[Biojava-l] Elementar Computing Processes

Mon, 7 May 2001 15:03:11 +0200 (EET)

Dear Madams/Sirs,

On behalf of the SCI 2001 Organizing Committee we would like to invite you
to participate in The Fifth Multi-Conference on Systemics, Cybernetics and
Informatics, Invited Session: "Elementar Processes in Atomic-Molecular
Level of Classical, Quantum and DNA Computing".
which will be held in Orlando, Florida, USA, from July 22 - 25, 2001.
Therefore, we are sending you the respective Call for Papers.

We are making emphasis on the area of Nanotechnologies.

You can find information about the suggested steps for invited session
organization in the Call for papers and in the conference web site
(http://www.iiis.org/sci/).

After reviewing the enclosed extended abstracts included in our invited
session: 'Elementar Processes in Atomic-Molecular Level of Classical,
Quantum and DNA Computing' the Organizing Committee informed us that our
invited session has been definitely approved, therefore, it will be
inserted in the conference program, as long as we receive the camera-ready
papers and authors registrations in the conference, on the respective
deadlines:
May 09, 2001. Deadline for papers acceptation's.
May 23, 2001. Deadline for camera-ready papers: hard copies and
              electronic versions

With best regards.
Yours sincerely, Arvydas Tamulis
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           Arvydas Tamulis

Doctor of Natural Sciences, senior research fellow

Institute of Theoretical Physics and Astronomy,
Theoretical Molecular Electronics Research Group,
A. Gostauto 12, Vilnius 2600, Lithuania
e-mail: TAMULIS@ITPA.lt; WEBsite: http://www.itpa.lt/~tamulis/
fax: +(370-2)-225361  or  +(370-2)-224694
Phone: +(370-2)-620861
Home address: Didlaukio 27-40, Vilnius 2057, Lithuania
Phone: +(370-2)-778743
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P.S. List of included to our invited session 'Elementar Processes...'
extended abstracts:

1. P. Kosobutsky, M. Lobur, Ja. Kosobutskyy, T. Slyusarchyk, (Ukraine)
"Modelling of Time Relaxation of Oscillator Energy and Correlation with
Spectrum of its
Forced Vibrations", applied to The Fifth Multi-Conference on Systemics,
Cybernetics and Informatics, Invited Session: "Elementar Processes in
Atomic-Molecular Level of Classical, Quantum and DNA Computintg", 2001.

Modeling of time relaxation of oscillator energy [1] is based on the
integral of one-dimensional motion investigations of a harmonic oscillator
in the context of the model of linear approximation. Authors show, that
some oscillator vibrates could be modulated with long-wave oscillations.
They presented functions that describes the dynamic of medium resistance
to the natural vibrations of the linear harmonic oscillator. Thus the
energy loses of the oscillators in the resistance medium could be
described. The energy exchange between the oscillator and the external
source is described also. The studies indicate that oscillating damps with
time, whereas the forced power of source increases
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2. J. Tamuliene, A. Tamulis, Z. Rinkevicius, V. Tamulis (Lithuania),
"Quantum Chemical Design of Logic Gates of Classical and Quantum Molecular
Computers and Light Driven Molecular Logical Machines", applied to The
Fifth
Multi-Conference on Systemics, Cybernetics and Informatics, Invited
Session:
"Elementar Processes in Atomic-Molecular Level of Classical, Quantum and
DNA
Computintg", 2001.

Computational investigations of azo-benzene [2] show that most probable
way of trans-cis isomerization is rotation around of -N=N- where almost
not
exist potential barrier. Other investigated reaction coordinates are
related
with per linear transition state or with one N atom in-plane inversion
pathway. These other reaction coordinates possess relatively large
potential barriers. The experimentally observing temperature dependance on
trans-cis reaction yield allow to predict that exist small probability of
these other reaction coordinates. Most probably that reaction pathway is
in coherence of all three above mentioned isomerization ways.
OR logically controlled molecule machine designed from
thiobenzene-N=N-benzene-NO2 with electron acceptor fragment -(Ph-NO2)
(moving part after excitation) and two photoelectron donor parts:
dithieno[3,2-b:2',3'-d]thiophene and ferocene molecules show some not
intensive absorption in infrared region. Applied DFT B3PW91/SVP-Time
Dependent (TD) method and our modified visualization program showed from
which fragments electron is hopping in first excited state.
We performed design and calculations of molecular logical devices based on
organic electron donor: dithieno[3,2-b:2',3'-d]thiophene and ferocene
(C10H10Fe) and electron acceptor molecules:
1,3-bis(dicyanomethylidene)indane and endohedral fullerene ErSc2N@C80
substituted derivative ErSc2N@(CH2CH2NH)C80, electron
donor-bridge-electron acceptor dyads and triads including electron donor
and acceptor molecules joined with -CH=CH- bridge. Design of new series
molecular implementations of two variable logic functions: AND (NAND), OR
(NOR) is based on quantum chemical ab initio HF/6-31G geometry
optimization procedure which shows that our newly designed logical gates
based on ErSc2N@C80 substituted derivativeErSc2N@(CH2CH2NH)C80 are more
stable rather than based on ErSc2N@C80 substituted derivative
ErSc2N@(CH2)C80.
It have been optimized CdS model structure without benzenes using DFT
B3PW91 method usingLanL2DZ basis. The band gap between HOMO and LUMO after
such a geometry optimization is equal to 4.190 eV. After we have attached
four
benzenes to initial CdS model structure and after DFT B3PW91/LanL2DZ
geometry optimization the gap between HOMO and LUMO become equal to 4.151
eV. The band gap is indeed close to the expected (experimentally measured
by Dr. N. Kotov) value for these clusters. Therefore it was decided to
design and calculate the CdS cluster with 8 phenyl ligands because
experimentally, there are the data that show the decrease of the band gap
with addition of phenyls.
It was performed design and DFT B3PW91/6-311G** calculation of biliverdin
derivatives which possess from one to six Quantum Bits generating by
proton NMR for closed shell species (not including Fermi Contact
interaction and other relativistic effects). Theory of our obtained
different relativistic terms for open shell paramagnetically shifted
proton NMR calculations is given in this paper.
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3. N. Moiseyev, I. Vorobeichik, (Israel) "Solving Problems in Optical
Communications by Theories, Computational algorithms and Methods
Originally Developed in Molecular Dynamics and Laser Phsics", applied to
The Fifth Multi-Conference on Systemics, Cybernetics and Informatics,
Invited Session: "Elementar Processes in Atomic-Molecular Level of
Classical,
Quantum and DNA Computintg", 2001.

Solving problems in optical communications by computational algorithms in
molecular dynamics and laser physics [3] are performing using the electric
field in optical wave-guides with in-homogeneous refractive index along
the propagation axis and as solutions of time-depended Schrodinger
equations. The possibilities to control the power exchange between
different types of optical wave-guides and cavities are investigates. The
novel mechanism of power exchange control in optical couplers is induced
by periodic variations of refractive index. They proposed devices that can
be used for optical power coupling, optical switching, wave-length
filtering and so on. The new techniques for calculation of the reflected
waves are proposed.
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4. S. Folling, O. Turel, K. Likharev, (USA) "Single-Electron Latching
Nanoswitshes as Synapses for Self-Evolving Neuromorphic Networks", applied
to The Fifth Multi-Conference on Systemics, Cybernetics and Informatics,
Invited Session: "Elementar Processes in Atomic-Molecular Level of
Classical,
Quantum and DNA Computintg", 2001.

Single-electron latching nano-switches are using for self-evolving
neuromorphic networks [4]. Authors are developing new kind of a
single-electron device. According to the Monte -Carlo simulation the
device is typical for latching switch. The preliminary studies of two
promising architectures of adaptive neuromorphic networks are based on 2D
square arrays of the single-electron synaptic nodes. The architecture of
"randomized distributed crossbar" are investigated also. This network
actively uses virtually the whole chip area.
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5. D. Kirvelis, (Lithuania) "CODING-DECODING as General Principle of the
Bio-systems
Functional Organization", applied to The Fifth Multi-Conference on
Systemics, Cybernetics and Informatics, Invited Session: "Elementar
Processes
in Atomic-Molecular Level of Classical, Quantum and DNA Computintg", 2001.

General CODING-DECODING principle of BioComputing systems is developing in
paper [5]. Author describes informational coding-decoding processes that
are in living organisms. Some typical phenomena of living nature using the
terms of informational technologies are presented. Biological evolution is
discussed as a changing formation and reproduction of hierarchically
organized dynamic structures of coding-decoding.
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6. A. Tamulis, A.K. Gaigalas (USA-NIST), Rinkevicius, J. Tamuliene, V.
Tamulis (Lithuania), "Quantum Chemical Design of Molecular Logic,
Fluorescencing and
Nano-Medicine Robots", applied to The Fifth Multi-Conference on Systemics,
Cybernetics and Informatics, Invited Session: "Elementar Processes in
Atomic-Molecular Level of Classical, Quantum and DNA Computing", 2001.

Quantum chemical first principles calculations [6] along with full
geometry optimizations of dianion and monoanion fluorescein molecules in
the
ground state were performed applying the method of DFT B3PW91/6-311G**
model.
Dianion charge transfer investigations made by B3PW91/6-311G**-TD method
showed that electron transfer incomes in fluorescein dianion molecule in
during most transitions localize on one C atom joining tricycle and
monocycle rings. Such a transferred electron localization on one C atom
prevents the energy dissipation during HOMO-LUMO and other excitations and
therefore the absorption intensity of HOMO-LUMO transition is large and
fluorescence in fluorescein is efficient. Energy dissipation in monoanion
transitions makes not so intensive absorption lines in comparison with
dianion in first, HOMO-LUMO and other transition absorption lines because
of more mixing of atomic orbitals from far situated atoms or fragments
inducing charge transfer energy dissipation.
Based on detailed DFT-TD spectra and charge transfer investigations of
various
fluorescein derivatives and electronic structure and proton NMR
calculations of biliverdin derivatives such a CuOEB and others were
designed molecular devices which moving and possessing fluorescence and
anti-oxidant biological features. These device wer optimized by HF/6-31G
method. Optimized supermolecules possess stable electronic structure and
previous features of fluorescencing and anti-oxidant activities that allow
to use them for nano-medicine robots.
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On May 02 we have received fax message from Dr. Rao (University of
Massachusetts, Boston, MA, USA) who informed that sent abstract "Optical
computing and Information processing with biomaterials"