Urs P. Wild, Alois Renn · 1991
Each dye molecule embedded in an amorphous material such as a a polymer host experiences a specific molecular environment which strongly influences its electronic transition energies. At low temperatures the different microenvironments result in an inhomogeneously broadened absorption band. The invention of the laser brought new spectroscopic techniques based on energy selection, such as fluorescence line narrowing and spectral hole-burning [1]. These techniques enable convenient addressing of thousands of molecular subsets selected by their transition energy.
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Soichiro Tsuda · 2014
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Weng-Long Chang, Athanasios V. Vasilakos · Studies in big data · 2014
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Michael Conrad · Advances in computers · 1990
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Soichiro Tsuda · 2016
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Donald Beaver · 2007
We design a molecular Turing machine and determine the complexity of the problems solvable by molecular computers. In [A94], a combinatorial molecular experiment to solve the NP-complete problem of Hamiltonian Path was proposed and implemented. Using our design, we show that such molecular computers can in fact compute PSPACE, under the generous assumptions implicit in [A94]. Under stronger and somewhat more practical restrictions, which [A94] fails to satisfy, we show that molecular computers are limited to solving problems in P. 1 Introduction Molecular and quantum computers have recently been considered as alternatives to standard models such as Turing machines, PRAM's, or logical circuits [S94, Si94, A94, B94]. Shor has shown that quantum computers can factor large numbers and calculate discrete logarithms in polynomial time, even though no known polynomial-time algorithm is known [S94]. Adleman has proposed a molecular "computer" that solves the NPcomplete Hamiltonian Path proble...
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Max Garzón, Sambriddhi Mainali · 2022
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Yaakov Benenson, Ehud Shapiro · 2004
Biopolymers such as nucleic acids and proteins encode biological data and may be viewed as strings of chemical letters. While electronic computers manipulate strings of 0’s and 1’s encoded in electric signals, biologically encoded data might, in principle, be manipulated by biochemical means. During the last decade, several approaches to compute with biomolecules were developed, and the field has become known as biomolecular or DNA computing. The approaches varied widely with respect to the model of computation they employed, the problems they attempted to solve, and the degree of human intervention. One approach focused on the application of the Turing machine model and, more generally, string-processing automata to biomolecular information processing. Its goal is to construct computers made of biomolecules that are capable of autonomous conversion of an input dataencoding molecule to an output molecule according to a set of rules defined by a molecular program. Here we survey the field of biomolecular computing machines and discuss possible future directions.
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Konrad Szaciłowski · 2012
This chapter contains sections titled: Introduction Reconfigurable and Superimposed Molecular Logic Devices Concatenated Chemical Logic Systems Molecular-Scale Digital Communication Molecular Arithmetics: Adders and Subtractors Molecular-Scale Security Systems Noise and Error Propagation in Concatenated Systems References
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Max Garzón, Russell Deaton, John A. Rose · DIMACS series in discrete mathematics and theoretical computer science · 2000
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Masami Hagiya · Lecture notes in computer science · 2001
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Masami Hagiya · 2001
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Wataru Yahiro, Nathanaël Aubert-Kato, Masami Hagiya · 2018
In this paper, we apply the Polymerase-Exonuclease-Nickase Dynamic Network Assembly (PEN DNA) toolbox, a modular framework for molecular computing, to reservoir computing. While reservoir computing...
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James M. Tour, Dustin K. James · 2018
This chapter discusses several general architectural approaches that researchers are considering to build computers based on molecular-scale electronics and the advances made in these several areas in the years 1998 to 2001. It focuses upon the progress made in measuring the electrical characteristics of molecular switches and in designing logic devices using molecular electronics components. Technology development and industrial competition have been driving the semiconductor industry to produce smaller, faster, and more powerful logic devices. Carbon nanotubes are known to exhibit either metallic or semiconductor properties. Avouris and coworkers at IBM have developed a method of engineering both multiwalled nanotubes and single-walled carbon nanotubes using electrical breakdown methods. Molecular electronics as a field of research is rapidly expanding with almost weekly announcements of new discoveries and breakthroughs. Many cycles of testing and feedback analysis must occur with a working nanocell before we know the programming of the nanocell is successful.
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A. Prasanna de Silva, Seiichi Uchiyama · Nature Nanotechnology · 2007
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James Pustell · Nucleic Acids Research · 1988
It is clear that the selection of the best possible algorithm for a computer program is essential for the creation of a useful tool. After this first step is taken, however, the usefulness of such a program may be greatly enhanced or impeded by the way it is implemented. We illustrate this point by describing our implementation of the well known FASTP/FASTIN algorithm in an interactive software environment.
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Milan N. Stojanović · Progress in nucleic acid research and molecular biology · 2008
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Milan N. Stojanović, Darko Stefanović, Sergei Rudchenko · Accounts of Chemical Research · 2014
CONSPECTUS: The successes of electronic digital logic have transformed every aspect of human life over the last half-century. The word "computer" now signifies a ubiquitous electronic device, rather than a human occupation. Yet evidently humans, large assemblies of molecules, can compute, and it has been a thrilling challenge to develop smaller, simpler, synthetic assemblies of molecules that can do useful computation. When we say that molecules compute, what we usually mean is that such molecules respond to certain inputs, for example, the presence or absence of other molecules, in a precisely defined but potentially complex fashion. The simplest way for a chemist to think about computing molecules is as sensors that can integrate the presence or absence of multiple analytes into a change in a single reporting property. Here we review several forms of molecular computing developed in our laboratories. When we began our work, combinatorial approaches to using DNA for computing were used to search for solutions to constraint satisfaction problems. We chose to work instead on logic circuits, building bottom-up from units based on catalytic nucleic acids, focusing on DNA secondary structures in the design of individual circuit elements, and reserving the combinatorial opportunities of DNA for the representation of multiple signals propagating in a large circuit. Such circuit design directly corresponds to the intuition about sensors transforming the detection of analytes into reporting properties. While this approach was unusual at the time, it has been adopted since by other groups working on biomolecular computing with different nucleic acid chemistries. We created logic gates by modularly combining deoxyribozymes (DNA-based enzymes cleaving or combining other oligonucleotides), in the role of reporting elements, with stem-loops as input detection elements. For instance, a deoxyribozyme that normally exhibits an oligonucleotide substrate recognition region is modified such that a stem-loop closes onto the substrate recognition region, making it unavailable for the substrate and thus rendering the deoxyribozyme inactive. But a conformational change can then be induced by an input oligonucleotide, complementary to the loop, to open the stem, allow the substrate to bind, and allow its cleavage to proceed, which is eventually reported via fluorescence. In this Account, several designs of this form are reviewed, along with their application in the construction of large circuits that exhibited complex logical and temporal relationships between the inputs and the outputs. Intelligent (in the sense of being capable of nontrivial information processing) theranostic (therapy + diagnostic) applications have always been the ultimate motivation for developing computing (i.e., decision-making) circuits, and we review our experiments with logic-gate elements bound to cell surfaces that evaluate the proximal presence of multiple markers on lymphocytes.
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Alys Hugo, Douglas J. Baxter, William R. Cannon et al. · 2012
We report the development of a novel high performance computing method for the identification of proteins from unknown (environmental) samples. The method uses computational optimization to provide an effective way to control the false discovery rate for environmental samples and complements de novo peptide sequencing. Furthermore, the method provides information based on the expressed protein in a microbial community, and thus complements DNA-based identification methods. Testing on blind samples demonstrates that the method provides 79-95 % overlap with analogous results from searches involving only the correct genomes. We provide scaling and performance evaluations for the software that demonstrate the ability to carry out large-scale optimizations on 1258 genomes containing 4.2M proteins. 1.
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Bin Fu, Richard Beigel · Biosystems · 1999
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