WorldCat Identities

Winfree, Erik 1969-

Overview
Works: 26 works in 59 publications in 1 language and 370 library holdings
Genres: Conference proceedings  Academic theses 
Roles: Editor, Thesis advisor, Author
Classifications: QA76.618, 511.3
Publication Timeline
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Most widely held works by Erik Winfree
Evolution as computation : DIMACS workshop, Princeton, January 1999 by Laura F Landweber( Book )

10 editions published between 2000 and 2013 in English and held by 127 WorldCat member libraries worldwide

The study of the genetic basis for evolution has flourished in this century, as well as our understanding of the evolvability and programmability of biological systems. Genetic algorithms meanwhile grew out of the realization that a computer program could use the biologically-inspired processes of mutation, recombination, and selection to solve hard optimization problems. Genetic and evolutionary programming provide further approaches to a wide variety of computational problems. A synthesis of these experiences reveals fundamental insights into both the computational nature of biological evolution and processes of importance to computer science. Topics include biological models of nucleic acid information processing and genome evolution; molecules, cells, and metabolic circuits that compute logical relationships; the origin and evolution of the genetic code; and the interface with genetic algorithms, genetic and evolutionary programming. This research combines theory and experiments to understand the computations that take place in cells and the combinatorial processes that drive evolution at the molecular level
DNA Based Computers V : DIMACS Workshop DNA Based Computers V, June 14-15, 1999, Massachusetts Institute of Technology by DIMACS Workshop on DNA Based Computers( Book )

7 editions published in 2000 in English and held by 125 WorldCat member libraries worldwide

Algorithmic bioprocesses by Anne Condon( )

9 editions published between 2009 and 2013 in English and Undetermined and held by 47 WorldCat member libraries worldwide

Offers a comprehensive overview of research into algorithmic self-assembly, RNA folding, the algorithmic foundations for biochemical reactions, and the algorithmic nature of developmental processes. This book addresses subjects such as sequence discovery, generation, and analysis; nanoconstructions and self-assembly; and membrane computing
Beyond Watson and Crick : programming the self-assembly and reconfiguration of DNA nanostructures based on stacking interactions by Sungwook Woo( )

2 editions published in 2013 in English and held by 2 WorldCat member libraries worldwide

Dynamic DNA strand displacement circuits by David Yu Zhang( )

2 editions published in 2010 in English and held by 2 WorldCat member libraries worldwide

Algorithms for nucleic acid sequence design by Joseph N Zadeh( Book )

2 editions published in 2010 in English and held by 2 WorldCat member libraries worldwide

Information processing in the interaural time difference pathway of the barn owl by Gestur Bjorn Christianson( Book )

1 edition published in 2006 in English and held by 2 WorldCat member libraries worldwide

Stochastic simulation of the kinetics of multiple interacting nucleic acid strands by Joseph Malcolm Schaeffer( Book )

2 editions published in 2013 in Undetermined and held by 2 WorldCat member libraries worldwide

The Self-Replication and Evolution of DNA Crystals by Rebecca Schulman( )

2 editions published in 2007 in English and held by 2 WorldCat member libraries worldwide

Compiling and verifying DNA-based chemical reaction network implementations by Seung Woo Shin( )

2 editions published in 2011 in English and held by 2 WorldCat member libraries worldwide

"One goal of molecular programming and synthetic biology is to build chemical circuits that can control chemical processes at the molecular level. Remarkably, it has been shown that synthesized DNA molecules can be used to construct complex chemical circuits that operate without any enzyme or cellular component. However, designing DNA molecules at the individual nucleotide base level is often difficult and laborious, and thus chemical reaction networks (CRNs) have been proposed as a higher-level programming language. So far, several general-purpose schemes have been described for designing synthetic DNA molecules that simulate the behavior of arbitrary CRNs, and many more are being actively investigated."
Olfactory object recognition and generalization in the insect brain by Kai Shen( )

2 editions published in 2010 in English and held by 2 WorldCat member libraries worldwide

Sensory object recognition is the most fundamental of operations performed by the brain. A key computational difficulty of object recognition is that it requires both selectivity to particular objects (e.g., exact odor mixture identification) and generalization across objects (identifying particular features or components common to different odors). Although previous results (1) suggest that odor identity and intensity are represented in the activity of both PNs and KCs, it is not clear how these representations generalize across complex odor mixtures. In particular, it is not clear what types of information are available in KC population (or if its even possible to decode across KC populations?) and how is this information represented? Using the locust olfactory system as a model system, we found that Kenyon cells (KCs), the principal neurons of the mushroom body, an area required for associative learning can identify the presence of components in mixtures and thus enable odor segmentation. As a population, small groups of KCs can both identify and categorize odors with high accuracy. We identified and tested simple circuit requirements for this computation, and propose that odor representations in mushroom bodies are optimized for odor memorization, identification and generalization. These rules may be relevant for pattern classifying circuits in general
Gene regulatory circuit dynamics : analysis and synthesis by Joseph H Levine( )

2 editions published in 2012 in English and held by 2 WorldCat member libraries worldwide

How can cells shape and utilize dynamic gene regulation to enable complex cellular behaviors? I study this question in natural and synthetic contexts. The first project studies how a natural genetic network can imbue cells with a sense of 'time'. The second project proposes a method to rapidly generate and test complex genetic network dynamics in living cells
The multistrand simulator : stochastic simulation of the kinetics of multiple interacting DNA strands by Joseph Malcolm Schaeffer( Book )

2 editions published in 2012 in English and held by 2 WorldCat member libraries worldwide

Networks of relations by Matthew M Cook( Book )

1 edition published in 2005 in English and held by 2 WorldCat member libraries worldwide

Crystals that count! : physical principles and experimental investigations of DNA tile self-assembly by Constantine Glen Evans( )

2 editions published in 2014 in English and held by 2 WorldCat member libraries worldwide

Algorithmic DNA tiles systems are fascinating. From a theoretical perspective, they can result in simple systems that assemble themselves into beautiful, complex structures through fundamental interactions and logical rules. As an experimental technique, they provide a promising method for programmably assembling complex, precise crystals that can grow to considerable size while retaining nanoscale resolution. In the journey from theoretical abstractions to experimental demonstrations, however, lie numerous challenges and complications. In this thesis, to examine these challenges, we consider the physical principles behind DNA tile self-assembly
Algorithmic Self-Assembly of DNA: Theoretical Motivations and 2D Assembly Experiments by Erik Winfree( )

1 edition published in 2000 in Undetermined and held by 1 WorldCat member library worldwide

Biology makes things far smaller and more complex than anything produced by human engineering. The biotechnology revolution has for the first time given us the tools necessary to consider engineering on the molecular level. Research in DNA computation, launched by Len Adleman, has opened the door for experimental study of programmable biochemical reactions. Here we focus on a single biochemical mechanism, the self-assembly of DNA structures, that is theoretically sufficient for Turing-universal computation. The theory combines Hao Wang?s purely mathematical Tiling Problem with the branched DNA constructions of Ned Seeman. In the context of mathematical logic, Wang showed how jigsaw-shaped tiles can be designed to simulate the operation of any Turing Machine. For a biochemical implementation, we will need molecular Wang tiles. DNA molecular structures and intermolecular interactions are particularly amenable to design and are sufficient for the creation of complex molecular objects. The structure of individual molecules can be designed by maximizing desired and minimizing undesired Watson-Crick complementarity. Intermolecular interactions are programmed by the design of sticky ends that determine which molecules associate, and how. The theory has been demonstrated experimentally using a system of synthetic DNA double-crossover molecules that self-assemble into two-dimensional crystals that have been visualized by atomic force microscopy. This experimental system provides an excellent platform for exploring the relationship between computation and molecular self-assembly, and thus represents a first step toward the ability to program molecular reactions and molecular structures
Algorithmic self-assembly of DNA by Erik Winfree( Book )

1 edition published in 1998 in English and held by 1 WorldCat member library worldwide

Molecules computing : self-assembled nanostructures, molecular automata, and chemical reaction networks by David Soloveichik( Book )

1 edition published in 2008 in English and held by 1 WorldCat member library worldwide

Algorithmic self-assembly of DNA by Erik Winfree( )

1 edition published in 1998 in Undetermined and held by 1 WorldCat member library worldwide

How can molecules compute? In his early studies of reversible computation, Bennett imagined an enzymatic Turing Machine which modified a hetero-polymer (such as DNA) to perform computation with asymptotically low energy expenditures. Adleman's recent experimental demonstration of a DNA computation, using an entirely different approach, has led to a wealth of ideas for how to build DNA-based computers in the laboratory, whose energy efficiency, information density, and parallelism may have potential to surpass conventional electronic computers for some purposes. In this thesis, I examine one mechanism used in all designs for DNA-based computer -- the self-assembly of DNA by hybridization and formation of the double helix -- and show that this mechanism alone in theory can perform universal computation. To do so, I borrow an important result in the mathematical theory of tiling: Wang showed how jigsaw-shaped tiles can be designed to simulate the operation of any Turing Machine. I propose constructing molecular Wang tiles using the branched DNA constructions of Seeman, thereby producing self-assembled and algorithmically patterned two-dimensional lattices of DNA. Simulations of plausible self-assembly kinetics suggest that low error rates can be obtained near the melting temperature of the lattice; under these conditions, self-assembly is performing reversible computation with asymptotically low energy expenditures. Thus encouraged, I have begun an experimental investigation of algorithmic self-assembly. A competition experiment suggests that an individual logical step can proceed correctly by self-assembly, while a companion experiment demonstrates that unpatterned two dimensional lattices of DNA will self-assemble and can be visualized. We have reason to hope, therefore, that this experimental system will prove fruitful for investigating issues in the physics of computation by self-assembly. It may also lead to interesting new materials
Algorithmic Self-Assembly of DNA by Erik Winfree( Book )

1 edition published in 2006 in Undetermined and held by 1 WorldCat member library worldwide

Nucleic acids have proven to be remarkably versatile as an engineering material for chemical tasks including the storage of information, catalyzing reactions creating and breaking bonds, mechanical manipulation using molecular motors, and constructing supramolecular structures. This talk will focus particularly on molecular self-assembly, giving examples of engineered DNA "tiles" that crystallize into two-dimensional sheets, one-dimensional tubes and ribbons, and information-guided patterns such as a Sierpinski triangle and a binary counter. A theme is how cooperative binding can be used to control nucleation and direct selective tile attachment. Such "algorithmic" self-assembly may provide a bottom-up fabrication method for creating complex, well-defined supramolecular structures that can be used as scaffolds or templates for applications such as arranging molecular electronic components into active circuits
 
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Evolution as computation : DIMACS workshop, Princeton, January 1999
Alternative Names
Erik Winfree American computer scientist

Languages
English (47)

Covers
DNA Based Computers V : DIMACS Workshop DNA Based Computers V, June 14-15, 1999, Massachusetts Institute of TechnologyAlgorithmic bioprocesses