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quant-ph/0009089 | Nikolaos Mavromatos | N.E. Mavromatos (King's College London) | Cell Microtubules as Cavities: Quantum Coherence and Energy Transfer? | 7 pages LATEX. Invited talk at the 2000 International Conference on
Mathematics and Engineering Techniques in Medicine and Biological Sciences,
Monte Carlo Resort, Las Vegas (USA), June 26-29 2000, published in the
proceedings | null | null | null | quant-ph physics.bio-ph | null | A model is presented for dissipationless energy transfer in cell microtubules
due to quantum coherent states. The model is based on conjectured (hydrated)
ferroelectric properties of microtubular arrangements. Ferroelectricity is
essential in providing the necessary isolation against thermal losses in thin
interior regions, full of ordered water, near the tubulin dimer walls of the
microtubule. These play the role of cavity regions, which are similar to
electromagnetic cavities of quantum optics. As a result, the formation of
(macroscopic) quantum coherent states of electric dipoles on the tubulin dimers
may occur. Some experiments, inspired by quantum optics, are suggested for the
falsification of this scenario.
| 2007-05-23 |
quant-ph/0101019 | Dr Matthew J. Donald | Matthew J. Donald | A review of Johnjoe McFadden's book ``Quantum Evolution'' | 11 pages, plain TeX | null | null | null | quant-ph physics.bio-ph | null | In ``Quantum Evolution: Life in the Multiverse'' (HarperCollins, 2000), ISBN
0-00-255948-X, 0-00-655128-9, Johnjoe McFadden makes far-reaching claims for
the importance of quantum physics in the solution of problems in biological
science. In this review, I discuss the relevance of unitary wavefunction
dynamics to biological systems, analyse the inverse quantum Zeno effect, and
argue that McFadden's use of quantum theory is deeply flawed.
| 2007-05-23 |
quant-ph/0102034 | Apoorva D. Patel | Apoorva Patel (CTS and SERC, IISc, Bangalore) | Testing Quantum Dynamics in Genetic Information Processing | 4 pages, latex. (v2) Several points elaborated. Published version,
formatted according to the journal style | Journal of Genetics 80 (2001) 39-43 | null | IISc-CTS-4/01 | quant-ph physics.bio-ph q-bio.GN | null | Does quantum dynamics play a role in DNA replication? What type of tests
would reveal that? Some statistical checks that distinguish classical and
quantum dynamics in DNA replication are proposed.
| 2007-05-23 |
quant-ph/0103017 | Apoorva D. Patel | Apoorva Patel (CTS and SERC, IISc, Bangalore) | Carbon--The First Frontier of Information Processing | (v1) 9 pages, revtex. (v2) 10 pages. Several arguments expanded to
make the article self-contained and to increase clarity. Applications pointed
out. (v3) 11 pages. Published version. Well-known properties of proteins
shifted to an appendix. Reformatted according to journal style | Journal of Biosciences 27 (2002) 207-218 | null | IISc-CTS-8/01 | quant-ph cond-mat physics.bio-ph q-bio.BM | null | Information is often encoded as an aperiodic chain of building blocks. Modern
digital computers use bits as the building blocks, but in general the choice of
building blocks depends on the nature of the information to be encoded. What
are the optimal building blocks to encode structural information? This can be
analysed by substituting the operations of addition and multiplication of
conventional arithmetic with translation and rotation. It is argued that at the
molecular level, the best component for encoding discretised structural
information is carbon. Living organisms discovered this billions of years ago,
and used carbon as the back-bone for constructing proteins that function
according to their structure. Structural analysis of polypeptide chains shows
that an efficient and versatile structural language of 20 building blocks is
needed to implement all the tasks carried out by proteins. Properties of amino
acids indicate that the present triplet genetic code was preceded by a more
primitive one, coding for 10 amino acids using two nucleotide bases.
| 2007-05-23 |
quant-ph/0103085 | Azhar Iqbal | A.Iqbal and A.H.Toor | Darwinism in quantum systems? | Revised in the light of referee's comments. To appear in Physics
Letters A. LaTex, 15 pages, 1 figure | Physics Letters, A 294/5-6 (2002) pp. 261-270 | 10.1016/S0375-9601(02)00067-1 | null | quant-ph nlin.AO physics.bio-ph | null | We investigate the role of quantum mechanical effects in the central
stability concept of evolutionary game theory i.e. an Evolutionarily Stable
Strategy (ESS). Using two and three-player symmetric quantum games we show how
the presence of quantum phenomenon of entanglement can be crucial to decide the
course of evolutionary dynamics in a population of interacting individuals.
| 2009-11-07 |
quant-ph/0105001 | Apoorva D. Patel | Apoorva Patel (CTS and SERC, IISc, Bangalore) | Why Genetic Information Processing could have a Quantum Basis | 6 pages, latex, formatted according to journal style. This is an
introductory article, aimed at biologists. (v2) Minor grammatical changes.
Title slightly modified. Published version | Journal of Biosciences 26 (2001) 145-151 | null | IISc-CTS-5/01 | quant-ph physics.bio-ph q-bio.GN | null | Living organisms are not just random collections of organic molecules. There
is continuous information processing going on in the apparent bouncing around
of molecules of life. Optimisation criteria in this information processing can
be searched for using the laws of physics. Quantum dynamics can explain why
living organisms have 4 nucleotide bases and 20 amino acids, as optimal
solutions of the molecular assembly process. Experiments should be able to tell
whether evolution indeed took advantage of quantum dynamics or not.
| 2007-05-23 |
quant-ph/0106123 | Mikhail Altaisky | M.V.Altaisky and F.P.Filatov | Genetic information and quantum gas | LaTeX, 3 pages | null | null | null | quant-ph physics.bio-ph q-bio.BM | null | Possible explanation of the 64/20 redundancy of the triplet genetic code
based on the assumption of quantum nature of genetic information is proposed.
| 2007-05-23 |
quant-ph/0110084 | H. N. M. Gheorghiu | S. Gheorghiu-Svirschevski | From Davydov solitons to decoherence-free subspaces: self-consistent
propagation of coherent-product states | revtex3, latex2e; 22 pages, no figs.; to appear in Phys.Rev.E
(Nov.2001) | null | 10.1103/PhysRevE.64.051907 | null | quant-ph cond-mat.stat-mech physics.bio-ph | null | The self-consistent propagation of generalized $D_{1}$ [coherent-product]
states and of a class of gaussian density matrix generalizations is examined,
at both zero and finite-temperature, for arbitrary interactions between the
localized lattice (electronic or vibronic) excitations and the phonon modes. It
is shown that in all legitimate cases, the evolution of $D_{1}$ states reduces
to the disentangled evolution of the component $D_{2}$ states. The
self-consistency conditions for the latter amount to conditions for
decoherence-free propagation, which complement the $D_{2}$ Davydov soliton
equations in such a way as to lift the nonlinearity of the evolution for the
on-site degrees of freedom. Although it cannot support Davydov solitons, the
coherent-product ansatz does provide a wide class of exact density-matrix
solutions for the joint evolution of the lattice and phonon bath in compatible
systems. Included are solutions for initial states given as a product of a
[largely arbitrary] lattice state and a thermal equilibrium state of the
phonons. It is also shown that external pumping can produce self-consistent
Frohlich-like effects. A few sample cases of coherent, albeit not solitonic,
propagation are briefly discussed.
| 2009-11-07 |
quant-ph/0202015 | Fariel Shafee | Fariel Shafee | Semiclassical Neural Network | 8 pages 2 figures; new sections and figures added on short term
memory and period | stochastics and dynamics, Vol. 7, No. 3 (2007) 403-416 | null | null | quant-ph cond-mat.dis-nn cs.AI q-bio | null | We have constructed a simple semiclassical model of neural network where
neurons have quantum links with one another in a chosen way and affect one
another in a fashion analogous to action potentials. We have examined the role
of stochasticity introduced by the quantum potential and compare the system
with the classical system of an integrate-and-fire model by Hopfield. Average
periodicity and short term retentivity of input memory are noted.
| 2007-10-11 |
quant-ph/0202016 | Fariel Shafee | Fariel Shafee | Neural Networks with c-NOT Gated Nodes | 4 pages 6 figures; minor corrections made; clearer explanations
added; Engineering Applications of Artificial Intelligence, online Nov 1,
2006 | null | null | null | quant-ph cond-mat.dis-nn cs.AI q-bio | null | We try to design a quantum neural network with qubits instead of classical
neurons with deterministic states, and also with quantum operators replacing
teh classical action potentials. With our choice of gates interconnecting teh
neural lattice, it appears that the state of the system behaves in ways
reflecting both the strengths of coupling between neurons as well as initial
conditions. We find that depending whether there is a threshold for emission
from excited to ground state, the system shows either aperiodic oscillations or
coherent ones with periodicity depending on the strength of coupling.
| 2007-05-23 |
quant-ph/0202022 | Apoorva D. Patel | Apoorva Patel (CTS and SERC, IISc, Bangalore) | Mathematical Physics and Life | 20 pages, latex, Review article to appear in {\it Computing and
Information Sciences: Recent Trends}, ed. J.C.Misra, Narosa Publishing House.
(v2) Typos corrected, published version, p.271-294 (2003) | null | null | IISc-CTS-1/02 | quant-ph cond-mat physics.bio-ph q-bio.BM | null | It is a fascinating subject to explore how well we can understand the
processes of life on the basis of fundamental laws of physics. It is emphasised
that viewing biological processes as manipulation of information extracts their
essential features. This information processing can be analysed using
well-known methods of computer science. The lowest level of biological
information processing, involving DNA and proteins, is the easiest one to link
to physical properties. Physical underpinnings of the genetic information that
could have led to the universal language of 4 nucleotide bases and 20 amino
acids are pointed out. Generalisations of Boolean logic, especially features of
quantum dynamics, play a crucial role.
| 2007-05-23 |
quant-ph/0204021 | Nikolaos Mavromatos | N.E. Mavromatos (King's Coll. London), A. Mershin and D.V. Nanopoulos
(Texas A and M Univ.) | QED-Cavity model of microtubules implies dissipationless energy transfer
and biological quantum teleportation | 20 pages LATEX, three ps figures incorporated | Int. J. Modern Physics B 16 No 24, p3623-3642 (2002) | 10.1142/S0217979202011512 | null | quant-ph cond-mat.dis-nn physics.bio-ph | null | We refine a QED-cavity model of microtubules (MTs), proposed earlier by two
of the authors (N.E.M. and D.V.N.), and suggest mechanisms for the formation of
biomolecular mesoscopic coherent and/or entangled quantum states, which may
avoid decoherence for times comparable to biological characteristic times. This
refined model predicts dissipationless energy transfer along such "shielded"
macromolecules at near room temperatures as well as quantum teleportation of
states across MTs and perhaps neurons.
| 2009-11-07 |
quant-ph/0205161 | Diederik Aerts | Liane Gabora and Diederik Aerts | Contextualizing Concepts using a Mathematical Generalization of the
Quantum Formalism | 44 pages | Journal of Experimental and Theoretical Artificial Intelligence,
14, pp. 327-358 (2002) | null | null | quant-ph cs.AI q-bio.NC | null | We outline the rationale and preliminary results of using the State Context
Property (SCOP) formalism, originally developed as a generalization of quantum
mechanics, to describe the contextual manner in which concepts are evoked,
used, and combined to generate meaning. The quantum formalism was developed to
cope with problems arising in the description of (1) the measurement process,
and (2) the generation of new states with new properties when particles become
entangled. Similar problems arising with concepts motivated the formal
treatment introduced here. Concepts are viewed not as fixed representations,
but entities existing in states of potentiality that require interaction with a
context--a stimulus or another concept--to 'collapse' to an instantiated form
(e.g. exemplar, prototype, or other possibly imaginary instance). The stimulus
situation plays the role of the measurement in physics, acting as context that
induces a change of the cognitive state from superposition state to collapsed
state. The collapsed state is more likely to consist of a conjunction of
concepts for associative than analytic thought because more stimulus or concept
properties take part in the collapse. We provide two contextual measures of
conceptual distance--one using collapse probabilities and the other weighted
properties--and show how they can be applied to conjunctions using the pet fish
problem
| 2013-11-02 |
quant-ph/0206014 | Apoorva D. Patel | Apoorva Patel (CTS and SERC, IISc, Bangalore) | Survival of the Fittest and Zero Sum Games | 6 pages, formatted according to journal style. Special Issue on Game
Theory and Evolutionary Processes. (v2) Published version. Some
clarifications added. Topological interpretation pointed out | Fluctuation and Noise Letters 2 (2002) L279-L284 | null | IISc-CTS-5/02 | quant-ph physics.bio-ph q-bio.PE | null | Competition for available resources is natural amongst coexisting species,
and the fittest contenders dominate over the rest in evolution. The dynamics of
this selection is studied using a simple linear model. It has similarities to
features of quantum computation, in particular conservation laws leading to
destructive interference. Compared to an altruistic scenario, competition
introduces instability and eliminates the weaker species in a finite time.
| 2007-05-23 |
quant-ph/0208068 | Maoxin Wu | Huping Hu, Maoxin Wu | Spin-Mediated Consciousness: Theory, Experimental Studies, Further
Development & Related Topics | 92 pages; expanded content; minor corrections; for additional
information, please visit http://quantumbrain.org | Medical Hypotheses (2004) 63(4): 633-646 | null | BCG-01-2002 | quant-ph cond-mat physics.bio-ph | null | We postulate that consciousness is intrinsically connected to quantum spin
since the latter is the origin of quantum effects in both Bohm and Hestenes
quantum formulisms and a fundamental quantum process associated with the
structure of space-time. Applying these ideas to the particular structures and
dynamics of the brain, we have developed a detailed model of quantum
consciousness. We have also carried out experiments from the perspective of our
theory to test the possibility of quantum-entangling the quantum entities
inside the brain with those of an external chemical substance. We found that
applying magnetic pulses to the brain when an anaesthetic was placed in between
caused the brain to feel the effect of said anaesthetic as if the test subject
had actually inhaled the same. We further found that drinking water exposed to
magnetic pulses, laser light or microwave when an anaesthetic was placed in
between also causes brain effects in various degrees. Additional experiments
indicate that the said brain effect is indeed the consequence of quantum
entanglement. Recently we have studied non-local effects in simple physics
systems. We have found that the pH value, temperature and gravity of a liquid
in the detecting reservoirs can be non-locally affected through manipulating
another liquid in a remote reservoir quantum-entangled with the former. In
particular, the pH value changes in the same direction as that being
manipulated; the temperature can change against that of local environment; and
the gravity can change against local gravity. We suggest that they are mediated
by quantum entanglement between nuclear and/or electron spins in treated liquid
and discuss the profound implications of these results. This paper now also
includes materials on further development of the theory and related topics.
| 2007-11-08 |
quant-ph/0208104 | Martin Lopez Corredoira | M. Lopez-Corredoira | Quantum mechanics and free will: counter-arguments | postscript or pdf, 10 pages, to be published in "The Journal of
Non-Locality and Remote Mental Interactions" | Neuroquantology, 7(3), 449 [2009] | null | null | quant-ph physics.bio-ph physics.pop-ph | null | Since quantum mechanics (QM) was formulated, many voices have claimed this to
be the basis of free will in the human beings. Basically, they argue that free
will is possible because there is an ontological indeterminism in the natural
laws, and that the mind is responsible for the wave function collapse of
matter, which leads to a choice among the different possibilities for the body.
However, I defend the opposite thesis, that free will cannot be defended in
terms of QM. First, because indeterminism does not imply free will, it is
merely a necessary condition but not enough to defend it. Second, because all
considerations about an autonomous mind sending orders to the body is against
our scientific knowledge about human beings; in particular, neither
neurological nor evolutionary theory can admit dualism. The quantum theory of
measurement can be interpreted without the intervention of human minds, but
other fields of science cannot contemplate the mentalist scenario, so it is
concluded that QM has nothing to say about the mind or free will, and its
scientific explanation is more related to biology than to physics. A fatalistic
or materialist view, which denies the possibility of a free will, makes much
more sense in scientific terms.
| 2010-09-07 |
quant-ph/0209047 | Rui Qi | Rui Qi | A quantum method to test the existence of consciousness | 5 pages, no figures | null | null | null | quant-ph physics.bio-ph | null | As we know, "Who can be said to be a conscious being?" is one of the hard
problems in present science, and no method has been found to strictly
differentiate the conscious being from the being without consciousness or usual
matter. In this short paper, we present a strict physical method based on
revised quantum dynamics to test the existence of consciousness, and the
principle is to use the distinguishability of nonorthogonal single states. We
demonstrate that although the dynamical collapse time can't be measured by a
physical measuring device, a conscious being can perceive it under the assumed
QSC condition, thus can distinguish the nonorthogonal single states in the
framework of revised quantum dynamics This in principle provides a quantum
method to differentiate man and machine, or to test the existence of
consciousness. We further discuss the rationality of the assumed QSC condition,
and denote that some experimental evidences have indicated that our human being
can satisfy the condition. This not only provides some confirmation of our
method, but also indicates that the method is a practical proposal, which can
be implemented in the near future experiments.
| 2007-05-23 |
quant-ph/0210176 | Carlo A. Trugenberger | Carlo A. Trugenberger | Quantum Pattern Recognition | Invited Talk at the 1st Feynman Festival, Univ. of Maryland, College
Park, August 2002 | null | null | null | quant-ph cond-mat.dis-nn cs.IR nlin.AO q-bio.NC | null | I review and expand the model of quantum associative memory that I have
recently proposed. In this model binary patterns of n bits are stored in the
quantum superposition of the appropriate subset of the computational basis of n
qbits. Information can be retrieved by performing an input-dependent rotation
of the memory quantum state within this subset and measuring the resulting
state. The amplitudes of this rotated memory state are peaked on those stored
patterns which are closest in Hamming distance to the input, resulting in a
high probability of measuring a memory pattern very similar to it. The accuracy
of pattern recall can be tuned by adjusting a parameter playing the role of an
effective temperature. This model solves the well-known capacity shortage
problem of classical associative memories, providing an exponential improvement
in capacity. The price to pay is the probabilistic nature of information
retrieval, a feature that, however, this model shares with our own brain.
| 2007-05-23 |
quant-ph/0211105 | Marek Czachor | D. Aerts, M. Czachor, L. Gabora, M. Kuna, A. Posiewnik, J. Pykacz, M.
Syty | Quantum morphogenesis: A variation on Thom's catastrophe theory | published version | Phys. Rev. E 67, 051926 (2003) | 10.1103/PhysRevE.67.051926 | null | quant-ph q-bio.QM | null | Non-commutative propositions are characteristic of both quantum and
non-quantum (sociological, biological, psychological) situations. In a Hilbert
space model states, understood as correlations between all the possible
propositions, are represented by density matrices. If systems in question
interact via feedback with environment their dynamics is nonlinear. Nonlinear
evolutions of density matrices lead to phenomena of morphogenesis which may
occur in non-commutative systems. Several explicit exactly solvable models are
presented, including `birth and death of an organism' and `development of
complementary properties'.
| 2009-11-07 |
quant-ph/0301075 | Chris Adami | Charles Ofria (Michigan State University), Christoph Adami (JPL,
Caltech), Travis C. Collier (UCLA) | Selective pressures on genomes in molecular evolution | 16 pages, 3 figures, to be published in J. theor. Biology | J. theor. Biol. 222 (2003) 477-483 | 10.1016/S0022-5193(03)00062-6 | null | quant-ph cs.NE nlin.AO physics.bio-ph q-bio.PE | null | We describe the evolution of macromolecules as an information transmission
process and apply tools from Shannon information theory to it. This allows us
to isolate three independent, competing selective pressures that we term
compression, transmission, and neutrality selection. The first two affect
genome length: the pressure to conserve resources by compressing the code, and
the pressure to acquire additional information that improves the channel,
increasing the rate of information transmission into each offspring. Noisy
transmission channels (replication with mutations) gives rise to a third
pressure that acts on the actual encoding of information; it maximizes the
fraction of mutations that are neutral with respect to the phenotype. This
neutrality selection has important implications for the evolution of
evolvability. We demonstrate each selective pressure in experiments with
digital organisms.
| 2007-05-23 |
quant-ph/0306158 | Apoorva D. Patel | Apoorva Patel (CHEP and SERC, IISc, Bangalore) | Information Processing beyond Quantum Computation | 6 pages, revtex, pedagogical write-up based on talk presented at the
National Conference on Quantum Computing (NQC-2002), Gwalior, October 2002
(v2) Possible directions for future development are pointed out. Presented at
the First World Congress on Lateral Computing (WCLC 2004), Bangalore,
December 2004 | null | null | IISc-CTS-3/03 | quant-ph cond-mat cs.DM physics.bio-ph | null | Recent developments in quantum computation have made it clear that there is a
lot more to computation than the conventional Boolean algebra. Is quantum
computation the most general framework for processing information? Having
gathered the courage to go beyond the traditional definitions, we are now in a
position to answer: Certainly not. The meaning of a message being ``a
collection of building blocks'' can be explored in a variety of situations. A
generalised framework is proposed based on group theory, and it is illustrated
with well-known physical examples. A systematic information theoretical
approach is yet to be developed in many of these situations. Some directions
for future development are pointed out.
| 2007-05-23 |
quant-ph/0401127 | Przemyslaw Gralewicz | P. Gralewicz | Quantum computing in neural networks | Minor changes, improved discussion, added references, 10 pages, 4 eps
figures, LaTeX2e | null | null | null | quant-ph q-bio.NC | null | According to the statistical interpretation of quantum theory, quantum
computers form a distinguished class of probabilistic machines (PMs) by
encoding n qubits in 2n pbits (random binary variables). This raises the
possibility of a large-scale quantum computing using PMs, especially with
neural networks which have the innate capability for probabilistic information
processing. Restricting ourselves to a particular model, we construct and
numerically examine the performance of neural circuits implementing universal
quantum gates. A discussion on the physiological plausibility of proposed
coding scheme is also provided.
| 2007-05-23 |
quant-ph/0401140 | Gombojav Ariunbold O. | G.O. Ariunbold, G.S. Agarwal, Z. Wang, H. Walther and M.O. Scully | Nanosecond Dynamics of Single-Molecule Fluorescence Resonance Energy
Transfer | 8 pages, 1 figure. accepted to J.Phys.Chem.B | null | 10.1021/jp037609h | null | quant-ph physics.bio-ph | null | Motivated by recent experiments on photon statistics from individual dye
pairs planted on biomolecules and coupled by fluorescence resonance energy
transfer (FRET), we show here that the FRET dynamics can be modelled by
Gaussian random processes with colored noise. Using Monte-Carlo numerical
simulations, the photon intensity correlations from the FRET pairs are
calculated, and are turned out to be very close to those observed in
experiment. The proposed stochastic description of FRET is consistent with
existing theories for microscopic dynamics of the biomolecule that carries the
FRET coupled dye pairs.
| 2016-09-28 |
quant-ph/0406157 | Taksu Cheon | Taksu Cheon | Altruistic Contents of Quantum Prisoner's Dilemma | Revised according to publisher's request: 4 pgs, 2 fgs, ReVTeX4. For
more info, go to http://www.mech.kochi-tech.ac.jp/cheon/ | Europhysics Letters 69 (2005) 149-155 | 10.1209/epl/i2004-10343-x | null | quant-ph cond-mat.mes-hall math-ph math.MP q-bio.PE | null | We examine the classical contents of quantum games. It is shown that a
quantum strategy can be interpreted as a classical strategies with effective
density-dependent game matrices composed of transposed matrix elements. In
particular, successful quantum strategies in dilemma games are interpreted in
terms of a symmetrized game matrix that corresponds to an altruistic game plan.
| 2009-02-27 |
quant-ph/0406161 | Giuseppe Vitiello | Eliano Pessa, Giuseppe Vitiello | Quantum noise induced entanglement and chaos in the dissipative quantum
model of brain | 14 pages | Int. J. Mod. Phys. B 18 (2004) 841-858 | 10.1142/S0217979204024045 | null | quant-ph q-bio.OT | null | We discuss some features of the dissipative quantum model of brain in the
frame of the formalism of quantum dissipation. Such a formalism is based on the
doubling of the system degrees of freedom. We show that the doubled modes
account for the quantum noise in the fluctuating random force in the
system-environment coupling. Remarkably, such a noise manifests itself through
the coherent structure of the system ground state. The entanglement of the
system modes with the doubled modes is shown to be permanent in the infinite
volume limit. In such a limit the trajectories in the memory space are
classical chaotic trajectories.
| 2009-11-10 |
quant-ph/0409071 | Ciro Minichini | C. Minichini and A. Sciarrino | Quantum spin model fitting the Yule distribution of oligonucleotides in
DNA | 12 pages, 4 figures | null | null | DSF 29/2004 | quant-ph q-bio.BM | null | A quantum spin chain is identified by the labels of a vector state of a
Kashiwara crystal basis. The intensity of the one-spin flip is assumed to
depend from the variation of the labels. The rank ordered plot of the
numerically computed, averaged in time, transition probabilities is nicely
fitted by a Yule distribution, which is the observed distribution of the ranked
short oligonucleotides frequency in DNA.
| 2007-05-23 |
quant-ph/0412170 | Joel Gilmore | Joel Gilmore and Ross H. McKenzie | Criteria for quantum coherent transfer of excitons between chromophores
in a polar solvent | 5 pages, 2 figures | null | null | null | quant-ph cond-mat.other q-bio.BM q-bio.OT | null | We show that the quantum decoherence of Forster resonant energy transfer
between two optically active molecules can be described by a spin-boson model.
This allows us to give quantitative criteria, in terms of experimentally
measurable system parameters, that are necessary for coherent Bloch
oscillations of excitons between the chromophores. Experimental tests of our
results should be possible with Flourescent Resonant Energy Transfer (FRET)
spectroscopy. Although we focus on the case of protein-pigment complexes our
results are also relevant to quantum dots and organic molecules in a dielectric
medium.
| 2007-05-23 |
quant-ph/0503233 | Taksu Cheon | Taksu Cheon and Izumi Tsutsui | Classical and Quantum Contents of Solvable Game Theory on Hilbert Space | 4 Pages, REVTeX, 3 Figures, 1 Table. Abstract, introduction and
conclusion are revised. For higher resolution figures, go to
http://www.mech.kochi-tech.ac.jp/cheon/index_j.html | Physics Letters A 348 (2006) 147-152 | 10.1016/j.physleta.2005.08.066 | null | quant-ph cond-mat.other math-ph math.MP nlin.CD nlin.SI physics.bio-ph | null | A simple and general formulation of the quantum game theory is presented,
accommodating all possible strategies in the Hilbert space for the first time.
The theory is solvable for the two strategy quantum game, which is shown to be
equivalent to a family of classical games supplemented by quantum interference.
Our formulation gives a clear perspective to understand why and how quantum
strategies outmaneuver classical strategies. It also reveals novel aspects of
quantum games such as the stone-scissor-paper phase sub-game and the
fluctuation-induced moderation.
| 2016-09-08 |
quant-ph/0509042 | Fred Thaheld H | Fred H. Thaheld | Does consciousness really collapse the wave function? A possible
objective biophysical resolution of the measurement problem | 36 pages, 5 figures, Comment and references added to Sec. 4 regarding
whether Spontaneous Localization or decoherence can lead to a single
subjective outcome in the visual cortex | BioSystems 81 (2005) 113-124 | null | null | quant-ph q-bio.NC | null | An analysis has been performed of the theories and postulates advanced by von
Neumann, London and Bauer, and Wigner, concerning the role that consciousness
might play in the collapse of the wave function, which has become known as the
measurement problem. This reveals that an error may have been made by them in
the area of biology and its interface with quantum mechanics, when they called
for the reduction of any superposition states in the brain through the mind or
consciousness. Many years later Wigner changed his mind to reflect a simpler
and more realistic objective position, expanded upon by Shimony, which appears
to offer a way to resolve this issue. The argument is therefore made that the
wave function of any superposed photon state or states is always objectively
changed within the complex architecture of the eye in a continuous linear
process initially for most of the superposed photons, followed by a
discontinuous nonlinear collapse process later for any remaining superposed
photons, thereby guaranteeing that only final, measured information is
presented to the brain, mind or consciousness. An experiment to be conducted in
the near future may enable us to simultaneously resolve the measurement problem
and also determine if the linear nature of quantum mechanics is violated by the
perceptual process.
| 2007-05-23 |
quant-ph/0602144 | Tetsuo Matsui | Takashi Hiramatsu, Tetsuo Matsui, and Kazuhiko Sakakibara | Self-Reduction Rate of a Microtubule | 7 pages, 9 figures, Extended version | International Journal of Modern Physics C19(2008)291-305. | 10.1142/S0129183108012194 | null | quant-ph q-bio.NC q-bio.SC | null | We formulate and study a quantum field theory of a microtubule, a basic
element of living cells. Following the quantum theory of consciousness by
Hameroff and Penrose, we let the system to reduce to one of the classical
states without measurement if certain conditions are
satisfied(self-reductions), and calculate the self-reduction time $\tau_N$ (the
mean interval between two successive self-reductions) of a cluster consisting
of more than $N$ neighboring tubulins (basic units composing a microtubule).
$\tau_N$ is interpreted there as an instance of the stream of consciousness. We
analyze the dependence of $\tau_N$ upon $N$ and the initial conditions, etc.
For relatively large electron hopping amplitude, $\tau_N$ obeys a power law
$\tau_N \sim N^b$, which can be explained by the percolation theory. For
sufficiently small values of the electron hopping amplitude, $\tau_N$ obeys an
exponential law, $\tau_N \sim \exp(c' N)$. By using this law, we estimate the
condition for $\tau_N $ to take realistic values $\tau_N$
\raisebox{-0.5ex}{$\stackrel{>}{\sim}$} $10^{-1}$ sec as $N$ \raisebox{-0.5ex}
{$\stackrel{>}{\sim}$} 1000.
| 2008-09-08 |
quant-ph/0602190 | Fred Thaheld H | Fred H. Thaheld | Comment on "Experimental motivation and empirical consistency in minimal
no-collapse quantum mechanics" | A comment on quant-ph/0506199 v3, 5 pages | null | null | null | quant-ph q-bio.NC | null | Schlosshauer has advanced a theory of minimal no-collapse quantum mechanics
for a decoherence-based subjective resolution of the measurement problem. The
basic premise being that superposition states are maintained beyond the retinal
apparatus, becoming correlated with neuronal arrays located in the occipital
lobe of the brain. Decoherence for these neurons in a superposition of firing
and resting, leads to an irreversible dynamical decoupling of the two branches,
resulting in the emergence of a single subjective perception. Based upon prior
retinal research, it is shown that his theory is untenable for several reasons.
| 2007-05-23 |
quant-ph/0604181 | Fred Thaheld H | Fred H. Thaheld | The argument for an objective wave function collapse: Why spontaneous
localization collapse or no-collapse decoherence cannot solve the measurement
problem in a subjective fashion | 8 pages, no figures | null | null | null | quant-ph physics.bio-ph | null | A more detailed analysis of the measurement problem continues to support the
position taken by Shimony and the author that collapse of the wave function
takes place in an objective manner in the rhodopsin molecule of the retina.
This casts further doubts on the theories involving a spontaneous localization
collapse process or a no-collapse decoherence process taking place in the
visual cortex in a subjective fashion. The possibility is then raised, as per
Anandan, as to whether the solution of the measurement problem in quantum
theory allows one to address the problem of quantizing gravitation.
| 2007-05-23 |
quant-ph/0607127 | Fred Thaheld H | Fred H. Thaheld | A modified approach to the measurement problem: Objective reduction in
the retinal molecule prior to conformational change | 8 pages. A new theory is advanced where the collapse of the wave
function now takes place within the retinal molecule, specifically the
retinal chromophore. This occurs prior to any retinal molecule conformational
change and before any CSL-type reduction mechanism in the retinal rod cells | BioSystems 92 (2008) 114-116 | null | null | quant-ph physics.bio-ph | null | A new analysis of the measurement problem reveals the possibility that
collapse of the wavefunction may now take place just before photoisomerization
of the rhodopsin molecule in the retinal rods. It is known that when a photon
is initially absorbed by the retinal molecule which, along with opsin comprises
the rhodopsin molecule, an electron in the highest pi orbital is immediately
excited to a pi* orbital. This means that a measurement or transfer of
information takes place at the quantum level before the retinal molecule
commences the conformational change from cis to trans. This could have profound
implications for resolving some of the foundational issues confronting quantum
mechanics.
| 2008-04-17 |
quant-ph/0609216 | Rolando Somma | Rolando D. Somma, Cristian D. Batista, Gerardo Ortiz | A Quantum Approach to Classical Statistical Mechanics | 4 pages, no figures | null | 10.1103/PhysRevLett.99.030603 | null | quant-ph cond-mat.other cond-mat.stat-mech q-bio.OT | null | We present a new approach to study the thermodynamic properties of
$d$-dimensional classical systems by reducing the problem to the computation of
ground state properties of a $d$-dimensional quantum model. This
classical-to-quantum mapping allows us to deal with standard optimization
methods, such as simulated and quantum annealing, on an equal basis.
Consequently, we extend the quantum annealing method to simulate classical
systems at finite temperatures. Using the adiabatic theorem of quantum
mechanics, we derive the rates to assure convergence to the optimal
thermodynamic state. For simulated and quantum annealing, we obtain the
asymptotic rates of $T(t) \approx (p N) /(k_B \log t)$ and $\gamma(t) \approx
(Nt)^{-\bar{c}/N}$, for the temperature and magnetic field, respectively. Other
annealing strategies, as well as their potential speed-up, are also discussed.
| 2009-11-13 |
quant-ph/9907009 | Max Tegmark | Max Tegmark | The importance of quantum decoherence in brain processes | Minor changes to match accepted PRE version. 15 pages with 5 figs
included. Color figures and links at
http://www.physics.upenn.edu/~max/brain.html or from [email protected].
Physical Review E, in press | Phys.Rev.E61:4194-4206,2000 | 10.1103/PhysRevE.61.4194 | null | quant-ph cond-mat.dis-nn cs.NE physics.bio-ph q-bio | null | Based on a calculation of neural decoherence rates, we argue that that the
degrees of freedom of the human brain that relate to cognitive processes should
be thought of as a classical rather than quantum system, i.e., that there is
nothing fundamentally wrong with the current classical approach to neural
network simulations. We find that the decoherence timescales ~10^{-13}-10^{-20}
seconds are typically much shorter than the relevant dynamical timescales
(~0.001-0.1 seconds), both for regular neuron firing and for kink-like
polarization excitations in microtubules. This conclusion disagrees with
suggestions by Penrose and others that the brain acts as a quantum computer,
and that quantum coherence is related to consciousness in a fundamental way.
| 2009-10-07 |
quant-ph/9912070 | Giuseppe Vitiello | Eliano Pessa and Giuseppe Vitiello | Quantum dissipation and neural net dynamics | latex file Published: Bioelectrochemistry and Bioenergetics,
48:339-342, 1999 | Bioelectrochem.Bioenerg 48 (1999) 339-342 | null | null | quant-ph cond-mat.other hep-th physics.bio-ph q-bio.OT | null | Inspired by the dissipative quantum model of brain, we model the states of
neural nets in terms of collective modes by the help of the formalism of
Quantum Field Theory. We exhibit an explicit neural net model which allows to
memorize a sequence of several informations without reciprocal destructive
interference, namely we solve the overprinting problem in such a way last
registered information does not destroy the ones previously registered.
Moreover, the net is able to recall not only the last registered information in
the sequence, but also anyone of those previously registered.
| 2007-05-23 |
quant-ph/9912120 | Matteo Beccaria | Eleonora Alfinito and Giuseppe Vitiello | Life-time and hierarchy of memory in the dissipative quantum model of
brain | 4pages, no figures, paper accepted for publication in the JCIS 2000
Proceedings | null | 10.1142/S0217979200001734 | null | quant-ph cond-mat nlin.AO physics.bio-ph q-bio | null | Some recent developments of the dissipative quantum model of brain are
reported. In particular, the time-dependent frequency case is considered with
its implications on the different life-times of the collective modes.
| 2009-10-31 |
solv-int/9807001 | Juhi-Lian Julian Ting | Julian Juhi-Lian Ting | DNA Transcription Mechanism with a Moving Enzyme | paper published long time ago. 11 pages RevTeX 4 EPS files | Int. J. Bifurcat. Chaos.7:5, 1125-1132 (1997) | null | null | solv-int nlin.SI q-bio | null | Previous numerical investigations of an one-dimensional DNA model with an
extended modified coupling constant by transcripting enzyme are integrated to
longer time and demonstrated explicitly the trapping of breathers by DNA chains
with realistic parameters obtained from experiments. Furthermore, collective
coordinate method is used to explain a previously observed numerical evidence
that breathers placed far from defects are difficult to trap, and the motional
effect of RNA-polymerase is investigated.
| 2021-01-21 |
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