Nabble - Bio.net - Biophys

GRADUATE TRAINING, COGNITIVE & NEURAL SYSTEMS, BOSTON UNIVERSITY

2009-11-03T10:41:19Z

The Department of Cognitive and Neural Systems at Boston University
Relating brain and behavior through computational approaches

The Department of Cognitive and Neural Systems (CNS) offers comprehensive graduate training in the neural and computational principles, mechanisms, and architectures that underlie human and animal behavior, as well as the application of neural network architectures to technological problems. CNS offers 17 distinct graduate courses and other training leading to PhD and MA degrees.

For program details, see the CNS Brochure http://cns.bu.edu/brochure/ and
the Graduate School Bulletin http://www.bu.edu/bulletins/grs/

For information regarding application procedures, visit
Graduate School of Arts & Sciences Admissions http://www.bu.edu/cas/admissions/graduate/

Application forms and instructions are available at
http://www.bu.edu/cas/admissions/graduate/apply/

Applications for admission and financial aid should be received in the Graduate School Admissions Office by December 15, 2009 but will be given full consideration if received by no later than January 15, 2010.

Applicants are required to submit undergraduate (and, if applicable, graduate) transcripts, three letters of recommendation, and Graduate Record Examination (GRE) scores. GRE scores may be waived for MA candidates and, in exceptional cases, for PhD candidates, but absence of these scores may decrease an applicant's chances for admission and financial aid.

All application materials must be submitted directly to the Graduate School Admissions Office.

CNS also offers joint BA/MA programs to Boston University undergraduates majoring in Biology, Computer Science, Mathematics & Statistics, Psychology, and Neuroscience (new, pending final approval).

Please direct questions regarding CNS admissions applications to Mr. Robin Amos, ramos(at)cns.bu.edu; 617-353-9481.

.......................................................................
Department of Cognitive and Neural Systems
Boston University
677 Beacon Street
Boston, MA 02215
Phone: 617/353-9481
Fax: 617/353-7755
Email: ramos-AT-cns.bu.edu
Web: http://www.cns.bu.edu/
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Practical Course in Biomolecular Modelling

2009-09-25T05:51:01Z

Dear colleagues,

please be informed that online applications are still accepted for the
following course until October 16, 2009:

8TH NCCR PRACTICAL COURSE IN BIOMOLECULAR MODELLING

January 10 - 15, 2010
Kandersteg, Switzerland
http://www.structuralbiology.uzh.ch/course2010.asp

Course topics include
Simulation techniques, force-field development, conformational search,
computation of free energy and entropy, treatment of electrostatic
forces, simulation of folding, comparison of simulation with experiment

This course is primarily directed to PhD students and postdocs from
experimental structural biology groups wishing to learn more on
biomolecular modelling. The course format will include morning lectures
and late-afternoon/early evening tutorials, and provide ample
opportunities for discussions with experts and fellow participants.
Participants will be invited to bring own problems for tutorials and/or
discussion. The course will be organized as a winter retreat in the
Swiss Alps offering a stimulating learning atmosphere with the
afternoons available for informal participation in discussions, reading
and self-study or recreational activities in the area.

Interested candidates are encouraged to apply online on
http://www.structuralbiology.uzh.ch/course2010_application.asp.
Application deadline will be October 16, 2010. We will be able to accept
20 participants to this course.

Best regards,
Patrick Sticher

--
_________________________________
Visit the NCCR on the Internet
www.structuralbiology.uzh.ch

Dr. Patrick Sticher Moser
NCCR Scientific Officer
Institute of Biochemistry
University of Zürich
Winterthurerstrasse 190
CH - 8057 Zürich

Phone +41 / (0)44 / 635 54 84
Fax +41 / (0)44 / 635 59 08
Mail sticher@...

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National Conference on Stem cell Research, Computational Biology ans Chemistry on 8th &9th of August'09 at Hotel Green Park, Chennai

2009-06-17T05:35:31Z

Dear all,

BionteQ Bioscience Private Limited, a company located in Chennai,
venturing into Bioinformatics, Cheminformatics and Bio-Medical
Engineering providing software and research solutions to the life
science world. The company also provides Consultancy Services in the
area of computational biology and chemistry with its own research and
development team working on these areas.

BionteQ is organizing Technobia ’09, a National Conference on Stem
cell Research, Computational Biology and Chemistry on 8th and 9th of
August at Hotel Green Park.

Technobia’09 aims to bring together researchers, scientists, students,
engineers, and academic and R&D scholars to exchange and share their
experiences, new ideas, and research results about all aspects of
Computational Biology & Chemistry and also Stem cell research, and
discuss the practical challenges encountered and the solutions
adopted. The event addresses the development and application of
computational methods for biological problems from the perspectives of
both research and industry. Eminent well known speakers come together
to enlighten the audience with their research, academic and industry
experiences, also highlighting the recent research and scope in these
fields.

The Conference covers the following topics:

STEM CELL RESEARCH

1. Dr. Rama Shanker Verma, Associate Professor, Stem and Molecular
Biology lab, Department of Biotechnology, IITM, Chennai

2. Dr. Shaji R.V, Assistant Professor, Department of Haematology, CMC,
Vellore.

CHEMINFORMATICS

• Dr. Chandan Raychaudhury, Solutions Scientist, Life Science,
Accelrys, Bangalore

DRUG DESIGNING

• Mrs. Rohini Srinivasan, Senior Consultant, Lifesciences and Pharma,
HCL Technologies, Chennai

SAS & CLINICAL DATA MANAGEMENT

• Mr. Ahmed Z Kabeer, Project Manager, Laxai, Hyderabad.

STRUCTURAL BIOINFORMATICS

• Dr. Swagatha Das Gupta, Associate Professor, Department of
Chemistry, IIT Karaghpur.

SYSTEMS BIOLOGY

• Mr. Saurabh Bundela, Senior Scientist, Systems Biology India Pvt
Ltd, Pune.

MICRO ARRAY

• Dr. Kshitish Acharya, Faculty Scientist, IBAB, Bangalore.

REGISTRATION

Early Bird Offer
Upto June 30, 2009 July 1 onwards
Students INR 1850/- INR 2000/-
Academic and R&D professionals INR 2850/- INR 3000/-
Industry INR 3850/- INR 4000/-

The registration fee is to be paid through demand draft drawn in
favor of BionteQ Bioscience Private Limited payable at Chennai.

Registration fee includes the following:
Conference kit, Certificate, Lunch and refreshments.

ACCOMODATION

Participants should arrange their own accommodation, however,
accommodation in hotels, paying guest houses may be booked on request,
against an advance booking amount sent. A special request must be made
for accommodation assistance during the registration.

The request for accomodation must reach BionteQ by July 31, 2009.
Payments should be made through a demand draft in favor of BionteQ
Bioscience Private Limited payable at Chennai.

For any further information please contact:

Coordinator (Technobia ‘09),
BionteQ Bioscience Private Limited
No.97/5, Periyar Pathai,
Choolaimedu,
Chennai-600094
Tel:+91-44-64536777
Mob: 9282348999
Email: info@...
www.bionteq.com

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ISBMR 9th Course: Biophysics and Structure, Erice-Sicily, 22 Jun-2 Jul '09

2009-04-08T22:18:33Z

We like to bring to your attention the 9th Biophysics and Structure
Course of the Int'l School of Biological Magnetic Resonance (ISBMR).
We kindly ask you share this information with graduate students,
postdoctoral fellows, and other colleagues and interested individuals,
particularly in the areas of Structural Biology, NMR, Biophysics,
Crystallography, Computational Biology, and Biochemistry. Details
follow:

COURSE TITLE: ISBMR 9th Course: Biophysics and Structure
WHEN: 22 June - 2 July 2009
WHERE: Ettore Majorana Foundation and Centre for Scientific Culture,
Erice-Sicily, Italy.
URL: http://smrl.stanford.edu/erice2009/
Apply online: http://www.stanford.edu/~manolia/erice2009app.fb

* COURSE FORMAT and PURPOSE: The format is an Advanced Study Institute
(ASI). This course will provide an overview of physical and
structural methods in biology and will present technologies related to
pathogen detection and treatment using these methods. Both, basic
principles and concrete examples will be presented in a long course
format. It is an ideal course for graduate students and postdoctoral
fellows. Please note that the structure of the course provides a
great opportunity for young scientists to present their work.

* TOPICS Include: Principles of NMR spectroscopy; Principles of X-ray
diffraction; Single-molecule methods; Cryoelectron Microscopy;
Molecular dynamics and other computational approaches; Mass
spectrometry; Use of NMR data to calculate protein and nucleic acid
structures; New RNA and protein NMR methods; Viral pathogens;
Bacterial pathogens; Antivirals; Ribosome structure; Translational
mechanism and antibiotics; New technologies to study proteins; Solid
state NMR; Peptides as drugs; Membrane proteins as drug targets;
Structure-based drug design in biotechnology; NMR and physical studies
of pathogenic proteins; Coupling genomics and structural studies.

APPLICATION PROCEDURE: Applications are now accepted online:
http://www.stanford.edu/~manolia/erice2009app.fb

Thank you in advance for your time and consideration.
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7th International NCCR Symposium on New Trends in Structural Biology

2009-04-06T08:20:36Z

Dear colleagues,

please be informed that the registration slot for the

7th International NCCR Symposium on New Trends in Structural Biology
7 + 8 September 2009, ETH Zürich, Lecture Hall HG E7, Zürich, Switzerland

is now open. Online registration is possible directly from the symposium
website:
www.structuralbiology.uzh.ch/symposium2009
where you will also find further information about this event.

Confirmed plenary lecturer to date:
Pietro de Camilli, Arthur Horwich, Brian Kobilka, Harry Noller, Anna
Marie Pyle, David Wemmer, Masasuke Yoshida

Please do not hesitate to contact me anytime if you need further
information (sticher@...).

With best regards,
Patrick Sticher

The NCCR Structural Biology is a research initiative of the Swiss
Science Foundation. Its research encompasses the fields of recombinant
protein technologies, macromolecular structure determination and
computational biomolecular sciences with a special focus on membrane
proteins and supramolecular assemblies/interactions. 19 research groups
from Swiss Universities and Research Institutions participate in this
network. www.structuralbiology.uzh.ch/

_________________________________
Dr. Patrick Sticher Moser
NCCR Scientific Officer
Institute of Biochemistry
University of Zürich
Winterthurerstrasse 190
CH - 8057 Zürich

Phone +41 / (0)44 / 635 54 84
Fax +41 / (0)44 / 635 59 08

--
_________________________________
Visit the NCCR on the Internet
www.structuralbiology.uzh.ch

Dr. Patrick Sticher Moser
NCCR Scientific Officer
Institute of Biochemistry
University of Zürich
Winterthurerstrasse 190
CH - 8057 Zürich

Phone +41 / (0)44 / 635 54 84
Fax +41 / (0)44 / 635 59 08
Mail sticher@...

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Influence of magnetic fields on human body

2009-03-11T18:27:23Z

Hi,

I am looking for information on the influnce of low frequency magnetic
fields on the human body.

Low frequency means in this case pulsating magnetic fields with a frequency
of 0-3 Hz modulated with another frequency of 10-50 Hz. My current circuit
doesn't match these figures, but that's what I had in thought.

I personally have clear sensations in hands, arms and belly when exposed to
such fields. Call it an itching feeling.

The force must be relatively strong, while I am using 2-3 A at 12 V. So,
basically, 20-30 W of electrical power is used in the coil. The effciency I
don't know, but my compas reacts from an arm's length.

My question is whether or not exposure to such fields could cause adverse
effects, and if so what? Or could such fields used for magnetic therapies?
Through which mechanism is it possible that I have undeniable sensations
when exposed to such fields.

Googling didn't yield much useful information yet. Hopefully anyone here has
something useful.

Thanks on beforehand.

Ron
Norway

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"Hands-On" Workshop on Computational Biophysics, July 6-10 & August 10-14, 2009, Champaign, IL

2009-01-28T08:41:13Z

"Hands-On" Workshop on Computational Biophysics

http://www.ks.uiuc.edu/Training/Workshop/Champaign09J/
http://www.ks.uiuc.edu/Training/Workshop/Champaign09A/

Application Deadline: May 3, 2009

The Theoretical and Computational Biophysics Group, NIH Resource for
Macromolecular Modeling and Bioinformatics (www.ks.uiuc.edu) at the
University of Illinois at Urbana-Champaign (www.uiuc.edu), will
organize an

"'Hands-On' Workshop on Computational Biophysics"

to be held at the following dates and location:

* July 6 to July 10, 2009 at the I Hotel and Conference Center in
Champaign, Illinois
* August 10 to August 14, 2009 at the I Hotel and Conference Center in
Champaign, Illinois

The workshop will explore physical models and computational approaches
used for the simulation of biological systems and the investigation of
their function at an atomic level. The course will be based on case
studies including the properties of membranes and membrane proteins,
mechanisms of molecular motors, trafficking in the living cell through
water and ion channels, and signaling pathways. Relevant physical
concepts, mathematical techniques, and computational methods will be
introduced, including force fields and algorithms used in molecular
modeling, molecular dynamics simulations on parallel computers and
steered molecular dynamics simulations.

The workshop is designed for graduate students and postdoctoral
researchers in computational and/or biophysical fields who seek to
extend their research skills to include computational and theoretical
expertise, as well as other researchers interested in theoretical and
computational biophysics. Theory sessions in the morning will be
followed by hands-on computer labs in the afternoon in which
participants will be able to set up and run simulations.

Applications to the workshop are due by May 3, 2009. Selection and
notification of participants from the application pool will be
completed by May 13, 2009. Those selected to attend must register and
pay a workshop fee by May 23, 2009. The base registration fee is $200
for students, $300 for non-student academics, and $400 for all other
applicants. Double-occupancy housing and all course materials are
included in the fee. All participants are required to bring their own
laptop for use in workshop tutorial sessions. The workshop can neither
fund nor arrange participant travel.

Due to space and equipment constraints, each workshop is limited to 20
participants. For further information, and online application, please
visit the appropriate sites for each date:
* July 6-10 workshop: http://www.ks.uiuc.edu/Training/Workshop/Champaign09J/
* August 10-14 workshop: http://www.ks.uiuc.edu/Training/Workshop/Champaign09A/

Workshop Organizers e-mail contacts by date:
* July 6-10 workshop: workshop+champaign09J@...
* August 10-14 workshop: workshop+champaign09A@...

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Pressure/Patch-Clamp Methods

2008-12-29T21:19:58Z

It is approaching 20 years since the introduction of the single-
channel patch-clamp recording technique (Neher and Sakmann, 1976), and
over the last two decades its refinements and diverse applications
have served to maintain it as the dominant technique in membrane
physiology (Neher, 1992; Sakmann, 1992). Historical accounts of the
development of the technique have been given (Sigworth, 1986), and an
extensive literature exists detailing and updating various aspects of
the method (Sakmann and Neher, 1983, 1995; and this volume). In this
chapter we focus on a critical yet some-what neglected aspect of the
method, namely the magnitude and time course of the suction/pressure
applied to the patch and its consequent effects on membrane and
channel properties. Although suction is most often used in obtaining
the tight seal, it has also been shown that excessive suction alters
the properties of specific membrane ion channels (Hamill and McBride,
1992). In particular we describe here recent development of pressure
clamp techniques that allow the application of precise and rapid
suction/pressure steps to membrane patches and whole cells (McBride
and Hamill, 1992, 1993, 1995).
Tonny
--------------
More bio-med news & videos
Portal to share biological information-data between people
http://biospace.ethz.ch
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Re: melting wood

2008-12-09T07:58:26Z

"Dr Engelbert Buxbaum" <engelbert_buxbaum@...> wrote in
news:op.uf4xy2do66vu6s@...:

> Am 12.08.2008, 22:58 Uhr, schrieb Olli Holliday
> <olli.holliday@...>:
>
>> I am trying to find further information about melting wood, all I've
>> found so far are messages from this forum from 1994, 1999 and 2003
>> that seem to be without any follow-up.
>>
>> has any progress been made on this topic in the years since the last
>> post?
>
> Wood is mainly composed of cellulose and lignin. These macromolecules
> do not melt, but decompose when heated, producing charcoal.

Ok, you may be right, but couldn't we just produce wood with other
chemicals that do melt? Or, if that's not likely, could there be a way of
creating a genetically modified wood that did melt?

I'm not a scientist, but I know that at least some people out there are
scientists. I really would love to see molten wood in my lifetime (however
long that turns out to be).

I'd be really grateful for any further information!

Cheers,
Kelvin
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Re: Stem Cells Seeds of Hope

2008-09-05T11:12:44Z

Am 04.09.2008, 03:15 Uhr, schrieb j_thomas <julianthomasp@...>:

> Some tissues continue to stem cells after it become specialized, but
> these cells are less flexible than embryonic stem cells,

That view is perhaps a little outdated now, see
T. Aoi et al: Generation of Pluripotent Stem Cells from Adult Mouse Liver
and Stomach Cells, Science 321 (2008) 699 - 702
DOI: 10.1126/science.1154884,
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Re: melting wood

2008-08-19T06:19:40Z

Am 12.08.2008, 22:58 Uhr, schrieb Olli Holliday <olli.holliday@...>:

> I am trying to find further information about melting wood, all I've
> found so far are messages from this forum from 1994, 1999 and 2003
> that seem to be without any follow-up.
>
> has any progress been made on this topic in the years since the last
> post?

Wood is mainly composed of cellulose and lignin. These macromolecules do
not melt, but decompose when heated, producing charcoal.
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6th NCCR Symposium on New Trends in Structural Biology: New Program / Registration deadline August 29

2008-08-18T08:36:40Z

Dear colleagues,

6th International NCCR Symposium on New Trends in Structural Biology
8 + 9 September 2008, University of Zürich, Zürich, Switzerland

NEW PROGRAM.

The opening lecture will now be given by Gebhard Schertler about "Structure of the stress hormone receptor: beta1 adrenergic receptor".

Confirmed plenary lecturers are Markus Grütter, Stephen C. Kowalczykowski, Kaspar Locher, Keiichi Namba, Poul Nissen, Andrej Sali, Gebhard F.X. Schertler, Jeffrey Skolnick, and A. Joshua Wand. The meeting will be held together with the Annual Meeting of the Swiss Society for Crystallography. Speakers of the society are Clemens Schulze-Briese and Colin Nave. Please see the symposium website for the complete program.

REGISTRATION SLOT EXPIRES AUGUST 29.

Please note that online registrations can be accepted for only a few more days until August 29.

INFORMATION AND REGISTRATION.

www.structuralbiology.uzh.ch/symposium2008.asp

Please do not hesitate to contact me anytime if you need further information (sticher@...).

With best regards,
Patrick Sticher

The NCCR Structural Biology is a research initiative of the Swiss Science Foundation. Its research encompasses the fields of recombinant protein technologies, macromolecular structure determination and computational biomolecular sciences with a special focus on membrane proteins and supramolecular assemblies/interactions. 19 research groups from Swiss Universities and Research Institutions participate in this network. www.structuralbiology.uzh.ch/

_________________________________
Dr. Patrick Sticher Moser
NCCR Scientific Officer
Institute of Biochemistry
University of Zürich
Winterthurerstrasse 190
CH - 8057 Zürich

Phone +41 / (0)44 / 635 54 84
Fax +41 / (0)44 / 635 59 08

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re: melting wood

2008-08-12T19:58:56Z

I am trying to find further information about melting wood, all I've
found so far are messages from this forum from 1994, 1999 and 2003
that seem to be without any follow-up.

has any progress been made on this topic in the years since the last
post?
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Re: Mitochondrial DNA

2008-08-11T18:43:22Z

In article <52bc96c6-ebe4-4597-b79c-63cac0da9b19@...>,
j_thomas <julianthomasp@...> wrote:
>
>Mitochondrial DNA
>
>http://bioisolutions.blogspot.com/2008/05/mitochondrial-dna.html

What does this mean?

"mtDNA is particularly susceptible to reactive oxygen species
generated by the respiratory chain due to its close proximity."
<op. cit.>

--bks

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6th NCCR Symposium New Trends in Structural Biology - Program online

2008-07-22T02:33:35Z

Dear colleagues,

6th International NCCR Symposium on New Trends in Structural Biology
8 + 9 September 2008, University of Zürich, Lecture Hall KOH-B10,
Zürich, Switzerland
www.structuralbiology.uzh.ch/symposium2008.asp

The lecture program is available online at:
http://www.structuralbiology.uzh.ch/symposium2008_lectures.asp

Plenary lecturers:
Markus G. Grütter, Stephen C. Kowalczykowski, Kaspar Locher, Keiichi
Namba, Poul Nissen, Andrej Sali, Ilme Schlichting, Titia Sixma, Jeffrey
Skolnick, A. Joshua Wand

The meeting will be held together with the Annual Meeting of the Swiss
Crystallography Society.
Society lectures will be given by Clemens Schulze-Briese and Colin Nave

Online registration to this event is still possible through the
symposium homepage or directly at:
http://www.structuralbiology.uzh.ch/registration08.asp

Please do not hesitate to contact me anytime if you need further
information (sticher@...).

With best regards,
Patrick Sticher

The NCCR Structural Biology is a research initiative of the Swiss
Science Foundation. Its research encompasses the fields of recombinant
protein technologies, macromolecular structure determination and
computational biomolecular sciences with a special focus on membrane
proteins and supramolecular assemblies/interactions. 19 research groups
from Swiss Universities and Research Institutions participate in this
network. www.structuralbiology.uzh.ch/

_________________________________
Dr. Patrick Sticher Moser
NCCR Scientific Officer
Institute of Biochemistry
University of Zürich
Winterthurerstrasse 190
CH - 8057 Zürich

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Biology videos

2008-04-15T05:03:48Z

Gleevecs Effects on tryosine Kinase

http://bioisolutions.blogspot.com/2008/03/gleevecs-effects-on-tryosine-kinase.html

Cell Cycle Control

http://bioisolutions.blogspot.com/2008/03/cell-cycle-control.html

Comparison of Mitosis and Meiosis

http://bioisolutions.blogspot.com/2008/03/comparison-of-mitosis-and-meiosis.html

How The Cell Cycle Works

http://bioisolutions.blogspot.com/2008/03/how-cell-cycle-works.html
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Biology videos

2008-03-24T22:28:55Z

HIV Replication Animation
http://bioisolutions.blogspot.com/2008/02/hiv-replication-animation.html
or

ttp://tinyurl.com/37zo4n

Muscle contraction Animation

http://bioisolutions.blogspot.com/2008/02/muscle-contraction.html

http://tinyurl.com/2k7kux

Stroke Animation
http://bioisolutions.blogspot.com/2008/02/stroke-animation_21.html

http://tinyurl.com/33qntr

Sarcomere Contraction Animation

http://bioisolutions.blogspot.com/2008/02/sarcomere-contraction-animation.html

http://tinyurl.com/33n2hv

Function of the Neuromuscular Junction

http://bioisolutions.blogspot.com/2008/02/function-of-neuromuscular-junction.html

http://tinyurl.com/325xgl
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Re: Call for papers on NSCs

2008-03-24T09:36:56Z

On Jan 30, 8:15 pm, neural.stem.cells.EJ...@... wrote:

> Call for papers on Neural Stem Cells!
>
> You are now invited to submit Neural stem cell studies being conducted
> in your own labs. This special issue will be a great chance for peer
> communication and seeking for national collaborations. Please submit
> such contributions before March 1.
>
> Further, you may contribute short-reviews as well as original articles
> on topics in but not limitted to following lists:
>
> Neural Stem Cells transplantation;
> Neural Stem Cell differentiation;
> Adult neurogenesis & neural stem cell niche;
> History and opinions on Neural Stem Cell research (especially in your
> own country);
> New methdology for Neural Stem Cell research;
> Therapeutical application.
>
> Manuscripts could be submitted via WORD (DOC) attachment in email and
> you will soon acknowledge with a receipt.
>
> submission to: n...@...
> submission to: neural.stem.cells.ej...@...
>
> Cheers,
>
> Special Issue on Neural Stem Cells
>
> eJBio Editoral Broad
> __________________________________
>
> Electronic Journal of Biology

sir,
i am working as a lecturer in engineering college and wishes to carry
out the research work in the biophysics field by expecting your
guidance i am writing here and by seeing your reply i will contribute
my knowledge about neuralogy
with regards
srinivas
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Re: biotech videos

2008-03-21T10:46:04Z

Am 19.03.2008, 08:52 Uhr, schrieb j_thomas <julianthomasp@...>:

> Sodium-Potassium pump
>
> http://bioisolutions.blogspot.com/2008/02/sodium-potassium-pump.html

One should however point out that the model used is somewhat
oversimplified, it does not account for E1/E2 transition or the
oligoprotomeric nature of the enzyme. For highschools certainly ok, for
undergrads perhaps but insufficient for advanced students.
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First Announcement: 6th International NCCR Symposium on New Trends in Structural Biology, September 8 + 9, 2008

2008-02-11T00:31:12Z

Dear colleagues,

it is our pleasure to announce the 6th International NCCR Symposium
taking place this September.

First Announcement:

6th INTERNATIONAL NCCR SYMPOSIUM ON NEW TRENDS IN STRUCTURAL BIOLOGY
September 8 + 9, 2008
Lecture Hall KOH B10, University of Zurich, Switzerland

Confirmed speakers to date:
Stephen Kowalczykowski ¦ Keiichi Namba ¦ Poul Nissen ¦ Andrej Sali ¦ A.
Joshua Wand

www.structuralbiology.uzh.ch/symposium2008.asp

The registration slot opens end of March.
Online registration will be possible directly from the above mentioned
web site.

The symposium will be followed directly by the Annual Meeting of the
Swiss Society for Crystallography with two or three additional short
lectures. Participants of the NCCR Symposium are invited to join this
event as well.

We do hope that this conference is of interest to you and would be
pleased to welcome you in Zurich this fall.

With best regards,
Patrick Sticher

_________________________________
Visit the NCCR on the Internet
www.structuralbiology.uzh.ch

Dr. Patrick Sticher Moser
NCCR Scientific Officer
Institute of Biochemistry
University of Zürich
Winterthurerstrasse 190
CH - 8057 Zürich

Phone +41 / (0)44 / 635 54 84
Fax +41 / (0)44 / 635 59 08
Mail sticher@...

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George Mrevlishvili

2008-02-10T10:50:51Z

The internationally renowned biophysicist, our mentor, colleague, and
dear friend George Mrevlishvili has passed away on February 8, 2008 at
age 69. George Mrevlishvili was an extraordinary stimulating teacher
deeply committed to the highest standards in academic achievement and
the advancement of young scientists.

His creativity, foresight, generous heart, humanity and sense of
humor, as well as his many other talents made him a vibrant
personality who greatly influenced his students, colleagues and
scientific collaborators. The significance of his work goes beyond the
boundaries of biophysics and thermodynamics of biological
macromolecules. It will influence our minds and hearts for years to
come.
We will always treasure his dear memory and strive to apply his high
standards to our research and teaching.

Condolences can be sent to Tbilisi State University at
usc@...
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chemical pinging mechanism?

2008-01-23T14:37:10Z

Dear all,

I am wondering if anyone knows any biological examples of the following
mechanism, or something close to it:

A cell emits a chemical A that diffuses outward and comes in contact
with another cell (or target). The target is then triggered to produce
another chemical B, that diffuses back to the cell that prodiced A. This
cell then uses B as a chemoattractant/repellent to move towards or away
from the target. Are there any examples of
such chemical pinging mechanisms in Nature? I think bacterial
aggregation is different from what I have in mind.

Thank you,

Tom

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Lecture on Protein Ligand Modelling

2008-01-01T08:20:25Z

Lecture on Protein Ligand Modelling

http://bioisolutions.blogspot.com/2007/12/protein-ligand-modelling.html

or

http://tinyurl.com/227kty

--
Sincerely,
Julian Thomas
http://bioisolutions.blogspot.com/
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Practical Course on Biomolecular Modelling

2007-07-26T04:15:23Z

Dear colleagues,

please be informed that online applications are accepted for the
following course:

6TH NCCR PRACTICAL COURSE ON BIOMOLECULAR MODELLING

January 6 - 11, 2008
Kandersteg, Switzerland
www.structuralbiology.unizh.ch/course2008.asp

Course topics include
Simulation techniques, force-field development, conformational search,
computation of free energy and entropy, treatment of electrostatic
forces, simulation of folding, comparison of simulation with experiment

This course is primarily directed to PhD students and postdocs from
experimental structural biology groups wishing to learn more on
biomolecular modelling. The course format will include morning lectures
and late-afternoon/early evening tutorials, and provide ample
opportunities for discussions with experts and fellow participants. The
course will be organized as a winter retreat in the Swiss Alps offering
a stimulating learning atmosphere with the afternoons available for
informal participation in discussions, reading, self-study or
recreational activities in the area.

Interested candidates are encouraged to apply online on
www.structuralbiology.unizh.ch/course2008.asp. Application deadline will
be October 10. We will be able to accept 20 participants to this course.

Best regards,
Patrick Sticher

--

Dr. Patrick Sticher Moser
NCCR Scientific Officer
Institute of Biochemistry
University of Zürich
Winterthurerstrasse 190
CH - 8057 Zürich

Phone +41 / (0)44 / 635 54 84
Fax +41 / (0)44 / 635 59 08
Mail sticher@...

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Unraveling the physics of DNA's double helix

2007-07-13T02:56:31Z

Researchers at Duke University's Pratt School of Engineering have
uncovered a missing link in scientists' understanding of the physical
forces that give DNA its famous double helix shape.

http://theanalystmagazine.com/pr/368.htm

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Re: Dagan 8100-1 Single Electrode Voltage Clamp on eBay

2007-06-11T13:53:08Z

On Jun 4, 1:22 pm, timewarptradingp...@... wrote:
> Dagan 8100-1 Single Electrode Clamp Electrophysiology
> Intracellular Clamping Study Cell Membrane Electricity Item number:
> 290125397744
>
> Thought this Voltage Clamp Instrument would be of interest to the
> research community.
> Seems a rarity on eBay. Hope someone could use it!
>
> http://cgi.ebay.com/ws/eBayISAPI.dll?ViewItem&ih=019&sspagename=STRK%...

Still no bids? Maybe you should ship it to the customer for free (say,
a reputable buyer such as a university) and then let them pay you what
they think it's worth. Worst case for you is an underpaid item that
you're unlikely to sell otherwise.

--
Joe

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Dagan 8100-1 Single Electrode Voltage Clamp on eBay

2007-06-04T11:22:35Z

Dagan 8100-1 Single Electrode Clamp Electrophysiology
Intracellular Clamping Study Cell Membrane Electricity Item number:
290125397744

Thought this Voltage Clamp Instrument would be of interest to the
research community.
Seems a rarity on eBay. Hope someone could use it!

http://cgi.ebay.com/ws/eBayISAPI.dll?ViewItem&ih=019&sspagename=STRK%3AMESE%3AIT&viewitem=&item=290125397744&rd=1&rd=1

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Final Call for Papers--BIC-TA2007

2007-04-19T08:54:41Z

I'd like to apologize if you receive multiple emails.

****************************************************************************

CALL FOR PAPERS

2nd International Conference on

BIO-INSPIRED COMPUTING: THEORIES AND APPLICATIONS (BIC-TA2007)

Zhengzhou University of Light Industry, Zhengzhou, China

September 14-17, 2007

****************************************************************************

BIC-TA2007 paper submission Deadline has been extended to May 10, 2007

****************************************************************************

Organized by

Peking University, China
Zhengzhou University of Light Industry, China
Huazhong University of Science & Technology, China

Hosted by

Zhengzhou University of Light Industry, China

Co-Hosted by

Zhengzhou University, China
Zhongyuan University of Technology, China

Sponsors

National Natural Science Foundation of China
Henan Engineering Research Center for Biotechnology

****************************************************************************

BIC-TA2007 aims to provide a high-level international forum for researchers
working in the main areas of natural computing inspired from biology to
present their recent results and exchange ideas.

The conference includes, but not limited to the following topics:

A. Theories and Methodologies
A1 Neural Networks
A2 Evolutionary Computing and Genetic Algorithms
A3 DNA and Molecular Computing
A4 Membrane Computing
A5 Biological Computing
A6 Swarm Intelligence
A7 Autonomy-Oriented Computing
A8 Cellular and Molecular Automata

B. Applications
B1 Bioinformatics and Cheminformatics
B2 Computational Biology and Drug Design
B3 Systems Biology and Synthetic Biology
B4 Computational Genomics and Proteomics
B5 Computational Neuroscience
B6 Artificial Life and Artificial Immune Systems
B7 Signal Processing and Pattern Recognition
B8 Financial Engineering and Electronic Commerce
B9 Data Fusion, Knowledge Discovery and Data Mining
B10 Natural Language Processing and Expert Systems
B11 Computer Security and Computer Vision
B12 Circuit Design and Signal Processing
B13 Biological Implementation and Molecular Implementation
B14 DNA Nanotechnology
B15 Web and Network Application
B16 Multi-Objective Optimization
B17 Other Applications

****************************************************************************

Deadlines

Submission Deadline: 10 May, 2007
Notification of Acceptance: 10 June, 2007
Final Version for the Pre-proceedings: 25 June, 2007

****************************************************************************

Authors should submit a soft copy of their manuscripts with pdf format only
to the conference via the online submission systems.

The submission of a paper implies that the paper is original and has not been
submitted to elsewhere for possible publication. All submissions will be
peer-reviewed by experts in the field based on originality, significance,
quality and clarity. The papers will be prepared in LNCS style (available at
http://www.springer.de or our website) with no more than 12 pages.

A pre-proceedings volume will be available during the conference. The expanded
and revised version of all accepted papers at BIC-TA 2007 will be published
after the conference in international journals indexed by SCI-Expanded.

The latest information on BIC-TA2007 and related Special Issues of journals are
available at: http://www.bic-ta.org

****************************************************************************

Tel: +86-371-63627289

Fax: +86-371-63556791

Email: bicta2007@...; sec@...

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Re: A Thought Experiment: Impications of Quantum Physics in Genetics - A New Paradigm

2007-04-14T11:45:32Z

On Apr 14, 8:45 am, "Morpheal" <morph...@...> wrote:

> Implications of Quantum Physics in Genetics - A New Paradigm
>
> This is a thought experiment with broad implications for the
> understanding of genetics
> and the relation of genetics to quantum physics.
>
> The fundamental question we are going to consider is whether amino
> acids are a sufficient basis for storing all of the necessary
> information for the reproduction of an organism.
>
> Those who know what it takes to convey all of the information to build
> a relatively simple machine, such as an automobile will have a better
> appreciation of the analogy we are going to utilize in attempting to
> answer the fundamental question. Every part that comprises the
> automobile requries fully detailed drawings.

If we take a sand castle and somehow could measure the quantum
distribution of effects and fields, and then scattered the structure,
leaving different arrangements of distribution and effects, then
brought it back together, would this arrangement of sand micro rocks,
subsume the same field arrangment as before?

If we gather matter together could it be possible to remotely arrange
quantum fields and particle through subsumption architecture by
influence scaler phenonemon?

A subsumption architecture is a way of decomposing complicated
intelligent behaviour into many "simple" behaviour modules, which are
in turn orgnized into layers. Each layer implements a particular goal
of the agent, and higher layers are increasingly more abstract. Each
layer's goal subsumes that of the underlying layers, e.g. the decision
to move forward by the eat-food layer takes into account the decision
of the lowest obstacle-avoidance layer.

http://en.wikipedia.org/wiki/Subsumption_architecture

Genghis - Subsumption Architecture.

...Brooks's ideas gelled in a cockroachlike contraption the size of a
football called "Genghis." Brooks had pushed his downsizing to an
extreme. Genghis had six legs but no "brain" at all. All of its 12
motors and 21 sensors were distributed in a decomposable network
without a centralized controller. Yet the interaction of these 12
muscles and 21 sensors yielded an amazingly complex and lifelike
behavior.

Each of Genghis's six tiny legs worked on its own, independent of the
others. Each leg had its own ganglion of neural cells-a tiny
microprocessor-that controlled the leg's actions. Each leg thought for
itself! Walking for Genghis then became a group project with at least
six small minds at work. Other small semiminds within its body
coordinated communication between the legs. Entomologists say this is
how ants and real cockroaches cope-they have neurons in their legs
that do the leg's thinking.

In the mobot Genghis, walking emerges out of the collective behavior
of the 12 motors. Two motors at each leg lift, or not, depending on
what the other legs around them are doing. If they activate in the
right sequence-Okay, hup! One, three, six, two, five, four!-walking
"happens."

No one place in the contraption governs walking. Without a smart
central controller, control can trickle up from the bottom. Brooks
called it "bottom-up control." Bottom-up walking. Bottom-up smartness.
If you snip off one leg of a cockroach, it will shift gaits with the
other five without losing a stride. The shift is not learned; it is an
immediate self-reorganization. If you disable one leg of Genghis, the
other legs organize walking around the five that work. They find a new
gait as easily as the cockroach.

In one of his papers, Rod Brooks first laid out his instructions on
how to make a creature walk without knowing how:

There is no central controller which directs the body where to put
each foot or how high to lift a leg should there be an obstacle ahead.
Instead, each leg is granted a few simple behaviors and each
independently knows what to do under various circumstances. For
instance, two basic behaviors can be thought of as "If I'm a leg and
I'm up, put myself down, " or "If I'm a leg and I'm forward, put the
other five legs back a little."

These processes exist independently, run at all times, and fire
whenever the sensory preconditions are true. To create walking then,
there just needs to be a sequencing of lifting legs (this is the only
instance where any central control is evident). As soon as a leg is
raised it automatically swings itself forward, and also down. But the
act of swinging forward triggers all the other legs to move back a
little. Since those legs happen to be touching the ground, the body
moves forward.

Once the beast can walk on a flat smooth floor without tripping, other
behaviors can be added to improve the walk. For Genghis to get up and
over a mound of phone books on the floor, it needs a pair of sensing
whiskers to send information from the floor to the first set of legs.
A signal from a whisker can suppress a motor's action. The rule might
be, "If you feel something, I'll stop; if you don't, I'll keep
going."

While Genghis learns to climb over an obstacle, the foundational
walking routine is never fiddled with. This is a universal biological
principle that Brooks helped illuminate-a law of god: When something
works, don't mess with it; build on top of it. In natural systems,
improvements are "pasted" over an existing debugged system. The
original layer continues to operate without even being (or needing to
be) aware that it has another layer above it.

http://www.kk.org/outofcontrol/ch3-b.html

There are three kinds of "scopes" we can look through at one time and
one scale of observation;

Microscope
Mesoscope
Macroscope

Pretext: will become "mico-scale"
Text: will become "root-scale" or "middle-scale"
Context: will become "macr-scale"

THREE SCALES:

(-1) - Micro-scale: A prefix denoting very small size; e.g.
microgamete, micronucleus.

( 0) - Meso-scale: In meteorology, describing systems, or patterns of
systems between small and synoptic [The term means 'simultaneous']
scale; dimensions of between about 10 and 100 km across, in the
horizontal, have been suggested.

(+1) - Macro-scale: Large-scale. Thus, a macroclimate is the general
climate of a region extending across several hundred kilometres, such
as the Great Plains of North America, macrometeorology is the study of
large scale meteorological phenomena which can cover hundreds of
kilometres or may encompass the whole globe, from monsoons to the
general circulation of the atmosphere, and macro-economics is the
study of an economy as a whole.

Shifting focus upon different "scales" (attention to one area of a
hierarchy) can be illustrated with an analogy from grammatical
stucture and hierarchy. [In music theory a scale is those notes within
a group that don't repeat the same tone at a higher of lower octives.
When the same note is reached in a different scale of a higher or
lower pitch then it is another octive. (you can ignore this part)]

If we focus upon a word it becomes the "meso-scale" in which the micro-
scale is letters it consists (reductionism) and the macro-scale is the
sentence in which it might fit (productionism or synductionism).

At the next level up the scale the sentence would become the "meso-
scale" with words being micro-scale in which the sentence consists
(reductionism) and a paragraph would be a macro-scale, where a
sentence is a part (productionism or synductionism).

------------------------------

If a morpheme is the smallest language unit that carries a semantic
interpretation I am wondering what the morpheme_root "duction" means.

The root is the primary lexical unit of a word, which carries the most
significant aspects of semantic content and cannot be reduced into
smaller constituents.

Duction: The act of leading, bringing, or conducting.

re: backa, gain, repeatedly

meso: middle

syn: together, united, at the same time

Making this up today but I need the meaning of the ;

re-duction-ism
meso-duction-ism
syn-duction-ism

micro-analysis
meso-analysis
macro-analysis

super-structure
root-structure
sub-structure

Why hasn't this awesome perspective elaborated in current metaphysics?

http://www.virtualsalt.com/roots.htm
http://en.wikipedia.org/wiki/List_of_prefixes_in_the_English_language
http://en.wikipedia.org/wiki/Morpheme

http://xrefer.com/entry/462106
http://xrefer.com/entry.jsp?xrefid=610070
http://xrefer.com/entry.jsp?xrefid=609978

Microtubules are cylindrical molecules made by gluing together 13
strands of the protein, tubulin, to make a tube 25 nanometres across,
with a central channel about 15 nanometres wide. Each microtubule is
covered by a fuzz of protein stubs, known as MAPs (microtubule
associated proteins), and these can be used to hook clusters of
microtubules together into larger lattices. Both microtubules and MAPs
seem to be capable of a certain amount of movement, meaning that they
can be woven into plastic structures, able to give and bend.

The structural properties of microtubule assemblies make them a
valuable building material within cells. For example, a bundle of 20
microtubules form the beating, hair-like cilia that coat the surface
of many small single-celled animals, allowing them to swim. However
the main use for microtubules appears to be to make an internal
skeleton for cells-an intricate scaffolding that gives a cell its
shape but also can deform and bend enough to allow it to move.

The existence of the microtubule cytoskeleton was discovered only
relatively recently in the 1970s-previously the fixative chemicals
used in electron microscopy was having the unfortunate effect of
dissolving the tubules-so biologists still have much to learn about
what the cytoskeleton does and how it operates. Yet biologists believe
that it not only holds a cell in shape but also plays an important
role in cell metabolism, acting as a piping system or an internal
highway to move plasma and other essential cell products about the
cell. Some have suggested microtubules might do this by using their
MAP spurs to drag cell protoplasm along, hand over hand, in a
miniature bucket brigade running up the sides of a tubule.

There is also evidence that the cytoskeleton could serve as a
primitive brain. Biologists have long been puzzled how a simple single-
celled animal, like the slipper-shaped paramecium, could behave so
intelligently when it has no nervous system. A paramecium is
surprisingly nimble as it swims about in pond-bottom detritus,
twisting in and out of tight spaces in search of its dinner. Somehow
the protozoan manages to respond swiftly to information coming in from
a light-sensitive eyespot and its touch-sensitive cilia to co-ordinate
its swimming action. Several biologists have speculated that the
cytoskeleton could serve as the communication and information
processing link needed to organise such relatively complex behaviour.

This suggestion that the cytoskeleton could be a "brain within a
brain" has particularly excited the quantum theorists. In casting
around for a suitable cell structure to operate as a go-between,
connecting the sub-atomic realm with the macroscopic world of firing
brain cells, some theorists had considered that the membranes at the
synaptic junctions between nerve cells might be the site of quantum
interactions. Others had wondered whether the ion channels down the
flanks of neurons could be ruled by quantum effects. But quickly,
microtubules began to look a far better bet. While microtubules are
not unique to neurons, they are found there in particular abundance (a
fact that does not surprise neurologists given that nerve cells are so
metabolically-active and microtubules seem essential to metabolic
activity). Furthermore, the speed at which microtubules can switch
state between relaxation and contraction is believed to be of the
order of a nanosecond. This may be slow by the usual time scales of
quantum events, but it is about a million times faster than the cell
firing events usually believed to underlie consciousness and so at
least appears to get the biology of the system within striking
distance of a quantum explanation.

http://www.btinternet.com/~neuronaut/webtwo_articles.html

> Nowadays parts are often
> modeled in three dimensional representations showing all of the
> necessary features, to scale, so that the component can be reproduced
> accurately. Then the process for its production has to be described in
> sufficient detail to enable the component to be produced. Information
> about what types of material it is to be made from, and what is to be
> done to that material is included along with the representational
> model, drawing of digital file. We also have to consider all of the
> information necessary for making the machines, and operating them.
> This becomes a very large amount of data. Those who work in
> engineering, or manufacturing, know how much data, in digital form,
> can be required for even the simplest part to be described. It is
> staggering as to how much data would be required to describe all of
> the machines and processes going into making that part. It is even
> more staggering if one has to add the human element. Whether the part
> is made by robots, or with human involvement we have to allow for the
> software required to run all of the necessary processes.
>
> Now, compare the complexity of one organ, the human eye, and its
> function, with the complexity of our manufactured machines. The eye
> and its function is incredibly more complex, in both structure and
> function. We now need the representations for every manufacturing
> detail and every process necessary to make every component of the eye,
> and its related structures enabling effective sensory, perceptual, and
> visual memory functions. Not only do we have to detail every
> component but we have to write all of the software to make the system
> function. Although we cannot put a meaningful number to the number of
> bytes of data that would be required, we know that it is very large.
> The software programs necessary to emulate human vision would
> themselves be extremely large, and would challenge most computers.
> Understanding visual information is not a simple process. Storing
> visual memory is not a simple process either. The eye is infinitely
> more complex than the most complex automobile. Its function is
> similarly infinitely more complex than the function of an automobile.
>
> What we then have to do is to extrapolate that understanding to
> include all of the structures and functions of the entire body and the
> mind-brain. If we had the means we could attempt a computer simulation
> of how much data would be required to define a specific structure and
> a function, then extrapolate that to give us a rough idea of how much
> data might really be involved.
>
> I am arguing here that amino acid sequences are insufficient means to
> store the necessary data required to build a functioning organism.
> Similarly, we are faced with the problem of data transmission which at
> least cannot fully explain the transfer of sufficient software to
> enable function. It is not simply a question of putting the right
> molecules into place, the way bricks are mortared together onto a
> newly built wall.
>
> What I would suggest is that the amino acid sequences in the DNA helix
> are in fact only the filing cabinets for the balance of the necessary
> information, which is stored at the quantum level. What we have is the
> equivalent of a vast hard drive that stores information at the
> subatomic, quantum, level. When we look at the DNA helix, at the
> molecular level we look at the file folders, without being able to see
> the contents that is stored within those file folders. It is only at
> the quantum level that we can find what I suggest must be best
> described as a quantum holographic model of structure, linked to its
> "software" programs, required for function. A quantum holographic
> model would be the most probable paradigm because it appears to be the
> only way to reduce the total data requirement for the complete package
> of structure and function. Nevertheless, more complex functions
> certainly do require complex "software" programs that a traditional,
> purely mechanistic, paradigm cannot accomodate.
>
> A further implication includes inherent knowledge, learned by
> predecessor organisms, providing information for survival, not having
> to be relearned with each new, successive, generation. Plato's
> anamnesis, recollection of knowledge outside of immediate experience,
> is then a reality, as some information could be conveyed on the DNA
> helix beyond what is necessary to provide for basic structure and
> function. (As a footnote, citing unpublished experiments performed
> almost two decades ago, we have experimental indications that provide
> some strong indications that inherent information of that type does
> exist and plays a role in human reactions to their lived environments.
> This accounts for such phenomena as "collective unconscious" mind,
> where there is a sharing of some common threads of similar information
> inherent from past generations indicating historic socio-cultural
> group affinities as being definitive of its variants. We may also have
> the answer to some instances of alleged "reincarnation" where entire,
> historically verifiable, memories can be idenfitied without that
> information being learned within an individual's own lifetime. Our
> expectation is that such instances do occur, and that experiences that
> are deemed more significant to survival, having had what is felt to be
> a strong impact on the previous generation organism's survival, and
> potentially an impact on species survival, tend to be the type of
> experiences that are recorded onto the DNA helix. Studies of
> "reincarnation" anomalies support that contention.)
>
> Bob Ezergailis
> Hamilton, Canada
> April 13, 2007

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A Thought Experiment: Implications of Quantum Physics in Genetics - A New Paradigm

2007-04-14T09:52:04Z

Implications of Quantum Physics in Genetics - A New Paradigm

This is a thought experiment with broad implications for the
understanding of genetics
and the relation of genetics to quantum physics.

The fundamental question we are going to consider is whether amino
acids are a sufficient basis for storing all of the necessary
information for the reproduction of an organism.

Those who know what it takes to convey all of the information to build
a relatively simple machine, such as an automobile will have a better
appreciation of the analogy we are going to utilize in attempting to
answer the fundamental question. Every part that comprises the
automobile requries fully detailed drawings. Nowadays parts are often
modeled in three dimensional representations showing all of the
necessary features, to scale, so that the component can be reproduced
accurately. Then the process for its production has to be described in
sufficient detail to enable the component to be produced. Information
about what types of material it is to be made from, and what is to be
done to that material is included along with the representational
model, drawing of digital file. We also have to consider all of the
information necessary for making the machines, and operating them.
This becomes a very large amount of data. Those who work in
engineering, or manufacturing, know how much data, in digital form,
can be required for even the simplest part to be described. It is
staggering as to how much data would be required to describe all of
the machines and processes going into making that part. It is even
more staggering if one has to add the human element. Whether the part
is made by robots, or with human involvement we have to allow for the
software required to run all of the necessary processes.

Now, compare the complexity of one organ, the human eye, and its
function, with the complexity of our manufactured machines. The eye
and its function is incredibly more complex, in both structure and
function. We now need the representations for every manufacturing
detail and every process necessary to make every component of the eye,
and its related structures enabling effective sensory, perceptual, and
visual memory functions. Not only do we have to detail every
component but we have to write all of the software to make the system
function. Although we cannot put a meaningful number to the number of
bytes of data that would be required, we know that it is very large.
The software programs necessary to emulate human vision would
themselves be extremely large, and would challenge most computers.
Understanding visual information is not a simple process. Storing
visual memory is not a simple process either. The eye is infinitely
more complex than the most complex automobile. Its function is
similarly infinitely more complex than the function of an automobile.

What we then have to do is to extrapolate that understanding to
include all of the structures and functions of the entire body and the
mind-brain. If we had the means we could attempt a computer simulation
of how much data would be required to define a specific structure and
a function, then extrapolate that to give us a rough idea of how much
data might really be involved.

I am arguing here that amino acid sequences are insufficient means to
store the necessary data required to build a functioning organism.
Similarly, we are faced with the problem of data transmission which at
least cannot fully explain the transfer of sufficient software to
enable function. It is not simply a question of putting the right
molecules into place, the way bricks are mortared together onto a
newly built wall.

What I would suggest is that the amino acid sequences in the DNA helix
are in fact only the filing cabinets for the balance of the necessary
information, which is stored at the quantum level. What we have is the
equivalent of a vast hard drive that stores information at the
subatomic, quantum, level. When we look at the DNA helix, at the
molecular level we look at the file folders, without being able to see
the contents that is stored within those file folders. It is only at
the quantum level that we can find what I suggest must be best
described as a quantum holographic model of structure, linked to its
"software" programs, required for function. A quantum holographic
model would be the most probable paradigm because it appears to be the
only way to reduce the total data requirement for the complete package
of structure and function. Nevertheless, more complex functions
certainly do require complex "software" programs that a traditional,
purely mechanistic, paradigm cannot accomodate.

A further implication includes inherent knowledge, learned by
predecessor organisms, providing information for survival, not having
to be relearned with each new, successive, generation. Plato's
anamnesis, recollection of knowledge outside of immediate experience,
is then a reality, as some information could be conveyed on the DNA
helix beyond what is necessary to provide for basic structure and
function. (As a footnote, citing unpublished experiments performed
almost two decades ago, we have experimental indications that provide
some strong indications that inherent information of that type does
exist and plays a role in human reactions to their lived environments.
This accounts for such phenomena as "collective unconscious" mind,
where there is a sharing of some common threads of similar information
inherent from past generations indicating historic socio-cultural
group affinities as being definitive of its variants. We may also have
the answer to some instances of alleged "reincarnation" where entire,
historically verifiable, memories can be idenfitied without that
information being learned within an individual's own lifetime. Our
expectation is that such instances do occur, and that experiences that
are deemed more significant to survival, having had what is felt to be
a strong impact on the previous generation organism's survival, and
potentially an impact on species survival, tend to be the type of
experiences that are recorded onto the DNA helix. Studies of
"reincarnation" anomalies support that contention.)

Bob Ezergailis
Hamilton, Canada
April 13, 2007

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Re: Enthalpy of proteins

2007-04-06T09:17:10Z

Jafari wrote:

> My simple question is: is Ha>Hb? or Hb>Ha?

Without further knowledge on what you have to do to get from state A to
state B this question can not be answered. Perhaps you have to break
another ionic bond, or get two equal charges uncomfortably close
together?
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Enthalpy of proteins

2007-03-25T06:01:05Z

Hello
I have a very simple question.
Suppose in a protein folding pathway we have two opposite charged
residues seperated by "d" angstrom such that there is a weak
interaction between them. We name it state A, so its enthalpy is Ha.
As protein conformation changes through folding pathway we suppose
"d"
decreases, so interaction between charges become stronger. Now we
name
it State B and its enthalpy as Hb.

My simple question is: is Ha>Hb? or Hb>Ha?

Thanks

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BIC-TA 2007 Call for Paper

2007-01-28T18:04:13Z

Dear colleague,
Happy New Year! We cordially invite you to attend the 2007 International Conference on Bio-Inspired Computing: Theories and Applications (BIC-TA 2007), which will be held on September 14�C17, 2007 in Zhengzhou Henan Province, China.
The conference is organized by the Peking University, the Zhengzhou University of Light Industry as well as the Huazhong University of Science & Technology, and technically co-sponsored by the Zhongyuan University of Technology, the North China University of Water Conservancy and Electric Power, and financially supported by the National Natural Science Foundation of China.
Just like the name of the conference, the theme for this conference is Bio-Inspired Computing: Theories and Applications. Only original high quality papers related to this theme are especially solicited, including theories, methodologies, and applications in science and technology. Topics covering industrial issues/applications and academic research into bio-inspired computing will be welcome.
All submissions will be thoroughly peer-reviewed by experts in the field based on originality, significance and clarity, only papers presenting novel research results or successful innovative applications are seriously considered for publication.
A pre-proceedings volume will be available during the conference. The expanded and revised version of all accepted papers at BIC-TA 2007 will be published after the conference in international journals indexed by SCI-Expanded.
● Main Topics
The conference includes, but not limited to the following topics.
A. Theories and Methodologies
A1 Neural Networks
A2 Evolutionary Computing and Genetic Algorithms
A3 DNA and Molecular Computing
A4 Membrane Computing
A5 Biological Computing
A6 Swarm Intelligence
A7 Autonomy-Oriented Computing
A8 Cellular and Molecular Automata
B. Applications
B1 Bioinformatics and Cheminformatics
B2 Computational Biology and Drug Design
B3 Systems Biology and Synthetic Biology
B4 Computational Genomics and Proteomics
B5 Computational Neuroscience
B6 Artificial Life and Artificial Immune Systems
B7 Signal Processing and Pattern Recognition
B8 Financial Engineering and Electronic Commerce
B9 Data Fusion, Knowledge Discovery and Data Mining
B10 Natural Language Processing and Expert Systems
B11 Computer Security and Computer Vision
B12 Circuit Design and Signal Processing
B13 Biological Implementation and Molecular Implementation
B14 DNA Nanotechnology
B15 Web and Network Application
B16 Multi-Objective Optimization
B17 Other Applications
● Important Dates
Submission Deadline: 20 April, 2007
Notification of Acceptance: 10 June, 2007
Final Version for the Pre-proceedings: 25 June, 2007
● Web Site: http://www.bic-ta.org/
● E-mail: mailto:bicta2007@...; mailto:sec@...
● Tel: +86-(0)371-63627289
● Fax: +86-(0)371-63556790

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Mechanism of cold denaturation

2007-01-16T02:41:15Z

Hi all
I'm confused about cold denaturation, I read "cold denaturation of
proteins" by privalov, but beside thermodynamics explanation of
this phenomenon there must be molecular mechanism by which
this type of denaturation can be described. for example why
hydrophobic interactionof proteins weakened at low temperature
in spite of lower entropy and what is the role ofwater.
I would be appreciated if anybody give simple description of
thermodynamics concept of this event and also molecular
mechanism of that.
sorry for bad english

Thanks for your help
Protenger

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Postdoc position in biophysics / neuroengineering

2006-08-31T02:59:52Z

I have a postdoc position available in my lab to work on the multinational

European project "VSNs, voltage-sensitive nanoparticles". The project focuses

on the development of a novel technology to monitor membrane potential in

electrogenic cells using nanoparticle plasmon resonance. The selected

candidate will be familiar with electrophysiological techniques and/or

optics. Salary dependent on experience. Start date October 2006.

Send CV, the emails of three people who can provide reference letters and a

brief statement on career goals to: claverol@...

------------------------------------------------------------
Dr. Enric Claverol-Tinturé
Technical University of Catalonia
Lab. Nanobioenginyeria
c/ Josep Samitier 1-5
Barcelona 08028
Spain
Phone: 34 934 037 180
-----------------------------------------------------------

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