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 Computater Simulations, 30.08 - 01.09, 2001. Saturday, September 1 - Monday, September 3, 2001 Technical University of Gdansk, Gdansk, Poland

Second Announcement Registration Form - Call for Contributed Papers

Program | Abstracts | Site Map (JPEG 700 KB),

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 and amorphous 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):
   • prediction of properties of inorganic and organic compounds and materials;
   • reaction path calculations;
   • quantum mechanics of biomolecular systems;
   • 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 - "Fast Quantum-Mechanical Generators of the Potential Energy Function for Simulations of Biomolecular and Materials Systems"
• 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 - "Hierarchical ab initio calculation of protein structure"
• 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;
• MSc. Mscislaw Nakonieczny, Gdansk, 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:

• By e-mail to biomol@task.gda.pl. 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 TEX/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, plain TEX, and WordPerfect are recommended. All non-standard stylefiles used when preparing the abstract with LATEX must be included with the abstract.
• On-line submission using the Conference web site. Follow the instructions of the submission form.
• 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.

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 to 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) Workshop 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: smm@holidayinn.gdansk.pl, 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

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 Workshop (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 Workshop 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 Workshop 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 biomol@task.gda.pl. 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

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