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> DNA 'Music.", see also: DNA Grammar. DNA, Structure of.
Warren Bonesteel
post May 29, 2006, 08:46 AM
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http://news.bbc.co.uk/1/hi/sci/tech/222591.stm
By BBC News Online Science Editor Dr David Whitehouse
Advances in the science of biotechnology are breathtaking. We have the ability to read the information encoded in DNA, the blueprint of life, and can even manipulate the building blocks of life themselves.

Listen to the sound of DNA

But as science advances there are some that take a different view of this progress, regarding it not with the eye of a scientist but from the viewpoint of an artist.

Susan Alexjander holds an MA in music, which she teaches in Sacramento, California. Her compositions are fusing science and art, producing music that is a collaboration between her and DNA itself.

"Sound and the body interested me," she says, "so did maths, physics and their relationship with sound. Because of this, I started collecting frequencies in nature."

Melodic atoms

She asked if the movements of the atoms and molecules that make up our DNA could be recorded and heard. If so, what would they sound like? Random noise? Melodic?

Susan Alexjander: The music sounds alive
She wanted to measure the actual molecular vibrations of DNA. So she approached University of California biologist Dr David Deamer and discovered it was actually quite easy to do.

The vibrations were easily measurable using an infrared spectrophotometer. By exposing each section of DNA to infrared light and measuring the wavelength of the light absorbed, it was possible to determine distinctive frequencies for each DNA molecule.

But how to turn them into music?

"I wanted to go inside the chemistry and hear the frequencies. I did the science with Dr David Deamer and then the artist's hat went on."

Frequency combination

The ratios of the light frequencies were converted into ratios of sound. The relative relationship between light frequencies was kept. The result was strange, beautiful music.

Susan Alexjander: Some people have a deep reaction to the music
"Some of the combinations of frequencies," Alexjander adds, "are just stunning. I find it very arresting. It sounds alive to me."

Most of the changes of pitches in her DNA music are microtonal - that is, their frequencies occur in the area between the half-tone steps of the western musical scale.

Microtonal pitches are nothing new in music, however. Some cultures have a long history of their use, especially those of India and the Middle and Far East.

These sounds from the molecular world are remarkable. They may mean something - they may mean nothing.

Alexjander says her music produces a strong reaction. She speculates: "Perhaps on a very deep level the body recognises itself - hears something familiar in the music. It's a theory. I don't know."

The music is available on CD from Science and the Arts, PO Box 428, Aptos, California 95010, USA

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Warren Bonesteel
post May 29, 2006, 08:47 AM
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http://www.oursounduniverse.com/infraredfreq.html
In 1988 the author and biologist Dr. David Deamer collaborated on a science/art project which consisted of measuring the vibrational frequencies of the four DNA base molecules, translating them into 'sound,' programming them into a Yamaha synthesizer and using this tuning system as the basis for original compositions entitled Sequencia (1990 and '94 CD). The realization of biological, infrared frequencies into sound has resulted in unusual insights into the harmonic fabric of DNA, and reactions from listeners suggest that our bodies may have a way of recognizing their own electromagnetic patterns through the resonance of tone.
"See deep enough, and you see musically;
the heart of Nature being everywhere music,
if you can only reach it."
Thomas Carlyle



http://www.toshima.ne.jp/~edogiku/index.html
Genes and music are two heritable systems that underlie our life. Both of them are made of linear and quantized information. I try to explore the correspondence and metaphor between them by converting gene (DNA, RNA and protein) sequences to MIDI sequences. Hopefully, gene music can capture and inspire appreciation of the diversity, mystery and beauty of life.
http://www.toshima.ne.jp/~edogiku/FlaMov05...xMicroTGV1.html
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Warren Bonesteel
post May 29, 2006, 08:48 AM
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http://algoart.com/music.htm
Genetic Music From DNA and Protein
The music on this page was composed algorithmically with Algorithmic Arts software from the raw genetic data that is available as free downloads on the internet .
Currently there are 3 CD albums available, with more to follow. On this page, you can either audition or download the full tracks as free .mp3 files.


http://www.aber.ac.uk/~phiwww/pm/
ProteinMusic is a Java program converting DNA sequences into music. The original idea for this project came from R. D. King here at the University of Wales, Aberystwyth and C. G Angus from the Shamen (King, R.D. & Angus, C.G. (1996)). They developed a program written in C on an Apple Mac together with a MIDI connection to a synthesizer in 1996. This program here is a complete re-write of the original program in Java.



http://ndbserver.rutgers.edu/atlas/music/musical_atlas.html
ATLAS: The Musical Atlas
The Nucleic Acid Database has been developing different musical algorithms to provide a unique look into the structure of DNA.


http://www.botany.hawaii.edu/faculty/bridg...nflections/mp3/
Music from DNA by John Dunn and K. W. Bridges



http://www.helenwhitehead.com/Dissert/genetic17.htm
You wouldn't think there was music in me. But beautiful and strange music has been developed from the sequence of nucleotides in my DNA.
Using special software John Dunn selected and/or developed synthesizer sounds to be used to create music by translating the individual DNA codons, the strings of guanine, adenine, cytosine and thymine, into the proteins they form, taking account of "start" and "stop" signals.
The amino acids of each protein sequence plus chemical properties of the amino acids and the bases themselves were interpreted as pitches, pan positions, transpose values, tempi, tone, colors and so on. The realization of the piece was developed manually, until the piece was right.



http://www.dnamusic.com/articles/music_and_metamusic.htm
Hidden right there in plain sight is one of the most profound truths of our existence. From ancient Hindu mystics to modern quantum physicists the collective wisdom of humankind has repeatedly discovered that the universe is an immense energy field vibrating on a score of frequencies. No matter how we separate the individual notes, they all play together to create a single harmonious song.[2]
The Bible, so central to the beliefs of many Western cultures, tells us that “In the beginning was the Word.” Yet many Eastern and aboriginal cultures maintain that the world was not spoken, but, rather, SUNG into existence. For a growing number of scientists, their research into the impacts of music on the brain and consciousness now favors the influence of song over speech. In fact, quantum string theory describes our bodies, all physical matter, and even the Earth itself, as cosmic instruments staying in tune with a larger universal orchestra.



http://www.artic.edu/~pgena/genexs.html
Peter Dena: DNA music for Genesis



http://www.artic.edu/~pgena/DNAmus.html
The physio-musical conversion of DNA sequences occurs via a series of formulae that were worked out in a manner based on physical properties of DNA and musical parameters. Once the sequences are converted by my custom algorithms they are played by the DNA Mixer, which reads linearly much like the ribosomes—organelles that read codons for amino acid conversion—traverse the mRNA, mixing multiple sequences simultaneously just like in our cells.

From the onset I believed that a musical reading of DNA ought to be rendered literally. As the sequences represent life of many sorts, I am reluctant to tamper with the “score.” The DNA mixer can realize sequences as digital sound and/or print them out in musical notation. Ideally, performances of the gene sequences should be executed live from the computer as in an installation, where the ribosome simulations can be positioned spontaneously before playing. Red Blood Cells is a mix of five genes that are present in human blood: alpha and beta globin, heme synthetase, transaldolase, and glucose 6 phosphate. These are realized simultaneously, just as they are produced in the body. The piece was premiered in November, 1995 at the XI Colloquium on Musical Informatics at the University of Bologna. In May, 1996 it was aired over Icelandic National Radio during a series on American Electronic Music, and in August of the same year it was presented in Hong Kong at the 1996 International Computer Music Conference.

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Warren Bonesteel
post May 29, 2006, 08:48 AM
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http://www.nslij-genetics.org/dnamusic/
DNA and music?? What is the connection? And why is it included in a page on correlation structure of DNA sequences? Because: the correlation stucture "1/f spectra" have been found in both musical signals and DNA sequences.

Prof. Susumu Ohno (of Beckman Research Institute of the City of Hope, who died on January 13, 2000, at the age of 71) proposed years ago that the repetition process governs both the musical composition and the DNA sequence construction . see this paper by Ohno in Immunogenetics (1986) titled: "The all pervasive principle of repetitious recurrence governs not only coding sequence construction but also human endeavor in musical composition".

when DNA sequences are converted to music, it sounds musical!

models with duplication and mutation operations, such as the "expansion-modification model" are able to generate sequences with 1/f spectra.


http://whozoo.org/mac/Music/
Human protein sequences from the Gene Project Reports at Texas Wesleyan University
Projects for 2001
Projects for 2002
Note: all of the sequences from the links immediately above are simple linear readouts of the amino acid sequences of the proteins indicated. However some sense of the protein's higher order structure emerges from the alternation between the higher-pitched polar amino acids and the lower-pitched nonpolar amino acids. http://whozoo.org/mac/Music/samples.htm


http://www.molecularmusic.com/
The site for music derived from the molecules of life.
Listen to mp3 clips of music derived from herbs, medicinal plants and the human body. Visit our online education section with a preview version of Molecular Music's first interactive exhibit currently showing at Bristol.

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Warren Bonesteel
post May 29, 2006, 08:51 AM
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http://www.fractal.org/Life-Science-Techno...ter-Gariaev.htm
In order to achieve success in our attempts to treat various medical problems and curb the processes of human aging, it is clearly necessary to understand the languages by which cells communicate. To some extent, those of us who have pioneered the field of "wave-genetics" have managed to accomplish this. It appears that the languages we were looking for exist, in fact, in the 98% or "junk" DNA contained in our own genetic apparatus. The foundational principle of these genetic languages is similar to the language of holographic images as well as texts constructed from human speech



http://www.rialian.com/rnboyd/dna-phantom.htm
Original Research: Poponin, V., The DNA Phantom Effect: Direct Measurement of a New field in the Vacuum Substructure, unpublished laboratory notes, 1995. Duplicating Experiments: Poponin,V.V. and Gariaev, P., Vacuum DNA Phantom Effect In Vitro and its Possible Rational Explanation, Nanobiology, 1995.
http://www.plasmacosmology.net/electric.html
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Warren Bonesteel
post May 29, 2006, 08:53 AM
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http://www.fosar-bludorf.com
DNA
The human DNA is a biological Internet and superior in many aspects to
the artificial one. The latest Russian scientific research directly or
indirectly explains phenomena such as clairvoyance, intuition,
spontaneous and remote acts of healing, self healing, affirmation
techniques, unusual light-auras around people (namely spiritual
masters), mind's influence on weather-patterns and much more. In
addition, there is evidence for a whole new type of medicine in which
DNA can be influenced and reprogrammed by words and frequencies WITHOUT
cutting out and replacing single genes.

Only 10% of our DNA is being used for building proteins. It is this
subset of DNA that is of interest to western researchers and is being
examined and categorized. The other 90% are considered "junk DNA". The
Russian researchers, however, convinced that nature was not dumb,
joined linguists and geneticists in a venture to explore those 90% of "junk
DNA". Their results, findings and conclusions are simply revolutionary!
According to them, our DNA is not only responsible for the construction
of our body, but also serves as data storage and in communication. The
Russian linguists found that the genetic code, especially in the
apparently useless 90%, follows the same rules as all our human
languages. To this end they compared the rules of syntax (the way in
which words are put together to form phrases and sentences), semantics
(the study of meaning in language forms) and the basic rules of
grammar.
They found that the alkalines of our DNA follow a regular grammar and
do have set rules just like our languages. So human languages did not
appear coincidentally but are a reflection of our inherent DNA.
The Russian biophysici stand molecular biologist Pjotr Garjajev and his
colleagues also explored the vibrational behaviour of the DNA. [For the
sake of brevity I will give only a summary here. For further
exploration please refer to the appendix at the end of this article.] The bottom
line was: "Living chromosomes function just like solitonic-holographic
computers using the endogenous DNA laser radiation." This means that
they managed for example to modulate certain frequency patterns onto a
laser ray and with it influenced the DNA frequency and thus the genetic
information itself. Since the basic structure of DNA-alkaline pairs and
of language (as explained earlier) are of the same structure, no DNA
decoding is necessary. One can simply use words and sentences of the
human language! This, too, was experimentally proven! Living DNA
substance (in living tissue, not in vitro) will always react to
language-modulated laser rays and even to radio waves, if the proper
frequencies are being used. This finally and scientifically explains
why affirmations, autogenous training, hypnosis and the like can have such
strong effects on humans and their bodies. It is entirely normal and
natural for our DNA to react to language. While western researchers cut
single genes from the DNA strands and insert them elsewhere, the
Russians enthusiastically worked on devices that can influence the
cellular metabolism through suitable modulated radio and light
frequencies and thus repair genetic defects.

Garjajev's research group succeeded in proving that with this method
chromosomes damaged by x-rays for example can be repaired. They even
captured information patterns of a particular DNA and transmitted it
onto another, thus reprogramming cells to another genome. So they
successfully transformed, for example, frog embryos to salamander
embryos simply by transmitting the DNA information patterns! This way
the entire information was transmitted without any of the side effects
or disharmonies encountered when cutting out and re-introducing single
genes from the DNA. This represents an unbelievable, world-transforming
revolution and sensation! All this by simply applying vibration and
language instead of the archaic cutting-out procedure! This experiment
points to the immense power of wave genetics, which obviously has a
greater influence on the formation of organisms than the biochemical
processes of alkaline sequences. Esoteric and spiritual teachers have
known for ages that our body is programmable by language, words and
thought. This has now been scientifically proven and explained. Of
course the frequency has to be correct. And this is why not everybody
is equally successful or can do it with always the same strength. The
individual person must work on the inner processes and maturity in
order to establish a conscious communication with the DNA. The Russian
researchers work on a method that is not dependent on these factors but
will ALWAYS work, provided one uses the correct frequency.

But the higher developed an individual's consciousness is, the less
need is there for any type of device! One can achieve these results by
oneself, and science will finally stop to laugh at such ideas and will
confirm and explain the results. And it doesn't end there. The Russian
scientists also found out that our DNA can cause disturbing patterns in
the vacuum, thus producing magnetized wormholes! Wormholes are the
microscopic equivalents of the so-called Einstein-Rosen bridges in the
vicinity of black holes (left by burned-out stars). These are tunnel
connections between entirely different areas in the universe through
which information can be transmitted outside of space and time. The DNA
attracts these bits of information and passes them on to our
consciousness. This process of hypercommunication is most effective in
a state of relaxation. Stress, worries or a hyperactive intellect prevent
successful hypercommunication or the information will be totally
distorted and useless. In nature hypercommunication has been
successfully applied for millions of years. The organized flow of life
in insect states proves this dramatically.

Modern man knows it only on a much more subtle level, as "intuition".
But we, too, can regain full use of it. An example from Nature: When a
queen ant is spatially separated from her colony, building still
continues fervently and according to plan. If the queen is killed,
however, all work in the colony stops. No ant knows what to do.
Apparently the queen sends the "building plans" also from far away via
the group consciousness of her subjects. She can be as far away as she
wants, as long as she is alive. In man hypercommunication is most often
encountered when one suddenly gains access to information that is
outside one's knowledge base. Such hypercommunication is then
experienced as inspiration or intuition. The Italian composer Giuseppe
Tartini for instance dreamt one night that a devil sat at his bedside
playing the violin. The next morning Tartini was able to note down the
piece exactly from memory, he called it the Devil's Trill Sonata. For
years, a 42-year old male nurse dreamt of a situation in which he was
hooked up to a kind of knowledge CD-ROM. Verifiable knowledge from all
imaginable fields was then transmitted to him that he was able to
recall in the morning. There was such a flood of information that it seemed a
whole encyclopaedia was transmitted at night. The majority of facts
were outside his personal knowledge base and reached technical details about
which he knew absolutely nothing.

When hypercommunication occurs, one can observe in the DNA as well as
in the human being special phenomena. The Russian scientists irradiated
DNA samples with laser light. On screen a typical wave pattern was formed.
When they removed the DNA sample, the wave pattern did not disappear,
it remained. Many control experiments showed that the pattern still came
from the removed sample, whose energy field apparently remained by
itself. This effect is now called phantom DNA effect. It is surmised
that energy from outside of space and time still flows through the
activated wormholes after the DNA was removed. The side effect
encountered most often in hypercommunication also in human beings are
inexplicable electromagnetic fields in the vicinity of the persons
concerned. Electronic devices like CD players and the like can be
irritated and cease to function for hours. When the electromagnetic
field slowly dissipates, the devices function normally again. Many
healers and psychics know this effect from their work. The better the
atmosphere and the energy, the more frustrating it is that the
recording device stops functioning and recording exactly at that moment. And
repeated switching on and off after the session does not restore
function yet, but next morning all is back to normal. Perhaps this is
reassuring to read for many, as it has nothing to do with them being
technically inept, it means they are good at hypercommunication.
In their book Vernetzte Intelligenz (Networked Intelligence), Grazyna
Gosar and Franz Bludorf explain these connections precisely and
clearly.
The authors also quote sources presuming that in earlier times humanity
had been, just like the animals, very strongly connected to the group
consciousness and acted as a group. To develop and experience
individuality we humans however had to forget hypercommunication almost
completely. Now that we are fairly stable in our individual
consciousness, we can create a new form of group consciousness, namely
one, in which we attain access to all information via our DNA, without
being forced or remotely controlled about what to do with that
information. We now know that just as on the internet our DNA can feed
its proper data into the network, can call up data from the network and
can establish contact with other participants in the network. Remote
healing, telepathy or "remote sensing" about the state of relatives
etc. can thus be explained. Some animals know also from afar when their
owners plan to return home. That can be freshly interpreted and
explained via the concepts of group consciousness and
hypercommunication.

Any collective consciousness cannot be sensibly used over any period of
time without a distinctive individuality. Otherwise we would revert to
a primitive herd instinct that is easily manipulated. Hypercommunication
in the new millennium means something quite different:
Researchers think that if humans with full individuality would regain
group consciousness, they would have a god-like power to create, alter
and shape things on Earth! [I am overjoyed. Finally orders from the
Universe are scientifically explained!!!] AND humanity is collectively
moving toward such a group consciousness of the new kind. Fifty percent
of today's children will be problem children as soon as they go to
school. The system lumps everyone together and demands adjustment. But
the individuality of today's children is so strong that that they
refuse this adjustment and giving up their idiosyncrasies in the most diverse
ways. At the same time more and more clairvoyant children are born [see
the book Chinas Indigo Children by Paul Dong or the chapter about
Indigos in my book Nutze die taeglichen Wunder (Make Use of the Daily
Wonders)]. Something in those children is striving more and more
towards the group consciousness of the new kind, and it will no longer be
suppressed. As a rule, weather for example is rather difficult to
influence by a single individual. But it may be influenced by a group
consciousness (nothing new to some tribes doing it in their rain
dances). Weather is strongly influenced by Earth resonance frequencies,
the so-called Schumann frequencies. But those same frequencies are also
produced in our brains, and when many people synchronise their
thinking, or individuals (spiritual masters, for instance) focus their thoughts
in a laser-like fashion, then it is scientifically speaking not at all
surprising if they can thus influence weather.

Researchers in group consciousness have formulated the theory of Type I
civilisations. A humanity that developed a group consciousness of the
new kind would have neither environmental problems nor scarcity of
energy. For if it were to use its mental power as a unified
civilisation, it would have control of the energies of its home planet
as a natural consequence. And that includes all natural catastrophes!!!
A theoretical Type II civilisation would even be able to control all
energies of their home galaxy. In my book Nutze die taeglichen Wunder I
have described an example of this: Whenever a great many people focus
their attention or consciousness on something similar like Christmas
time, football world championship or the funeral of Lady Diana in
England then certain random number generators in computers start to
deliver ordered numbers instead of the random ones. An ordered group
consciousness creates order in its whole surroundings!!!

When a great number of people get together very closely, potentials of
violence also dissolve. It looks as if here, too, a kind of
humanitarian consciousness of all humanity is created. At the Love Parade, for
example, where every year about one million of young people congregate,
there has never been any brutal riots as they occur for instance at
sports events. The name of the event alone is not seen as the cause
here. The result of an analysis indicated rather that the number of
people was TOO GREAT to allow a tipping over to violence. To come back
to the DNA: It apparently is also an organic superconductor that can
work at normal body temperature. Artificial superconductors require
extremely low temperatures of between 200 and 140°C to function. As one
recently learned, all superconductors are able to store light and thus
information. This is a further explanation of how the DNA can store
information. There is another phenomenon linked to DNA and wormholes.
Normally, these supersmall wormholes are highly unstable and are
maintained only for the tiniest fractions of a second. Under certain
conditions (read about it in the Fosar/Bludorf book above) stable
wormholes can organise themselves which then form distinctive vacuum
domains in which for example gravity can transform into electricity.
Vacuum domains are self-radiant balls of ionised gas that contain
considerable amounts of energy. There are regions in Russia where such
radiant balls appear very often. Following the ensuing confusion the
Russians started massive research programmes leading finally to some of
the discoveries mentions above. Many people know vacuum domains as
shiny balls in the sky. The attentive look at them in wonder and ask
themselves, what they could be. I thought once: "Hello up there. If you
happen to be a UFO, fly in a triangle." And suddenly, the light balls
moved in a triangle. Or they shot across the sky like ice hockey pucks.
They accelerated from zero to crazy speeds while sliding gently across
the sky.

One is left gawking and I have, as many others, too, thought them to be
UFOs. Friendly ones, apparently, as they flew in triangles just to
please me. Now the Russians found in the regions, where vacuum domains
appear often that sometimes fly as balls of light from the ground
upwards into the sky, that these balls can be guided by thought. One
has found out since that vacuum domains emit waves of low frequency as they
are also produced in our brains. And because of this similarity of
waves they are able to react to our thoughts. To run excitedly into one that
is on ground level might not be such a great idea, because those balls
of light can contain immense energies and are able to mutate our genes.
They can, they don't necessarily have to, one has to say. For many
spiritual teachers also produce such visible balls or columns of light
in deep meditation or during energy work which trigger decidedly
pleasant feelings and do not cause any harm. Apparently this is also
dependent on some inner order and on the quality and provenance of the
vacuum domain. There are some spiritual teachers (the young Englishman
Ananda, for example) with whom nothing is seen at first, but when one
tries to take a photograph while they sit and speak or meditate in
hypercommunication, one gets only a picture of a white cloud on a
chair.
In some Earth healing projects such light effects also appear on
photographs. Simply put, these phenomena have to do with gravity and
anti-gravity forces that are also exactly described in the book and
with ever more stable wormholes and hypercommunication and thus with
energies from outside our time and space structure. Earlier generations that got
in contact with such hypercommunication experiences and visible vacuum
domains were convinced that an angel had appeared before them. And we
cannot be too sure to what forms of consciousness we can get access
when using hypercommunication.

Not having scientific proof for their actual existence (people having
had such experiences do NOT all suffer from hallucinations) does not
mean that there is no metaphysical background to it. We have simply
made another giant step towards understanding our reality. Official science
also knows of gravity anomalies on Earth (that contribute to the
formation of vacuum domains), but only of ones of below one percent.
But recently gravity anomalies have been found of between three and four
percent. One of these places is Rocca di Papa, south of Rome (exact
location in the book Vernetzte Intelligenz plus several others). Round
objects of all kinds, from balls to full buses, roll uphill. But the
stretch in Rocca di Papa is rather short, and defying logic sceptics
still flee to the theory of optical illusion (which it cannot be due to
several features of the location).

All informations are from the book ""Vernetzte Intelligenz" von Grazyna
Fosar und Franz Bludorf ISBN 3930243237, summarized and commented by
Baerbel.

The book is unfortunately only available in German so far. You can reach
the authors here: http://www.fosar-bludorf.com
<http://www.fosar-bludorf.com/>
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Warren Bonesteel
post May 29, 2006, 08:55 AM
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http://www.cymatics.org.uk/

From June 19 to 25, 2005, Dr. Anthony Fleming will attend the 27th annual meeting of Bioelectromagnetics Society (BEMS) in Dublin. Dr. Fleming will present findings of an acoustic therapy device, the Cyma 1000, successfully trialed on thoroughbred racehorses. The work presents the photon and the phonon as two particles having the same structure, but a different propagation vector. The phonon is orthogonal to the photon of equivalent energy. The phonon has the important advantage of being able to penetrate far deeper into biological tissues than EM radiation. Delivery of precise frequencies enable control over the DNA bases during replication. This can be used to promote healing within injured tissues. The method is a generic process for a number of different important therapies




Spin resonance in DNA


http://www.biophysj.org/cgi/content/full/81/2/1195
Biophys J, August 2001, p. 1195-1204, Vol. 81, No. 2
Substrate Binding to DNA Photolyase Studied by Electron Paramagnetic Resonance Spectroscopy

Structural changes in Escherichia coli DNA photolyase induced by binding of a (cis,syn)-cyclobutane pyrimidine dimer (CPD) are studied by continuous-wave electron paramagnetic resonance and electron-nuclear double resonance spectroscopies, using the flavin adenine dinucleotide (FAD) cofactor in its neutral radical form as a naturally occurring electron spin probe. The electron paramagnetic resonance/electron-nuclear double resonance spectral changes are consistent with a large distance ( 0.6 nm) between the CPD lesion and the 7,8-dimethyl isoalloxazine ring of FAD, as was predicted by recent model calculations on photolyase enzyme-substrate complexes. Small shifts of the isotropic proton hyperfine coupling constants within the FAD's isoalloxazine moiety can be understood in terms of the cofactor binding site becoming more nonpolar because of the displacement of water molecules upon CPD docking to the enzyme. Molecular orbital calculations of hyperfine couplings using density functional theory, in conjunction with an isodensity polarized continuum model, are presented to rationalize these shifts in terms of the changed polarity of the medium surrounding the FAD cofa



http://www.etsu.edu/physics/yuripub.htm
Publications (last 10 years)
Y. Razskazovskiy, M. G. Debije, S. B. Howerton, L. D. Williams, W. A. Bernhard, Strand breaks produced in X-irradiated crystalline DNA: Alternating CG-oligomers. Radiat. Res. In Press (2003)

Y. Razskazovskiy, M. G. Debije, W. A. Bernhard, Strand breaks produced in X-irradiated crystalline DNA: Influence of base sequence. Radiat. Res 159, 663-669 (2003)

Y. Razskazovskiy, Radiation-activated nuclease activity of o,o‘-diphenyleneiodononium cations (DPI): A reductively initiated chain reaction involving the C1‘-chemistry. Radiat. Res. 159, 543-549 (2003)

Y. Razskazovskiy, M. G. Debije, W. A. Bernhard, The yield of strand breaks resulting from direct-type effects in crystalline DNA X-irradiated at 4 K and room temperature. J. Am. Chem. Soc. 123, 2917-2918 (2001)

Y. Razskazovskiy, M. G. Debije, W. A. Bernhard, Direct radiation damage to crystalline DNA: What is the source of unaltered base release? Radiat. Res. 153, 436-441 (2000)

Y. Razskazovskiy, M. Roginskaya, A. Jacobs, M. D. Sevilla, Reductively activated cleavage of DNA mediated by o,o‘-diphenylenehalonium cations. Radiat. Res. 154, 319-325 (2000)

K. Messer, K. Carpenter, K. Forzley, J. Buchanan, S. Yang, Y. Razskazovkiy, Z. Cai and M. D. Sevilla, Electron Spin Resonance study of electron transfer rates in DNA: Determination of the tunneling constant  for single step excess electron transfer. J. Phys. Chem. 104, 1128-1136 (2000)

W. A Bernhard, M. G. Debije, M. T. Milano and Y. Razskazovskiy. Influence of structure on electron and hole transfer in directly ionized DNA. Proceedings of the Eleventh International Congress of Radiation Research, M Moriarty, C. Mothersill, C. Seymour, M. Edington, J. F. Ward, and R. J. M. Fry, eds., Vol. 2, 321-324 (2000)

Y. Razskazovskiy, M. J. Raiti and M. D. Sevilla, Electron spin resonance and molecular orbital study of one-electron-reduced O,O ‘-diphenylenehalonium cations: First evidence for a diaryliodine radical, Ar2I. or simply a new *-radical? J. Phys. Chem. A 103, 6351-6359 (1999)

Y. Razskazovskiy, D. Becker and M. D. Sevilla, Sulfoxyl radicals: formation, structure and kinetics. In S-Centered radicals,Vol. (Z. B. Alfassi, Ed.), pp. 245-276. John Wiley & Sons, Chichester - New York - Weinheim - Brisbane - Singapore - Toronto, 1999

Y. V. Razskazovskiy, and M. Y. Mel’nikov, Reactions of thiyl radicals in the solid phase. In S-Centered radicals,Vol. (Z. B. Alfassi, Ed.), pp. 225-244. John Wiley & Sons, Chichester - New York - Weinheim - Brisbane - Singapore - Toronto, 1999

Y. Razskazovskiy, M. Roginskaya and M. D. Sevilla, Modification of the reductive pathway in gamma-irradiated DNA by electron scavengers: targeting the sugar-phosphate backbone. Radiat. Res. 149, 422-432 (1998)

W. Wang, Y. Razskazovskiy and M. D. Sevilla, Secondary radical attack on DNA nucleotides: reaction by addition to DNA bases and abstraction from sugar. Int. J. Radiat. Biol. 71, 387-399 (1997)

. M. D. Sevilla, D. Becker and Y. Razskazovskiy, Electron and hole transfer within DNA and its hydration layer. Abstr. Pap. Am. Chem. Soc. 214, 171-Phys, Part 172 (1997)

Y. Razskazovskiy, S. G. Swarts, J. M. Falcone, C. Taylor and M. D. Sevilla, Competitive electron scavenging by chemically modified pyrimidine bases in bromine-doped DNA: relative efficiencies and relevance to intrastrand electron migration distances. J. Phys. Chem. 101, 1460-1467 (1997)

. D. Becker, Y. Razskazovskiy, M. U. Callaghan and M. D. Sevilla, Electron spin resonance of DNA irradiated with a heavy-ion beam (O-16(8+)): Evidence for damage to the deoxyribose phosphate backbone. Radiat. Res. 146, 361-368 (1996)

Y. Razskazovskiy, and M. D. Sevilla, Reactions of Sulfonyl Peroxyl Radicals with DNA and its Components: Hydrogen Abstraction from the Sugar Backbone versus Addition to Pyrimidine Double Bonds. Int. J. Radiat. Biol. 69, 75-87 (1996)

Y. Razskazovskiy, and M. D. Sevilla, One-electron oxidation and reduction of sulfites and sulfinic acids in oxygenated media: the formation of sulfonyl and sulfuranyl peroxyl radicals. J. Phys. Chem. 100, 4090-4096 (1996)

Y. Razskazovskiy, A.-O. Colson and M. D. Sevilla, On the nature of thiyl peroxyl radical: ESR and ab initio MO evidence for intermolecular stabilization of the charge transfer state, RS(+)OO-. J. Phys. Chem. 99, 7993-8001 (1995)

Y. V. Razskazovskiy, M. V. Roginskaya and M. Y. Melnikov, Two pathways of SO2 addition to carbon-centered free radicals grafted to a silica surface - sulfonyl and oxysulfinyl radical formation. J. Phys. Chem. 98, 12003-12007 (1994)




http://www.acert.cornell.edu/acert_pubs.phtml

PUBLICATIONS 1996-2005

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(Updated 3/25/05)
Coexisting Domains in the Plasma Membranes of Live Cells Characterized by ESR. M.J. Swamy, L. Ciani, M. Ge, D. Holowka, B. Baird, and J.H. Freed, (submitted).

A Variable Temperature EPR Study of Mn2-doped NH4Cl0.9I0.1Single Crystal at 170 GHz: Zero-field Splitting Parameter and its Absolute Sign. S. Misra, S. Andronenko, P. Chand, K.A. Earle, S. Paschenko, and J.H. Freed, J. Magn. Res. (in press, 2005).

Pulsed 3D Electron Spin Resonance Microscopy. A. Blank, C.R. Dunnam, P.P. Borbat, J.H. Freed, Applied Phys. Letters 85, 5430-5432 (2004).

The Determination of Pair Distance Distributions by Pulsed ESR Using Tikhonov Regularization. Y.-W. Chiang, P.P. Borbat, and J.H. Freed, J. Magn. Res. 172, 279-295 (2005).

New Method for Determining Tie-lines in Coexisting Membrane Phases using Spin-label ESR. Y.-W. Chiang, J. Zhao, J. Wu, Y. Shimoyama, G.W. Feigenson, J.H. Freed, Biophysica-Biochimica Acta 1668, 99-105 (2005).

ESR and Molecular Dynamics. J.H. Freed, in Biomedical EPR, Part B: Methodology, Instrumentation and Dynamics. Eds. S.S. Eaton, G.R. Eaton, and L.J. Berliner, Kluwer, NY, Ch. 9, Biological Magnetic Resonance, 24, 239-268 (2005).

Dynamic Molecular Structure of DPPC-DLPC-Cholesterol Ternary Lipid System by Spin-Labeling ESR. Y.-W. Chiang, Y. Shimoyama, G.W. Feigenson, and J.H. Freed, Biophys. J. 87, 2483-2496 (2004).

Spin-Labeled Gramicidin A. Channel Formation and Dissociation. B.G. Dzikovski, Petr P. Borbat, and J.H. Freed, Biophys. J. 87, 3504-3517 (2004).

A Multifrequency ESR Study of T4 Lysozyme Dynamics using the Slowly Relaxing Local Structure Model. Z. Liang, Y. Lou, J.H. Freed, L. Columbus, and W.L. Hubbell, J. Phys. Chem. 108, 17649-17659 (2004).

Enrichment of Endoplasmic Reticulum with Cholesterol Inhibits SERCA2b Activity in Parallel with Increased Order of Membrane Lipids. Y. Li, M. Ge, L. Ciani, G. Kuriakose, E. Westover, M. Dura, D. Covey, F. Maxfield, J. Lytton, I. Tabas, J.H. Freed, J. Biol. Chem. 279, 37030-37039 (2004).

Measurement of Large Distances in Biomolecules Using Double-Quantum-Filtered Refocused Electron-Spin-Echoes. P.P. Borbat, J.H. Davis, S.E. Butcher, and J.H. Freed, J. Am. Chem. Soc, 126, 7746-7747 (2004).

A 3D Electron Spin Resonance Microscope. A. Blank, C.R. Dunnam, P.P. Borbat and J.H. Freed, Rev. Sci. Instrum. 75, 3050-3061 (2004).

A High-power 95 GHz pulsed ESR Spectrometer. W. Hofbauer, K.A. Earle, C.R. Dunnam, J.K. Moscicki, and J.H. Freed, Rev. Sci. Instrum. 75, 1194-1208 (2004).

Variable-Frequency EPR Study of Mn2+-doped NH4Cl0.9I0.1Single Crystal at 9.6, 36 and 249.9 GHz: Structural Phase Transition. S.K. Misra, S.I. Andronenko, G. Rinaldi, P. Chand, K.A. Earle and J.H. Freed, J. Magn. Res. 160, 131-138, (2003). PDF

The Development of High Field/High Frequency ESR: Historical Overview, J.H. Freed in Very High Frequency ESR, Biological Magnetic Resonance . 22, O. Grinberg and L.J. Berliner, Eds., Kluwer, NY Ch. 2, 19-43 (2004).

High Resolution Electron Spin Resonance Microscopy. A. Blank, C. Dunnam, P. Borbat, and J.H. Freed, J. Magn. Res. 165, 116-127 (2003). PDF

Mode-Coupling SRLS versus Mode-Decoupled Model-Free N-H Bond Dynamics: Mode-Mixing and Renormalization . E. Meirovitch, Y.E. Shapiro, Z. Liang, and J.H. Freed, J. Phys. Chem. B 107, 9898-9904 (2003). PDF

Mode-coupling Analysis of 15N CSA-15N-1H Dipolar Cross-correlated Relaxation in Proteins. E. Meirovitch, Y.E. Shapiro, V. Tugarinov, Z. Liang, and J.H. Freed, J. Phys. Chem. B 107, 9883-9897 (2003). PDF

Hydration, Structure, and Molecular Interactions in the Headgroup Region of Dioleoylphosphatidylcholine Bilayers: An ESR Study. M. Ge and J.H. Freed, Biophys. J. 85, 4023-44 . (2003).

ESR and Molecular Dynamics. J.H. Freed, in Biomedical ESR, Eds. S.S. Eaton, G.R. Eaton, and L.J. Berliner, Kluwer, NY (in press).

Ordered and Disordered Phases Coexist in Plasma Membrane Vesicles of RBL-2H3 Mast Cells. An ESR Study. , M. Ge, A. Gidwani, H. Alex Brown, D. Holowka, B. Baird, and J.H. Freed, Biophys. J. 85, 1278-1288 (2003). PDF

End to End Correlation for a C12 Hydrocarbon Chain. S. Wagner, A. Nevzorov, J.H. Freed, R.G. Bryant, J. Magn. Res. 160, 161-165 (2003). PDF

Lipid-Gramicidin Interactions: Dynamic Structure of the Boundary Lipid by 2D-ELDOR. A.J. Costa-Filho, R.H. Crepeau, P.P. Borbat, M. Ge, and J.H. Freed, Biophysical J. 84, 3364-3378 (2003). PDF

A 2D-ELDOR Study of the Liquid Ordered Phase in Multilamellar Vesicle Membranes. A.J. Costa-Filho, Y. Shimoyama, and J.H. Freed, Biophys. J. 84, 2619-2633, (2003) PDF

Modern ESR Methods in Studies of the Dynamic Structure of Proteins and Membranes . J.H. Freed, EPR in the 2lst. Century, A. Kawamori, J. Yamauchi and H. Ohta, Eds. Elsevier Science, Amsterdam, Netherlands, 719-730 (2002).

Phase Relaxation in a Many-Body System of Diffusing Spins: Slow Motional Limit. A.A.Nevzorov and J.H. Freed, J. Chem. Phys. 117, 282-287 (2002). PDF

Domain Flexibility in Ligand-Free and Inhibitor-Bound E. coli Adenylate Kinase Based on a Mode-Coupling Analysis of 15N Spin Relaxation. Y.E. Shapiro, E. Kahana, V. Tugarinov, Z. Liang, J.H. Freed, and E. Meirovitch, Biochemistry 41, 6271-6281 (2002). PDF

Protein Structure Determination Using Long-Distance Constraints from Double-Quantum Coherence ESR: Study of T4-Lysozyme. P.P. Borbat, H.S. Mchaourab, and J.H. Freed, J. Am. Chem. Soc. 124, (19) 5304-5314 (2002). PDF

A Novel View of Domain Flexibility in E. Coli Adenylate Kinase Based on a Structural Mode-Coupling Approach to 15N NMR Relaxation. V. Tugarinov, Y.E. Shapiro, Z. Liang, J.H. Freed, E. Meirovitch, J. Mol. Biol. 315, 155-170 (2002). PDF

Single-Crystal EPR Studies of Transition-Metal Ions in Inorganic Crystals at Very High Frequencies. S.K. Misra, S.A. Andronenko, K.A. Earle, J.H. Freed, Appl. Magn. Res. 21, 549-561 (2001).

A Multifrequency ESR Study of the Complex Dynamics of Membranes. Y.Lou, M. Ge, and J.H. Freed, J. Phys. Chem. B 105, 11053-11056 (2001). PDF

A Many-Body Analysis of the Effects of the Matrix Protons and their Diffusional Motion on ESR Lineshapes and Electron Spin Echoes. A.A. Nevzorov and J.H. Freed, J. Chem. Phys. 115, 2416-2429 (2001). PDF

Direct Product Formalism for Calculating Magnetic Resonance Relaxation in Many-Body Systems of Interacting Spins. A.A. Nevzorov and J.H. Freed, J. Chem. Phys. 115, 2401-2415 (2001). PDF

A Structural Mode-Coupling Approach to 15N NMR Relaxation in Proteins. V. Tugarinov. Z. Liang, Y. E. Shapiro, J.H. Freed, E. Meirovitch, J. Am. Chem. Soc. 123, 3055-3063 (2001). PDF

ARF6 Binding to PIP2-Containing Vesicles Creates Defects in the Bilayer Structure: ESR Studies on Model Membranes. M. Ge, J.S. Cohen, H.A. Brown, and J.H. Freed, Biophys. J. 81, 994-1005 (2001). PDF

Electron Spin Resonance in Studies of Membranes and Proteins. P.P. Borbat, A.J. Costa-Filho, K.A. Earle, J.K. Moscicki and J.H. Freed, Science 291, 266-269, (2001).

Segmental Rotational Diffusion of Spin Labeled Polystyrene in Dilute Toluene Solution by 9 and 250 GHz. J. Pilar, J. Labsky, A. Marek, D. E. Budil, K.A. Earle, and J.H. Freed, Macromolecules 33, 4438-4444 (2000). PDF

Double Quantum ESR and Distance Measurements. P.P. Borbat and J.H. Freed, Biol. Magn. Res. 19, 383-459 (2000), Ch. 9.

Jones Matrix Formalism for Quasioptical EPR. D.E. Budil, Z. Ding, G.R. Smith, and K.A. Earle, J. Magn. Res. 144, 20-34 (2000). PDF

New Technologies in Electron Spin Resonance. J.H. Freed, Annual Review of Physical Chemistry, Vol. 51 655-689 (2000). PDF

An Electron Spin Resonance Study of DNA Dynamics Using the Slowly Relaxing Local Structure Model. Z. Liang, J.H. Freed, R.S. Keyes, A.M. Bobst, J. Phys. Chem. B104, 5372-5381 (2000). PDF

Dipolar Relaxation in a Many-Body System of Spin of 1/2. A.A. Nevzorov and J.H. Freed J. Chem. Phys., 112, 1425-1443 (2000). PDF

Spin Relaxation by Dipolar Coupling: From Motional Narrowing to the Rigid Limit. A.A. Nevzorov and J.H. Freed, J. Chem. Phys., 112, 1413-1424 (2000). PDF

Multiple-Quantum ESR and Distance Measurements. P.P. Borbat and J.H. Freed, Chem. Phys. Letts., 313, 145-154 (1999). PDF

An Assessment of the Applicability of Multifrequency ESR to Study the Complex Dynamics of Biomolecules. Z. Liang and J.H. Freed, J. Phys. Chem. B, 103, 6384-6396 (1999). PDF

Quasioptical Hardware for a Flexible FIR-EPR Spectrometer. K.A. Earle and J.H. Freed, Appl. Magn. Res. 16, 247-272 (1999).

Study of Motional Dynamics in Complex Fluids by Very High-Field, Very High-Frequency EPR (VHF-EPR). A.K. Hassan, J. van Tol, A.L. Maniero, L.C. Brunel, K.A. Earle, and J.H. Freed, Physical Phenomena at High Magnetic Fields -III. Eds. Z. Fisk, L. Gor'kov, J.R. Schrieffer, World Scientific Publishers, NJ, 453-456 (1999).

A Multi-Frequency ESR Study of T4 Lysozyme Dynamics. J. Barnes, Z. Liang, H. Mchaourab, J.H. Freed, and W. Hubbell, Biophys. J. 76, 3298-3306, (1999).

An EPR Study of Some Highly Distorted Tetrahedral Manganese (II) Complexes at 250 GHz. R. M. Wood, D.M. Stucker, W.B. Lynch, S.K. Misra, and J.H. Freed, Inorgan. Chem. 38, 5384-5388 (1999). PDF

Multi-Frequency EPR Determination of Zero-Field Splitting of High-Spin Species in Liquids: Gd (III) Chelates in Water. R.B. Clarkson, A.I. Smirnov, T.I. Smirnova, H. Kang, R.L. Belford, K.A. Earle, and J.H. Freed, Molec. Phys. 95, 1325-1332 (1998). PDF

Response to "Comment on 'A 250 GHz ESR Study of o-terphenyl Dynamic Cage Effects above Tc'". K.A. Earle, J.K. Moscicki, A. Polimeno, and J.H. Freed, J. Chem. Phys. 109, 10525-10526, (1998). PDF

Dynamics and Ordering in Mixed Model Membranes of DMPC and DMPS: A 250 GHz. ESR Study. J.P. Barnes and J.H. Freed, Biophys. J. 75, 2532-2546 (1998).


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Research Topic: Enzyme structure and mechanism of action; enzymes of DNA synthesis and hydrolysis; isomerases; nuclear magnetic resonance and electron spin resonance

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