12,064 research outputs found
Quantum Genetics, Quantum Automata and Quantum Computation
The concepts of quantum automata and quantum computation are studied in the context of quantum genetics and genetic networks with nonlinear dynamics. In a previous publication (Baianu,1971a) the formal concept of quantum automaton was introduced and its possible implications for genetic and metabolic activities in living cells and organisms were considered. This was followed by a report on quantum and abstract, symbolic computation based on the theory of categories, functors and natural transformations (Baianu,1971b). The notions of topological semigroup, quantum automaton,or quantum computer, were then suggested with a view to their potential applications to the analogous simulation of biological systems, and especially genetic activities and nonlinear dynamics in genetic networks. Further, detailed studies of nonlinear dynamics in genetic networks were carried out in categories of n-valued, Lukasiewicz Logic Algebras that showed significant dissimilarities (Baianu, 1977) from Bolean models of human neural networks (McCullough and Pitts,1945). Molecular models in terms of categories, functors and natural transformations were then formulated for uni-molecular chemical transformations, multi-molecular chemical and biochemical transformations (Baianu, 1983,2004a). Previous applications of computer modeling, classical automata theory, and relational biology to molecular biology, oncogenesis and medicine were extensively reviewed and several important conclusions were reached regarding both the potential and limitations of the computation-assisted modeling of biological systems, and especially complex organisms such as Homo sapiens sapiens(Baianu,1987). Novel approaches to solving the realization problems of Relational Biology models in Complex System Biology are introduced in terms of natural transformations between functors of such molecular categories. Several applications of such natural transformations of functors were then presented to protein biosynthesis, embryogenesis and nuclear transplant experiments. Other possible realizations in Molecular Biology and Relational Biology of Organisms are here suggested in terms of quantum automata models of Quantum Genetics and Interactomics. Future developments of this novel approach are likely to also include: Fuzzy Relations in Biology and Epigenomics, Relational Biology modeling of Complex Immunological and Hormonal regulatory systems, n-categories and Topoi of Lukasiewicz Logic Algebras and Intuitionistic Logic (Heyting) Algebras for modeling nonlinear dynamics and cognitive processes in complex neural networks that are present in the human brain, as well as stochastic modeling of genetic networks in Lukasiewicz Logic Algebras
Programming Quantum Computers Using Design Automation
Recent developments in quantum hardware indicate that systems featuring more
than 50 physical qubits are within reach. At this scale, classical simulation
will no longer be feasible and there is a possibility that such quantum devices
may outperform even classical supercomputers at certain tasks. With the rapid
growth of qubit numbers and coherence times comes the increasingly difficult
challenge of quantum program compilation. This entails the translation of a
high-level description of a quantum algorithm to hardware-specific low-level
operations which can be carried out by the quantum device. Some parts of the
calculation may still be performed manually due to the lack of efficient
methods. This, in turn, may lead to a design gap, which will prevent the
programming of a quantum computer. In this paper, we discuss the challenges in
fully-automatic quantum compilation. We motivate directions for future research
to tackle these challenges. Yet, with the algorithms and approaches that exist
today, we demonstrate how to automatically perform the quantum programming flow
from algorithm to a physical quantum computer for a simple algorithmic
benchmark, namely the hidden shift problem. We present and use two tool flows
which invoke RevKit. One which is based on ProjectQ and which targets the IBM
Quantum Experience or a local simulator, and one which is based on Microsoft's
quantum programming language Q.Comment: 10 pages, 10 figures. To appear in: Proceedings of Design, Automation
and Test in Europe (DATE 2018
Design Automation and Design Space Exploration for Quantum Computers
A major hurdle to the deployment of quantum linear systems algorithms and
recent quantum simulation algorithms lies in the difficulty to find inexpensive
reversible circuits for arithmetic using existing hand coded methods. Motivated
by recent advances in reversible logic synthesis, we synthesize arithmetic
circuits using classical design automation flows and tools. The combination of
classical and reversible logic synthesis enables the automatic design of large
components in reversible logic starting from well-known hardware description
languages such as Verilog. As a prototype example for our approach we
automatically generate high quality networks for the reciprocal , which is
necessary for quantum linear systems algorithms.Comment: 6 pages, 1 figure, in 2017 Design, Automation & Test in Europe
Conference & Exhibition, DATE 2017, Lausanne, Switzerland, March 27-31, 201
A variational approach to the stochastic aspects of cellular signal transduction
Cellular signaling networks have evolved to cope with intrinsic fluctuations,
coming from the small numbers of constituents, and the environmental noise.
Stochastic chemical kinetics equations govern the way biochemical networks
process noisy signals. The essential difficulty associated with the master
equation approach to solving the stochastic chemical kinetics problem is the
enormous number of ordinary differential equations involved. In this work, we
show how to achieve tremendous reduction in the dimensionality of specific
reaction cascade dynamics by solving variationally an equivalent quantum field
theoretic formulation of stochastic chemical kinetics. The present formulation
avoids cumbersome commutator computations in the derivation of evolution
equations, making more transparent the physical significance of the variational
method. We propose novel time-dependent basis functions which work well over a
wide range of rate parameters. We apply the new basis functions to describe
stochastic signaling in several enzymatic cascades and compare the results so
obtained with those from alternative solution techniques. The variational
ansatz gives probability distributions that agree well with the exact ones,
even when fluctuations are large and discreteness and nonlinearity are
important. A numerical implementation of our technique is many orders of
magnitude more efficient computationally compared with the traditional Monte
Carlo simulation algorithms or the Langevin simulations.Comment: 15 pages, 11 figure
OpenFermion: The Electronic Structure Package for Quantum Computers
Quantum simulation of chemistry and materials is predicted to be an important
application for both near-term and fault-tolerant quantum devices. However, at
present, developing and studying algorithms for these problems can be difficult
due to the prohibitive amount of domain knowledge required in both the area of
chemistry and quantum algorithms. To help bridge this gap and open the field to
more researchers, we have developed the OpenFermion software package
(www.openfermion.org). OpenFermion is an open-source software library written
largely in Python under an Apache 2.0 license, aimed at enabling the simulation
of fermionic models and quantum chemistry problems on quantum hardware.
Beginning with an interface to common electronic structure packages, it
simplifies the translation between a molecular specification and a quantum
circuit for solving or studying the electronic structure problem on a quantum
computer, minimizing the amount of domain expertise required to enter the
field. The package is designed to be extensible and robust, maintaining high
software standards in documentation and testing. This release paper outlines
the key motivations behind design choices in OpenFermion and discusses some
basic OpenFermion functionality which we believe will aid the community in the
development of better quantum algorithms and tools for this exciting area of
research.Comment: 22 page
Quantum Genetics and Quantum Automata Models of Quantum-Molecular Evolution Involved in the Evolution of Organisms and Species
Previous theoretical or general approaches to the problems of Quantum Genetics and Molecular Evolution are considered in this article from the point of view of Quantum Automata Theory first published by the author in 1971 and further developed in several recent articles. The representation of genomes and Interactome networks in categories of many-valued logic LMn –algebras that are naturally transformed during biological evolution, or evolve through interactions with the environment provide a new insight into the mechanisms of molecular evolution, as well as organismal evolution, in terms of sequences of quantum automata. Phenotypic changes are expressed only when certain environmentally-induced quantum-molecular changes are coupled with an internal re-structuring of major submodules of the genome and Interactome networks related to cell cycling and cell growth. Contrary to the commonly held view of `standard’ Darwinist models of evolution, the evolution of organisms and species occurs through coupled multi-molecular transformations induced not only by the environment but actually realized through internal re-organizations of genome and interactome networks. The biological, evolutionary processes involve certain epigenetic transformations that are responsible for phenotypic expression of the genome and Interactome transformations initiated at the quantum-molecular level. It can thus be said that only quantum genetics can provide correct explanations of evolutionary processes that are initiated at the quantum--multi-molecular levels and propagate to the higher levels of organismal and species evolution.

Biological evolution should be therefore regarded as a multi-scale process which is initiated by underlying quantum (coupled) multi-molecular transformations of the genomic and interactomic networks, followed by specific phenotypic transformations at the level of organism and the variable biogroupoids associated with the evolution of species which are essential to the survival of the species. The theoretical framework introduced in this article also paves the way to a Quantitative Biology approach to biological evolution at the quantum-molecular, as well as at the organismal and species levels. This is quite a substantial modification of the 'established’ modern Darwinist, and also of several so-called `molecular evolution’ theories
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