6 during the priming phase, but enhanced growth factor levels through peak hepatocyte replication. By contrast, supraphysiological concentrations of Adn resulting from rosiglitazone treatment suppressed regeneration by reducing growth factor levels during S phase, consistent with computational predictions. Together, these results revealed that Adn fine-tunes the progression of liver regeneration through dynamically modulating molecular mediator networks and cellular interactions within the liver. PMID:25630259
Adiponectin fine-tuning of liver regeneration dynamics revealed through cellular network modelling
Correnti, Jason M; Cook, Daniel; Aksamitiene, Edita; Swarup, Aditi; Ogunnaike, Babatunde; Vadigepalli, Rajanikanth; Hoek, Jan B
2015-01-01
Following partial hepatectomy, the liver initiates a regenerative programme involving hepatocyte priming and replication driven by the coordinated actions of cytokine and growth factors. We investigated the mechanisms underlying adiponectin's (Adn) regulation of liver regeneration through modulation of these mediators. Adn–/– mice showed delayed onset of hepatocyte replication, but accelerated cell cycle progression relative to wild-type mice, suggesting Adn has multiple effects fine-tuning the kinetics of liver regeneration. We developed a computational model describing the molecular and physiological kinetics of liver regeneration in Adn–/– mice. We employed this computational model to evaluate the underlying regulatory mechanisms. Our analysis predicted that Adn is required for an efficient early cytokine response to partial hepatectomy, but is inhibitory to later growth factor actions. Consistent with this prediction, Adn knockout reduced hepatocyte responses to interleukin-6 during the priming phase, but enhanced growth factor levels through peak hepatocyte replication. By contrast, supraphysiological concentrations of Adn resulting from rosiglitazone treatment suppressed regeneration by reducing growth factor levels during S phase, consistent with computational predictions. Together, these results revealed that Adn fine-tunes the progression of liver regeneration through dynamically modulating molecular mediator networks and cellular interactions within the liver. PMID:25630259
Localization microscopy: mapping cellular dynamics with single molecules.
Nelson, A J; Hess, S T
2014-04-01
Resolution describes the smallest details within a sample that can be recovered by a microscope lens system. For optical microscopes detecting visible light, diffraction limits the resolution to ∼200-250 nm. In contrast, localization measures the position of an isolated object using its image. Single fluorescent molecules can be localized with an uncertainty of a few tens of nanometres, and in some cases less than one nanometre. Superresolution fluorescence localization microscopy (SRFLM) images and localizes fluorescent molecules in a sample. By controlling the visibility of the fluorescent molecules with light, it is possible to cause a sparse subset of the tags to fluoresce and be spatially separated from each other. A movie is acquired with a camera, capturing images of many sets of visible fluorescent tags over a period of time. The movie is then analysed by a computer whereby all of the single molecules are independently measured, and their positions are recorded. When the coordinates of a sufficient number of molecules are collected, an image can be rendered by plotting the coordinates of the localized molecules. The spatial resolution of these rendered images can be better than 20 nm, roughly an order of magnitude better than the diffraction limited resolution. The invention of SRFLM has led to an explosion of related techniques. Through the use of specialized optics, the fluorescent signal can be split into multiple detection channels. These channels can capture additional information such as colour (emission wavelength), orientation and three-dimensional position of the detected molecules. Measurement of the colour of the detected fluorescence can allow researchers to distinguish multiple types of fluorescent tags and to study the interaction between multiple molecules of interest. Three-dimensional imaging and determination of molecular orientations offer insight into structural organization of the sample. SRFLM is compatible with living samples and
NASA Astrophysics Data System (ADS)
Van De Wiel, Marco J.; Coulthard, Tom J.; Macklin, Mark G.; Lewin, John
2007-10-01
We introduce a new computational model designed to simulate and investigate reach-scale alluvial dynamics within a landscape evolution model. The model is based on the cellular automaton concept, whereby the continued iteration of a series of local process 'rules' governs the behaviour of the entire system. The model is a modified version of the CAESAR landscape evolution model, which applies a suite of physically based rules to simulate the entrainment, transport and deposition of sediments. The CAESAR model has been altered to improve the representation of hydraulic and geomorphic processes in an alluvial environment. In-channel and overbank flow, sediment entrainment and deposition, suspended load and bed load transport, lateral erosion and bank failure have all been represented as local cellular automaton rules. Although these rules are relatively simple and straightforward, their combined and repeatedly iterated effect is such that complex, non-linear geomorphological response can be simulated within the model. Examples of such larger-scale, emergent responses include channel incision and aggradation, terrace formation, channel migration and river meandering, formation of meander cutoffs, and transitions between braided and single-thread channel patterns. In the current study, the model is illustrated on a reach of the River Teifi, near Lampeter, Wales, UK.
Dynamic cellular uptake of mixed-monolayer protected nanoparticles.
Carney, Randy P; Carney, Tamara M; Mueller, Marie; Stellacci, Francesco
2012-12-01
Nanoparticles (NPs) are gaining increasing attention for potential application in medicine; consequently, studying their interaction with cells is of central importance. We found that both ligand arrangement and composition on gold nanoparticles play a crucial role in their cellular internalization. In our previous investigation, we showed that 66-34OT nanoparticles coated with stripe-like domains of hydrophobic (octanethiol, OT, 34%) and hydrophilic (11-mercaptoundecane sulfonate, MUS, 66%) ligands permeated through the cellular lipid bilayer via passive diffusion, in addition to endo-/pino-cytosis. Here, we show an analysis of NP internalization by DC2.4, 3T3, and HeLa cells at two temperatures and multiple time points. We study four NPs that differ in their surface structures and ligand compositions and report on their cellular internalization by intracellular fluorescence quantification. Using confocal laser scanning microscopy we have found that all three cell types internalize the 66-34OT NPs more than particles coated only with MUS, or particles coated with a very similar coating but lacking any detectable ligand shell structure, or 'striped' particles but with a different composition (34-66OT) at multiple data points. PMID:22589060
Computer simulation of microstructural dynamics
Grest, G.S.; Anderson, M.P.; Srolovitz, D.J.
1985-01-01
Since many of the physical properties of materials are determined by their microstructure, it is important to be able to predict and control microstructural development. A number of approaches have been taken to study this problem, but they assume that the grains can be described as spherical or hexagonal and that growth occurs in an average environment. We have developed a new technique to bridge the gap between the atomistic interactions and the macroscopic scale by discretizing the continuum system such that the microstructure retains its topological connectedness, yet is amenable to computer simulations. Using this technique, we have studied grain growth in polycrystalline aggregates. The temporal evolution and grain morphology of our model are in excellent agreement with experimental results for metals and ceramics.
A cellular automata model of Ebola virus dynamics
NASA Astrophysics Data System (ADS)
Burkhead, Emily; Hawkins, Jane
2015-11-01
We construct a stochastic cellular automaton (SCA) model for the spread of the Ebola virus (EBOV). We make substantial modifications to an existing SCA model used for HIV, introduced by others and studied by the authors. We give a rigorous analysis of the similarities between models due to the spread of virus and the typical immune response to it, and the differences which reflect the drastically different timing of the course of EBOV. We demonstrate output from the model and compare it with clinical data.
Computational fluid dynamics - A personal view
NASA Technical Reports Server (NTRS)
Hussaini, M. Y.
1989-01-01
This paper provides a personal view of computational fluid dynamics. The main theme is divided into two categories - one dealing with algorithms and engineering applications and the other with scientific investigations. The former category may be termed computational aerodynamics, with the objective of providing reliable aerodynamic or engineering predictions. The latter category is essentially basic research, where the algorithmic tools are used to unravel and elucidate fluid-dynamic phenomena hard to obtain in a laboratory. A critique of the numerical solution techniques for both compressible and incompressible flows is included. The discussion on scientific investigations deals in particular with transition and turbulence.
Traffic Dynamics of Computer Networks
NASA Astrophysics Data System (ADS)
Fekete, Attila
2008-10-01
Two important aspects of the Internet, namely the properties of its topology and the characteristics of its data traffic, have attracted growing attention of the physics community. My thesis has considered problems of both aspects. First I studied the stochastic behavior of TCP, the primary algorithm governing traffic in the current Internet, in an elementary network scenario consisting of a standalone infinite-sized buffer and an access link. The effect of the fast recovery and fast retransmission (FR/FR) algorithms is also considered. I showed that my model can be extended further to involve the effect of link propagation delay, characteristic of WAN. I continued my thesis with the investigation of finite-sized semi-bottleneck buffers, where packets can be dropped not only at the link, but also at the buffer. I demonstrated that the behavior of the system depends only on a certain combination of the parameters. Moreover, an analytic formula was derived that gives the ratio of packet loss rate at the buffer to the total packet loss rate. This formula makes it possible to treat buffer-losses as if they were link-losses. Finally, I studied computer networks from a structural perspective. I demonstrated through fluid simulations that the distribution of resources, specifically the link bandwidth, has a serious impact on the global performance of the network. Then I analyzed the distribution of edge betweenness in a growing scale-free tree under the condition that a local property, the in-degree of the "younger" node of an arbitrary edge, is known in order to find an optimum distribution of link capacity. The derived formula is exact even for finite-sized networks. I also calculated the conditional expectation of edge betweenness, rescaled for infinite networks.
Fast Parallel Computation Of Multibody Dynamics
NASA Technical Reports Server (NTRS)
Fijany, Amir; Kwan, Gregory L.; Bagherzadeh, Nader
1996-01-01
Constraint-force algorithm fast, efficient, parallel-computation algorithm for solving forward dynamics problem of multibody system like robot arm or vehicle. Solves problem in minimum time proportional to log(N) by use of optimal number of processors proportional to N, where N is number of dynamical degrees of freedom: in this sense, constraint-force algorithm both time-optimal and processor-optimal parallel-processing algorithm.
Quantifying cellular interaction dynamics in 3-D fluorescence microscopy data
Klauschen, Frederick; Ishii, Masaru; Qi, Hai; Bajénoff, Marc; Egen, Jackson G.; Germain, Ronald N.; Meier-Schellersheim, Martin
2012-01-01
The wealth of information available from advanced fluorescence imaging techniques used to analyze biological processes with high spatial and temporal resolution calls for high-throughput image analysis methods. Here, we describe a fully automated approach to analyzing cellular interaction behavior in 3-D fluorescence microscopy images. As example application we present the analysis of drug-induced and S1P1-knock-out-related changes in bone-osteoclast interactions. Moreover, we apply our approach to images showing the spatial association of dendritic cells with the fibroblastic reticular cell network within lymph nodes and to microscopy data about T-B lymphocyte synapse formation. Such analyses that yield important information about the molecular mechanisms determining cellular interaction behavior would be very difficult to perform with approaches that rely on manual/semi-automated analyses. This protocol integrates adaptive threshold segmentation, object detection, adaptive color channel merging and neighborhood analysis and permits rapid, standardized, quantitative analysis and comparison of the relevant features in large data sets. PMID:19696749
Use of computer and cellular phone technology by older rural adults.
O'Brien, Tara Renee; Treiber, Frank; Jenkins, Carolyn; Mercier, Angela
2014-08-01
The objective of this study was to explore the use of computer and cellular phone technology among older adults living in the rural Appalachian region of North Carolina. A 21-item questionnaire on access to and use of computer and cellular phone technology was administered to 43 older adults, using dichotomous and frequency-rated questions. The sample was recruited from two rural senior centers in the Appalachian region of North Carolina. Forty percent of the participants earned $20 000 or less annually. The majority owned a cellular phone (79.9%), and nearly half had a desktop computer (44.2%). High-speed Internet coverage was the most frequent type (42%) of in-home coverage. This study provides insights into the needs and challenges of older rural Appalachians with regard to technology. Computer technology may be more accessible and have fewer barriers by older adults than other forms of technology. Future research should explore the levels of computer literacy of older adults. PMID:24949713
Dynamics of HIV infection on 2D cellular automata
NASA Astrophysics Data System (ADS)
Benyoussef, A.; HafidAllah, N. El; ElKenz, A.; Ez-Zahraouy, H.; Loulidi, M.
2003-05-01
We use a cellular automata approach to describe the interactions of the immune system with the human immunodeficiency virus (HIV). We study the evolution of HIV infection, particularly in the clinical latency period. The results we have obtained show the existence of four different behaviours in the plane of death rate of virus-death rate of infected T cell. These regions meet at a critical point, where the virus density and the infected T cell density remain invariant during the evolution of disease. We have introduced two kinds of treatments, the protease inhibitors and the RT inhibitors, in order to study their effects on the evolution of HIV infection. These treatments are powerful in decreasing the density of the virus in the blood and the delay of the AIDS onset.
Phenomenological study of a cellular material behaviour under dynamic loadings
NASA Astrophysics Data System (ADS)
Bouix, R.; Viot, Ph.; Lataillade, J.-L.
2006-08-01
Polypropylene foams are cellular materials, which are often use to fill structures subjected to crash or violent impacts. Therefore, it is necessary to know and to characterise in experiments their mechanical behaviour in compression at high strain rates. So, several apparatus have been used in order to highlight the influence of strain rate, material density and also temperature. A split Hopkinson Pressure Bar has been used for impact tests, a fly wheel to test theses materials at medium strain rate and an electro-mechanical testing machine associated to a climatic chamber for temperature tests. Then, a rheological model has been used in order to describe the material behaviour. The mechanical response to compression of these foams presents three typical domains: a linear elastic step, a wide collapse plateau stress, which leads to a densification, which are related to a standard rheological model.
Statistical analysis of nanoparticle dosing in a dynamic cellular system.
Summers, Huw D; Rees, Paul; Holton, Mark D; Brown, M Rowan; Chappell, Sally C; Smith, Paul J; Errington, Rachel J
2011-03-01
The delivery of nanoparticles into cells is important in therapeutic applications and in nanotoxicology. Nanoparticles are generally targeted to receptors on the surfaces of cells and internalized into endosomes by endocytosis, but the kinetics of the process and the way in which cell division redistributes the particles remain unclear. Here we show that the chance of success or failure of nanoparticle uptake and inheritance is random. Statistical analysis of nanoparticle-loaded endosomes indicates that particle capture is described by an over-dispersed Poisson probability distribution that is consistent with heterogeneous adsorption and internalization. Partitioning of nanoparticles in cell division is random and asymmetric, following a binomial distribution with mean probability of 0.52-0.72. These results show that cellular targeting of nanoparticles is inherently imprecise due to the randomness of nature at the molecular scale, and the statistical framework offers a way to predict nanoparticle dosage for therapy and for the study of nanotoxins. PMID:21258333
Statistical analysis of nanoparticle dosing in a dynamic cellular system
NASA Astrophysics Data System (ADS)
Summers, Huw D.; Rees, Paul; Holton, Mark D.; Rowan Brown, M.; Chappell, Sally C.; Smith, Paul J.; Errington, Rachel J.
2011-03-01
The delivery of nanoparticles into cells is important in therapeutic applications and in nanotoxicology. Nanoparticles are generally targeted to receptors on the surfaces of cells and internalized into endosomes by endocytosis, but the kinetics of the process and the way in which cell division redistributes the particles remain unclear. Here we show that the chance of success or failure of nanoparticle uptake and inheritance is random. Statistical analysis of nanoparticle-loaded endosomes indicates that particle capture is described by an over-dispersed Poisson probability distribution that is consistent with heterogeneous adsorption and internalization. Partitioning of nanoparticles in cell division is random and asymmetric, following a binomial distribution with mean probability of 0.52-0.72. These results show that cellular targeting of nanoparticles is inherently imprecise due to the randomness of nature at the molecular scale, and the statistical framework offers a way to predict nanoparticle dosage for therapy and for the study of nanotoxins.
Visualization of unsteady computational fluid dynamics
NASA Astrophysics Data System (ADS)
Haimes, Robert
1994-11-01
A brief summary of the computer environment used for calculating three dimensional unsteady Computational Fluid Dynamic (CFD) results is presented. This environment requires a super computer as well as massively parallel processors (MPP's) and clusters of workstations acting as a single MPP (by concurrently working on the same task) provide the required computational bandwidth for CFD calculations of transient problems. The cluster of reduced instruction set computers (RISC) is a recent advent based on the low cost and high performance that workstation vendors provide. The cluster, with the proper software can act as a multiple instruction/multiple data (MIMD) machine. A new set of software tools is being designed specifically to address visualizing 3D unsteady CFD results in these environments. Three user's manuals for the parallel version of Visual3, pV3, revision 1.00 make up the bulk of this report.
Visualization of unsteady computational fluid dynamics
NASA Technical Reports Server (NTRS)
Haimes, Robert
1994-01-01
A brief summary of the computer environment used for calculating three dimensional unsteady Computational Fluid Dynamic (CFD) results is presented. This environment requires a super computer as well as massively parallel processors (MPP's) and clusters of workstations acting as a single MPP (by concurrently working on the same task) provide the required computational bandwidth for CFD calculations of transient problems. The cluster of reduced instruction set computers (RISC) is a recent advent based on the low cost and high performance that workstation vendors provide. The cluster, with the proper software can act as a multiple instruction/multiple data (MIMD) machine. A new set of software tools is being designed specifically to address visualizing 3D unsteady CFD results in these environments. Three user's manuals for the parallel version of Visual3, pV3, revision 1.00 make up the bulk of this report.
Graphics supercomputer for computational fluid dynamics research
NASA Astrophysics Data System (ADS)
Liaw, Goang S.
1994-11-01
The objective of this project is to purchase a state-of-the-art graphics supercomputer to improve the Computational Fluid Dynamics (CFD) research capability at Alabama A & M University (AAMU) and to support the Air Force research projects. A cutting-edge graphics supercomputer system, Onyx VTX, from Silicon Graphics Computer Systems (SGI), was purchased and installed. Other equipment including a desktop personal computer, PC-486 DX2 with a built-in 10-BaseT Ethernet card, a 10-BaseT hub, an Apple Laser Printer Select 360, and a notebook computer from Zenith were also purchased. A reading room has been converted to a research computer lab by adding some furniture and an air conditioning unit in order to provide an appropriate working environments for researchers and the purchase equipment. All the purchased equipment were successfully installed and are fully functional. Several research projects, including two existing Air Force projects, are being performed using these facilities.
Keränen, Soile VE; Fowlkes, Charless C; Luengo Hendriks, Cris L; Sudar, Damir; Knowles, David W; Malik, Jitendra; Biggin, Mark D
2006-01-01
Background To accurately describe gene expression and computationally model animal transcriptional networks, it is essential to determine the changing locations of cells in developing embryos. Results Using automated image analysis methods, we provide the first quantitative description of temporal changes in morphology and gene expression at cellular resolution in whole embryos, using the Drosophila blastoderm as a model. Analyses based on both fixed and live embryos reveal complex, previously undetected three-dimensional changes in nuclear density patterns caused by nuclear movements prior to gastrulation. Gene expression patterns move, in part, with these changes in morphology, but additional spatial shifts in expression patterns are also seen, supporting a previously proposed model of pattern dynamics based on the induction and inhibition of gene expression. We show that mutations that disrupt either the anterior/posterior (a/p) or the dorsal/ventral (d/v) transcriptional cascades alter morphology and gene expression along both the a/p and d/v axes in a way suggesting that these two patterning systems interact via both transcriptional and morphological mechanisms. Conclusion Our work establishes a new strategy for measuring temporal changes in the locations of cells and gene expression patterns that uses fixed cell material and computational modeling. It also provides a coordinate framework for the blastoderm embryo that will allow increasingly accurate spatio-temporal modeling of both the transcriptional control network and morphogenesis. PMID:17184547
Final Report Computational Analysis of Dynamical Systems
Guckenheimer, John
2012-05-08
This is the final report for DOE Grant DE-FG02-93ER25164, initiated in 1993. This grant supported research of John Guckenheimer on computational analysis of dynamical systems. During that period, seventeen individuals received PhD degrees under the supervision of Guckenheimer and over fifty publications related to the grant were produced. This document contains copies of these publications.
Computational fluid dynamics in oil burner design
Butcher, T.A.
1997-09-01
In Computational Fluid Dynamics, the differential equations which describe flow, heat transfer, and mass transfer are approximately solved using a very laborious numerical procedure. Flows of practical interest to burner designs are always turbulent, adding to the complexity of requiring a turbulence model. This paper presents a model for burner design.
Probing Cellular Mechanoadaptation Using Cell-Substrate De-Adhesion Dynamics: Experiments and Model
S S, Soumya; Sthanam, Lakshmi Kavitha; Padinhateeri, Ranjith; Inamdar, Mandar M.; Sen, Shamik
2014-01-01
Physical properties of the extracellular matrix (ECM) are known to regulate cellular processes ranging from spreading to differentiation, with alterations in cell phenotype closely associated with changes in physical properties of cells themselves. When plated on substrates of varying stiffness, fibroblasts have been shown to exhibit stiffness matching property, wherein cell cortical stiffness increases in proportion to substrate stiffness up to 5 kPa, and subsequently saturates. Similar mechanoadaptation responses have also been observed in other cell types. Trypsin de-adhesion represents a simple experimental framework for probing the contractile mechanics of adherent cells, with de-adhesion timescales shown to scale inversely with cortical stiffness values. In this study, we combine experiments and computation in deciphering the influence of substrate properties in regulating de-adhesion dynamics of adherent cells. We first show that NIH 3T3 fibroblasts cultured on collagen-coated polyacrylamide hydrogels de-adhere faster on stiffer substrates. Using a simple computational model, we qualitatively show how substrate stiffness and cell-substrate bond breakage rate collectively influence de-adhesion timescales, and also obtain analytical expressions of de-adhesion timescales in certain regimes of the parameter space. Finally, by comparing stiffness-dependent experimental and computational de-adhesion responses, we show that faster de-adhesion on stiffer substrates arises due to force-dependent breakage of cell-matrix adhesions. In addition to illustrating the utility of employing trypsin de-adhesion as a biophysical tool for probing mechanoadaptation, our computational results highlight the collective interplay of substrate properties and bond breakage rate in setting de-adhesion timescales. PMID:25197799
Parallel computation of manipulator inverse dynamics
NASA Technical Reports Server (NTRS)
Fijany, Amir; Bejczy, Antal K.
1991-01-01
In this article, parallel computation of manipulator inverse dynamics is investigated. A hierarchical graph-based mapping approach is devised to analyze the inherent parallelism in the Newton-Euler formulation at several computational levels, and to derive the features of an abstract architecture for exploitation of parallelism. At each level, a parallel algorithm represents the application of a parallel model of computation that transforms the computation into a graph whose structure defines the features of an abstract architecture, i.e., number of processors, communication structure, etc. Data-flow analysis is employed to derive the time lower bound in the computation as well as the sequencing of the abstract architecture. The features of the target architecture are defined by optimization of the abstract architecture to exploit maximum parallelism while minimizing architectural complexity. An architecture is designed and implemented that is capable of efficient exploitation of parallelism at several computational levels. The computation time of the Newton-Euler formulation for a 6-degree-of-freedom (dof) general manipulator is measured as 187 microsec. The increase in computation time for each additional dof is 23 microsec, which leads to a computation time of less than 500 microsec, even for a 12-dof redundant arm.
Optimal dynamic remapping of parallel computations
NASA Technical Reports Server (NTRS)
Nicol, David M.; Reynolds, Paul F., Jr.
1987-01-01
A large class of computations are characterized by a sequence of phases, with phase changes occurring unpredictably. The decision problem was considered regarding the remapping of workload to processors in a parallel computation when the utility of remapping and the future behavior of the workload is uncertain, and phases exhibit stable execution requirements during a given phase, but requirements may change radically between phases. For these problems a workload assignment generated for one phase may hinder performance during the next phase. This problem is treated formally for a probabilistic model of computation with at most two phases. The fundamental problem of balancing the expected remapping performance gain against the delay cost was addressed. Stochastic dynamic programming is used to show that the remapping decision policy minimizing the expected running time of the computation has an extremely simple structure. Because the gain may not be predictable, the performance of a heuristic policy that does not require estimnation of the gain is examined. The heuristic method's feasibility is demonstrated by its use on an adaptive fluid dynamics code on a multiprocessor. The results suggest that except in extreme cases, the remapping decision problem is essentially that of dynamically determining whether gain can be achieved by remapping after a phase change. The results also suggest that this heuristic is applicable to computations with more than two phases.
Dynamic fragmentation of cellular, ice-templated alumina scaffolds
NASA Astrophysics Data System (ADS)
Tan, Yi Ming; Cervantes, Octavio; Nam, SeanWoo; Molitoris, John D.; Hooper, Joseph P.
2016-01-01
We examine the dynamic failure of ice-templated freeze-cast alumina scaffolds that are being considered as biomimetic hierarchical structures. Three porosities of alumina freeze-cast structures were fabricated, and a systematic variation in microstructural properties such as lamellar width and thickness was observed with changing porosity. Dynamic impact tests were performed in a light-gas gun to examine the failure properties of these materials under high strain-rate loading. Nearly complete delamination was observed following impact, along with characteristic cracking across the lamellar width. Average fragment size decreases with increasing porosity, and a theoretical model was developed to explain this behavior based on microstructural changes. Using an energy balance between kinetic, strain, and surface energies within a single lamella, we are able to accurately predict the characteristic fragment size using only standard material properties of bulk alumina.
Chromatin Dynamics in Lineage Commitment and Cellular Reprogramming
Shchuka, Virlana M.; Malek-Gilani, Nakisa; Singh, Gurdeep; Langroudi, Lida; Dhaliwal, Navroop K.; Moorthy, Sakthi D.; Davidson, Scott; Macpherson, Neil N.; Mitchell, Jennifer A.
2015-01-01
Dynamic structural properties of chromatin play an essential role in defining cell identity and function. Transcription factors and chromatin modifiers establish and maintain cell states through alteration of DNA accessibility and histone modifications. This activity is focused at both gene-proximal promoter regions and distally located regulatory elements. In the three-dimensional space of the nucleus, distal elements are localized in close physical proximity to the gene-proximal regulatory sequences through the formation of chromatin loops. These looping features in the genome are highly dynamic as embryonic stem cells differentiate and commit to specific lineages, and throughout reprogramming as differentiated cells reacquire pluripotency. Identifying these functional distal regulatory regions in the genome provides insight into the regulatory processes governing early mammalian development and guidance for improving the protocols that generate induced pluripotent cells. PMID:26193323
Chromatin Dynamics in Lineage Commitment and Cellular Reprogramming.
Shchuka, Virlana M; Malek-Gilani, Nakisa; Singh, Gurdeep; Langroudi, Lida; Dhaliwal, Navroop K; Moorthy, Sakthi D; Davidson, Scott; Macpherson, Neil N; Mitchell, Jennifer A
2015-01-01
Dynamic structural properties of chromatin play an essential role in defining cell identity and function. Transcription factors and chromatin modifiers establish and maintain cell states through alteration of DNA accessibility and histone modifications. This activity is focused at both gene-proximal promoter regions and distally located regulatory elements. In the three-dimensional space of the nucleus, distal elements are localized in close physical proximity to the gene-proximal regulatory sequences through the formation of chromatin loops. These looping features in the genome are highly dynamic as embryonic stem cells differentiate and commit to specific lineages, and throughout reprogramming as differentiated cells reacquire pluripotency. Identifying these functional distal regulatory regions in the genome provides insight into the regulatory processes governing early mammalian development and guidance for improving the protocols that generate induced pluripotent cells. PMID:26193323
Dynamical modeling and analysis of large cellular regulatory networks
NASA Astrophysics Data System (ADS)
Bérenguier, D.; Chaouiya, C.; Monteiro, P. T.; Naldi, A.; Remy, E.; Thieffry, D.; Tichit, L.
2013-06-01
The dynamical analysis of large biological regulatory networks requires the development of scalable methods for mathematical modeling. Following the approach initially introduced by Thomas, we formalize the interactions between the components of a network in terms of discrete variables, functions, and parameters. Model simulations result in directed graphs, called state transition graphs. We are particularly interested in reachability properties and asymptotic behaviors, which correspond to terminal strongly connected components (or "attractors") in the state transition graph. A well-known problem is the exponential increase of the size of state transition graphs with the number of network components, in particular when using the biologically realistic asynchronous updating assumption. To address this problem, we have developed several complementary methods enabling the analysis of the behavior of large and complex logical models: (i) the definition of transition priority classes to simplify the dynamics; (ii) a model reduction method preserving essential dynamical properties, (iii) a novel algorithm to compact state transition graphs and directly generate compressed representations, emphasizing relevant transient and asymptotic dynamical properties. The power of an approach combining these different methods is demonstrated by applying them to a recent multilevel logical model for the network controlling CD4+ T helper cell response to antigen presentation and to a dozen cytokines. This model accounts for the differentiation of canonical Th1 and Th2 lymphocytes, as well as of inflammatory Th17 and regulatory T cells, along with many hybrid subtypes. All these methods have been implemented into the software GINsim, which enables the definition, the analysis, and the simulation of logical regulatory graphs.
Cellular Proteome Dynamics during Differentiation of Human Primary Myoblasts.
Le Bihan, Marie-Catherine; Barrio-Hernandez, Inigo; Mortensen, Tenna Pavia; Henningsen, Jeanette; Jensen, Søren Skov; Bigot, Anne; Blagoev, Blagoy; Butler-Browne, Gillian; Kratchmarova, Irina
2015-08-01
Muscle stem cells, or satellite cells, play an important role in the maintenance and repair of muscle tissue and have the capacity to proliferate and differentiate in response to physiological or environmental changes. Although they have been extensively studied, the key regulatory steps and the complex temporal protein dynamics accompanying the differentiation of primary human muscle cells remain poorly understood. Here, we demonstrate the advantages of applying a MS-based quantitative approach, stable isotope labeling by amino acids in cell culture (SILAC), for studying human myogenesis in vitro and characterize the fine-tuned changes in protein expression underlying the dramatic phenotypic conversion of primary mononucleated human muscle cells during in vitro differentiation to form multinucleated myotubes. Using an exclusively optimized triple encoding SILAC procedure, we generated dynamic expression profiles during the course of myogenic differentiation and quantified 2240 proteins, 243 of which were regulated. These changes in protein expression occurred in sequential waves and underlined vast reprogramming in key processes governing cell fate decisions, i.e., cell cycle withdrawal, RNA metabolism, cell adhesion, proteolysis, and cytoskeletal organization. In silico transcription factor target analysis demonstrated that the observed dynamic changes in the proteome could be attributed to a cascade of transcriptional events involving key myogenic regulatory factors as well as additional regulators not yet known to act on muscle differentiation. In addition, we created of a dynamic map of the developing myofibril, providing valuable insights into the formation and maturation of the contractile apparatus in vitro. Finally, our SILAC-based quantitative approach offered the possibility to follow the expression profiles of several muscle disease-associated proteins simultaneously and therefore could be a valuable resource for future studies investigating
Atlas of Cellular Dynamics during Zebrafish Adult Kidney Regeneration
McCampbell, Kristen K.; Springer, Kristin N.; Wingert, Rebecca A.
2015-01-01
The zebrafish is a useful animal model to study the signaling pathways that orchestrate kidney regeneration, as its renal nephrons are simple, yet they maintain the biological complexity inherent to that of higher vertebrate organisms including mammals. Recent studies have suggested that administration of the aminoglycoside antibiotic gentamicin in zebrafish mimics human acute kidney injury (AKI) through the induction of nephron damage, but the timing and details of critical phenotypic events associated with the regeneration process, particularly in existing nephrons, have not been characterized. Here, we mapped the temporal progression of cellular and molecular changes that occur during renal epithelial regeneration of the proximal tubule in the adult zebrafish using a platform of histological and expression analysis techniques. This work establishes the timing of renal cell death after gentamicin injury, identifies proliferative compartments within the kidney, and documents gene expression changes associated with the regenerative response of proliferating cells. These data provide an important descriptive atlas that documents the series of events that ensue after damage in the zebrafish kidney, thus availing a valuable resource for the scientific community that can facilitate the implementation of zebrafish research to delineate the mechanisms that control renal regeneration. PMID:26089919
Computed optical interferometric tomography for high-speed volumetric cellular imaging
Liu, Yuan-Zhi; Shemonski, Nathan D.; Adie, Steven G.; Ahmad, Adeel; Bower, Andrew J.; Carney, P. Scott; Boppart, Stephen A.
2014-01-01
Three-dimensional high-resolution imaging methods are important for cellular-level research. Optical coherence microscopy (OCM) is a low-coherence-based interferometry technology for cellular imaging with both high axial and lateral resolution. Using a high-numerical-aperture objective, OCM normally has a shallow depth of field and requires scanning the focus through the entire region of interest to perform volumetric imaging. With a higher-numerical-aperture objective, the image quality of OCM is affected by and more sensitive to aberrations. Interferometric synthetic aperture microscopy (ISAM) and computational adaptive optics (CAO) are computed imaging techniques that overcome the depth-of-field limitation and the effect of optical aberrations in optical coherence tomography (OCT), respectively. In this work we combine OCM with ISAM and CAO to achieve high-speed volumetric cellular imaging. Experimental imaging results of ex vivo human breast tissue, ex vivo mouse brain tissue, in vitro fibroblast cells in 3D scaffolds, and in vivo human skin demonstrate the significant potential of this technique for high-speed volumetric cellular imaging. PMID:25401012
Computed optical interferometric tomography for high-speed volumetric cellular imaging.
Liu, Yuan-Zhi; Shemonski, Nathan D; Adie, Steven G; Ahmad, Adeel; Bower, Andrew J; Carney, P Scott; Boppart, Stephen A
2014-09-01
Three-dimensional high-resolution imaging methods are important for cellular-level research. Optical coherence microscopy (OCM) is a low-coherence-based interferometry technology for cellular imaging with both high axial and lateral resolution. Using a high-numerical-aperture objective, OCM normally has a shallow depth of field and requires scanning the focus through the entire region of interest to perform volumetric imaging. With a higher-numerical-aperture objective, the image quality of OCM is affected by and more sensitive to aberrations. Interferometric synthetic aperture microscopy (ISAM) and computational adaptive optics (CAO) are computed imaging techniques that overcome the depth-of-field limitation and the effect of optical aberrations in optical coherence tomography (OCT), respectively. In this work we combine OCM with ISAM and CAO to achieve high-speed volumetric cellular imaging. Experimental imaging results of ex vivo human breast tissue, ex vivo mouse brain tissue, in vitro fibroblast cells in 3D scaffolds, and in vivo human skin demonstrate the significant potential of this technique for high-speed volumetric cellular imaging. PMID:25401012
Stochasticity and universal dynamics in communicating cellular populations
NASA Astrophysics Data System (ADS)
Noorbakhsh, Javad; Mehta, Pankaj; Allyson Sgro Collaboration; David Schwab Collaboration; Troy Mestler Collaboration; Thomas Gregor Collaboration
2014-03-01
A fundamental problem in biology is to understand how biochemical networks within individual cells coordinate and control population-level behaviors. Our knowledge of these biochemical networks is often incomplete, with little known about the underlying kinetic parameters. Here, we present a general modeling approach for overcoming these challenges based on universality. We apply our approach to study the emergence of collective oscillations of the signaling molecule cAMP in populations of the social amoebae Dictyostelium discoideum and show that a simple two-dimensional dynamical system can reproduce signaling dynamics of single cells and successfully predict novel population-level behaviors. We reduce all the important parameters of our model to only two and will study its behavior through a phase diagram. This phase diagram determines conditions under which cells are quiet or oscillating either coherently or incoherently. Furthermore it allows us to study the effect of different model components such as stochasticity, multicellularity and signal preprocessing. A central finding of our model is that Dictyostelium exploit stochasticity within biochemical networks to control population level behaviors.
The brain dynamics of linguistic computation
Murphy, Elliot
2015-01-01
Neural oscillations at distinct frequencies are increasingly being related to a number of basic and higher cognitive faculties. Oscillations enable the construction of coherently organized neuronal assemblies through establishing transitory temporal correlations. By exploring the elementary operations of the language faculty—labeling, concatenation, cyclic transfer—alongside neural dynamics, a new model of linguistic computation is proposed. It is argued that the universality of language, and the true biological source of Universal Grammar, is not to be found purely in the genome as has long been suggested, but more specifically within the extraordinarily preserved nature of mammalian brain rhythms employed in the computation of linguistic structures. Computational-representational theories are used as a guide in investigating the neurobiological foundations of the human “cognome”—the set of computations performed by the nervous system—and new directions are suggested for how the dynamics of the brain (the “dynome”) operate and execute linguistic operations. The extent to which brain rhythms are the suitable neuronal processes which can capture the computational properties of the human language faculty is considered against a backdrop of existing cartographic research into the localization of linguistic interpretation. Particular focus is placed on labeling, the operation elsewhere argued to be species-specific. A Basic Label model of the human cognome-dynome is proposed, leading to clear, causally-addressable empirical predictions, to be investigated by a suggested research program, Dynamic Cognomics. In addition, a distinction between minimal and maximal degrees of explanation is introduced to differentiate between the depth of analysis provided by cartographic, rhythmic, neurochemical, and other approaches to computation. PMID:26528201
Fokkelman, Michiel; Balcıoğlu, Hayri E.; Klip, Janna E.; Yan, Kuan; Verbeek, Fons J.; Danen, Erik H. J.; van de Water, Bob
2016-01-01
Cancer cells migrate from the primary tumour into surrounding tissue in order to form metastasis. Cell migration is a highly complex process, which requires continuous remodelling and re-organization of the cytoskeleton and cell-matrix adhesions. Here, we aimed to identify genes controlling aspects of tumour cell migration, including the dynamic organization of cell-matrix adhesions and cellular traction forces. In a siRNA screen targeting most cell adhesion-related genes we identified 200+ genes that regulate size and/or dynamics of cell-matrix adhesions in MCF7 breast cancer cells. In a subsequent secondary screen, the 64 most effective genes were evaluated for growth factor-induced cell migration and validated by tertiary RNAi pool deconvolution experiments. Four validated hits showed significantly enlarged adhesions accompanied by reduced cell migration upon siRNA-mediated knockdown. Furthermore, loss of PPP1R12B, HIPK3 or RAC2 caused cells to exert higher traction forces, as determined by traction force microscopy with elastomeric micropillar post arrays, and led to considerably reduced force turnover. Altogether, we identified genes that co-regulate cell-matrix adhesion dynamics and traction force turnover, thereby modulating overall motility behaviour. PMID:27531518
Visualization of unsteady computational fluid dynamics
NASA Astrophysics Data System (ADS)
Haimes, Robert
1995-10-01
The current computing environment that most researchers are using for the calculation of 3D unsteady Computational Fluid Dynamic (CFD) results is a super-computer class machine. The Massively Parallel Processors (MPP's) such as the 160 node IBM SP2 at NAS and clusters of workstations acting as a single MPP (like NAS's SGI Power-Challenge array) provide the required computation bandwidth for CFD calculations of transient problems. Work is in progress on a set of software tools designed specifically to address visualizing 3D unsteady CFD results in these super-computer-like environments. The visualization is concurrently executed with the CFD solver. The parallel version of Visual3, pV3 required splitting up the unsteady visualization task to allow execution across a network of workstation(s) and compute servers. In this computing model, the network is almost always the bottleneck so much of the effort involved techniques to reduce the size of the data transferred between machines.
Visualization of unsteady computational fluid dynamics
NASA Technical Reports Server (NTRS)
Haimes, Robert
1995-01-01
The current computing environment that most researchers are using for the calculation of 3D unsteady Computational Fluid Dynamic (CFD) results is a super-computer class machine. The Massively Parallel Processors (MPP's) such as the 160 node IBM SP2 at NAS and clusters of workstations acting as a single MPP (like NAS's SGI Power-Challenge array) provide the required computation bandwidth for CFD calculations of transient problems. Work is in progress on a set of software tools designed specifically to address visualizing 3D unsteady CFD results in these super-computer-like environments. The visualization is concurrently executed with the CFD solver. The parallel version of Visual3, pV3 required splitting up the unsteady visualization task to allow execution across a network of workstation(s) and compute servers. In this computing model, the network is almost always the bottleneck so much of the effort involved techniques to reduce the size of the data transferred between machines.
Logical Modeling and Dynamical Analysis of Cellular Networks
Abou-Jaoudé, Wassim; Traynard, Pauline; Monteiro, Pedro T.; Saez-Rodriguez, Julio; Helikar, Tomáš; Thieffry, Denis; Chaouiya, Claudine
2016-01-01
The logical (or logic) formalism is increasingly used to model regulatory and signaling networks. Complementing these applications, several groups contributed various methods and tools to support the definition and analysis of logical models. After an introduction to the logical modeling framework and to several of its variants, we review here a number of recent methodological advances to ease the analysis of large and intricate networks. In particular, we survey approaches to determine model attractors and their reachability properties, to assess the dynamical impact of variations of external signals, and to consistently reduce large models. To illustrate these developments, we further consider several published logical models for two important biological processes, namely the differentiation of T helper cells and the control of mammalian cell cycle. PMID:27303434
Imaging cellular dynamics in vivo with multicolor fluorescent proteins
NASA Astrophysics Data System (ADS)
Hoffman, Robert M.
2005-04-01
The new field of in vivo cell biology is being developed with multi-colored fluorescent proteins. With the use of fluorescent proteins, the behavior of individual cells can be visualized in the living animal. An example of the new cell biology is dual-color fluorescence imaging using red fluorescent protein (RFP)-expressing tumors transplanted in green fluorescent protein (GFP)-expressing transgenic mice. These models show with great clarity the details of the tumor-stroma cell-cell interaction especially tumor-induced angiogenesis, tumor-infiltrating lymphocytes, stromal fibroblasts and macrophages. Another example is the color-coding of cells with RFP or GFP such that both cell types and their interaction can be simultaneously visualized in vivo. Stem cells can also be visualized and tracked in vivo with fluorescent proteins. Mice, in which the regulatory elements of the stem-cell marker nestin drive GFP expression, can be used to visualize hair follicle stem cells including their ability to form hair follicles as well as blood vessels. Dual-color cells expressing GFP in the nucleus and RFP in the cytoplasm enable real-time visualization of nuclear-cytoplasm dynamics including cell cycle events and apoptosis. Dual-color cells also enable the in vivo imaging of cell and nuclear deformation as well as trafficking in capillaries in living animals. Multiple-color labeling of cells will enable multiple events to be simultaneously visualized in vivo including cell-cell interaction, gene expression, ion fluxes, protein and organelle trafficking, chromosome dynamics and numerous other processes currently still studied in vitro.
Spectral Methods for Computational Fluid Dynamics
NASA Technical Reports Server (NTRS)
Zang, T. A.; Streett, C. L.; Hussaini, M. Y.
1994-01-01
As a tool for large-scale computations in fluid dynamics, spectral methods were prophesized in 1944, born in 1954, virtually buried in the mid-1960's, resurrected in 1969, evangalized in the 1970's, and catholicized in the 1980's. The use of spectral methods for meteorological problems was proposed by Blinova in 1944 and the first numerical computations were conducted by Silberman (1954). By the early 1960's computers had achieved sufficient power to permit calculations with hundreds of degrees of freedom. For problems of this size the traditional way of computing the nonlinear terms in spectral methods was expensive compared with finite-difference methods. Consequently, spectral methods fell out of favor. The expense of computing nonlinear terms remained a severe drawback until Orszag (1969) and Eliasen, Machenauer, and Rasmussen (1970) developed the transform methods that still form the backbone of many large-scale spectral computations. The original proselytes of spectral methods were meteorologists involved in global weather modeling and fluid dynamicists investigating isotropic turbulence. The converts who were inspired by the successes of these pioneers remained, for the most part, confined to these and closely related fields throughout the 1970's. During that decade spectral methods appeared to be well-suited only for problems governed by ordinary diSerential eqllations or by partial differential equations with periodic boundary conditions. And, of course, the solution itself needed to be smooth. Some of the obstacles to wider application of spectral methods were: (1) poor resolution of discontinuous solutions; (2) inefficient implementation of implicit methods; and (3) drastic geometric constraints. All of these barriers have undergone some erosion during the 1980's, particularly the latter two. As a result, the applicability and appeal of spectral methods for computational fluid dynamics has broadened considerably. The motivation for the use of spectral
The use of computers for instruction in fluid dynamics
NASA Technical Reports Server (NTRS)
Watson, Val
1987-01-01
Applications for computers which improve instruction in fluid dynamics are examined. Computers can be used to illustrate three-dimensional flow fields and simple fluid dynamics mechanisms, to solve fluid dynamics problems, and for electronic sketching. The usefulness of computer applications is limited by computer speed, memory, and software and the clarity and field of view of the projected display. Proposed advances in personal computers which will address these limitations are discussed. Long range applications for computers in education are considered.
Computation in Dynamically Bounded Asymmetric Systems
Rutishauser, Ueli; Slotine, Jean-Jacques; Douglas, Rodney
2015-01-01
Previous explanations of computations performed by recurrent networks have focused on symmetrically connected saturating neurons and their convergence toward attractors. Here we analyze the behavior of asymmetrical connected networks of linear threshold neurons, whose positive response is unbounded. We show that, for a wide range of parameters, this asymmetry brings interesting and computationally useful dynamical properties. When driven by input, the network explores potential solutions through highly unstable ‘expansion’ dynamics. This expansion is steered and constrained by negative divergence of the dynamics, which ensures that the dimensionality of the solution space continues to reduce until an acceptable solution manifold is reached. Then the system contracts stably on this manifold towards its final solution trajectory. The unstable positive feedback and cross inhibition that underlie expansion and divergence are common motifs in molecular and neuronal networks. Therefore we propose that very simple organizational constraints that combine these motifs can lead to spontaneous computation and so to the spontaneous modification of entropy that is characteristic of living systems. PMID:25617645
A computational model for dynamic vision
NASA Technical Reports Server (NTRS)
Moezzi, Saied; Weymouth, Terry E.
1990-01-01
This paper describes a novel computational model for dynamic vision which promises to be both powerful and robust. Furthermore the paradigm is ideal for an active vision system where camera vergence changes dynamically. Its basis is the retinotopically indexed object-centered encoding of the early visual information. Specifically, the relative distances of objects to a set of referents is encoded in image registered maps. To illustrate the efficacy of the method, it is applied to the problem of dynamic stereo vision. Integration of depth information over multiple frames obtained by a moving robot generally requires precise information about the relative camera position from frame to frame. Usually, this information can only be approximated. The method facilitates the integration of depth information without direct use or knowledge of camera motion.
Arterioportal shunts on dynamic computed tomography
Nakayama, T.; Hiyama, Y.; Ohnishi, K.; Tsuchiya, S.; Kohno, K.; Nakajima, Y.; Okuda, K.
1983-05-01
Thirty-two patients, 20 with hepatocelluar carcinoma and 12 with liver cirrhosis, were examined by dynamic computed tomography (CT) using intravenous bolus injection of contrast medium and by celiac angiography. Dynamic CT disclosed arterioportal shunting in four cases of hepatocellular carcinoma and in one of cirrhosis. In three of the former, the arterioportal shunt was adjacent to a mass lesion on CT, suggesting tumor invasion into the portal branch. In one with hepatocellular carcinoma, the shunt was remote from the mass. In the case with cirrhosis, there was no mass. In these last two cases, the shunt might have been caused by prior percutaneous needle puncture. In another case of hepatocellular carcinoma, celiac angiography but not CT demonstrated an arterioportal shunt. Thus, dynamic CT was diagnostic in five of six cases of arteriographically demonstrated arterioportal shunts.
Human systems dynamics: Toward a computational model
NASA Astrophysics Data System (ADS)
Eoyang, Glenda H.
2012-09-01
A robust and reliable computational model of complex human systems dynamics could support advancements in theory and practice for social systems at all levels, from intrapersonal experience to global politics and economics. Models of human interactions have evolved from traditional, Newtonian systems assumptions, which served a variety of practical and theoretical needs of the past. Another class of models has been inspired and informed by models and methods from nonlinear dynamics, chaos, and complexity science. None of the existing models, however, is able to represent the open, high dimension, and nonlinear self-organizing dynamics of social systems. An effective model will represent interactions at multiple levels to generate emergent patterns of social and political life of individuals and groups. Existing models and modeling methods are considered and assessed against characteristic pattern-forming processes in observed and experienced phenomena of human systems. A conceptual model, CDE Model, based on the conditions for self-organizing in human systems, is explored as an alternative to existing models and methods. While the new model overcomes the limitations of previous models, it also provides an explanatory base and foundation for prospective analysis to inform real-time meaning making and action taking in response to complex conditions in the real world. An invitation is extended to readers to engage in developing a computational model that incorporates the assumptions, meta-variables, and relationships of this open, high dimension, and nonlinear conceptual model of the complex dynamics of human systems.
Dynamic self-organization of microwell-aggregated cellular mixtures.
Song, Wei; Tung, Chih-Kuan; Lu, Yen-Chun; Pardo, Yehudah; Wu, Mingming; Das, Moumita; Kao, Der-I; Chen, Shuibing; Ma, Minglin
2016-06-29
Cells with different cohesive properties self-assemble in a spatiotemporal and context-dependent manner. Previous studies on cell self-organization mainly focused on the spontaneous structural development within a short period of time during which the cell numbers remained constant. However the effect of cell proliferation over time on the self-organization of cells is largely unexplored. Here, we studied the spatiotemporal dynamics of self-organization of a co-culture of MDA-MB-231 and MCF10A cells seeded in a well defined space (i.e. non-adherent microfabricated wells). When cell-growth was chemically inhibited, high cohesive MCF10A cells formed a core surrounded by low cohesive MDA-MB-231 cells on the periphery, consistent with the differential adhesion hypothesis (DAH). Interestingly, this aggregate morphology was completely inverted when the cells were free to grow. At an initial seeding ratio of 1 : 1 (MDA-MB-231 : MCF10A), the fast growing MCF10A cells segregated in the periphery while the slow growing MDA-MB-231 cells stayed in the core. Another morphology developed at an inequal seeding ratio (4 : 1), that is, the cell mixtures developed a side-by-side aggregate morphology. We conclude that the cell self-organization depends not only on the cell cohesive properties but also on the cell seeding ratio and proliferation. Furthermore, by taking advantage of the cell self-organization, we purified human embryonic stem cells-derived pancreatic progenitors (hESCs-PPs) from co-cultured feeder cells without using any additional tools or labels. PMID:27275624
Computational fluid dynamics uses in fluid dynamics/aerodynamics education
NASA Technical Reports Server (NTRS)
Holst, Terry L.
1994-01-01
The field of computational fluid dynamics (CFD) has advanced to the point where it can now be used for the purpose of fluid dynamics physics education. Because of the tremendous wealth of information available from numerical simulation, certain fundamental concepts can be efficiently communicated using an interactive graphical interrogation of the appropriate numerical simulation data base. In other situations, a large amount of aerodynamic information can be communicated to the student by interactive use of simple CFD tools on a workstation or even in a personal computer environment. The emphasis in this presentation is to discuss ideas for how this process might be implemented. Specific examples, taken from previous publications, will be used to highlight the presentation.
Statistical analysis of cellular detonation dynamics from numerical simulations: one-step chemistry
NASA Astrophysics Data System (ADS)
Sharpe, G. J.; Radulescu, M. I.
2011-10-01
In this paper, two methods are developed for statistically analysing the nonlinear cellular dynamics from numerical simulations of gaseous detonations, one use of which is the systematic determination of detonation cell sizes from such simulations. Both these methods rely on signed vorticity records in which the individual families of transverse waves are captured independently. The first method involves an automated extraction of the main triple-point tracks from the vorticity records, allowing statistical analysis of the spacings between neighbouring tracks. The second method uses the autocorrelation function to spectrally analyse the vorticity records. These methods are then employed for a preliminary analysis of the cellular dynamics of the standard, idealized one-step chemistry model. Evidence is found for 'cell size doubling' bifurcations in the one-step model as the cellular dynamics become more irregular (e.g. as the activation is increased). It is also shown that the statistical models converge slowly due to systematic 'shot-to-shot' variation in the cellular dynamics for fixed parameters with different initial perturbations. Instead, it appears that a range of equally probable cell sizes can be obtained for given parameters.
A SIMPLE CELLULAR AUTOMATON MODEL FOR HIGH-LEVEL VEGETATION DYNAMICS
We have produced a simple two-dimensional (ground-plan) cellular automata model of vegetation dynamics specifically to investigate high-level community processes. The model is probabilistic, with individual plant behavior determined by physiologically-based rules derived from a w...
NASA Astrophysics Data System (ADS)
Karamooz Ravari, M. R.; Kadkhodaei, M.
2015-01-01
As the fabrication and characterization of cellular lattice structures are time consuming and expensive, development of simple models is vital. In this paper, a new approach is presented to model the mechanical stress-strain curve of cellular lattices with low computational efforts. To do so, first, a single strut of the lattice is modeled with its imperfections and defects. The stress-strain of a specimen fabricated with the same processing parameters as those used for the lattice is used as the base material. Then, this strut is simulated in simple tension, and its stress-strain curve is obtained. After that, a unit cell of the lattice is simulated without any imperfections, and the material parameters of the single strut are attributed to the bulk material. Using this method, the stress-strain behavior of the lattice is obtained and shown to be in a good agreement with the experimental result. Accordingly, this paper presents a computationally efficient method for modeling the mechanical properties of cellular lattices with a reasonable accuracy using the material parameters of simple tension tests. The effects of the single strut's length and its micropores on its mechanical properties are also assessed.
Computational Fluid Dynamics of rising droplets
Wagner, Matthew; Francois, Marianne M.
2012-09-05
The main goal of this study is to perform simulations of droplet dynamics using Truchas, a LANL-developed computational fluid dynamics (CFD) software, and compare them to a computational study of Hysing et al.[IJNMF, 2009, 60:1259]. Understanding droplet dynamics is of fundamental importance in liquid-liquid extraction, a process used in the nuclear fuel cycle to separate various components. Simulations of a single droplet rising by buoyancy are conducted in two-dimensions. Multiple parametric studies are carried out to ensure the problem set-up is optimized. An Interface Smoothing Length (ISL) study and mesh resolution study are performed to verify convergence of the calculations. ISL is a parameter for the interface curvature calculation. Further, wall effects are investigated and checked against existing correlations. The ISL study found that the optimal ISL value is 2.5{Delta}x, with {Delta}x being the mesh cell spacing. The mesh resolution study found that the optimal mesh resolution is d/h=40, for d=drop diameter and h={Delta}x. In order for wall effects on terminal velocity to be insignificant, a conservative wall width of 9d or a nonconservative wall width of 7d can be used. The percentage difference between Hysing et al.[IJNMF, 2009, 60:1259] and Truchas for the velocity profiles vary from 7.9% to 9.9%. The computed droplet velocity and interface profiles are found in agreement with the study. The CFD calculations are performed on multiple cores, using LANL's Institutional High Performance Computing.
NASA Astrophysics Data System (ADS)
Aono, Masashi; Gunji, Yukio-Pegio
2004-08-01
How can non-algorithmic/non-deterministic computational syntax be computed? "The hyperincursive system" introduced by Dubois is an anticipatory system embracing the contradiction/uncertainty. Although it may provide a novel viewpoint for the understanding of complex systems, conventional digital computers cannot run faithfully as the hyperincursive computational syntax specifies, in a strict sense. Then is it an imaginary story? In this paper we try to argue that it is not. We show that a model of complex systems "Elementary Conflictable Cellular Automata (ECCA)" proposed by Aono and Gunji is embracing the hyperincursivity and the nonlocality. ECCA is based on locality-only type settings basically as well as other CA models, and/but at the same time, each cell is required to refer to globality-dominant regularity. Due to this contradictory locality-globality loop, the time evolution equation specifies that the system reaches the deadlock/infinite-loop. However, we show that there is a possibility of the resolution of these problems if the computing system has parallel and/but non-distributed property like an amoeboid organism. This paper is an introduction to "the slime mold computing" that is an attempt to cultivate an unconventional notion of computation.
Almendro, Vanessa; Cheng, Yu -Kang; Randles, Amanda; Itzkovitz, Shalev; Marusyk, Andriy; Ametller, Elisabet; Gonzalez-Farre, Xavier; Muñoz, Montse; Russnes, Hege G.; Helland, Åslaug; et al
2014-02-01
Cancer therapy exerts a strong selection pressure that shapes tumor evolution, yet our knowledge of how tumors change during treatment is limited. Here, we report the analysis of cellular heterogeneity for genetic and phenotypic features and their spatial distribution in breast tumors pre- and post-neoadjuvant chemotherapy. We found that intratumor genetic diversity was tumor-subtype specific, and it did not change during treatment in tumors with partial or no response. However, lower pretreatment genetic diversity was significantly associated with pathologic complete response. In contrast, phenotypic diversity was different between pre- and post-treatment samples. We also observed significant changes in the spatialmore » distribution of cells with distinct genetic and phenotypic features. We used these experimental data to develop a stochastic computational model to infer tumor growth patterns and evolutionary dynamics. Our results highlight the importance of integrated analysis of genotypes and phenotypes of single cells in intact tissues to predict tumor evolution.« less
Almendro, Vanessa; Cheng, Yu -Kang; Randles, Amanda; Itzkovitz, Shalev; Marusyk, Andriy; Ametller, Elisabet; Gonzalez-Farre, Xavier; Muñoz, Montse; Russnes, Hege G.; Helland, Åslaug; Rye, Inga H.; Borresen-Dale, Anne -Lise; Maruyama, Reo; van Oudenaarden, Alexander; Dowsett, Mitchell; Jones, Robin L.; Reis-Filho, Jorge; Gascon, Pere; Gönen, Mithat; Michor, Franziska; Polyak, Kornelia
2014-02-01
Cancer therapy exerts a strong selection pressure that shapes tumor evolution, yet our knowledge of how tumors change during treatment is limited. Here, we report the analysis of cellular heterogeneity for genetic and phenotypic features and their spatial distribution in breast tumors pre- and post-neoadjuvant chemotherapy. We found that intratumor genetic diversity was tumor-subtype specific, and it did not change during treatment in tumors with partial or no response. However, lower pretreatment genetic diversity was significantly associated with pathologic complete response. In contrast, phenotypic diversity was different between pre- and post-treatment samples. We also observed significant changes in the spatial distribution of cells with distinct genetic and phenotypic features. We used these experimental data to develop a stochastic computational model to infer tumor growth patterns and evolutionary dynamics. Our results highlight the importance of integrated analysis of genotypes and phenotypes of single cells in intact tissues to predict tumor evolution.
Advances in computational fluid dynamics solvers for modern computing environments
NASA Astrophysics Data System (ADS)
Hertenstein, Daniel; Humphrey, John R.; Paolini, Aaron L.; Kelmelis, Eric J.
2013-05-01
EM Photonics has been investigating the application of massively multicore processors to a key problem area: Computational Fluid Dynamics (CFD). While the capabilities of CFD solvers have continually increased and improved to support features such as moving bodies and adjoint-based mesh adaptation, the software architecture has often lagged behind. This has led to poor scaling as core counts reach the tens of thousands. In the modern High Performance Computing (HPC) world, clusters with hundreds of thousands of cores are becoming the standard. In addition, accelerator devices such as NVIDIA GPUs and Intel Xeon Phi are being installed in many new systems. It is important for CFD solvers to take advantage of the new hardware as the computations involved are well suited for the massively multicore architecture. In our work, we demonstrate that new features in NVIDIA GPUs are able to empower existing CFD solvers by example using AVUS, a CFD solver developed by the Air Force Research Labratory (AFRL) and the Volcanic Ash Advisory Center (VAAC). The effort has resulted in increased performance and scalability without sacrificing accuracy. There are many well-known codes in the CFD space that can benefit from this work, such as FUN3D, OVERFLOW, and TetrUSS. Such codes are widely used in the commercial, government, and defense sectors.
Baroux, Célia; Autran, Daphné
2015-07-01
Sexual reproduction in flowering plants offers a number of remarkable aspects to developmental biologists. First, the spore mother cells - precursors of the plant reproductive lineage - are specified late in development, as opposed to precocious germline isolation during embryogenesis in most animals. Second, unlike in most animals where meiosis directly produces gametes, plant meiosis entails the differentiation of a multicellular, haploid gametophyte, within which gametic as well as non-gametic accessory cells are formed. These observations raise the question of the factors inducing and modus operandi of cell fate transitions that originate in floral tissues and gametophytes, respectively. Cell fate transitions in the reproductive lineage imply cellular reprogramming operating at the physiological, cytological and transcriptome level, but also at the chromatin level. A number of observations point to large-scale chromatin reorganization events associated with cellular differentiation of the female spore mother cells and of the female gametes. These include a reorganization of the heterochromatin compartment, the genome-wide alteration of the histone modification landscape, and the remodeling of nucleosome composition. The dynamic expression of DNA methyltransferases and actors of small RNA pathways also suggest additional, global epigenetic alterations that remain to be characterized. Are these events a cause or a consequence of cellular differentiation, and how do they contribute to cell fate transition? Does chromatin dynamics induce competence for immediate cellular functions (meiosis, fertilization), or does it also contribute long-term effects in cellular identity and developmental competence of the reproductive lineage? This review attempts to review these fascinating questions. PMID:26031902
A Mathematical Model to study the Dynamics of Epithelial Cellular Networks
Abate, Alessandro; Vincent, Stéphane; Dobbe, Roel; Silletti, Alberto; Master, Neal; Axelrod, Jeffrey D.; Tomlin, Claire J.
2013-01-01
Epithelia are sheets of connected cells that are essential across the animal kingdom. Experimental observations suggest that the dynamical behavior of many single-layered epithelial tissues has strong analogies with that of specific mechanical systems, namely large networks consisting of point masses connected through spring-damper elements and undergoing the influence of active and dissipating forces. Based on this analogy, this work develops a modeling framework to enable the study of the mechanical properties and of the dynamic behavior of large epithelial cellular networks. The model is built first by creating a network topology that is extracted from the actual cellular geometry as obtained from experiments, then by associating a mechanical structure and dynamics to the network via spring-damper elements. This scalable approach enables running simulations of large network dynamics: the derived modeling framework in particular is predisposed to be tailored to study general dynamics (for example, morphogenesis) of various classes of single-layered epithelial cellular networks. In this contribution we test the model on a case study of the dorsal epithelium of the Drosophila melanogaster embryo during early dorsal closure (and, less conspicuously, germband retraction). PMID:23221083
NASA Astrophysics Data System (ADS)
Vanag, Vladimir K.
1999-05-01
Spatially extended dynamical systems are ubiquitous and include such things as insect and animal populations; complex chemical, technological, and geochemical processes; humanity itself, and much more. It is clearly desirable to have a certain universal tool with which the highly complex behaviour of nonlinear dynamical systems can be analyzed and modelled. For this purpose, cellular automata seem to be good candidates. In the present review, emphasis is placed on the possibilities that various types of probabilistic cellular automata (PCA), such as DSMC (direct simulation Monte Carlo) and LGCA (lattice-gas cellular automata), offer. The methods are primarily designed for modelling spatially extended dynamical systems with inner fluctuations accounted for. For the Willamowskii-Roessler and Oregonator models, PCA applications to the following problems are illustrated: the effect of fluctuations on the dynamics of nonlinear systems; Turing structure formation; the effect of hydrodynamic modes on the behaviour of nonlinear chemical systems (stirring effects); bifurcation changes in the dynamical regimes of complex systems with restricted geometry or low spatial dimension; and the description of chemical systems in microemulsions.
Stone, John E.; Hallock, Michael J.; Phillips, James C.; Peterson, Joseph R.; Luthey-Schulten, Zaida; Schulten, Klaus
2016-01-01
Many of the continuing scientific advances achieved through computational biology are predicated on the availability of ongoing increases in computational power required for detailed simulation and analysis of cellular processes on biologically-relevant timescales. A critical challenge facing the development of future exascale supercomputer systems is the development of new computing hardware and associated scientific applications that dramatically improve upon the energy efficiency of existing solutions, while providing increased simulation, analysis, and visualization performance. Mobile computing platforms have recently become powerful enough to support interactive molecular visualization tasks that were previously only possible on laptops and workstations, creating future opportunities for their convenient use for meetings, remote collaboration, and as head mounted displays for immersive stereoscopic viewing. We describe early experiences adapting several biomolecular simulation and analysis applications for emerging heterogeneous computing platforms that combine power-efficient system-on-chip multi-core CPUs with high-performance massively parallel GPUs. We present low-cost power monitoring instrumentation that provides sufficient temporal resolution to evaluate the power consumption of individual CPU algorithms and GPU kernels. We compare the performance and energy efficiency of scientific applications running on emerging platforms with results obtained on traditional platforms, identify hardware and algorithmic performance bottlenecks that affect the usability of these platforms, and describe avenues for improving both the hardware and applications in pursuit of the needs of molecular modeling tasks on mobile devices and future exascale computers. PMID:27516922
Computational fluid dynamics: Transition to design applications
NASA Technical Reports Server (NTRS)
Bradley, R. G.; Bhateley, I. C.; Howell, G. A.
1987-01-01
The development of aerospace vehicles, over the years, was an evolutionary process in which engineering progress in the aerospace community was based, generally, on prior experience and data bases obtained through wind tunnel and flight testing. Advances in the fundamental understanding of flow physics, wind tunnel and flight test capability, and mathematical insights into the governing flow equations were translated into improved air vehicle design. The modern day field of Computational Fluid Dynamics (CFD) is a continuation of the growth in analytical capability and the digital mathematics needed to solve the more rigorous form of the flow equations. Some of the technical and managerial challenges that result from rapidly developing CFD capabilites, some of the steps being taken by the Fort Worth Division of General Dynamics to meet these challenges, and some of the specific areas of application for high performance air vehicles are presented.
Computational dynamics of acoustically driven microsphere systems.
Glosser, Connor; Piermarocchi, Carlo; Li, Jie; Dault, Dan; Shanker, B
2016-01-01
We propose a computational framework for the self-consistent dynamics of a microsphere system driven by a pulsed acoustic field in an ideal fluid. Our framework combines a molecular dynamics integrator describing the dynamics of the microsphere system with a time-dependent integral equation solver for the acoustic field that makes use of fields represented as surface expansions in spherical harmonic basis functions. The presented approach allows us to describe the interparticle interaction induced by the field as well as the dynamics of trapping in counter-propagating acoustic pulses. The integral equation formulation leads to equations of motion for the microspheres describing the effect of nondissipative drag forces. We show (1) that the field-induced interactions between the microspheres give rise to effective dipolar interactions, with effective dipoles defined by their velocities and (2) that the dominant effect of an ultrasound pulse through a cloud of microspheres gives rise mainly to a translation of the system, though we also observe both expansion and contraction of the cloud determined by the initial system geometry. PMID:26871188
Computational dynamics of acoustically driven microsphere systems
NASA Astrophysics Data System (ADS)
Glosser, Connor; Piermarocchi, Carlo; Li, Jie; Dault, Dan; Shanker, B.
2016-01-01
We propose a computational framework for the self-consistent dynamics of a microsphere system driven by a pulsed acoustic field in an ideal fluid. Our framework combines a molecular dynamics integrator describing the dynamics of the microsphere system with a time-dependent integral equation solver for the acoustic field that makes use of fields represented as surface expansions in spherical harmonic basis functions. The presented approach allows us to describe the interparticle interaction induced by the field as well as the dynamics of trapping in counter-propagating acoustic pulses. The integral equation formulation leads to equations of motion for the microspheres describing the effect of nondissipative drag forces. We show (1) that the field-induced interactions between the microspheres give rise to effective dipolar interactions, with effective dipoles defined by their velocities and (2) that the dominant effect of an ultrasound pulse through a cloud of microspheres gives rise mainly to a translation of the system, though we also observe both expansion and contraction of the cloud determined by the initial system geometry.
Bursac, P; Arnoczky, S; York, A
2009-01-01
The menisci of the knee play a significant role in the complex biomechanics of the joint and are critically important in maintaining articular cartilage health. While a general form-function relationship has been identified for the structural orientation of the extra-cellular matrix of the meniscus, the role of individual biochemical components has yet to be fully explored. To determine if correlations exist between the dynamic and static compressive modulus of human menisci and their major extra-cellular matrix constituents (collagen, glycosoaminoglycan and water content), 12 lateral and 11 medial menisci from 13 adult donors were examined. The results showed that in dynamic compression at high loading frequencies (0.1-1 Hz) the menisci behave as a rubber-like elastic material while at lower frequencies (0.01-0.03 Hz) significant viscous dissipation occurs. While regional variations in compressive moduli and extra-cellular matrix composition were observed, the magnitude of both dynamic and static compressive moduli were found to be insensitive to collagen content (p>0.4). However, this magnitude was found to significantly increase with increasing glycosaminoglycan content (p<0.001) and significantly decrease with increasing water content (p<0.001). The results of this study identify significant relationships between the viscoelastic behavior of the meniscus and its extra-cellular matrix composition. PMID:19581729
Shuttle rocket booster computational fluid dynamics
NASA Technical Reports Server (NTRS)
Chung, T. J.; Park, O. Y.
1988-01-01
Additional results and a revised and improved computer program listing from the shuttle rocket booster computational fluid dynamics formulations are presented. Numerical calculations for the flame zone of solid propellants are carried out using the Galerkin finite elements, with perturbations expanded to the zeroth, first, and second orders. The results indicate that amplification of oscillatory motions does indeed prevail in high frequency regions. For the second order system, the trend is similar to the first order system for low frequencies, but instabilities may appear at frequencies lower than those of the first order system. The most significant effect of the second order system is that the admittance is extremely oscillatory between moderately high frequency ranges.
LaRC computational dynamics overview
NASA Technical Reports Server (NTRS)
Husner, J. M.
1989-01-01
Present research centers on the development of advanced computational methods for transient simulation analyses. Aircraft, launch vehicles and space structure components are potential applications, but primary focus is presently on large space structures. There are both in-house and out-of-house activities. The in-house activity centers around the development of a multibody simulation tool for truss-like structures called LATDYN for Large Angle Transient DYNamics. Multibody analysis involves articulation of structural components as well as robotic maneuvers. These items are necessary for construction (erection or deployment) of large space structures in orbit and the carrying out of certain operations on board the space station. Thus, part of the in-house activity involves the development of methods which treat the changing mass, stiffness and constraints associated with articulating systems. The out-of-house activity involves subcycling, development of large deformation/motion beam formulation, constraint stabilization and direct time integration transient algorithms in parallel computing.
Computational fluid dynamics of reaction injection moulding
NASA Astrophysics Data System (ADS)
Mateus, Artur; Mitchell, Geoffrey; Bártolo, Paulo
2012-09-01
The modern approach to the development of moulds for injection moulding (Reaction Injection Moulding - RIM, Thermoplastic Injection Moulding - TIM and others) differs from the conventional approach based exclusively on the designer's experience and hypotheses. The increasingly complexityof moulds and the requirement by the clients for the improvement of their quality, shorter delivery times, and lower prices, demand the development of novel approaches to developed optimal moulds and moulded parts. The development of more accurate computational tools is fundamental to optimize both, the injection mouldingprocesses and the design, quality and durability of the moulds. This paper focuses on the RIM process proposing a novel thermo-rheo-kinetic model. The proposed model was implemented in generalpurpose Computational Fluid Dynamics (CFD) software. The model enables to accurately describe both flow and curing stages. Simulation results were validated against experimental results.
Computational fluid dynamics in cardiovascular disease.
Lee, Byoung-Kwon
2011-08-01
Computational fluid dynamics (CFD) is a mechanical engineering field for analyzing fluid flow, heat transfer, and associated phenomena, using computer-based simulation. CFD is a widely adopted methodology for solving complex problems in many modern engineering fields. The merit of CFD is developing new and improved devices and system designs, and optimization is conducted on existing equipment through computational simulations, resulting in enhanced efficiency and lower operating costs. However, in the biomedical field, CFD is still emerging. The main reason why CFD in the biomedical field has lagged behind is the tremendous complexity of human body fluid behavior. Recently, CFD biomedical research is more accessible, because high performance hardware and software are easily available with advances in computer science. All CFD processes contain three main components to provide useful information, such as pre-processing, solving mathematical equations, and post-processing. Initial accurate geometric modeling and boundary conditions are essential to achieve adequate results. Medical imaging, such as ultrasound imaging, computed tomography, and magnetic resonance imaging can be used for modeling, and Doppler ultrasound, pressure wire, and non-invasive pressure measurements are used for flow velocity and pressure as a boundary condition. Many simulations and clinical results have been used to study congenital heart disease, heart failure, ventricle function, aortic disease, and carotid and intra-cranial cerebrovascular diseases. With decreasing hardware costs and rapid computing times, researchers and medical scientists may increasingly use this reliable CFD tool to deliver accurate results. A realistic, multidisciplinary approach is essential to accomplish these tasks. Indefinite collaborations between mechanical engineers and clinical and medical scientists are essential. CFD may be an important methodology to understand the pathophysiology of the development and
Computational fluid dynamics symposium on aeropropulsion
Not Available
1991-01-01
Recognizing the considerable advances that have been made in computational fluid dynamics, the Internal Fluid Mechanics Division of NASA Lewis Research Center sponsored this symposium with the objective of providing a forum for exchanging information regarding recent developments in numerical methods, physical and chemical modeling, and applications. This conference publication is a compilation of 4 invited and 34 contributed papers presented in six sessions: algorithms one and two, turbomachinery, turbulence, components application, and combustors. Topics include numerical methods, grid generation, chemically reacting flows, turbulence modeling, inlets, nozzles, and unsteady flows.
Two-phase computational fluid dynamics
Rothe, P.H.
1991-07-26
The results of the project illustrate the feasibility of multiphase computerized fluid dynamics (CFD) software. Existing CFD software is capable of simulating particle fields, certain droplet fields, and certain free surface flows, and does so routinely in engineering applications. Stratified flows can be addressed by a multiphase CFD code, once one is developed with suitable capabilities. The groundwork for such a code has been laid. Calculations performed for stratified flows demonstrate the accuracy achievable and the convergence of the methodology. Extension of the stratified flow methodology to other segregated flows such as slug or annular faces no inherent limits. The research has commercial application in the development of multiphase CFD computer programs.
Computational Fluid Dynamics Technology for Hypersonic Applications
NASA Technical Reports Server (NTRS)
Gnoffo, Peter A.
2003-01-01
Several current challenges in computational fluid dynamics and aerothermodynamics for hypersonic vehicle applications are discussed. Example simulations are presented from code validation and code benchmarking efforts to illustrate capabilities and limitations. Opportunities to advance the state-of-art in algorithms, grid generation and adaptation, and code validation are identified. Highlights of diverse efforts to address these challenges are then discussed. One such effort to re-engineer and synthesize the existing analysis capability in LAURA, VULCAN, and FUN3D will provide context for these discussions. The critical (and evolving) role of agile software engineering practice in the capability enhancement process is also noted.
High performance computations using dynamical nucleation theory
NASA Astrophysics Data System (ADS)
Windus, T. L.; Kathmann, S. M.; Crosby, L. D.
2008-07-01
Chemists continue to explore the use of very large computations to perform simulations that describe the molecular level physics of critical challenges in science. In this paper, we describe the Dynamical Nucleation Theory Monte Carlo (DNTMC) model - a model for determining molecular scale nucleation rate constants - and its parallel capabilities. The potential for bottlenecks and the challenges to running on future petascale or larger resources are delineated. A 'master-slave' solution is proposed to scale to the petascale and will be developed in the NWChem software. In addition, mathematical and data analysis challenges are described.
Computational Fluid Dynamics Symposium on Aeropropulsion
NASA Technical Reports Server (NTRS)
1991-01-01
Recognizing the considerable advances that have been made in computational fluid dynamics, the Internal Fluid Mechanics Division of NASA Lewis Research Center sponsored this symposium with the objective of providing a forum for exchanging information regarding recent developments in numerical methods, physical and chemical modeling, and applications. This conference publication is a compilation of 4 invited and 34 contributed papers presented in six sessions: algorithms one and two, turbomachinery, turbulence, components application, and combustors. Topics include numerical methods, grid generation, chemically reacting flows, turbulence modeling, inlets, nozzles, and unsteady flows.
Verification and Validation in Computational Fluid Dynamics
OBERKAMPF, WILLIAM L.; TRUCANO, TIMOTHY G.
2002-03-01
Verification and validation (V and V) are the primary means to assess accuracy and reliability in computational simulations. This paper presents an extensive review of the literature in V and V in computational fluid dynamics (CFD), discusses methods and procedures for assessing V and V, and develops a number of extensions to existing ideas. The review of the development of V and V terminology and methodology points out the contributions from members of the operations research, statistics, and CFD communities. Fundamental issues in V and V are addressed, such as code verification versus solution verification, model validation versus solution validation, the distinction between error and uncertainty, conceptual sources of error and uncertainty, and the relationship between validation and prediction. The fundamental strategy of verification is the identification and quantification of errors in the computational model and its solution. In verification activities, the accuracy of a computational solution is primarily measured relative to two types of highly accurate solutions: analytical solutions and highly accurate numerical solutions. Methods for determining the accuracy of numerical solutions are presented and the importance of software testing during verification activities is emphasized.
Heijman, Jordi; Erfanian Abdoust, Pegah; Voigt, Niels; Nattel, Stanley; Dobrev, Dobromir
2016-02-01
The complexity of the heart makes an intuitive understanding of the relative contribution of ion channels, transporters and signalling pathways to cardiac electrophysiology challenging. Computational modelling of cardiac cellular electrophysiology has proven useful to integrate experimental findings, extrapolate results obtained in expression systems or animal models to other systems, test quantitatively ideas based on experimental data and provide novel hypotheses that are experimentally testable. While the bulk of computational modelling has traditionally been directed towards ventricular bioelectricity, increasing recognition of the clinical importance of atrial arrhythmias, particularly atrial fibrillation, has led to widespread efforts to apply computational approaches to understanding atrial electrical function. The increasing availability of detailed, atrial-specific experimental data has stimulated the development of novel computational models of atrial-cellular electrophysiology and Ca(2+) handling. To date, more than 300 studies have employed mathematical simulations to enhance our understanding of atrial electrophysiology, arrhythmogenesis and therapeutic responses. Future modelling studies are likely to move beyond current whole-cell models by incorporating new data on subcellular architecture, macromolecular protein complexes, and localized ion-channel regulation by signalling pathways. At the same time, more integrative multicellular models that take into account regional electrophysiological and Ca(2+) handling properties, mechano-electrical feedback and/or autonomic regulation will be needed to investigate the mechanisms governing atrial arrhythmias. A combined experimental and computational approach is expected to provide the more comprehensive understanding of atrial arrhythmogenesis that is required to develop improved diagnostic and therapeutic options. Here, we review this rapidly expanding area, with a particular focus on Ca(2+) handling, and
Direct modeling for computational fluid dynamics
NASA Astrophysics Data System (ADS)
Xu, Kun
2015-06-01
All fluid dynamic equations are valid under their modeling scales, such as the particle mean free path and mean collision time scale of the Boltzmann equation and the hydrodynamic scale of the Navier-Stokes (NS) equations. The current computational fluid dynamics (CFD) focuses on the numerical solution of partial differential equations (PDEs), and its aim is to get the accurate solution of these governing equations. Under such a CFD practice, it is hard to develop a unified scheme that covers flow physics from kinetic to hydrodynamic scales continuously because there is no such governing equation which could make a smooth transition from the Boltzmann to the NS modeling. The study of fluid dynamics needs to go beyond the traditional numerical partial differential equations. The emerging engineering applications, such as air-vehicle design for near-space flight and flow and heat transfer in micro-devices, do require further expansion of the concept of gas dynamics to a larger domain of physical reality, rather than the traditional distinguishable governing equations. At the current stage, the non-equilibrium flow physics has not yet been well explored or clearly understood due to the lack of appropriate tools. Unfortunately, under the current numerical PDE approach, it is hard to develop such a meaningful tool due to the absence of valid PDEs. In order to construct multiscale and multiphysics simulation methods similar to the modeling process of constructing the Boltzmann or the NS governing equations, the development of a numerical algorithm should be based on the first principle of physical modeling. In this paper, instead of following the traditional numerical PDE path, we introduce direct modeling as a principle for CFD algorithm development. Since all computations are conducted in a discretized space with limited cell resolution, the flow physics to be modeled has to be done in the mesh size and time step scales. Here, the CFD is more or less a direct
Utilizing parallel optimization in computational fluid dynamics
NASA Astrophysics Data System (ADS)
Kokkolaras, Michael
1998-12-01
General problems of interest in computational fluid dynamics are investigated by means of optimization. Specifically, in the first part of the dissertation, a method of optimal incremental function approximation is developed for the adaptive solution of differential equations. Various concepts and ideas utilized by numerical techniques employed in computational mechanics and artificial neural networks (e.g. function approximation and error minimization, variational principles and weighted residuals, and adaptive grid optimization) are combined to formulate the proposed method. The basis functions and associated coefficients of a series expansion, representing the solution, are optimally selected by a parallel direct search technique at each step of the algorithm according to appropriate criteria; the solution is built sequentially. In this manner, the proposed method is adaptive in nature, although a grid is neither built nor adapted in the traditional sense using a-posteriori error estimates. Variational principles are utilized for the definition of the objective function to be extremized in the associated optimization problems, ensuring that the problem is well-posed. Complicated data structures and expensive remeshing algorithms and systems solvers are avoided. Computational efficiency is increased by using low-order basis functions and concurrent computing. Numerical results and convergence rates are reported for a range of steady-state problems, including linear and nonlinear differential equations associated with general boundary conditions, and illustrate the potential of the proposed method. Fluid dynamics applications are emphasized. Conclusions are drawn by discussing the method's limitations, advantages, and possible extensions. The second part of the dissertation is concerned with the optimization of the viscous-inviscid-interaction (VII) mechanism in an airfoil flow analysis code. The VII mechanism is based on the concept of a transpiration velocity
Traffic dynamics of an on-ramp system with a cellular automaton model
NASA Astrophysics Data System (ADS)
Li, Xin-Gang; Gao, Zi-You; Jia, Bin; Jiang, Rui
2010-06-01
This paper uses the cellular automaton model to study the dynamics of traffic flow around an on-ramp with an acceleration lane. It adopts a parameter, which can reflect different lane-changing behaviour, to represent the diversity of driving behaviour. The refined cellular automaton model is used to describe the lower acceleration rate of a vehicle. The phase diagram and the capacity of the on-ramp system are investigated. The simulation results show that in the single cell model, the capacity of the on-ramp system will stay at the highest flow of a one lane system when the driver is moderate and careful; it will be reduced when the driver is aggressive. In the refined cellular automaton model, the capacity is always reduced even when the driver is careful. It proposes that the capacity drop of the on-ramp system is caused by aggressive lane-changing behaviour and lower acceleration rate.
Marquez-Lago, Tatiana T.
2015-01-01
The asymmetrical inheritance of plasmid DNA, as well as other cellular components, has been shown to be involved in replicative aging. In Saccharomyces cerevisiae, there is an ongoing debate regarding the mechanisms underlying this important asymmetry. Currently proposed models suggest it is established via diffusion, but differ on whether a diffusion barrier is necessary or not. However, no study so far incorporated key aspects to segregation, such as dynamic morphology changes throughout anaphase or plasmids size. Here, we determine the distinct effects and contributions of individual cellular variability, plasmid volume and moving boundaries in the asymmetric segregation of plasmids. We do this by measuring cellular nuclear geometries and plasmid diffusion rates with confocal microscopy, subsequently incorporating this data into a growing domain stochastic spatial simulator. Our modelling and simulations confirms that plasmid asymmetrical inheritance does not require an active barrier to diffusion, and provides a full analysis on plasmid size effects. PMID:26468952
Denton, Jai A; Ghosh, Atiyo; Marquez-Lago, Tatiana T
2015-01-01
The asymmetrical inheritance of plasmid DNA, as well as other cellular components, has been shown to be involved in replicative aging. In Saccharomyces cerevisiae, there is an ongoing debate regarding the mechanisms underlying this important asymmetry. Currently proposed models suggest it is established via diffusion, but differ on whether a diffusion barrier is necessary or not. However, no study so far incorporated key aspects to segregation, such as dynamic morphology changes throughout anaphase or plasmids size. Here, we determine the distinct effects and contributions of individual cellular variability, plasmid volume and moving boundaries in the asymmetric segregation of plasmids. We do this by measuring cellular nuclear geometries and plasmid diffusion rates with confocal microscopy, subsequently incorporating this data into a growing domain stochastic spatial simulator. Our modelling and simulations confirms that plasmid asymmetrical inheritance does not require an active barrier to diffusion, and provides a full analysis on plasmid size effects. PMID:26468952
Efficient gradient computation for dynamical models
Sengupta, B.; Friston, K.J.; Penny, W.D.
2014-01-01
Data assimilation is a fundamental issue that arises across many scales in neuroscience — ranging from the study of single neurons using single electrode recordings to the interaction of thousands of neurons using fMRI. Data assimilation involves inverting a generative model that can not only explain observed data but also generate predictions. Typically, the model is inverted or fitted using conventional tools of (convex) optimization that invariably extremise some functional — norms, minimum descriptive length, variational free energy, etc. Generally, optimisation rests on evaluating the local gradients of the functional to be optimized. In this paper, we compare three different gradient estimation techniques that could be used for extremising any functional in time — (i) finite differences, (ii) forward sensitivities and a method based on (iii) the adjoint of the dynamical system. We demonstrate that the first-order gradients of a dynamical system, linear or non-linear, can be computed most efficiently using the adjoint method. This is particularly true for systems where the number of parameters is greater than the number of states. For such systems, integrating several sensitivity equations – as required with forward sensitivities – proves to be most expensive, while finite-difference approximations have an intermediate efficiency. In the context of neuroimaging, adjoint based inversion of dynamical causal models (DCMs) can, in principle, enable the study of models with large numbers of nodes and parameters. PMID:24769182
Glass-like dynamics in the cell and in cellular collectives
Sadati, Monirosadat; Nourhani, Amir; Qazvini, Nader Taheri
2014-01-01
Prominent fluctuations, heterogeneity, and cooperativity dominate the dynamics of the cytoskeleton as well as the dynamics of the cellular collective. Such systems are out of equilibrium, disordered, and remain poorly understood. To explain these findings, here we consider a unifying mechanistic rubric that imagines these systems as comprising phases of soft condensed matter in proximity to a glass or jamming transition, with associated transitions between solid-like versus liquid-like phases. At the scale of the cytoskeleton, data suggest that intermittent dynamics, kinetic arrest and dynamic heterogeneity represent meso-scale features of glassy protein-protein interactions that link underlying biochemical events to integrative cellular behaviors such as crawling, contraction, and remodeling. At the scale of the multicellular collective, jamming has the potential to unify diverse biological factors that previously had been considered mostly as acting separately and independently. Although a quantitative relationship between intra- and intercellular dynamics is still lacking, glassy dynamics and jamming offer insights linking the mechanobiology of cell to human physiology and pathophysiology. PMID:24431332
Visualization of Unsteady Computational Fluid Dynamics
NASA Technical Reports Server (NTRS)
Haimes, Robert
1997-01-01
The current compute environment that most researchers are using for the calculation of 3D unsteady Computational Fluid Dynamic (CFD) results is a super-computer class machine. The Massively Parallel Processors (MPP's) such as the 160 node IBM SP2 at NAS and clusters of workstations acting as a single MPP (like NAS's SGI Power-Challenge array and the J90 cluster) provide the required computation bandwidth for CFD calculations of transient problems. If we follow the traditional computational analysis steps for CFD (and we wish to construct an interactive visualizer) we need to be aware of the following: (1) Disk space requirements. A single snap-shot must contain at least the values (primitive variables) stored at the appropriate locations within the mesh. For most simple 3D Euler solvers that means 5 floating point words. Navier-Stokes solutions with turbulence models may contain 7 state-variables. (2) Disk speed vs. Computational speeds. The time required to read the complete solution of a saved time frame from disk is now longer than the compute time for a set number of iterations from an explicit solver. Depending, on the hardware and solver an iteration of an implicit code may also take less time than reading the solution from disk. If one examines the performance improvements in the last decade or two, it is easy to see that depending on disk performance (vs. CPU improvement) may not be the best method for enhancing interactivity. (3) Cluster and Parallel Machine I/O problems. Disk access time is much worse within current parallel machines and cluster of workstations that are acting in concert to solve a single problem. In this case we are not trying to read the volume of data, but are running the solver and the solver outputs the solution. These traditional network interfaces must be used for the file system. (4) Numerics of particle traces. Most visualization tools can work upon a single snap shot of the data but some visualization tools for transient
Jabalee, J; Hillier, S; Franz-Odendaal, T A
2013-01-01
The development of intramembranous bone is a dynamic and complex process requiring highly coordinated cellular activities. Although the literature describes the detailed cellular dynamics of early mesoderm-derived endochondral bone, studies regarding neural crest-derived intramembranous bone have failed to keep pace. We analyzed the development of chick scleral ossicles from the onset of osteoid deposition to mineralization at morphological, histological, and ultrastructural levels. We find that the mesenchymal condensations from which ossicles develop change their shape from ellipsoidal to trapezoidal concurrent with an increase in size. Furthermore, the size of an ossicle is dependent upon its time of induction. Our histological analyses of condensation growth reveal cell migration and osteoid secretion as key cellular processes determining condensation size; these processes occur concomitantly to increase both the area and thickness of condensations. We also describe the formation of the zone of overlap between ossicles and conclude that the process is similar to that of cranial suture formation. Finally, transmission electron microscopy of early condensations demonstrates that early osteoblasts secrete collagen parallel to the long axis of the condensation. This study elucidates fundamental mechanisms of intramembranous bone development at the cellular level, furthering our knowledge of this important process among vertebrates. PMID:23930967
Jabalee, J; Hillier, S; Franz-Odendaal, T A
2013-10-01
The development of intramembranous bone is a dynamic and complex process requiring highly coordinated cellular activities. Although the literature describes the detailed cellular dynamics of early mesoderm-derived endochondral bone, studies regarding neural crest-derived intramembranous bone have failed to keep pace. We analyzed the development of chick scleral ossicles from the onset of osteoid deposition to mineralization at morphological, histological, and ultrastructural levels. We find that the mesenchymal condensations from which ossicles develop change their shape from ellipsoidal to trapezoidal concurrent with an increase in size. Furthermore, the size of an ossicle is dependent upon its time of induction. Our histological analyses of condensation growth reveal cell migration and osteoid secretion as key cellular processes determining condensation size; these processes occur concomitantly to increase both the area and thickness of condensations. We also describe the formation of the zone of overlap between ossicles and conclude that the process is similar to that of cranial suture formation. Finally, transmission electron microscopy of early condensations demonstrates that early osteoblasts secrete collagen parallel to the long axis of the condensation. This study elucidates fundamental mechanisms of intramembranous bone development at the cellular level, furthering our knowledge of this important process among vertebrates. PMID:23930967
Dynamic Finite Element Predictions for Mars Sample Return Cellular Impact Test #4
NASA Technical Reports Server (NTRS)
Fasanella, Edwin L.; Billings, Marcus D.
2001-01-01
The nonlinear, transient dynamic finite element code, MSC.Dytran, was used to simulate an impact test of an energy absorbing Earth Entry Vehicle (EEV) that will impact without a parachute. EEVOs are designed to return materials from asteroids, comets, or planets for laboratory analysis on Earth. The EEV concept uses an energy absorbing cellular structure designed to contain and limit the acceleration of space exploration samples during Earth impact. The spherical shaped cellular structure is composed of solid hexagonal and pentagonal foam-filled cells with hybrid graphite-epoxy/Kevlar cell walls. Space samples fit inside a smaller sphere at the center of the EEVOs cellular structure. Pre-test analytical predictions were compared with the test results from a bungee accelerator. The model used to represent the foam and the proper failure criteria for the cell walls were critical in predicting the impact loads of the cellular structure. It was determined that a FOAM1 model for the foam and a 20% failure strain criteria for the cell walls gave an accurate prediction of the acceleration pulse for cellular impact.
Dynamics of cellular immune responses in the acute phase of dengue virus infection.
Yoshida, Tomoyuki; Omatsu, Tsutomu; Saito, Akatsuki; Katakai, Yuko; Iwasaki, Yuki; Kurosawa, Terue; Hamano, Masataka; Higashino, Atsunori; Nakamura, Shinichiro; Takasaki, Tomohiko; Yasutomi, Yasuhiro; Kurane, Ichiro; Akari, Hirofumi
2013-06-01
In this study, we examined the dynamics of cellular immune responses in the acute phase of dengue virus (DENV) infection in a marmoset model. Here, we found that DENV infection in marmosets greatly induced responses of CD4/CD8 central memory T and NKT cells. Interestingly, the strength of the immune response was greater in animals infected with a dengue fever strain than in those infected with a dengue hemorrhagic fever strain of DENV. In contrast, when animals were re-challenged with the same DENV strain used for primary infection, the neutralizing antibody induced appeared to play a critical role in sterilizing inhibition against viral replication, resulting in strong but delayed responses of CD4/CD8 central memory T and NKT cells. The results in this study may help to better understand the dynamics of cellular and humoral immune responses in the control of DENV infection. PMID:23381396
Evidence for complex, collective dynamics and emergent, distributed computation in plants.
Peak, David; West, Jevin D; Messinger, Susanna M; Mott, Keith A
2004-01-27
It has been suggested that some biological processes are equivalent to computation, but quantitative evidence for that view is weak. Plants must solve the problem of adjusting stomatal apertures to allow sufficient CO(2) uptake for photosynthesis while preventing excessive water loss. Under some conditions, stomatal apertures become synchronized into patches that exhibit richly complicated dynamics, similar to behaviors found in cellular automata that perform computational tasks. Using sequences of chlorophyll fluorescence images from leaves of Xanthium strumarium L. (cocklebur), we quantified spatial and temporal correlations in stomatal dynamics. Our values are statistically indistinguishable from those of the same correlations found in the dynamics of automata that compute. These results are consistent with the proposition that a plant solves its optimal gas exchange problem through an emergent, distributed computation performed by its leaves. PMID:14732685
Verification and validation in computational fluid dynamics
NASA Astrophysics Data System (ADS)
Oberkampf, William L.; Trucano, Timothy G.
2002-04-01
Verification and validation (V&V) are the primary means to assess accuracy and reliability in computational simulations. This paper presents an extensive review of the literature in V&V in computational fluid dynamics (CFD), discusses methods and procedures for assessing V&V, and develops a number of extensions to existing ideas. The review of the development of V&V terminology and methodology points out the contributions from members of the operations research, statistics, and CFD communities. Fundamental issues in V&V are addressed, such as code verification versus solution verification, model validation versus solution validation, the distinction between error and uncertainty, conceptual sources of error and uncertainty, and the relationship between validation and prediction. The fundamental strategy of verification is the identification and quantification of errors in the computational model and its solution. In verification activities, the accuracy of a computational solution is primarily measured relative to two types of highly accurate solutions: analytical solutions and highly accurate numerical solutions. Methods for determining the accuracy of numerical solutions are presented and the importance of software testing during verification activities is emphasized. The fundamental strategy of validation is to assess how accurately the computational results compare with the experimental data, with quantified error and uncertainty estimates for both. This strategy employs a hierarchical methodology that segregates and simplifies the physical and coupling phenomena involved in the complex engineering system of interest. A hypersonic cruise missile is used as an example of how this hierarchical structure is formulated. The discussion of validation assessment also encompasses a number of other important topics. A set of guidelines is proposed for designing and conducting validation experiments, supported by an explanation of how validation experiments are different
Domain decomposition algorithms and computation fluid dynamics
NASA Technical Reports Server (NTRS)
Chan, Tony F.
1988-01-01
In the past several years, domain decomposition was a very popular topic, partly motivated by the potential of parallelization. While a large body of theory and algorithms were developed for model elliptic problems, they are only recently starting to be tested on realistic applications. The application of some of these methods to two model problems in computational fluid dynamics are investigated. Some examples are two dimensional convection-diffusion problems and the incompressible driven cavity flow problem. The construction and analysis of efficient preconditioners for the interface operator to be used in the iterative solution of the interface solution is described. For the convection-diffusion problems, the effect of the convection term and its discretization on the performance of some of the preconditioners is discussed. For the driven cavity problem, the effectiveness of a class of boundary probe preconditioners is discussed.
High performance computations using dynamical nucleation theory
Windus, Theresa L.; Kathmann, Shawn M.; Crosby, Lonnie D.
2008-07-14
Chemists continue to explore the use of very large computations to perform simulations that describe the molecular level physics of critical challenges in science. In this paper, the Dynamical Nucleation Theory Monte Carlo (DNTMC) model - a model for determining molecular scale nucleation rate constants - and its parallel capabilities are described. The potential for bottlenecks and the challenges to running on future petascale or larger resources are delineated. A "master-slave" solution is proposed to scale to the petascale and will be developed in the NWChem software. In addition, mathematical and data analysis challenges are also described. This work was supported by the U.S. Department of Energy's (DOE) Office of Basic Energy Sciences, Chemical Sciences program. The Pacific Northwest National Laboratory is operated by Battelle for DOE.
Domain decomposition methods in computational fluid dynamics
NASA Technical Reports Server (NTRS)
Gropp, William D.; Keyes, David E.
1992-01-01
The divide-and-conquer paradigm of iterative domain decomposition, or substructuring, has become a practical tool in computational fluid dynamic applications because of its flexibility in accommodating adaptive refinement through locally uniform (or quasi-uniform) grids, its ability to exploit multiple discretizations of the operator equations, and the modular pathway it provides towards parallelism. These features are illustrated on the classic model problem of flow over a backstep using Newton's method as the nonlinear iteration. Multiple discretizations (second-order in the operator and first-order in the preconditioner) and locally uniform mesh refinement pay dividends separately, and they can be combined synergistically. Sample performance results are included from an Intel iPSC/860 hypercube implementation.
Domain decomposition methods in computational fluid dynamics
NASA Technical Reports Server (NTRS)
Gropp, William D.; Keyes, David E.
1991-01-01
The divide-and-conquer paradigm of iterative domain decomposition, or substructuring, has become a practical tool in computational fluid dynamic applications because of its flexibility in accommodating adaptive refinement through locally uniform (or quasi-uniform) grids, its ability to exploit multiple discretizations of the operator equations, and the modular pathway it provides towards parallelism. These features are illustrated on the classic model problem of flow over a backstep using Newton's method as the nonlinear iteration. Multiple discretizations (second-order in the operator and first-order in the preconditioner) and locally uniform mesh refinement pay dividends separately, and they can be combined synergistically. Sample performance results are included from an Intel iPSC/860 hypercube implementation.
Computational fluid dynamics of airfoils and wings
NASA Technical Reports Server (NTRS)
Garabedian, P.; Mcfadden, G.
1982-01-01
It is pointed out that transonic flow is one of the fields where computational fluid dynamics turns out to be most effective. Codes for the design and analysis of supercritical airfoils and wings have become standard tools of the aircraft industry. The present investigation is concerned with mathematical models and theorems which account for some of the progress that has been made. The most successful aerodynamics codes are those for the analysis of flow at off-design conditions where weak shock waves appear. A major breakthrough was achieved by Murman and Cole (1971), who conceived of a retarded difference scheme which incorporates artificial viscosity to capture shocks in the supersonic zone. This concept has been used to develop codes for the analysis of transonic flow past a swept wing. Attention is given to the trailing edge and the boundary layer, entropy inequalities and wave drag, shockless airfoils, and the inverse swept wing code.
Lectures series in computational fluid dynamics
NASA Technical Reports Server (NTRS)
Thompson, Kevin W.
1987-01-01
The lecture notes cover the basic principles of computational fluid dynamics (CFD). They are oriented more toward practical applications than theory, and are intended to serve as a unified source for basic material in the CFD field as well as an introduction to more specialized topics in artificial viscosity and boundary conditions. Each chapter in the test is associated with a videotaped lecture. The basic properties of conservation laws, wave equations, and shock waves are described. The duality of the conservation law and wave representations is investigated, and shock waves are examined in some detail. Finite difference techniques are introduced for the solution of wave equations and conservation laws. Stability analysis for finite difference approximations are presented. A consistent description of artificial viscosity methods are provided. Finally, the problem of nonreflecting boundary conditions are treated.
Artificial Intelligence In Computational Fluid Dynamics
NASA Technical Reports Server (NTRS)
Vogel, Alison Andrews
1991-01-01
Paper compares four first-generation artificial-intelligence (Al) software systems for computational fluid dynamics. Includes: Expert Cooling Fan Design System (EXFAN), PAN AIR Knowledge System (PAKS), grid-adaptation program MITOSIS, and Expert Zonal Grid Generation (EZGrid). Focuses on knowledge-based ("expert") software systems. Analyzes intended tasks, kinds of knowledge possessed, magnitude of effort required to codify knowledge, how quickly constructed, performances, and return on investment. On basis of comparison, concludes Al most successful when applied to well-formulated problems solved by classifying or selecting preenumerated solutions. In contrast, application of Al to poorly understood or poorly formulated problems generally results in long development time and large investment of effort, with no guarantee of success.
Computational modeling of intraocular gas dynamics.
Noohi, P; Abdekhodaie, M J; Cheng, Y L
2015-01-01
The purpose of this study was to develop a computational model to simulate the dynamics of intraocular gas behavior in pneumatic retinopexy (PR) procedure. The presented model predicted intraocular gas volume at any time and determined the tolerance angle within which a patient can maneuver and still gas completely covers the tear(s). Computational fluid dynamics calculations were conducted to describe PR procedure. The geometrical model was constructed based on the rabbit and human eye dimensions. SF6 in the form of pure and diluted with air was considered as the injected gas. The presented results indicated that the composition of the injected gas affected the gas absorption rate and gas volume. After injection of pure SF6, the bubble expanded to 2.3 times of its initial volume during the first 23 h, but when diluted SF6 was used, no significant expansion was observed. Also, head positioning for the treatment of retinal tear influenced the rate of gas absorption. Moreover, the determined tolerance angle depended on the bubble and tear size. More bubble expansion and smaller retinal tear caused greater tolerance angle. For example, after 23 h, for the tear size of 2 mm the tolerance angle of using pure SF6 is 1.4 times more than that of using diluted SF6 with 80% air. Composition of the injected gas and conditions of the tear in PR may dramatically affect the gas absorption rate and gas volume. Quantifying these effects helps to predict the tolerance angle and improve treatment efficiency. PMID:26682529
Computational modeling of intraocular gas dynamics
NASA Astrophysics Data System (ADS)
Noohi, P.; Abdekhodaie, M. J.; Cheng, Y. L.
2015-12-01
The purpose of this study was to develop a computational model to simulate the dynamics of intraocular gas behavior in pneumatic retinopexy (PR) procedure. The presented model predicted intraocular gas volume at any time and determined the tolerance angle within which a patient can maneuver and still gas completely covers the tear(s). Computational fluid dynamics calculations were conducted to describe PR procedure. The geometrical model was constructed based on the rabbit and human eye dimensions. SF6 in the form of pure and diluted with air was considered as the injected gas. The presented results indicated that the composition of the injected gas affected the gas absorption rate and gas volume. After injection of pure SF6, the bubble expanded to 2.3 times of its initial volume during the first 23 h, but when diluted SF6 was used, no significant expansion was observed. Also, head positioning for the treatment of retinal tear influenced the rate of gas absorption. Moreover, the determined tolerance angle depended on the bubble and tear size. More bubble expansion and smaller retinal tear caused greater tolerance angle. For example, after 23 h, for the tear size of 2 mm the tolerance angle of using pure SF6 is 1.4 times more than that of using diluted SF6 with 80% air. Composition of the injected gas and conditions of the tear in PR may dramatically affect the gas absorption rate and gas volume. Quantifying these effects helps to predict the tolerance angle and improve treatment efficiency.
Baroux, Célia; Autran, Daphné
2015-01-01
Sexual reproduction in flowering plants offers a number of remarkable aspects to developmental biologists. First, the spore mother cells – precursors of the plant reproductive lineage – are specified late in development, as opposed to precocious germline isolation during embryogenesis in most animals. Second, unlike in most animals where meiosis directly produces gametes, plant meiosis entails the differentiation of a multicellular, haploid gametophyte, within which gametic as well as non-gametic accessory cells are formed. These observations raise the question of the factors inducing and modus operandi of cell fate transitions that originate in floral tissues and gametophytes, respectively. Cell fate transitions in the reproductive lineage imply cellular reprogramming operating at the physiological, cytological and transcriptome level, but also at the chromatin level. A number of observations point to large-scale chromatin reorganization events associated with cellular differentiation of the female spore mother cells and of the female gametes. These include a reorganization of the heterochromatin compartment, the genome-wide alteration of the histone modification landscape, and the remodeling of nucleosome composition. The dynamic expression of DNA methyltransferases and actors of small RNA pathways also suggest additional, global epigenetic alterations that remain to be characterized. Are these events a cause or a consequence of cellular differentiation, and how do they contribute to cell fate transition? Does chromatin dynamics induce competence for immediate cellular functions (meiosis, fertilization), or does it also contribute long-term effects in cellular identity and developmental competence of the reproductive lineage? This review attempts to review these fascinating questions. PMID:26031902
Computational fluid dynamics of left ventricular ejection.
Georgiadis, J G; Wang, M; Pasipoularides, A
1992-01-01
The present investigation addresses the effects of simple geometric variations on intraventricular ejection dynamics, by methods from computational fluid dynamics. It is an early step in incorporating more and more relevant characteristics of the ejection process, such as a continuously changing irregular geometry, in numerical simulations. We consider the effects of varying chamber eccentricities and outflow valve orifice-to-inner surface area ratios on instantaneous ejection gradients along the axis of symmetry of the left ventricle. The equation of motion for the streamfunction was discretized and solved iteratively with specified boundary conditions on a boundary-fitted adaptive grid, using an alternating-direction-implicit (ADI) algorithm. The unsteady aspects of the ejection process were subsequently introduced into the numerical simulation. It was shown that for given chamber volume and outflow orifice area, higher chamber eccentricities require higher ejection pressure gradients for the same velocity and local acceleration values at the aortic anulus than more spherical shapes. This finding is referable to the rise in local acceleration effects across the outflow axis. This is to be contrasted with the case of outflow orifice stenosis, in which it was shown that it is the convective acceleration effects that are intensified strongly. PMID:1562106
Nonlinear ship waves and computational fluid dynamics
MIYATA, Hideaki; ORIHARA, Hideo; SATO, Yohei
2014-01-01
Research works undertaken in the first author’s laboratory at the University of Tokyo over the past 30 years are highlighted. Finding of the occurrence of nonlinear waves (named Free-Surface Shock Waves) in the vicinity of a ship advancing at constant speed provided the start-line for the progress of innovative technologies in the ship hull-form design. Based on these findings, a multitude of the Computational Fluid Dynamic (CFD) techniques have been developed over this period, and are highlighted in this paper. The TUMMAC code has been developed for wave problems, based on a rectangular grid system, while the WISDAM code treats both wave and viscous flow problems in the framework of a boundary-fitted grid system. These two techniques are able to cope with almost all fluid dynamical problems relating to ships, including the resistance, ship’s motion and ride-comfort issues. Consequently, the two codes have contributed significantly to the progress in the technology of ship design, and now form an integral part of the ship-designing process. PMID:25311139
Computational Fluid Dynamics - Applications in Manufacturing Processes
NASA Astrophysics Data System (ADS)
Beninati, Maria Laura; Kathol, Austin; Ziemian, Constance
2012-11-01
A new Computational Fluid Dynamics (CFD) exercise has been developed for the undergraduate introductory fluid mechanics course at Bucknell University. The goal is to develop a computational exercise that students complete which links the manufacturing processes course and the concurrent fluid mechanics course in a way that reinforces the concepts in both. In general, CFD is used as a tool to increase student understanding of the fundamentals in a virtual world. A ``learning factory,'' which is currently in development at Bucknell seeks to use the laboratory as a means to link courses that previously seemed to have little correlation at first glance. A large part of the manufacturing processes course is a project using an injection molding machine. The flow of pressurized molten polyurethane into the mold cavity can also be an example of fluid motion (a jet of liquid hitting a plate) that is applied in manufacturing. The students will run a CFD process that captures this flow using their virtual mold created with a graphics package, such as SolidWorks. The laboratory structure is currently being implemented and analyzed as a part of the ``learning factory''. Lastly, a survey taken before and after the CFD exercise demonstrate a better understanding of both the CFD and manufacturing process.
Zhao, Yuchao; Conolly, Rory B; Andersen, Melvin E.
2006-11-21
This report describes the development of a computational systems biology approach to evaluate the hypotheses of molecular and cellular mechanisms of adaptive response to low dose ionizing radiation. Our concept is that computational models of signaling pathways can be developed and linked to biologically based dose response models to evaluate the underlying molecular mechanisms which lead to adaptive response. For development of quantitatively accurate, predictive models, it will be necessary to describe tissues consisting of multiple cell types where the different types each contribute in their own way to the overall function of the tissue. Such a model will probably need to incorporate not only cell type-specific data but also spatial information on the architecture of the tissue and on intercellular signaling. The scope of the current model was more limited. Data obtained in a number of different biological systems were synthesized to describe a chimeric, “average” population cell. Biochemical signaling pathways involved in sensing of DNA damage and in the activation of cell cycle checkpoint controls and the apoptotic path were also included. As with any computational modeling effort, it was necessary to develop these simplified initial descriptions (models) that can be iteratively refined. This preliminary model is a starting point which, with time, can evolve to a level of refinement where large amounts of detailed biological information are synthesized and a capability for robust predictions of dose- and time-response behaviors is obtained.
Computing cellular automata spectra under fixed boundary conditions via limit graphs
NASA Astrophysics Data System (ADS)
Ruivo, Eurico L. P.; de Oliveira, Pedro P. B.
2016-01-01
Cellular automata are fully discrete complex systems with parallel and homogeneous behavior studied both from the theoretical and modeling viewpoints. The limit behaviors of such systems are of particular interest, as they give insight into their emerging properties. One possible approach to investigate such limit behaviors is the analysis of the growth of graphs describing the finite time behavior of a rule in order to infer its limit behavior. Another possibility is to study the Fourier spectrum describing the average limit configurations obtained by a rule. While the former approach gives the characterization of the limit configurations of a rule, the latter yields a qualitative and quantitative characterisation of how often particular blocks of states are present in these limit configurations. Since both approaches are closely related, it is tempting to use one to obtain information about the other. Here, limit graphs are automatically adjusted by configurations directly generated by their respective rules, and use the graphs to compute the spectra of their rules. We rely on a set of elementary cellular automata rules, on lattices with fixed boundary condition, and show that our approach is a more reliable alternative to a previously described method from the literature.
Magneto-optical cellular chip model for intracellular orientational-dynamic-activity detection
NASA Astrophysics Data System (ADS)
Miyashita, Y.; Iwasaka, M.; Kurita, S.; Owada, N.
2012-04-01
In the present study, a magneto-optical cellular chip model (MoCCM) was developed to detect intracellular dynamics in macromolecules by using magneto-optical effects. For the purpose of cell-measurement under strong static magnetic fields of up to 10 T, we constructed a cellular chip model, which was a thin glass plate with a well for a cell culture. A cell line of osteoblast MC3T3-E1 was incubated in the glass well, and the well, 0.3 mm in depth, was sealed by a cover glass when the MoCCM was set in a fiber optic system. An initial intensity change of the polarized light transmission, which dispersed perpendicular to the cell's attaching surface, was collected for 10 to 60 min, and then magnetic fields were applied parallel and perpendicular to the surface and light direction, respectively. The magnetic birefringence signals that originated from the magnetic orientation of intracellular molecules such as cytoskeletons apparently appeared when the magnetic fields were constant at 10 T. A statistical analysis with 15 experiments confirmed that the cellular components under 10 T magnetic fields caused a stronger alignment, which was transferred into polarizing light intensity that increased more than the case before exposure. Cellular conditions such as generation and cell density affected the magnetic birefringence signals.
Weddell, Jared C.; Imoukhuede, P. I.
2014-01-01
Cell population heterogeneity can affect cellular response and is a major factor in drug resistance. However, there are few techniques available to represent and explore how heterogeneity is linked to population response. Recent high-throughput genomic, proteomic, and cellomic approaches offer opportunities for profiling heterogeneity on several scales. We have recently examined heterogeneity in vascular endothelial growth factor receptor (VEGFR) membrane localization in endothelial cells. We and others processed the heterogeneous data through ensemble averaging and integrated the data into computational models of anti-angiogenic drug effects in breast cancer. Here we show that additional modeling insight can be gained when cellular heterogeneity is considered. We present comprehensive statistical and computational methods for analyzing cellomic data sets and integrating them into deterministic models. We present a novel method for optimizing the fit of statistical distributions to heterogeneous data sets to preserve important data and exclude outliers. We compare methods of representing heterogeneous data and show methodology can affect model predictions up to 3.9-fold. We find that VEGF levels, a target for tuning angiogenesis, are more sensitive to VEGFR1 cell surface levels than VEGFR2; updating VEGFR1 levels in the tumor model gave a 64% change in free VEGF levels in the blood compartment, whereas updating VEGFR2 levels gave a 17% change. Furthermore, we find that subpopulations of tumor cells and tumor endothelial cells (tEC) expressing high levels of VEGFR (>35,000 VEGFR/cell) negate anti-VEGF treatments. We show that lowering the VEGFR membrane insertion rate for these subpopulations recovers the anti-angiogenic effect of anti-VEGF treatment, revealing new treatment targets for specific tumor cell subpopulations. This novel method of characterizing heterogeneous distributions shows for the first time how different representations of the same data set lead
Methodology for Uncertainty Analysis of Dynamic Computational Toxicology Models
The task of quantifying the uncertainty in both parameter estimates and model predictions has become more important with the increased use of dynamic computational toxicology models by the EPA. Dynamic toxicological models include physiologically-based pharmacokinetic (PBPK) mode...
Relating the sequential dynamics of excitatory neural networks to synaptic cellular automata.
Nekorkin, V I; Dmitrichev, A S; Kasatkin, D V; Afraimovich, V S
2011-12-01
We have developed a new approach for the description of sequential dynamics of excitatory neural networks. Our approach is based on the dynamics of synapses possessing the short-term plasticity property. We suggest a model of such synapses in the form of a second-order system of nonlinear ODEs. In the framework of the model two types of responses are realized-the fast and the slow ones. Under some relations between their timescales a cellular automaton (CA) on the graph of connections is constructed. Such a CA has only a finite number of attractors and all of them are periodic orbits. The attractors of the CA determine the regimes of sequential dynamics of the original neural network, i.e., itineraries along the network and the times of successive firing of neurons in the form of bunches of spikes. We illustrate our approach on the example of a Morris-Lecar neural network. PMID:22225361
Molecular modeling of the conformational dynamics of the cellular prion protein
NASA Astrophysics Data System (ADS)
Nguyen, Charles; Colling, Ian; Bartz, Jason; Soto, Patricia
2014-03-01
Prions are infectious agents responsible for transmissible spongiform encephalopathies (TSEs), a type of fatal neurodegenerative disease in mammals. Prions propagate biological information by conversion of the non-pathological version of the prion protein to the infectious conformation, PrPSc. A wealth of knowledge has shed light on the nature and mechanism of prion protein conversion. In spite of the significance of this problem, we are far from fully understanding the conformational dynamics of the cellular isoform. To remedy this situation we employ multiple biomolecular modeling techniques such as docking and molecular dynamics simulations to map the free energy landscape and determine what specific regions of the prion protein are most conductive to binding. The overall goal is to characterize the conformational dynamics of the cell form of the prion protein, PrPc, to gain insight into inhibition pathways against misfolding. NE EPSCoR FIRST Award to Patricia Soto.
NASA Astrophysics Data System (ADS)
Lazo, M. J.; Ferreira, A. A.; Alcaraz, F. C.
2015-11-01
We obtained the exact solution of a probabilistic cellular automaton related to the diagonal-to-diagonal transfer matrix of the six-vertex model on a square lattice. The model describes the flow of ants (or particles), traveling on a one-dimensional lattice whose sites are small craters containing sleeping or awake ants (two kinds of particles). We found the Bethe ansatz equations and the spectral gap for the time-evolution operator of the cellular automaton. From the spectral gap we show that in the asymmetric case it belongs to the Kardar-Parisi-Zhang (KPZ) universality class, exhibiting a dynamical critical exponent value z = 3/2. This result is also obtained from a direct Monte Carlo simulation, by evaluating the lattice-size dependence of the decay time to the stationary state.
Computational fluid dynamics modelling in cardiovascular medicine.
Morris, Paul D; Narracott, Andrew; von Tengg-Kobligk, Hendrik; Silva Soto, Daniel Alejandro; Hsiao, Sarah; Lungu, Angela; Evans, Paul; Bressloff, Neil W; Lawford, Patricia V; Hose, D Rodney; Gunn, Julian P
2016-01-01
This paper reviews the methods, benefits and challenges associated with the adoption and translation of computational fluid dynamics (CFD) modelling within cardiovascular medicine. CFD, a specialist area of mathematics and a branch of fluid mechanics, is used routinely in a diverse range of safety-critical engineering systems, which increasingly is being applied to the cardiovascular system. By facilitating rapid, economical, low-risk prototyping, CFD modelling has already revolutionised research and development of devices such as stents, valve prostheses, and ventricular assist devices. Combined with cardiovascular imaging, CFD simulation enables detailed characterisation of complex physiological pressure and flow fields and the computation of metrics which cannot be directly measured, for example, wall shear stress. CFD models are now being translated into clinical tools for physicians to use across the spectrum of coronary, valvular, congenital, myocardial and peripheral vascular diseases. CFD modelling is apposite for minimally-invasive patient assessment. Patient-specific (incorporating data unique to the individual) and multi-scale (combining models of different length- and time-scales) modelling enables individualised risk prediction and virtual treatment planning. This represents a significant departure from traditional dependence upon registry-based, population-averaged data. Model integration is progressively moving towards 'digital patient' or 'virtual physiological human' representations. When combined with population-scale numerical models, these models have the potential to reduce the cost, time and risk associated with clinical trials. The adoption of CFD modelling signals a new era in cardiovascular medicine. While potentially highly beneficial, a number of academic and commercial groups are addressing the associated methodological, regulatory, education- and service-related challenges. PMID:26512019
Computational fluid dynamics modelling in cardiovascular medicine
Morris, Paul D; Narracott, Andrew; von Tengg-Kobligk, Hendrik; Silva Soto, Daniel Alejandro; Hsiao, Sarah; Lungu, Angela; Evans, Paul; Bressloff, Neil W; Lawford, Patricia V; Hose, D Rodney; Gunn, Julian P
2016-01-01
This paper reviews the methods, benefits and challenges associated with the adoption and translation of computational fluid dynamics (CFD) modelling within cardiovascular medicine. CFD, a specialist area of mathematics and a branch of fluid mechanics, is used routinely in a diverse range of safety-critical engineering systems, which increasingly is being applied to the cardiovascular system. By facilitating rapid, economical, low-risk prototyping, CFD modelling has already revolutionised research and development of devices such as stents, valve prostheses, and ventricular assist devices. Combined with cardiovascular imaging, CFD simulation enables detailed characterisation of complex physiological pressure and flow fields and the computation of metrics which cannot be directly measured, for example, wall shear stress. CFD models are now being translated into clinical tools for physicians to use across the spectrum of coronary, valvular, congenital, myocardial and peripheral vascular diseases. CFD modelling is apposite for minimally-invasive patient assessment. Patient-specific (incorporating data unique to the individual) and multi-scale (combining models of different length- and time-scales) modelling enables individualised risk prediction and virtual treatment planning. This represents a significant departure from traditional dependence upon registry-based, population-averaged data. Model integration is progressively moving towards ‘digital patient’ or ‘virtual physiological human’ representations. When combined with population-scale numerical models, these models have the potential to reduce the cost, time and risk associated with clinical trials. The adoption of CFD modelling signals a new era in cardiovascular medicine. While potentially highly beneficial, a number of academic and commercial groups are addressing the associated methodological, regulatory, education- and service-related challenges. PMID:26512019
Dynamic Finite Element Predictions for Mars Sample Return Cellular Impact Test #4
NASA Technical Reports Server (NTRS)
Fasanella, Edwin L.; Billings, Marcus D.
2001-01-01
The nonlinear finite element program MSC.Dytran was used to predict the impact pulse for (he drop test of an energy absorbing cellular structure. This pre-test simulation was performed to aid in the design of an energy absorbing concept for a highly reliable passive Earth Entry Vehicle (EEV) that will directly impact the Earth without a parachute. In addition, a goal of the simulation was to bound the acceleration pulse produced and delivered to the simulated space cargo container. EEV's are designed to return materials from asteroids, comets, or planets for laboratory analysis on Earth. The EEV concept uses an energy absorbing cellular structure designed to contain and limit the acceleration of space exploration samples during Earth impact. The spherical shaped cellular structure is composed of solid hexagonal and pentagonal foam-filled cells with hybrid graphite-epoxy/Kevlar cell walls. Space samples fit inside a smaller sphere at the enter of the EEV's cellular structure. The material models and failure criteria were varied to determine their effect on the resulting acceleration pulse. Pre-test analytical predictions using MSC.Dytran were compared with the test results obtained from impact test #4 using bungee accelerator located at the NASA Langley Research Center Impact Dynamics Research Facility. The material model used to represent the foam and the proper failure criteria for the cell walls were critical in predicting the impact loads of the cellular structure. It was determined that a FOAMI model for the foam and a 20% failure strain criteria for the cell walls gave an accurate prediction of the acceleration pulse for drop test #4.
LaBarge, Mark A; Parvin, Bahram; Lorens, James B
2014-01-01
The field of bioengineering has pioneered the application of new precision fabrication technologies to model the different geometric, physical or molecular components of tissue microenvironments on solid-state substrata. Tissue engineering approaches building on these advances are used to assemble multicellular mimetic-tissues where cells reside within defined spatial contexts. The functional responses of cells in fabricated microenvironments has revealed a rich interplay between the genome and extracellular effectors in determining cellular phenotypes, and in a number of cases has revealed the dominance of microenvironment over genotype. Precision bioengineered substrata are limited to a few aspects, whereas cell/tissue-derived microenvironments have many undefined components. Thus introducing a computational module may serve to integrate these types of platforms to create reasonable models of drug responses in human tissues. This review discusses how combinatorial microenvironment microarrays and other biomimetic microenvironments have revealed emergent properties of cells in particular microenvironmental contexts, the platforms that can measure phenotypic changes within those contexts, and the computational tools that can unify the microenvironment-imposed functional phenotypes with underlying constellations of proteins and genes. Ultimately we propose that a merger of these technologies will enable more accurate pre-clinical drug discovery. PMID:24582543
Labarge, Mark A; Parvin, Bahram; Lorens, James B
2014-04-01
The field of bioengineering has pioneered the application of new precision fabrication technologies to model the different geometric, physical or molecular components of tissue microenvironments on solid-state substrata. Tissue engineering approaches building on these advances are used to assemble multicellular mimetic-tissues where cells reside within defined spatial contexts. The functional responses of cells in fabricated microenvironments have revealed a rich interplay between the genome and extracellular effectors in determining cellular phenotypes and in a number of cases have revealed the dominance of microenvironment over genotype. Precision bioengineered substrata are limited to a few aspects, whereas cell/tissue-derived microenvironments have many undefined components. Thus, introducing a computational module may serve to integrate these types of platforms to create reasonable models of drug responses in human tissues. This review discusses how combinatorial microenvironment microarrays and other biomimetic microenvironments have revealed emergent properties of cells in particular microenvironmental contexts, the platforms that can measure phenotypic changes within those contexts, and the computational tools that can unify the microenvironment-imposed functional phenotypes with underlying constellations of proteins and genes. Ultimately we propose that a merger of these technologies will enable more accurate pre-clinical drug discovery. PMID:24582543
Computational social dynamic modeling of group recruitment.
Berry, Nina M.; Lee, Marinna; Pickett, Marc; Turnley, Jessica Glicken; Smrcka, Julianne D.; Ko, Teresa H.; Moy, Timothy David; Wu, Benjamin C.
2004-01-01
The Seldon software toolkit combines concepts from agent-based modeling and social science to create a computationally social dynamic model for group recruitment. The underlying recruitment model is based on a unique three-level hybrid agent-based architecture that contains simple agents (level one), abstract agents (level two), and cognitive agents (level three). This uniqueness of this architecture begins with abstract agents that permit the model to include social concepts (gang) or institutional concepts (school) into a typical software simulation environment. The future addition of cognitive agents to the recruitment model will provide a unique entity that does not exist in any agent-based modeling toolkits to date. We use social networks to provide an integrated mesh within and between the different levels. This Java based toolkit is used to analyze different social concepts based on initialization input from the user. The input alters a set of parameters used to influence the values associated with the simple agents, abstract agents, and the interactions (simple agent-simple agent or simple agent-abstract agent) between these entities. The results of phase-1 Seldon toolkit provide insight into how certain social concepts apply to different scenario development for inner city gang recruitment.
Object Orientated Methods in Computational Fluid Dynamics.
NASA Astrophysics Data System (ADS)
Tabor, Gavin; Weller, Henry; Jasak, Hrvoje; Fureby, Christer
1997-11-01
We outline the aims of the FOAM code, a Finite Volume Computational Fluid Dynamics code written in C++, and discuss the use of Object Orientated Programming (OOP) methods to achieve these aims. The intention when writing this code was to make it as easy as possible to alter the modelling : this was achieved by making the top level syntax of the code as close as possible to conventional mathematical notation for tensors and partial differential equations. Object orientation enables us to define classes for both types of objects, and the operator overloading possible in C++ allows normal symbols to be used for the basic operations. The introduction of features such as automatic dimension checking of equations helps to enforce correct coding of models. We also discuss the use of OOP techniques such as data encapsulation and code reuse. As examples of the flexibility of this approach, we discuss the implementation of turbulence modelling using RAS and LES. The code is used to simulate turbulent flow for a number of test cases, including fully developed channel flow and flow around obstacles. We also demonstrate the use of the code for solving structures calculations and magnetohydrodynamics.
Computational fluid dynamics in ventilation: Practical approach
NASA Astrophysics Data System (ADS)
Fontaine, J. R.
The potential of computation fluid dynamics (CFD) for conceiving ventilation systems is shown through the simulation of five practical cases. The following examples are considered: capture of pollutants on a surface treating tank equipped with a unilateral suction slot in the presence of a disturbing air draft opposed to suction; dispersion of solid aerosols inside fume cupboards; performances comparison of two general ventilation systems in a silkscreen printing workshop; ventilation of a large open painting area; and oil fog removal inside a mechanical engineering workshop. Whereas the two first problems are analyzed through two dimensional numerical simulations, the three other cases require three dimensional modeling. For the surface treating tank case, numerical results are compared to laboratory experiment data. All simulations are carried out using EOL, a CFD software specially devised to deal with air quality problems in industrial ventilated premises. It contains many analysis tools to interpret the results in terms familiar to the industrial hygienist. Much experimental work has been engaged to validate the predictions of EOL for ventilation flows.
Computational study on cortical spreading depression based on a generalized cellular automaton model
NASA Astrophysics Data System (ADS)
Chen, Shangbin; Hu, Lele; Li, Bing; Xu, Changcheng; Liu, Qian
2009-02-01
Cortical spreading depression (CSD) is an important neurophysiological phenomenon correlating with some neural disorders, such as migraine, cerebral ischemia and epilepsy. By now, we are still not clear about the mechanisms of CSD's initiation and propagation, also the relevance between CSD and those neural diseases. Nevertheless, characterization of CSD, especially the spatiotemporal evolution, will promote the understanding of the CSD's nature and mechanisms. Besides the previous experimental work on charactering the spatiotemporal evolution of CSD in rats by optical intrinsic signal imaging, a computational study based on a generalized cellular automaton (CA) model was proposed here. In the model, we exploited a generalized neighborhood connection rule: a central CA cell is related with a group of surrounding CA cells with different weight coefficients. By selecting special parameters, the generalized CA model could be transformed to the traditional CA models with von Neumann, Moore and hexagon neighborhood connection means. Hence, the new model covered several properties of CSD simulated in traditional CA models: 1) expanding from the origin site like a circular wave; 2) annihilation of two waves traveling in opposite directions after colliding; 3) wavefront of CSD breaking and recovering when and after encountering an obstacle. By setting different refractory period in the different CA lattice field, different connection coefficient in different direction within the defined neighborhood, inhomogeneous propagation of CSD was simulated with high fidelity. The computational results were analogous to the reported time-varying CSD waves by optical imaging. So, the generalized CA model would be useful to study CSD because of its intuitive appeal and computational efficiency.
Synchrotron-based X-ray computed tomography during compression loading of cellular materials
Cordes, Nikolaus L.; Henderson, Kevin; Stannard, Tyler; Williams, Jason J.; Xiao, Xianghui; Robinson, Mathew W. C.; Schaedler, Tobias A.; Chawla, Nikhilesh; Patterson, Brian M.
2015-04-29
Three-dimensional X-ray computed tomography (CT) of in situ dynamic processes provides internal snapshot images as a function of time. Tomograms are mathematically reconstructed from a series of radiographs taken in rapid succession as the specimen is rotated in small angular increments. In addition to spatial resolution, temporal resolution is important. Thus temporal resolution indicates how close together in time two distinct tomograms can be acquired. Tomograms taken in rapid succession allow detailed analyses of internal processes that cannot be obtained by other means. This article describes the state-of-the-art for such measurements acquired using synchrotron radiation as the X-ray source.
Synchrotron-based X-ray computed tomography during compression loading of cellular materials
Cordes, Nikolaus L.; Henderson, Kevin; Stannard, Tyler; Williams, Jason J.; Xiao, Xianghui; Robinson, Mathew W. C.; Schaedler, Tobias A.; Chawla, Nikhilesh; Patterson, Brian M.
2015-04-29
Three-dimensional X-ray computed tomography (CT) of in situ dynamic processes provides internal snapshot images as a function of time. Tomograms are mathematically reconstructed from a series of radiographs taken in rapid succession as the specimen is rotated in small angular increments. In addition to spatial resolution, temporal resolution is important. Thus temporal resolution indicates how close together in time two distinct tomograms can be acquired. Tomograms taken in rapid succession allow detailed analyses of internal processes that cannot be obtained by other means. This article describes the state-of-the-art for such measurements acquired using synchrotron radiation as the X-ray source.
Computer aided analysis and optimization of mechanical system dynamics
NASA Technical Reports Server (NTRS)
Haug, E. J.
1984-01-01
The purpose is to outline a computational approach to spatial dynamics of mechanical systems that substantially enlarges the scope of consideration to include flexible bodies, feedback control, hydraulics, and related interdisciplinary effects. Design sensitivity analysis and optimization is the ultimate goal. The approach to computer generation and solution of the system dynamic equations and graphical methods for creating animations as output is outlined.
Trends in computational capabilities for fluid dynamics
NASA Technical Reports Server (NTRS)
Peterson, V. L.
1985-01-01
Milestones in the development of computational aerodynamics are reviewed together with past, present, and future computer performance (speed and memory) trends. Factors influencing computer performance requirements for both steady and unsteady flow simulations are identified. Estimates of computer speed and memory that are required to calculate both inviscid and viscous, steady and unsteady flows about airfoils, wings, and simple wing body configurations are presented and compared to computer performance which is either currently available, or is expected to be available before the end of this decade. Finally, estimates of the amounts of computer time that are required to determine flutter boundaries of airfoils and wings at transonic Mach numbers are presented and discussed.
Trends in computational capabilities for fluid dynamics
NASA Technical Reports Server (NTRS)
Peterson, V. L.
1984-01-01
Milestones in the development of computational aerodynamics are reviewed together with past, present, and future computer performance (speed and memory) trends. Factors influencing computer performance requirements for both steady and unsteady flow simulations are identified. Estimates of computer speed and memory that are required to calculate both inviscid and viscous, steady and unsteady flows about airfoils, wings, and simple wing body configurations are presented and compared to computer performance which is either currently available, or is expected to be available before the end of this decade. Finally, estimates of the amounts of computer time that are required to determine flutter boundaries of airfoils and wings at transonic Mach numbers are presented and discussed.
DNA-controlled dynamic colloidal nanoparticle systems for mediating cellular interaction.
Ohta, Seiichi; Glancy, Dylan; Chan, Warren C W
2016-02-19
Precise control of biosystems requires development of materials that can dynamically change physicochemical properties. Inspired by the ability of proteins to alter their conformation to mediate function, we explored the use of DNA as molecular keys to assemble and transform colloidal nanoparticle systems. The systems consist of a core nanoparticle surrounded by small satellites, the conformation of which can be transformed in response to DNA via a toe-hold displacement mechanism. The conformational changes can alter the optical properties and biological interactions of the assembled nanosystem. Photoluminescent signal is altered by changes in fluorophore-modified particle distance, whereas cellular targeting efficiency is increased 2.5 times by changing the surface display of targeting ligands. These concepts provide strategies for engineering dynamic nanotechnology systems for navigating complex biological environments. PMID:26912892
Emergence of density dynamics by surface interpolation in elementary cellular automata
NASA Astrophysics Data System (ADS)
Seck-Tuoh-Mora, Juan Carlos; Medina-Marin, Joselito; Martínez, Genaro J.; Hernández-Romero, Norberto
2014-04-01
A classic problem in elementary cellular automata (ECAs) is the specification of numerical tools to represent and study their dynamical behaviour. Mean field theory and basins of attraction have been commonly used; however, although the first case gives the long term estimation of density, frequently it does not show an adequate approximation for the step-by-step temporal behaviour; mainly for non-trivial behaviour. In the second case, basins of attraction display a complete representation of the evolution of an ECA, but they are limited up to configurations of 32 cells; and for the same ECA, one can obtain tens of basins to analyse. This paper is devoted to represent the dynamics of density in ECAs for hundreds of cells using only two surfaces calculated by the nearest-neighbour interpolation. A diversity of surfaces emerges in this analysis. Consequently, we propose a surface and histogram based classification for periodic, chaotic and complex ECA.
Clay, Matthew R.; Sherwood, David R.
2015-01-01
The nematode worm Caenorhabditis elegans has all the major basement membrane proteins found in vertebrates, usually with a smaller gene family encoding each component. With its powerful forward genetics, optical clarity, simple tissue organization, and the capability to functionally tag most basement membrane components with fluorescent proteins, C. elegans has facilitated novel insights into the assembly and function of basement membranes. Although basement membranes are generally thought of as static structures, studies in C. elegans have revealed their active properties and essential functions in tissue formation and maintenance. Here we review discoveries from C. elegans development that highlight dynamic aspects of basement membrane assembly, function, and regulation during organ growth, tissue polarity, cell migration, cell invasion, and tissue attachment. These studies have helped transform our view of basement membranes from static support structures to dynamic scaffoldings that play broad roles in regulating tissue organization and cellular behavior that are essential for development and have important implications in human diseases. PMID:26610919
DNA-controlled dynamic colloidal nanoparticle systems for mediating cellular interaction
NASA Astrophysics Data System (ADS)
Ohta, Seiichi; Glancy, Dylan; Chan, Warren C. W.
2016-02-01
Precise control of biosystems requires development of materials that can dynamically change physicochemical properties. Inspired by the ability of proteins to alter their conformation to mediate function, we explored the use of DNA as molecular keys to assemble and transform colloidal nanoparticle systems. The systems consist of a core nanoparticle surrounded by small satellites, the conformation of which can be transformed in response to DNA via a toe-hold displacement mechanism. The conformational changes can alter the optical properties and biological interactions of the assembled nanosystem. Photoluminescent signal is altered by changes in fluorophore-modified particle distance, whereas cellular targeting efficiency is increased 2.5 times by changing the surface display of targeting ligands. These concepts provide strategies for engineering dynamic nanotechnology systems for navigating complex biological environments.
Study of dynamic process of acetic acid induced-whitening in epithelial tissues at cellular level
NASA Astrophysics Data System (ADS)
Wu, Tao T.; Qu, Jianan Y.; Cheung, Tak Hong; Yim, So Fan; Wong, Yick Fu
2005-06-01
Acetic acid, inducing transient whitening (acetowhitening) when applied to epithelial tissues, is a commonly used contrast agent for detecting early cervical cancer. The goals of this research are to investigate the temporal characteristics of acetowhitening process in cervical epithelial tissue at cellular level and develop a clear understanding of the diagnostic information carried in the acetowhitening signal. A system measuring time-resolved reflectance was built to study the rising and decay processes of acetowhitening signal from the monolayered cell cultures of normal and cancerous cervical squamous cells. It is found that the dynamic processes of acetowhitening in normal and cancerous cells are significantly different. The results of this study provide insight valuable to further understand the acetowhitening process in epithelial cells and to encourage the development of an objective procedure to detect the early cervical cancers based on quantitative monitoring of the dynamic process of acetowhitening
Dynamic leaching test of personal computer components.
Li, Yadong; Richardson, Jay B; Niu, Xiaojun; Jackson, Ollie J; Laster, Jeremy D; Walker, Aaron K
2009-11-15
A dynamic leaching test (DLT) was developed and used to evaluate the leaching of toxic substances for electronic waste in the environment. The major components in personal computers (PCs) including motherboards, hard disc drives, floppy disc drives, and compact disc drives were tested. The tests lasted for 2 years for motherboards and 1.5 year for the disc drives. The extraction fluids for the standard toxicity characteristic leaching procedure (TCLP) and synthetic precipitation leaching procedure (SPLP) were used as the DLT leaching solutions. A total of 18 elements including Ag, Al, As, Au, Ba, Be, Cd, Cr, Cu, Fe, Ga, Ni, Pd, Pb, Sb, Se, Sn, and Zn were analyzed in the DLT leachates. Only Al, Cu, Fe, Ni, Pb, and Zn were commonly found in the DLT leachates of the PC components. Their leaching levels were much higher in TCLP extraction fluid than in SPLP extraction fluid. The toxic heavy metal Pb was found to continuously leach out of the components over the entire test periods. The cumulative amounts of Pb leached out of the motherboards in TCLP extraction fluid reached 2.0 g per motherboard over the 2-year test period, and that in SPLP extraction fluid were 75-90% less. The leaching rates or levels of Pb were largely affected by the content of galvanized steel in the PC components. The higher was the steel content, the lower the Pb leaching rate would be. The findings suggest that the obsolete PCs disposed of in landfills or discarded in the environment continuously release Pb for years when subjected to landfill leachate or rains. PMID:19616380
AIR INGRESS ANALYSIS: COMPUTATIONAL FLUID DYNAMIC MODELS
Chang H. Oh; Eung S. Kim; Richard Schultz; Hans Gougar; David Petti; Hyung S. Kang
2010-08-01
The Idaho National Laboratory (INL), under the auspices of the U.S. Department of Energy, is performing research and development that focuses on key phenomena important during potential scenarios that may occur in very high temperature reactors (VHTRs). Phenomena Identification and Ranking Studies to date have ranked an air ingress event, following on the heels of a VHTR depressurization, as important with regard to core safety. Consequently, the development of advanced air ingress-related models and verification and validation data are a very high priority. Following a loss of coolant and system depressurization incident, air will enter the core of the High Temperature Gas Cooled Reactor through the break, possibly causing oxidation of the in-the core and reflector graphite structure. Simple core and plant models indicate that, under certain circumstances, the oxidation may proceed at an elevated rate with additional heat generated from the oxidation reaction itself. Under postulated conditions of fluid flow and temperature, excessive degradation of the lower plenum graphite can lead to a loss of structural support. Excessive oxidation of core graphite can also lead to the release of fission products into the confinement, which could be detrimental to a reactor safety. Computational fluid dynamic model developed in this study will improve our understanding of this phenomenon. This paper presents two-dimensional and three-dimensional CFD results for the quantitative assessment of the air ingress phenomena. A portion of results of the density-driven stratified flow in the inlet pipe will be compared with results of the experimental results.
COMPUTATIONAL FLUID DYNAMICS MODELING ANALYSIS OF COMBUSTORS
Mathur, M.P.; Freeman, Mark; Gera, Dinesh
2001-11-06
In the current fiscal year FY01, several CFD simulations were conducted to investigate the effects of moisture in biomass/coal, particle injection locations, and flow parameters on carbon burnout and NO{sub x} inside a 150 MW GEEZER industrial boiler. Various simulations were designed to predict the suitability of biomass cofiring in coal combustors, and to explore the possibility of using biomass as a reburning fuel to reduce NO{sub x}. Some additional CFD simulations were also conducted on CERF combustor to examine the combustion characteristics of pulverized coal in enriched O{sub 2}/CO{sub 2} environments. Most of the CFD models available in the literature treat particles to be point masses with uniform temperature inside the particles. This isothermal condition may not be suitable for larger biomass particles. To this end, a stand alone program was developed from the first principles to account for heat conduction from the surface of the particle to its center. It is envisaged that the recently developed non-isothermal stand alone module will be integrated with the Fluent solver during next fiscal year to accurately predict the carbon burnout from larger biomass particles. Anisotropy in heat transfer in radial and axial will be explored using different conductivities in radial and axial directions. The above models will be validated/tested on various fullscale industrial boilers. The current NO{sub x} modules will be modified to account for local CH, CH{sub 2}, and CH{sub 3} radicals chemistry, currently it is based on global chemistry. It may also be worth exploring the effect of enriched O{sub 2}/CO{sub 2} environment on carbon burnout and NO{sub x} concentration. The research objective of this study is to develop a 3-Dimensional Combustor Model for Biomass Co-firing and reburning applications using the Fluent Computational Fluid Dynamics Code.
Integrated computer simulation on FIR FEL dynamics
Furukawa, H.; Kuruma, S.; Imasaki, K.
1995-12-31
An integrated computer simulation code has been developed to analyze the RF-Linac FEL dynamics. First, the simulation code on the electron beam acceleration and transport processes in RF-Linac: (LUNA) has been developed to analyze the characteristics of the electron beam in RF-Linac and to optimize the parameters of RF-Linac. Second, a space-time dependent 3D FEL simulation code (Shipout) has been developed. The RF-Linac FEL total simulations have been performed by using the electron beam data from LUNA in Shipout. The number of particles using in a RF-Linac FEL total simulation is approximately 1000. The CPU time for the simulation of 1 round trip is about 1.5 minutes. At ILT/ILE, Osaka, a 8.5MeV RF-Linac with a photo-cathode RF-gun is used for FEL oscillation experiments. By using 2 cm wiggler, the FEL oscillation in the wavelength approximately 46 {mu}m are investigated. By the simulations using LUNA with the parameters of an ILT/ILE experiment, the pulse shape and the energy spectra of the electron beam at the end of the linac are estimated. The pulse shape of the electron beam at the end of the linac has sharp rise-up and it slowly decays as a function of time. By the RF-linac FEL total simulations with the parameters of an ILT/ILE experiment, the dependencies of the start up of the FEL oscillations on the pulse shape of the electron beam at the end of the linac are estimated. The coherent spontaneous emission effects and the quick start up of FEL oscillations have been observed by the RF-Linac FEL total simulations.
2013-01-01
Background Cosmos caudatus is a local plant which has antioxidant properties and contains high calcium. It is also reported to be able to strengthen the bone. This report is an extension to previously published article in Evidence Based Complementary and Alternative Medicine (doi:10.1155/2012/817814). In this study, we determined the effectiveness of C. caudatus as an alternative treatment for osteoporosis due to post-menopause by looking at the dynamic and cellular paramaters of bone histomorphometry. Methods Forty female Wistar rats were divided into four groups i.e. sham operated, ovariectomized, ovariectomized treated with calcium 1% ad libitum and ovariectomized force-fed with 500 mg/kg C. caudatus extract. Treatment was given six days a week for eight weeks. Results Dynamic and cellular histomorphometry parameters were measured. C. caudatus increased double-labeled surface (dLS/BS), mineral appositional rate (MAR), osteoid volume (OV/BV) and osteoblast surface (Ob.S/BS). C. caudatus also gave better results compared to calcium 1% in the osteoid volume (OV/BV) parameter. Conclusions C. caudatus at the 500 mg/kg dose may be an alternative treatment in restoring bone damage that may occur in post-menopausal women. PMID:23800238
Dynamics of Cell Shape and Forces on Micropatterned Substrates Predicted by a Cellular Potts Model
Albert, Philipp J.; Schwarz, Ulrich S.
2014-01-01
Micropatterned substrates are often used to standardize cell experiments and to quantitatively study the relation between cell shape and function. Moreover, they are increasingly used in combination with traction force microscopy on soft elastic substrates. To predict the dynamics and steady states of cell shape and forces without any a priori knowledge of how the cell will spread on a given micropattern, here we extend earlier formulations of the two-dimensional cellular Potts model. The third dimension is treated as an area reservoir for spreading. To account for local contour reinforcement by peripheral bundles, we augment the cellular Potts model by elements of the tension-elasticity model. We first parameterize our model and show that it accounts for momentum conservation. We then demonstrate that it is in good agreement with experimental data for shape, spreading dynamics, and traction force patterns of cells on micropatterned substrates. We finally predict shapes and forces for micropatterns that have not yet been experimentally studied. PMID:24896113
Lappalainen, Pekka
2016-08-15
The actin cytoskeleton supports a vast number of cellular processes in nonmuscle cells. It is well established that the organization and dynamics of the actin cytoskeleton are controlled by a large array of actin-binding proteins. However, it was only 40 years ago that the first nonmuscle actin-binding protein, filamin, was identified and characterized. Filamin was shown to bind and cross-link actin filaments into higher-order structures and contribute to phagocytosis in macrophages. Subsequently many other nonmuscle actin-binding proteins were identified and characterized. These proteins regulate almost all steps of the actin filament assembly and disassembly cycles, as well as the arrangement of actin filaments into diverse three-dimensional structures. Although the individual biochemical activities of most actin-regulatory proteins are relatively well understood, knowledge of how these proteins function together in a common cytoplasm to control actin dynamics and architecture is only beginning to emerge. Furthermore, understanding how signaling pathways and mechanical cues control the activities of various actin-binding proteins in different cellular, developmental, and pathological processes will keep researchers busy for decades. PMID:27528696
Cellular Solid-State NMR Investigation of a Membrane Protein Using Dynamic Nuclear Polarization
Yamamoto, Kazutoshi; Caporini, Marc A.; Im, Sang-Choul; Waskell, Lucy; Ramamoorthy, Ayyalusamy
2014-01-01
While an increasing number of structural biology studies successfully demonstrate the power of high-resolution structures and dynamics of membrane proteins in fully understanding their function, there is considerable interest in developing NMR approaches to obtain such information in a cellular setting. As long as the proteins inside the living cell tumble rapidly in the NMR timescale, recently developed in-cell solution NMR approaches can be applied towards the determination of 3D structural information. However, there are numerous challenges that need to be overcome to study membrane proteins inside a cell. Research in our laboratory is focused on developing a combination of solid-state NMR and biological approaches to overcome these challenges with a specific emphasis on obtaining high-resolution structural insights into electron transfer biological processes mediated by membrane-bound proteins like mammalian cytochrome b5, cytochrome P450 and cytochrome P450 reductase. In this study, we demonstrate the feasibility of using the signal-enhancement rendered by dynamic nuclear polarization (DNP) magic angle spinning (MAS) NMR spectroscopy for in-cell studies on a membrane-anchored protein. Our experimental results obtained from 13C-labeled membrane-anchored cytochrome b5 in native Escherichia coli cells show a ~16-fold DNP signal enhancement (ε). Further, results obtained from a 2D 13C/13C chemical shift correlation MAS experiment demonstrates that it is highly possible to suppress the background signals from other cellular contents for high-resolution structural studies on membrane proteins. We believe that this study would pave new avenues for high-resolution 3D structural studies on a variety of membrane-associated proteins and their complexes in the cellular context to fully understand their functional roles in physiological processes. PMID:25017802
Cellular automata model based on GIS and urban sprawl dynamics simulation
NASA Astrophysics Data System (ADS)
Mu, Fengyun; Zhang, Zengxiang
2005-10-01
The simulation of land use change process needs the support of Geographical Information System (GIS) and other relative technologies. While the present commercial GIS lack capabilities of distribution, prediction, and simulation of spatial-temporal data. Cellular automata (CA) provide dynamically modeling "from bottom-to-top" framework and posses the capability of modeling spatial-temporal evolvement process of a complicated geographical system, which is composed of a fourfold: cells, states, neighbors and rules. The simplicity and flexibility make CA have the ability to simulate a variety of behaviors of complex systems. One of the most potentially useful applications of cellular automata from the point of view of spatial planning is their use in simulations of urban sprawl at local and regional level. The paper firstly introduces the principles and characters of the cellular automata, and then discusses three methods of the integration of CA and GIS. The paper analyses from a practical point of view the factors that effect urban activities in the science of spatial decision-making. The status of using CA to dynamic simulates of urban expansion at home and abroad is analyzed. Finally, the problems and tendencies that exist in the application of CA model are detailed discussed, such as the quality of the data that the CA needs, the self-organization of the CA roots in the mutual function among the elements of the system, the partition of the space scale, the time calibration of the CA and the integration of the CA with other modular such as artificial nerve net modular and population modular etc.
Computational fluid dynamics on a massively parallel computer
NASA Technical Reports Server (NTRS)
Jespersen, Dennis C.; Levit, Creon
1989-01-01
A finite difference code was implemented for the compressible Navier-Stokes equations on the Connection Machine, a massively parallel computer. The code is based on the ARC2D/ARC3D program and uses the implicit factored algorithm of Beam and Warming. The codes uses odd-even elimination to solve linear systems. Timings and computation rates are given for the code, and a comparison is made with a Cray XMP.
Mobility-Aware Caching and Computation Offloading in 5G Ultra-Dense Cellular Networks
Chen, Min; Hao, Yixue; Qiu, Meikang; Song, Jeungeun; Wu, Di; Humar, Iztok
2016-01-01
Recent trends show that Internet traffic is increasingly dominated by content, which is accompanied by the exponential growth of traffic. To cope with this phenomena, network caching is introduced to utilize the storage capacity of diverse network devices. In this paper, we first summarize four basic caching placement strategies, i.e., local caching, Device-to-Device (D2D) caching, Small cell Base Station (SBS) caching and Macrocell Base Station (MBS) caching. However, studies show that so far, much of the research has ignored the impact of user mobility. Therefore, taking the effect of the user mobility into consideration, we proposes a joint mobility-aware caching and SBS density placement scheme (MS caching). In addition, differences and relationships between caching and computation offloading are discussed. We present a design of a hybrid computation offloading and support it with experimental results, which demonstrate improved performance in terms of energy cost. Finally, we discuss the design of an incentive mechanism by considering network dynamics, differentiated user’s quality of experience (QoE) and the heterogeneity of mobile terminals in terms of caching and computing capabilities. PMID:27347975
Mobility-Aware Caching and Computation Offloading in 5G Ultra-Dense Cellular Networks.
Chen, Min; Hao, Yixue; Qiu, Meikang; Song, Jeungeun; Wu, Di; Humar, Iztok
2016-01-01
Recent trends show that Internet traffic is increasingly dominated by content, which is accompanied by the exponential growth of traffic. To cope with this phenomena, network caching is introduced to utilize the storage capacity of diverse network devices. In this paper, we first summarize four basic caching placement strategies, i.e., local caching, Device-to-Device (D2D) caching, Small cell Base Station (SBS) caching and Macrocell Base Station (MBS) caching. However, studies show that so far, much of the research has ignored the impact of user mobility. Therefore, taking the effect of the user mobility into consideration, we proposes a joint mobility-aware caching and SBS density placement scheme (MS caching). In addition, differences and relationships between caching and computation offloading are discussed. We present a design of a hybrid computation offloading and support it with experimental results, which demonstrate improved performance in terms of energy cost. Finally, we discuss the design of an incentive mechanism by considering network dynamics, differentiated user's quality of experience (QoE) and the heterogeneity of mobile terminals in terms of caching and computing capabilities. PMID:27347975
Bergemann, Claudia; Elter, Patrick; Lange, Regina; Weißmann, Volker; Hansmann, Harald; Klinkenberg, Ernst-Dieter; Nebe, Barbara
2015-01-01
Studies on bone cell ingrowth into synthetic, porous three-dimensional (3D) implants showed difficulties arising from impaired cellular proliferation and differentiation in the core region of these scaffolds with increasing scaffold volume in vitro. Therefore, we developed an in vitro perfusion cell culture module, which allows the analysis of cells in the interior of scaffolds under different medium flow rates. For each flow rate the cell viability was measured and compared with results from computer simulations that predict the local oxygen supply and shear stress inside the scaffold based on the finite element method. We found that the local cell viability correlates with the local oxygen concentration and the local shear stress. On the one hand the oxygen supply of the cells in the core becomes optimal with a higher perfusion flow. On the other hand shear stress caused by high flow rates impedes cell vitality, especially at the surface of the scaffold. Our results demonstrate that both parameters must be considered to derive an optimal nutrient flow rate. PMID:26539216
Computing Bisectors in a Dynamic Geometry Environment
ERIC Educational Resources Information Center
Botana, Francisco
2013-01-01
In this note, an approach combining dynamic geometry and automated deduction techniques is used to study the bisectors between points and curves. Usual teacher constructions for bisectors are discussed, showing that inherent limitations in dynamic geometry software impede their thorough study. We show that the interactive sketching of bisectors…
Biological pattern generation: the cellular and computational logic of networks in motion.
Grillner, Sten
2006-12-01
In 1900, Ramón y Cajal advanced the neuron doctrine, defining the neuron as the fundamental signaling unit of the nervous system. Over a century later, neurobiologists address the circuit doctrine: the logic of the core units of neuronal circuitry that control animal behavior. These are circuits that can be called into action for perceptual, conceptual, and motor tasks, and we now need to understand whether there are coherent and overriding principles that govern the design and function of these modules. The discovery of central motor programs has provided crucial insight into the logic of one prototypic set of neural circuits: those that generate motor patterns. In this review, I discuss the mode of operation of these pattern generator networks and consider the neural mechanisms through which they are selected and activated. In addition, I will outline the utility of computational models in analysis of the dynamic actions of these motor networks. PMID:17145498
Eleventh Workshop for Computational Fluid Dynamic Applications in Rocket Propulsion
NASA Technical Reports Server (NTRS)
Williams, R. W. (Compiler)
1993-01-01
Conference publication includes 79 abstracts and presentations and 3 invited presentations given at the Eleventh Workshop for Computational Fluid Dynamic Applications in Rocket Propulsion held at George C. Marshall Space Flight Center, April 20-22, 1993. The purpose of the workshop is to discuss experimental and computational fluid dynamic activities in rocket propulsion. The workshop is an open meeting for government, industry, and academia. A broad number of topics are discussed including computational fluid dynamic methodology, liquid and solid rocket propulsion, turbomachinery, combustion, heat transfer, and grid generation.
NASA Astrophysics Data System (ADS)
Acedo, L.; Villanueva-Oller, J.; Moraño, J. A.; Villanueva, R.-J.
2013-01-01
The Berkeley Open Infrastructure for Network Computing (BOINC) has become the standard open source solution for grid computing in the Internet. Volunteers use their computers to complete an small part of the task assigned by a dedicated server. We have developed a BOINC project called Neurona@Home whose objective is to simulate a cellular automata random network with, at least, one million neurons. We consider a cellular automata version of the integrate-and-fire model in which excitatory and inhibitory nodes can activate or deactivate neighbor nodes according to a set of probabilistic rules. Our aim is to determine the phase diagram of the model and its behaviour and to compare it with the electroencephalographic signals measured in real brains.
Ah Min, Kyoung; Zhang, Xinyuan; Yu, Jing-yu; Rosania, Gus R.
2013-01-01
Quantitative structure-activity relationship (QSAR) studies and mechanistic mathematical modeling approaches have been independently employed for analyzing and predicting the transport and distribution of small molecule chemical agents in living organisms. Both of these computational approaches have been useful to interpret experiments measuring the transport properties of small molecule chemical agents, in vitro and in vivo. Nevertheless, mechanistic cell-based pharmacokinetic models have been especially useful to guide the design of experiments probing the molecular pathways underlying small molecule transport phenomena. Unlike QSAR models, mechanistic models can be integrated from microscopic to macroscopic levels, to analyze the spatiotemporal dynamics of small molecule chemical agents from intracellular organelles to whole organs, well beyond the experiments and training data sets upon which the models are based. Based on differential equations, mechanistic models can also be integrated with other differential equations-based systems biology models of biochemical networks or signaling pathways. Although the origin and evolution of mathematical modeling approaches aimed at predicting drug transport and distribution has occurred independently from systems biology, we propose that the incorporation of mechanistic cell-based computational models of drug transport and distribution into a systems biology modeling framework is a logical next-step for the advancement of systems pharmacology research. PMID:24218242
Dynamics of the HIV infection under antiretroviral therapy: A cellular automata approach
NASA Astrophysics Data System (ADS)
González, Ramón E. R.; Coutinho, Sérgio; Zorzenon dos Santos, Rita Maria; de Figueirêdo, Pedro Hugo
2013-10-01
The dynamics of human immunodeficiency virus infection under antiretroviral therapy is investigated using a cellular automata model where the effectiveness of each drug is self-adjusted by the concentration of CD4+ T infected cells present at each time step. The effectiveness of the drugs and the infected cell concentration at the beginning of treatment are the control parameters of the cell population’s dynamics during therapy. The model allows describing processes of mono and combined therapies. The dynamics that emerges from this model when considering combined antiretroviral therapies reproduces with fair qualitative agreement the phases and different time scales of the process. As observed in clinical data, the results reproduce the significant decrease in the population of infected cells and a concomitant increase of the population of healthy cells in a short timescale (weeks) after the initiation of treatment. Over long time scales, early treatment with potent drugs may lead to undetectable levels of infection. For late treatment or treatments starting with a low density of CD4+ T healthy cells it was observed that the treatment may lead to a steady state in which the T cell counts are above the threshold associated with the onset of AIDS. The results obtained are validated through comparison to available clinical trial data.
A multi-objective model for designing a group layout of a dynamic cellular manufacturing system
NASA Astrophysics Data System (ADS)
Kia, Reza; Shirazi, Hossein; Javadian, Nikbakhsh; Tavakkoli-Moghaddam, Reza
2013-04-01
This paper presents a multi-objective mixed-integer nonlinear programming model to design a group layout of a cellular manufacturing system in a dynamic environment, in which the number of cells to be formed is variable. Cell formation (CF) and group layout (GL) are concurrently made in a dynamic environment by the integrated model, which incorporates with an extensive coverage of important manufacturing features used in the design of CMSs. Additionally, there are some features that make the presented model different from the previous studies. These features include the following: (1) the variable number of cells, (2) the integrated CF and GL decisions in a dynamic environment by a multi-objective mathematical model, and (3) two conflicting objectives that minimize the total costs (i.e., costs of intra and inter-cell material handling, machine relocation, purchasing new machines, machine overhead, machine processing, and forming cells) and minimize the imbalance of workload among cells. Furthermore, the presented model considers some limitations, such as machine capability, machine capacity, part demands satisfaction, cell size, material flow conservation, and location assignment. Four numerical examples are solved by the GAMS software to illustrate the promising results obtained by the incorporated features.