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

Cumulative index to NASA Tech Briefs, 1986-1990, volumes 10-14

Tech Briefs are short announcements of new technology derived from the R&D activities of the National Aeronautics and Space Administration. These briefs emphasize information considered likely to be transferrable across industrial, regional, or disciplinary lines and are issued to encourage commercial application. This cumulative index of Tech Briefs contains abstracts and four indexes (subject, personal author, originating center, and Tech Brief number) and covers the period 1986 to 1990. The abstract section is organized by the following subject categories: electronic components and circuits, electronic systems, physical sciences, materials, computer programs, life sciences, mechanics, machinery, fabrication technology, and mathematics and information sciences

An Initial Framework Assessing the Safety of Complex Systems

Trabajo presentado en la Conference on Complex Systems, celebrada online del 7 al 11 de diciembre de 2020.Atmospheric blocking events, that is large-scale nearly stationary atmospheric pressure patterns, are often associated with extreme weather in the mid-latitudes, such as heat waves and cold spells which have significant consequences on ecosystems, human health and economy. The high impact of blocking events has motivated numerous studies. However, there is not yet a comprehensive theory explaining their onset, maintenance and decay and their numerical prediction remains a challenge. In recent years, a number of studies have successfully employed complex network descriptions of fluid transport to characterize dynamical patterns in geophysical flows. The aim of the current work is to investigate the potential of so called Lagrangian flow networks for the detection and perhaps forecasting of atmospheric blocking events. The network is constructed by associating nodes to regions of the atmosphere and establishing links based on the flux of material between these nodes during a given time interval. One can then use effective tools and metrics developed in the context of graph theory to explore the atmospheric flow properties. In particular, Ser-Giacomi et al. [1] showed how optimal paths in a Lagrangian flow network highlight distinctive circulation patterns associated with atmospheric blocking events. We extend these results by studying the behavior of selected network measures (such as degree, entropy and harmonic closeness centrality)at the onset of and during blocking situations, demonstrating their ability to trace the spatio-temporal characteristics of these events.This research was conducted as part of the CAFE (Climate Advanced Forecasting of sub-seasonal Extremes) Innovative Training Network which has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 813844

Microfluidics and Nanofluidics Handbook

The Microfluidics and Nanofluidics Handbook: Two-Volume Set comprehensively captures the cross-disciplinary breadth of the fields of micro- and nanofluidics, which encompass the biological sciences, chemistry, physics and engineering applications. To fill the knowledge gap between engineering and the basic sciences, the editors pulled together key individuals, well known in their respective areas, to author chapters that help graduate students, scientists, and practicing engineers understand the overall area of microfluidics and nanofluidics. Topics covered include Finite Volume Method for Numerical Simulation Lattice Boltzmann Method and Its Applications in Microfluidics Microparticle and Nanoparticle Manipulation Methane Solubility Enhancement in Water Confined to Nanoscale Pores Volume Two: Fabrication, Implementation, and Applications focuses on topics related to experimental and numerical methods. It also covers fabrication and applications in a variety of areas, from aerospace to biological systems. Reflecting the inherent nature of microfluidics and nanofluidics, the book includes as much interdisciplinary knowledge as possible. It provides the fundamental science background for newcomers and advanced techniques and concepts for experienced researchers and professionals

Laboratory directed research and development. FY 1995 progress report

This document presents an overview of Laboratory Directed Research and Development Programs at Los Alamos. The nine technical disciplines in which research is described include materials, engineering and base technologies, plasma, fluids, and particle beams, chemistry, mathematics and computational science, atmic and molecular physics, geoscience, space science, and astrophysics, nuclear and particle physics, and biosciences. Brief descriptions are provided in the above programs

NASA patent abstracts bibliography: A continuing bibliography. Section 2: Indexes (supplement 46)

A subject index is provided for over 5600 patents and patent applications for the period May 1969 through December 1994. Additional indexes list personal authors, corporate authors, contract numbers, NASA case numbers, U.S. patent class numbers, U.S. patent numbers, and NASA accession numbers