21 research outputs found
Collective analog bioelectronic computation
Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2009.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.Cataloged from student submitted PDF version of thesis.Includes bibliographical references (p. 677-710).In this thesis, I present two examples of fast-and-highly-parallel analog computation inspired by architectures in biology. The first example, an RF cochlea, maps the partial differential equations that describe fluid-membrane-hair-cell wave propagation in the biological cochlea to an equivalent inductor-capacitor-transistor integrated circuit. It allows ultra-broadband spectrum analysis of RF signals to be performed in a rapid low-power fashion, thus enabling applications for universal or software radio. The second example exploits detailed similarities between the equations that describe chemical-reaction dynamics and the equations that describe subthreshold current flow in transistors to create fast-and-highly-parallel integrated-circuit models of protein-protein and gene-protein networks inside a cell. Due to a natural mapping between the Poisson statistics of molecular flows in a chemical reaction and Poisson statistics of electronic current flow in a transistor, stochastic effects are automatically incorporated into the circuit architecture, allowing highly computationally intensive stochastic simulations of large-scale biochemical reaction networks to be performed rapidly. I show that the exponentially tapered transmission-line architecture of the mammalian cochlea performs constant-fractional-bandwidth spectrum analysis with O(N) expenditure of both analysis time and hardware, where N is the number of analyzed frequency bins. This is the best known performance of any spectrum-analysis architecture, including the constant-resolution Fast Fourier Transform (FFT), which scales as O(N logN), or a constant-fractional-bandwidth filterbank, which scales as O (N2).(cont.) The RF cochlea uses this bio-inspired architecture to perform real-time, on-chip spectrum analysis at radio frequencies. I demonstrate two cochlea chips, implemented in standard 0.13m CMOS technology, that decompose the RF spectrum from 600MHz to 8GHz into 50 log-spaced channels, consume < 300mW of power, and possess 70dB of dynamic range. The real-time spectrum analysis capabilities of my chips make them uniquely suitable for ultra-broadband universal or software radio receivers of the future. I show that the protein-protein and gene-protein chips that I have built are particularly suitable for simulation, parameter discovery and sensitivity analysis of interaction networks in cell biology, such as signaling, metabolic, and gene regulation pathways. Importantly, the chips carry out massively parallel computations, resulting in simulation times that are independent of model complexity, i.e., O(1). They also automatically model stochastic effects, which are of importance in many biological systems, but are numerically stiff and simulate slowly on digital computers. Currently, non-fundamental data-acquisition limitations show that my proof-of-concept chips simulate small-scale biochemical reaction networks at least 100 times faster than modern desktop machines. It should be possible to get 103 to 106 simulation speedups of genome-scale and organ-scale intracellular and extracellular biochemical reaction networks with improved versions of my chips. Such chips could be important both as analysis tools in systems biology and design tools in synthetic biology.by Soumyajit Mandal.Ph.D
Using MapReduce Streaming for Distributed Life Simulation on the Cloud
Distributed software simulations are indispensable in the study of large-scale life models but often require the use of technically complex lower-level distributed computing frameworks, such as MPI. We propose to overcome the complexity challenge by applying the emerging MapReduce (MR) model to distributed life simulations and by running such simulations on the cloud. Technically, we design optimized MR streaming algorithms for discrete and continuous versions of Conway’s life according to a general MR streaming pattern. We chose life because it is simple enough as a testbed for MR’s applicability to a-life simulations and general enough to make our results applicable to various lattice-based a-life models. We implement and empirically evaluate our algorithms’ performance on Amazon’s Elastic MR cloud. Our experiments demonstrate that a single MR optimization technique called strip partitioning can reduce the execution time of continuous life simulations by 64%. To the best of our knowledge, we are the first to propose and evaluate MR streaming algorithms for lattice-based simulations. Our algorithms can serve as prototypes in the development of novel MR simulation algorithms for large-scale lattice-based a-life models.https://digitalcommons.chapman.edu/scs_books/1014/thumbnail.jp
A complex systems approach to education in Switzerland
The insights gained from the study of complex systems in biological, social, and engineered systems enables us not only to observe and understand, but also to actively design systems which will be capable of successfully coping with complex and dynamically changing situations. The methods and mindset required for this approach have been applied to educational systems with their diverse levels of scale and complexity. Based on the general case made by Yaneer Bar-Yam, this paper applies the complex systems approach to the educational system in Switzerland. It confirms that the complex systems approach is valid. Indeed, many recommendations made for the general case have already been implemented in the Swiss education system. To address existing problems and difficulties, further steps are recommended. This paper contributes to the further establishment complex systems approach by shedding light on an area which concerns us all, which is a frequent topic of discussion and dispute among politicians and the public, where billions of dollars have been spent without achieving the desired results, and where it is difficult to directly derive consequences from actions taken. The analysis of the education system's different levels, their complexity and scale will clarify how such a dynamic system should be approached, and how it can be guided towards the desired performance
Recent advances in petri nets and concurrency
CEUR Workshop Proceeding
MS FT-2-2 7 Orthogonal polynomials and quadrature: Theory, computation, and applications
Quadrature rules find many applications in science and engineering. Their analysis is a classical area of applied mathematics and continues to attract considerable attention. This seminar brings together speakers with expertise in a large variety of quadrature rules. It is the aim of the seminar to provide an overview of recent developments in the analysis of quadrature rules. The computation of error estimates and novel applications also are described
Generalized averaged Gaussian quadrature and applications
A simple numerical method for constructing the optimal generalized averaged Gaussian quadrature formulas will be presented. These formulas exist in many cases in which real positive GaussKronrod formulas do not exist, and can be used as an adequate alternative in order to estimate the error of a Gaussian rule. We also investigate the conditions under which the optimal averaged Gaussian quadrature formulas and their truncated variants are internal
The cell-transmission model : a new look at a dynamic network loading model
Thèse numérisée par la Direction des bibliothèques de l'Université de Montréal