AU Raymo, FM
TI Digital processing and communication with molecular switches
SO ADVANCED MATERIALS
AB Molecular switches based on chemical, electrical, or optical
   stimulations are a hot topic as they can provide the future for
   faster computers and internet applications. Basic logic
   operations of AND, NOT, and OR gates have been reproduced
   relying on simple molecular switches (see Figure). The
   fabrication of nanoelectronic circuits and all-optical networks
   from molecular components can be envisaged.
BP 401
EP +
PG 15
JI Adv. Mater.
PY 2002
PD MAR 18
VL 14
IS 6

AU Benenson, Y
   Paz-Elizur, T
   Adar, R
   Keinan, E
   Livneh, Z
   Shapiro, E
TI Programmable and autonomous computing machine made of
   biomolecules
SO NATURE
AB Devices that convert information from one form into another
   according to a definite procedure are known as automata. One
   such hypothetical device is the universal Turing machine(1),
   which stimulated work leading to the development of modern
   computers. The Turing machine and its special cases(2),
   including finite automata(3), operate by scanning a data tape,
   whose striking analogy to information-encoding biopolymers
   inspired several designs for molecular DNA computers(4-8).
   Laboratory-scale computing using DNA and human-assisted
   protocols has been demonstrated(9-15), but the realization of
   computing devices operating autonomously on the molecular scale
   remains rare(16-20). Here we describe a programmable finite
   automaton comprising DNA and DNA-manipulating enzymes that
   solves computational problems autonomously. The automaton's
   hardware consists of a restriction nuclease and ligase, the
   software and input are encoded by double-stranded DNA, and
   programming amounts to choosing appropriate software molecules.
   Upon mixing solutions containing these components, the
   automaton processes the input molecule via a cascade of
   restriction, hybridization and ligation cycles, producing a
   detectable output molecule that encodes the automaton's final
   state, and thus the computational result. In our implementation
   10(12) automata sharing the same software run independently and
   in parallel on inputs (which could, in principle, be distinct)
   in 120 mul solution at room temperature at a combined rate of
   10(9) transitions per second with a transition fidelity greater
   than 99.8%, consuming less than 10(-10) W.
BP 430
EP 434
PG 5
JI Nature
PY 2001
PD NOV 22
VL 414
IS 6862

AU Dongarra, JJ
   Walker, DW
TI The quest for petascale computing
SO COMPUTING IN SCIENCE & ENGINEERING
AB Although the challenges to achieving petascale computing within
   the next decade are daunting, several software and hardware
   technologies are emerging that could help us reach this goal.
   The authors review these technologies and consider new
   algorithms capable of exploiting a petascale computer's
   architecture.
BP 32
EP 39
PG 8
JI Comput. Sci. Eng.
PY 2001
PD MAY-JUN
VL 3
IS 3

AU Marrow, P
TI Nature-inspired computing technology and applications
SO BT TECHNOLOGY JOURNAL
AB Increasing demands upon current computer systems, along with
   technological changes, create a need for more flexible and
   adaptable systems. Natural systems provide many examples of the
   type of versatile system required This paper reviews examples
   of nature-inspired computing, drawing inspiration from many
   different areas of living systems including evolution, ecology,
   development and behaviour. The implications for the future
   development of computing technology and applications are also
   discussed
BP 13
EP 23
PG 11
JI BT Technol. J.
PY 2000
PD OCT
VL 18
IS 4

AU Krishnamurthy, V
   Krishnamurthy, EV
TI Rule-based programming paradigm: a formal basis for biological,
   chemical and physical computation
SO BIOSYSTEMS
AB A rule-based programming paradigm is described as a formal
   basis for biological, chemical and physical computations. In
   this paradigm, the computations are interpreted as the outcome
   arising out of interaction of elements in an object space. The
   interactions can create new elements (or same elements with
   modified attributes) or annihilate old elements according to
   specific rules. Since the interaction rules are inherently
   parallel, any number of actions can be performed cooperatively
   or competitively among the subsets of elements, so that the
   elements evolve toward an equilibrium or unstable or chaotic
   state. Such an evolution may retain certain invariant
   properties of the attributes of the elements. The object space
   resembles Gibbsian ensemble that corresponds to a distribution
   of points in the space of positions and momenta (called phase
   space). It permits the introduction of probabilities in rule
   applications. As each element of the ensemble changes over
   time, its phase point is carried into a new phase point. The
   evolution of this probability cloud in phase space corresponds
   to a distributed probabilistic computation. Thus, this paradigm
   can handle tor deterministic exact computation when the initial
   conditions are exactly specified and the trajectory of
   evolution is deterministic. Also, it can handle probabilistic
   mode of computation if we want to derive macroscopic or bulk
   properties of matter. We also explain how to support this rule-
   based paradigm using relational-database like query processing
   and transactions. (C) 1999 Elsevier Science Ireland Ltd. All
   rights reserved.
BP 205
EP 228
PG 24
JI Biosystems
PY 1999
PD MAR
VL 49
IS 3

AU Lusth, JC
   Dixon, B
TI A characterization of important algorithms for quantum-dot
   cellular automata
SO INFORMATION SCIENCES
AB Feature sizes in chip manufacturing are becoming so small that
   quantum mechanical behavior will. soon have a deleterious
   effect on the function of devices. Quantum-dot cellular
   automats (QDCA) have been proposed as computing devices which
   are helped, rather than hindered, by the quantum behavior of
   electrons. QDCA compute by relaxing to a configuration of
   minimal energy. Previously, it has been shown that a quantum-
   dot device may not compute properly if all of its relaxed
   configurations are not equal in energy level. Such an automaton
   is termed unbalanced. A necessary condition for an automaton to
   be balanced is that the number of distinguished configurations
   with minimum energy should equal the number of input
   combinations the automaton handles. Does an efficient algorithm
   for determining the number of distinguished ground states
   exist? If so, it will be difficult to find, as such an
   algorithm is shown to be NP-hard. Furthermore, the related
   problem of determining the minimum energy level of arbitrary
   automata is also shown to be NP-hard, These results have
   important implications for simulating and analyzing QDCA on
   conventional computers. (C) 1999 Elsevier Science Inc. All
   rights reserved.
BP 193
EP 204
PG 12
JI Inf. Sci.
PY 1999
PD FEB
VL 113
IS 3-4

AU Heath, JR
   Kuekes, PJ
   Snider, GS
   Williams, RS
TI A defect-tolerant computer architecture: Opportunities for
   nanotechnology
SO SCIENCE
AB Teramac is a massively parallel experimental computer built at
   Hewlett-Packard Laboratories to investigate a wide range of
   different computational architectures. This machine contains
   about 220,000 hardware defects, any one of which could prove
   fatal to a conventional computer, and yet it operated 100 times
   faster than a high-end single-processor workstation for some of
   its configurations. The defect-tolerant architecture of
   Teramac, which incorporates a high communication bandwith that
   enables it to easily route around defects, has significant
   implications for any future nanometer-scale computational
   paradigm. It may be feasible to chemically synthesize
   individual electronic components with less than a 100 percent
   yield, assemble them into systems with appreciable uncertainty
   in their connectivity, and still create a powerful and reliable
   data communications network. Future nanoscale computers may
   consist of extremely large-configuration memories that are
   programmed for specific tasks by a tutor that locates and tags
   the defects in the system.
BP 1716
EP 1721
PG 6
JI Science
PY 1998
PD JUN 12
VL 280
IS 5370

AU Pirrung, MC
   Connors, RV
   Montague-Smith, MP
TI Design and use of a solid phase DNA-based computational device
   to solve satisfiability (SAT) problems
SO FASEB JOURNAL
BP 2090
PG 1
JI Faseb J.
PY 1997
PD JUL 31
VL 11
IS 9
SU S