Subject: Summer school on "Parallel computing in biomolecular simulations" in Gdansk

From: Adam Liwo <[email-masked]>
Date: Wed, 2 May 2001 13:30:36 +0200 (CEST)

___________________________________________________________________________
|                                                                           |
|                            SUMMER SCHOOL ON                               |
|                                                                           |
|               PARALLEL COMPUTING IN BIOMOLECULAR SIMULATIONS              |
|                                                                           |
|                                                                           |
|                               organized by                                |
|                                                                           |
|                                                                           |
|             Faculty of Chemistry, University of Gdansk, Poland            |
|                                                                           |
|               Academic Computer Center in Gdansk TASK, Poland             |
|                                                                           |
|       Interdisciplinary Center of Mathematical and Computer Modeling      |
|                   (ICM) University of Warsaw, Poland                      |
|                                                                           |
|                              INTEL Poland                                 |
|                                                                           |
|                                                                           |
|           Held in conjunction with the annual meeting of the              |
|   Polish Society of Computational Simulations, 28.08 - 01.09, 2001.       |
|                                                                           |
|                                                                           |
|                                                                           |
|              Saturday, September 1 - Monday, September 3, 2001            |
|                Technical University of Gdansk, Gdansk, Poland             |
|                                                                           |
|                                                                           |
|___________________________________________________________________________|
|                                                                           |
|                         Second  Announcement                              |
|                                                                           |
|             Registration Form - Call for Contributed Papers               |
|                                                                           |
|  ________________________________________________________________________ |
|                                                                           |
|          Web page: http://www.task.gda.pl/ptsk-2001/biomol.html           |
|___________________________________________________________________________|

AIMS

	Computational molecular biology and computational chemistry play a
still increasing role in contemporary science, medicine, agriculture, and
industry. With the advent of high-speed parallel computers it appears now
possible to calculate the pathways of complex chemical reactions, predict
the reactivity of chemical compounds, predict the structure and properties
of crystalline, glassy and metallic systems, predict the structure of
proteins and nucleic acids, and simulate cellular processes at the molecular
level. This finds numerous applications in the design of novel drugs,
materials, fuels, etc. The purpose of this summer school is to give an
overview of the techniques and software used in modern computational
chemistry and molecular biology, as well as to give an insight into the
problems that are currently being investigated by the scientists working
in this field. Special attention will be devoted to the use of parallel
computers. The formula of the summer school should encourage participation
of researchers, students and industry engineers.

LOCATION

	The Summer school on "Parallel computing in biomolecular
simulations" will be held on 01-03.09.2001 on the premises of the
Technical University of Gdansk. The town of Gdansk is situated at the
coast of the Baltic Sea, with an international airport 20 minutes driving
> from the city, good rail and road connections with major cities in Poland
and Europe, and ferry links with Scandinavia.  Gdansk is one of the most
impressive industrial, historic and tourist sites in Poland. It is a
center of shipping, ship-building, commerce as well as chemical,
electronic, telecommunication and food industry. In 1997, Gdansk
celebrated its Millennium. Throughout turbulent times of the twentieth
century, Gdansk was a bone of contention at the eve of the second world
war.  More recently, it was a cradle of the Solidarity movement which
inspired the process of political and economic transformations in Central
and Eastern Europe. Gdansk offers a variety of places of cultural interest,
including old town architecture, museums, churches, and also places for
shopping and leisure.

TOPICS

	The topics of the summer school "Parallel computing in
biomolecular simulations" will include the following:

   1. Quantum chemistry (ab initio and semiempirical methods):

        o prediction of properties of inorganic and organic compounds and
	  materials;
        o reaction path calculations;
        o quantum mechanics of biomolecular systems;
        o photochemical and radiative processes, including DNA damage and
	  repair.

   2. Global optimization in the prediction of the structure of peptides,
      proteins, and crystals.
   3. Inclusion of solvation in quantum-mechanical calculations and
      empirical force fields.
   4. Effect of pH on protein conformation.
   5. Homology modeling and threading in the prediction of protein
      structure.
   6. Software demonstration:  AMBER, ECEPPAK, CRYSTALG, UNRES, GAMESS,
      MCSYM, and other.

KEYNOTE AND INVITED LECTURES

 Dr. Piotr Bala, Nicholas Copernicus University, Poland - "Parallelism in
	classical and quantum-classical molecular dynamics".

 Prof.  Maciej S. Gutowski, Pacific National Laboratories, USA -
	"Stabilization of the zwitterionic forms of amino acids by an
	excess electron in the gas phase".

 Prof.  Jooyoung Lee, Korea Institute for Advanced Study, Korea -
	"Massively parallel computation and conformational space annealing
	method".

 Prof. Bogdan Lesyng, ICM, Poland - TBA.

 Prof. Andrzej Kolinski, University of Warsaw, Poland - "Generalized
	comparative modeling (GENECOMP): a combination of sequence comparison,
	threading, lattice and off-lattice modeling for protein structure
	prediction".

 Prof. Gregory V. Nikiforovich, Washington University, USA - "Restoring
	small, medium and large (up to 60 residues) loops in proteins".

 Dr.  Krzysztof Olszewski, Molecular Simulations Inc., USA - "Automated
	knowledge extraction from predictive structural models".

 Prof.  Lucjan Piela, University of Warsaw, Poland - "Deformation methods
	in global optimization".

 Dr. Jaroslaw Pillardy, Cornell University, USA - "Structure prediction by
	global optimization of a potential function: proteins, polypeptides,
	and crystals".

 Dr. Daniel R. Ripoll, Cornell University, USA - "The ECEPPAK program for
	conformational analysis of peptides and proteins".

 Prof. Irena Roterman, Jagiellonian University, Poland - "Capabilities and
	restrictions of molecular dynamics".

 Prof. Harold A. Scheraga, Cornell University, USA - TBA.

 Dr. Mark D. Shenderovich, Structural Bioinformatics Inc., USA -
	"Computational phenotyping of HIV protease - inhibitor complexes".

 Prof. Jeffrey Skolnick, Danforth Plant Sciences Center, USA - "Genome
	scale prediction of protein structure and function".

 Prof. Andrzej Sokalski, Technical University of Wroclaw, Poland -
	"Modeling interactions in large molecular systems and inhibitor design".

 Prof. Jorge A. Vila, Universidad Nacional de San Luis, Argentina -
	"Theoretical study of linear tetrapeptides in solution. A test of
	different solvation models".

SCIENTIFIC COMMITTEE

Prof. Andrzej Kolinski, University of Warsaw, Poland; Prof. Jooyoung Lee,
Korea Institute for Advanced Study, Korea; Prof. Bogdan Lesyng, ICM,
Poland;  Prof. Adam Liwo, University of Gdansk, Poland; Prof.  Gregory V.
Nikiforovich, Washington University, USA; Prof.  Lucjan Piela, University
of Warsaw, Poland; Dr.  Daniel R. Ripoll, Cornell University, USA; Prof.
Irena Roterman, Jagiellonian University, Poland;  Prof. Harold A.
Scheraga, Cornell University, USA; Dr. Mark D. Shenderovich, Structural
Bioinformatics Inc., USA; Prof. Jeffrey Skolnick, Danforth Plant Sciences
Center, USA; Prof. Jorge A. Vila, Universidad Nacional de San Luis,
Argentina.

ORGANIZING COMMITTEE

Prof. Adam Liwo, Gdansk, Poland (Chairman); Dr. Jaroslaw Rybicki, Gdansk,
Poland (V-ce Chairman); Dr.  Sylwia Rodziewicz-Motowidlo, MSc.  Bartosz
Pliszka, Gdansk, Poland (Secretaries); Dr.  Cezary Czaplewski, Gdansk,
Poland; Dr.  Stanislaw Oldziej, Gdansk, Poland; Prof. Bogdan Lesyng,
Warsaw, Poland.

LANGUAGE

The official language of the Summer School will be English.

ABSTRACT SUBMISSION

Abstracts can be submitted by one of the following three ways:

    o By regular mail to: Dr.  Sylwia Rodziewicz-Motowidlo, Faculty of
      Chemistry, University of Gdansk, Sobieskiego 18, 80-952 Gdansk,
      Poland. Please submit two copies of your abstract.  The sheet(s)
      must not be folded to enable direct reproduction. LATEX and Word
      templates for abstract preparation are available on the Conference
      web site. An ASCII version of the template with instructions is
      also attached to this announcement.

    o By e-mail to [email-masked]. The subject line should begin with
      the word ABSTRACT and contain the name of the corresponding author.
      The electronic version of the abstract, together with all pertaining
      graphics files, should be included as an attachment. Virtually all
      mailers, such as pine or Netscape Mail contain the attachment
      utility. If you use an old-style mailer, encode the binary files
      for for 7-bit transmission, using the UNIX or DOS uuencode utility
      and include the uuencoded files in the body of the message.
      Abstracts prepared with LATEX, which are in ASCII format can be
      included in the message body directly. Any DOS, Windows or
      Unix-compatible word processor can be used. Using MacIntosh word
      processors is discouraged to avoid the risk of misconversion.
      Microsoft Word, LATEX, and WordPerfect are recommended. All
      non-standard stylevles used when preparing the abstract with LATEX
      must be included with the abstract.

    o On-line submission using the Conference web site:
      (http://www.task.gda.pl /ptsk-2001/biomol/submit.html). Follow the
      instructions of the submission form.

PUBLICATION

	Both lecturers and other participants will be asked to contribute
a paper to a special issue of TASK Quarterly.  All manuscripts will undergo
regular peer-reviewing process.  See http://www.task.gda.pl/quart/ for
instructions for authors.

ACCOMMODATION

	For participants who wish so accommodation will be provided in
Student Hostel DS1 (hotel standard; located within walking distance from
the Technical University of Gdansk) at a cost of 55 zl (approximately $14)
per night. The address is: ul. Traugutta 115 80-266 Gdansk Wrzeszcz, tel.
+48 58 347-15-97.

	The participants of the PTSK (Polish Society of Computer
Simulation) Workshops who wish to take part in the School can be
accommodated in the Workshops site at Sobieszewo or in the DS1 Students
Hostel. For participants who prefer to stay elsewhere, the organizers can
assist in arranging hotel accommodation; please indicate in the
registration form, if you wish so.  Below are the addresses and phone
numbers of the hotels located near the School site.

"SZYDLOWSKI" ul. Grunwaldzka 114, (+48 58) tel. 345-70-40 - 370 zl single
room, 420 zl double room.

"HEVELIUS" Orbis S.A. ul. Heweliusza 22, tel. 321-00-00 - 420 zl single
room, 515 zl double room.

"HOLIDAY INN" ul. Podwale Grodzkie 9, tel. 300-60-00, fax 300-60-11
e-mail: [email-masked], web page:
http://www.holidayinn.pl/gdansk/ - 150 ECU (550 zl) single room, 180 ECU
(650 zl) double room; the rates on weekends
 are 180 ECU (380 zl) and 126 ECU (450 zl), respectively.

"JANTAR" ul. Dlugi Targ 19, tel. (+48 58) 301-95-32 - 80 zl per person
(single and double rooms; breakfast included).

"RO-KO" ul. Traugutta 29, (+48 58) tel. 347-77-88 - 100 zl double room,
132 zl triple room.

Follow the "Turystyka" link of http://www.gdansk.pl/ for more hotel
information.

SOCIAL EVENTS

	Welcome Party and Conference Dinner are planned on September 1 and
September 3, respectively. Depending on the number of those interested, a
sightseeing trip to the Old Town of Gdansk and/or other interesting places
(the curort of Sopot, the Marine Life Museum in Gdynia) will be organized.
A special sightseeing program for accompanying persons will be organized
(costs included in accompanying persons' registration fee).

TRAVEL

	Gdansk (Danzig) is a part of the Gdansk-Sopot-Gdynia Tricity chain
located at southern Baltic. Gdansk's airport Rebiechowo is ~10-15 km away
> from the city center and serves limited international `ights (e.g., from
and to London, Hamburg, and Copenhagen), as well as domestic `ights from
and to Warsaw, whose international Okecie airport serves worldwide
connections by air. There is also a reliable express and InterCity train
service between Warsaw and Gdansk (4 h trip) and direct train connections
with Berlin (9 h trip). Trains between Warsaw and Gdansk run every hour
during daytime.

FEE

	The complete fee is 700 zl (180 USD) and 415 zl (104 USD) for
undergraduate and graduate students, as well as academic employees below
Ph.D. degree. The fee covers regi stration, accommodation in DS1 Students
Hostel (see "Accommodation"), and meals at the Technical University of
Gdansk caffeteria.  Participants who do not wish to stay at the DS1
Students Hostel pay 535 zl (138 USD) or 250 zl (63 USD), respectively.
Important: Participants of PTSK Workshops (August 30, September 1, 2001)
can participate in this Summer School at a fee of 400 zl covering the cost
of additional accommodation in the Workshops site at Sobieszewo or in the
vicinity of the School site. Those persons DO NOT pay the registration and
accommodation fee specived above.  For information about the Workshops see
http://www.task.gda.pl/ptsk-2001/

Payment should be made by bank transfer to

Wydzial FTiMS PG, ul. Narutowicza 11/12, 80-952 Gdansk, Poland
Summer school on "Parallel computing in biomolecular simulations"

bank account:

Wielkopolski Bank Kredytowy SA, Oddzial Gdansk 10901098-2903-128-00-0.

with the annotation "Zadanie nr 014772" (very important!).

Also, indicate the names of persons paid for.

REGISTRATION

	Participants can register by filling out the attached form. Mail
the form together with a copy of bank transfer record to:

Dr. Sylwia Rodziewicz-Motowidlo
Secretary, Summer School
"Parallel computing in biomolecular simulations"
Faculty of Chemistry, University of Gdansk
ul. Sobieskiego 18, 80-952 Gdansk, Poland
tel. +48 58 345 0361, fax +48 58 341 0357

The other option is to register on line at
http://www.task.gda.pl/ptsk-2001/biomol/registration.html.  If so, mail or
fax the copy of bank transfer record to the address given above. On-line
registration will open on May 9, 2001.

CORRESPONDENCE

	All regular-mail correspondence should be directed to the address
printed above. E-mail should be sent to [email-masked]. The web page
of the School is: http://www.task.gda.pl/ptsk-2001/biomol.html

PRESENTATIONS

	Poster stands will be provided for poster sessions.  Visual
equipment: overhead and slide projectors, as well as a computer projector
will be provided for oral presentations. An IMB PC machine with
Windows/Linux systems will be available for computer presentations.

IMPORTANT DEADLINES

    o Abstract submission - July 15, 2001.
    o Registration & Payment - July 22, 2001.

________________________________cut here_____________________________________

                    Registration and Accommodation Form

                             SUMMER SCHOOL ON

               Parallel computing in biomolecular simulations

               September 1 - September 3, 2001, Gdansk, Poland

   Family Name ______________________________________________________________

   Given Name _______________________________________________________________

   Title: Prof.___  Dr.___  MSc.___  Mr.___  Mrs.___  Ms.___

   Institution________________________________________________________________

   Mailing address____________________________________________________________

   ___________________________________________________________________________

   Country_____________Postal Code____________________________________________

   E-mail ____________________________________________________________________

                          *
   Presentation preference  oral ___     poster ___
                           #
   Regular registration fee  _______________________________________ 535zl ___

   or student's & young scientist registration _____________________ 250zl ___

   Accompanying person(s) _______________________________________ x 200 zl ___

   Accommodation at DS1 Students Hostel (Sept.1-Sept.3, 2001) ___ x 165 zl ___

   Extra night Aug. 29/Sept. 1 + supper __________________________ x 70 zl ___

   Total payment ______________________________________________________ zl ___

   Please pay by bank transfer to Wielkopolski  Bank  Kredytowy  SA,  Oddzial
   Gdansk, 10901098-2903-128-00-0; account owner: Wydzia_l FTiMS PG ul.
   Narutowicza 11/12 80-952 Gdansk, Poland with annotation "Zadanie nr
   014772" (very important!). Include the list of persons paid for.

   Need hotel reservation ___    Preferred hotel (list in decreasing order;
   see p .5 for hotels located closely to the School site) ___________________

   ___________________________________________________________________________

   Date of Arrival________________________________Date of Departure___________

   If you will arrive by plane in Gdansk, give arrival time and flight number

   ___________________________________________________________________________

   Sightseeing tours: Old Town of Gdansk ___  Westerplatte ___  Oliva Cathedral
   (including organ concert) ___   Sopot curor ___  Marine Life Museum
   in Gdynia ___
   (tours will be paid on site)

   Food preferences:  Kosher ___  Vegetarian ___  Diet  ___  Other (please
   describe):
   ___________________________________________________________________________

   ___________________________________________________________________________

   ___________________________________________________________________________

   Special wishes/Remarks ____________________________________________________

   ___________________________________________________________________________

   ___________________________________________________________________________

   ___________________________________________________________________________

   ___________________________________________________________________________

   ___________________________________________________________________________

   ___________________________________________________________________________

   Date________________Signature______________________________________________

     MAIL OR FAX THE FORM & A COPY OF BANK-TRANSFER RECORD TO:

     Dr. Sylwia Rodziewicz-Motowidlo, Secretary, Summer School
     "Parallel computing in biomolecular simulations",
     Faculty of Chemistry, University of Gdansk, Sobieskiego 18,
     80-952 Gdansk, Poland, FAX: +48 58 341 0357

     or e-mail the form to [email-masked] (this address will become
     active on May 9, 2000) and mail or fax a copy of bank-transfer
     record to the address above.

-----
   *
    For those interested in presenting a contribution. Final selection of
    contributions for oral presentations will be made by the Scientific
    Committee.

   #
    Registered participants of PTSK workshops (August 30 - September 1,
    2001) do not pay the above fee; instead they add 400 zl to their PTSK
    workshop registration fee. See http://www.task.gda.pl/ptsk-2001/ for
    more information.
_____________________________________________________________________________

            Web page: http://www.task.gda.pl/ptsk-2001/biomol.html
         e-mail: [email-masked] (will become active on May 9, 2001)

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

Dr. Adam Liwo
Faculty of Chemistry
University of Gdansk
Sobieskiego 18
80-952 Gdansk, Poland

phone: +48 58 345-0361
fax:   +48 58 341-0357

e-mail: [email-masked]