Physics and Biology of Proteins

Workshop | Monday, June 12, 2017 - Friday, June 30, 2017
Directors:
Gerald Kneller
Vitor Leite
Adam Liwo
Antti Niemi
Steve Plotkin

Overview

 

The mission of this workshop is to help building a bridge over the gap between physics, where one seeks to understand detailed properties of relatively simple systems, and biology, which studies the overall behavior of highly complex systems. A particularly interesting area where the relative simplicity of a physical system can profitably meet the complexity of life, is the study of biopolymers such as proteins, in particular the so-called protein folding problem.

 

 

A protein folding in a biological system has to be a robust process, the biological function of a protein depends critically on its three dimensional shape. Thus the goal to understand how a protein folds enables us to understand the functioning of living systems. Moreover, a wrong fold is a common cause for a protein to lose its function. A misfolded protein can be dangerous, even fatal, to a biological organism. Thus the ability to accurately describe and control the structure and dynamics of proteins is a problem of utmost importance for biology, pharmacy, and health sciences.

 There are powerful all-atom level computational molecular dynamics techniques developed to model biological macromolecules, to describe the way how a protein folds and the way how proteins interact with each other. The simulations are performed with the highest precision accessible and using the best computational power available, including both commercial and special purpose supercomputers. However, the task is computationally enormous: even the most powerful computer available today for all-atom  dynamics can at most cover a few microseconds of in vitro folding trajectory per a day in silico, and only in the case of a relatively short protein chain. At the same time it takes several seconds, sometimes even days, for a protein to fold into its biologically active conformation, inside a living organism.

 

The enormous computational task of modeling proteins and their dynamics has prompted the development of various coarse grained force fields, where the all-atom level interactions are systematically approximated by effective interactions, using a variety of techniques. Owing to the reduction of representation and averaging of fine-grain degrees of freedom, coarse-grained molecular dynamics enables us to extend the time scale of simulations by 4 and more orders of magnitude compared to all-atom treatment. At the same time, the problem of convergence of the coarse-grained simulations can be addressed by known well-developed techniques in theoretical physics, such as Landau-Wilson approach, originally developed to describe phase transitions and critical phenomena. Alternative approaches make it possible to introduce and utilise various new approximation techniques, such as an expansion in terms of slowly varying fields (small momentum/derivative expansions). Accordingly the goal of the workshop will be to find out, whether the powerful arsenal introduced in modern mathematical and theoretical physics, including the Landau-Wilson approach with ensuing geometry and topology, could be developed to understand why and how a protein folds the way it does.


In terms of the format the goal of the workshop is to organize a stimulative environment for the discussion of principle problems in proteins dynamics and contribute to the development of new techniques to approach them. It is expected that the joint participation of specialists in physics, math, chemistry and biology will increase the efficiency of the proposed meeting and lead to the generation of new interesting ideas in each field separately.

 

The event will be focused on, but not limited to, the following list of topics:

  • Phenomenology of proteins – structures vs physical/chemical/biological properties
  • Energy functions for protein folding and dynamics – all-atoms and beyond
  • Coarse graining
  • Universality – scaling properties and structural building blocks (protein solitons)
  • Computational challenges – what can lattice QCD give to proteins
  • Protein dynamics and energy landscapes
  • Knots in proteins – how they form

 

Program

 

Check this webpage for program updates.

 

The program will include the main conference on the week of June 19 to 23, when the most participation is expected. The details of the conference program can be found at the bottom of this page.

 

Besides the conference minicourses for graduate students on protein research are planned together with a post-conference workshop. The current program of the minicourses include

June 12 to 16

June 26 to 30

  • Hue Sun Chan -- set of 3 lectures on aspects of protein folding.

Poster session is planned for June 19.

 

 Talk titles and abstracts (if available) can be accessed at the bottom of this page.

 

Tentative list of speakers
  • Jørgen Andersen (Aarhus University, Denmark)]
  • Antonio Pereira de Araujo (University of Brasilia, Brazil)
  • Ugo Bastolla (Center of Molecular Biology - UAM, Spain)
  • Hue Sun Chan (University of Toronto, Canada)
  • Laurent Dardenne (National Laboratory of Scientific Computation - LNCC, Brazil)
  • Mark Dennis* (University of Bristol)
  • Yong Duan (University of California - Davis, USA)
  • Olga Dudko (University of California - San Diego, USA)
  • Diego Ferreiro (University of Buenos Aires, Argentina)
  • Hans Frauenfelder* (Los Alamos National Laboratory, USA)
  • Angel Garcia (Los Alamos National Laboratory, USA)
  • Kingshuk Ghosh (University of Denver, USA)
  • Valentin Gordeli (Eber Institute of Structural Biolology, France & ICS - Research Center Juelich, Germany)
  • Konrad Hinsen (Center of Molecular Biophysics - CNRS - Orleans, France)
  • Gerhard Hummer (Max Planck Institute for Biophysics - Frankfurt, Germany)
  • Andrzej Kolinski (University of Warsaw, Poland)
  • Roberto Lins (FIOCRUZ Pernambuco, Brazil)
  • Ralf Metzler (Institute for Physics and Astronomy - University of Potsdam, Germany)
  • Alexander Molochkov (Far Eastern Federal University, Russia)
  • Victor Muñoz (University of California - Merced, USA)
  • Thomas Needham (Ohio State University, USA)
  • Leandro Cristante de Oliveira (UNESP - Rio Preto, Brazil)
  • Ronaldo Junio Oliveira (Federal University of Triangulo Mineiro, Brazil)
  • Jose Onuchic (Rice University, USA)
  • Garegin Papoian (University of Maryland, USA)
  • Xubiao Peng (University of British Columbia, USA)
  • Stefano Piana* (D.E. Shaw Research, USA)
  • Jennifer Ross (University of Massachusetts - Amherst, USA)
  • Gregory Schehr* (LPTMS - Paris-Sud University - Orsay, France)
  • Adam Sieradzan (University of Gdansk, Poland)
  • Joanna Sulkowska (University of Warsaw, Poland)
  • Piotr Sulkowski* (University of Warsaw, Poland)
  • Dave Thirumalai (University of Maryland, USA)
  • Paul Whitford (Northeastern University, USA)
  • Peter Wolynes* (Rice University, USA)
  • Michael Woodside (University of Alberta, Canada)

 * - to be confirmed

 

Registration

In order to assist the organizing staff to timely issue invitation and visa letters, book accommodation and communicate important information, the prospective particpants are kindly asked to regsiter by clicking on the "Register" button at the top of this page.

 

Registration fee

The policy of the International Institute of Physics with respect to organization of events demands collecting a registration fee from the participants. The current ammount of the registration fee is set to

 

400 Brazilian reals for students;

800 Brazilian reals for professionals.

 

Registration deadline: May 14, 2017
 

Location


The city of Natal is located at the north-eastern part of Brazil, closest to Africa and Europe. Home of sandy dunes and magnificent beaches, it is an attractive destination for South American and, more recently, European tourists. We recommend to visit the Wikipedia page of Natal for general information about the city.

 

The event will take place in the new building of the International Institute of Physics on the campus of the Federal University of Rio Grande do Norte (UFRN) in Natal. The participants will have access to the facilities of the IIP, including auditorium, offices, seminar rooms and discussion rooms.

 


Accommodation and Transportation

 

We expect the participants to select their preferred accommodation type. For those participants staying for a short period (up to two weeks) the reasonable choice of the accommodation would be a room in the hotel. In the case of a longer stay, it is advisable to rent an apartment. The recommended location for the accommodation of the IIP guests is Ponta Negra, the coastal district of Natal. Both hotel and apartment reservations can be made through the organizing committee. During the program a bus transportation will be organized from one of the hotels in Ponta Negra to the IIP building.

 

Other practical information:

 
Visa: Please check whether you require a tourist visa to travel to Brazil. Nationals of the majority of European countries do not require a visa to enter Brazil as a tourist. Nationals of the USA, Canada, China, India and some other contries need to apply for a tourist visa. Please check the website of the Brazilian consulate nearest to you for the list of required documents. The IIP will be happy to assist you with the application process.

Flights: Natal has a regular flight connection with Lisbon, Portugal, operated by the Portuguese TAP. For those, coming through Europe, this is typically the most convenient option. The majority of flights operated from North America have connections in either Rio de Janeiro, or Sao Paulo. The closest direct flights (Americal Airlines from Miami and Copa Airlines from Panama City) arrive to Recife, 315 km away from Natal.

Airport: The two recommended ways to get to/from the airport is taxi and shuttle. Taxi ride from the airport to Ponta Negra will be around 80-150 reals, depending on the time of the day and traffic. Many commercial companies also operate shuttle service to/from the airport. The shuttle cost is around 35 reals one way and you will share the ride with several other passengers. Depending on the number of passengers it can take longer to arrive to your destination. 
 
 
For more information, please contact our events department at: events@iip.ufrn.br

Date/Time Speakers NameTalk Title

Tuesday

June 13, 2017

09:00 am - 10:00 am

Angel Garcia

Invited speaker

Los Alamos National Laboratory

  • Tuesday

    June 13, 2017

    10:30 am - 11:30 am

    Joanna Sulkowska

    Invited speaker

    University of Warsaw

  • Tuesday

    June 13, 2017

    02:00 pm - 03:00 pm

    Piotr Sulkowski

    Invited speaker

    University of Warsaw

  • Wednesday

    June 14, 2017

    09:00 am - 10:00 am

    Diego Ferreiro

    Invited speaker

    University of Buenos Aires

  • Wednesday

    June 14, 2017

    10:30 am - 11:30 am

    Diego Ferreiro

    Invited speaker

    University of Buenos Aires

  • Wednesday

    June 14, 2017

    02:00 pm - 03:00 pm

    Angel Garcia

    Invited speaker

    Los Alamos National Laboratory

  • Wednesday

    June 14, 2017

    03:00 pm - 04:00 pm

    Jennifer Ross

    Invited speaker

    University of Massachusetts - Amherst

  • Friday

    June 16, 2017

    09:00 am - 10:00 am

    Diego Ferreiro

    Invited speaker

    University of Buenos Aires

  • Friday

    June 16, 2017

    10:30 am - 11:30 am

    Diego Ferreiro

    Invited speaker

    University of Buenos Aires

  • Friday

    June 16, 2017

    02:00 pm - 03:00 pm

    Angel Garcia

    Invited speaker

    Los Alamos National Laboratory

  • Friday

    June 16, 2017

    03:00 pm - 04:00 pm

    Valentin Gordeli

    Invited speaker

    J.-P. Ebel Institute of Structural Biology & Institute of Complex Systems (ICS), Research Centre Juelich

  • Monday

    June 19, 2017

    09:00 am - 10:00 am

    Hue Sun Chan

    Invited speaker

    University of Toronto

  • Monday

    June 19, 2017

    10:00 am - 10:30 am

    Coffee break

    Monday

    June 19, 2017

    10:30 am - 11:15 am

    Ugo Bastolla

    Invited speaker

    Universidad Autonoma de Madrid

  • Monday

    June 19, 2017

    11:15 am - 12:00 pm

    Kingshuk Ghosh

    Invited speaker

    University of Denver

  • Monday

    June 19, 2017

    12:00 pm - 02:00 pm

    Lunch

    Monday

    June 19, 2017

    02:00 pm - 02:45 pm

    Konrad Hinsen

    Invited speaker

    Centre de Biophysique Moléculaire in Orléans

  • Monday

    June 19, 2017

    02:45 pm - 03:30 pm

    Dave Thirumalai

    Invited speaker

    University of Maryland

  • Monday

    June 19, 2017

    03:30 pm - 04:00 pm

    Coffee-break

    Monday

    June 19, 2017

    04:00 pm - 05:00 pm

    Gerhard Hummer

    Invited speaker

    Max Planck Institute for Biophysics

  • Monday

    June 19, 2017

    05:00 pm - 06:00 pm

    Poster session

    Tuesday

    June 20, 2017

    09:00 am - 10:00 am

    Garegin Papoian

    Invited speaker

    University of Maryland

  • Tuesday

    June 20, 2017

    10:00 am - 10:30 am

    Coffee break

    Tuesday

    June 20, 2017

    10:30 am - 11:15 am

    Cezary Czaplewski

    Invited speaker

    University of Gdansk

  • Tuesday

    June 20, 2017

    11:15 am - 12:00 pm

    Victor Munoz

    Invited speaker

    Universit of California

  • Tuesday

    June 20, 2017

    12:00 pm - 02:00 pm

    Lunch

    Tuesday

    June 20, 2017

    02:00 pm - 02:45 pm

    Ralf Metzler

    Invited speaker

    University of Potsdam

  • Tuesday

    June 20, 2017

    02:45 pm - 03:30 pm

    Thomas Needham

    Invited speaker

    Ohio State University

  • Tuesday

    June 20, 2017

    03:30 pm - 04:00 pm

    Coffee-break

    Tuesday

    June 20, 2017

    04:00 pm - 05:00 pm

    Hans Frauenfelder

    Invited speaker

    Los Alamos National Laboratory

  • Tuesday

    June 20, 2017

    05:00 pm - 05:45 pm

    Laurent Dardenne

    Invited speaker

    National Laboratory of Scientific Computation - LNCC

  • Wednesday

    June 21, 2017

    09:00 am - 10:00 am

    Paul Whitford

    Invited speaker

    Northeastern University

  • Wednesday

    June 21, 2017

    10:00 am - 10:30 am

    Coffee break

    Wednesday

    June 21, 2017

    10:30 am - 11:15 am

    Yong Duan

    Invited speaker

    University of California, Davis

  • Wednesday

    June 21, 2017

    11:15 am - 12:00 pm

    Angel Garcia

    Invited speaker

    Los Alamos National Laboratory

  • Wednesday

    June 21, 2017

    12:00 pm - 02:00 pm

    Lunch

    Wednesday

    June 21, 2017

    02:00 pm - 02:45 pm

    Adam Sieradzan

    Invited speaker

    University of Gdansk

  • Wednesday

    June 21, 2017

    02:45 pm - 03:30 pm

    Roberto Lins

    Invited speaker

    FIOCRUZ

  • Wednesday

    June 21, 2017

    03:30 pm - 04:00 pm

    Coffee-break

    Wednesday

    June 21, 2017

    04:00 pm - 05:00 pm

    Jose Onuchic

    Invited speaker

    Rice University

  • Wednesday

    June 21, 2017

    05:00 pm - 05:45 pm

    Antonio Francisco Pereira de Araujo

    Invited speaker

    University of Brasilia

  • Wednesday

    June 21, 2017

    07:30 pm - 10:00 pm

    Conference Dinner

    Thursday

    June 22, 2017

    09:00 am - 10:00 am

    Andrzej Kolinski

    Invited speaker

    University of Warsaw

  • Thursday

    June 22, 2017

    10:00 am - 10:30 am

    Coffee break

    Thursday

    June 22, 2017

    10:30 am - 11:15 am

    Olga Dudko

    Invited speaker

    University of California, San Diego

  • Thursday

    June 22, 2017

    11:15 am - 12:00 pm

    Alexander Molochkov

    Invited speaker

    Far Eastern Federal University

  • Thursday

    June 22, 2017

    12:00 pm - 02:00 pm

    Lunch

    Thursday

    June 22, 2017

    02:00 pm - 02:45 pm

    Mark Dennis

    Invited speaker

    University of Bristol

  • Thursday

    June 22, 2017

    02:45 pm - 03:30 pm

    Garegin Papoian

    Invited speaker

    University of Maryland

  • Thursday

    June 22, 2017

    03:30 pm - 04:00 pm

    Coffee-break

    Thursday

    June 22, 2017

    04:00 pm - 05:00 pm

    Peter Wolynes

    Invited speaker

    Rice University

  • Thursday

    June 22, 2017

    05:00 pm - 05:45 pm

    Valentin Gordeli

    Invited speaker

    J.-P. Ebel Institute of Structural Biology & Institute of Complex Systems (ICS), Research Centre Juelich

  • Friday

    June 23, 2017

    09:00 am - 10:00 am

    Dave Thirumalai

    Invited speaker

    University of Maryland

  • Friday

    June 23, 2017

    10:00 am - 10:30 am

    Coffee break

    Friday

    June 23, 2017

    10:30 am - 11:15 am

    Xubiao Peng

    Invited speaker

    University of British Columbia

  • Friday

    June 23, 2017

    11:15 am - 12:00 pm

    Pawel Dabrowski

    Invited speaker

    Centre of New Technology

  • Friday

    June 23, 2017

    12:00 pm - 02:00 pm

    Lunch

    Friday

    June 23, 2017

    02:00 pm - 02:45 pm

    Joanna Sulkowska

    Invited speaker

    University of Warsaw

  • Friday

    June 23, 2017

    02:45 pm - 03:30 pm

    Paul Whitford

    Invited speaker

    Northeastern University

  • Friday

    June 23, 2017

    03:30 pm - 04:00 pm

    Coffee-break

    Friday

    June 23, 2017

    04:00 pm - 05:00 pm

    Michael Woodside

    Invited speaker

    University of Alberta

  • Friday

    June 23, 2017

    05:00 pm - 05:45 pm

    Andrzej Kolinski

    Invited speaker

    University of Warsaw

  • Monday

    June 26, 2017

    09:30 am - 10:30 am

    Hue Sun Chan

    Invited speaker

    University of Toronto

  • Monday

    June 26, 2017

    11:00 am - 12:00 pm

    Michael Woodside

    Invited speaker

    University of Alberta

  • Monday

    June 26, 2017

    02:00 pm - 03:00 pm

    Ronaldo J. Oliveira

    Invited speaker

    Federal University of Triangulo Mineiro

  • Tuesday

    June 27, 2017

    09:00 am - 10:00 am

    Hue Sun Chan

    Invited speaker

    University of Toronto

  • Tuesday

    June 27, 2017

    11:00 am - 12:00 pm

    Leandro Cristante de Oliveira

    Invited speaker

    UNESP - Rio Preto

  • Wednesday

    June 28, 2017

    09:00 am - 10:00 am

    Hue Sun Chan

    Invited speaker

    University of Toronto

  • Wednesday

    June 28, 2017

    11:00 am - 12:00 pm

    Gerald Kneller

    Invited speaker

    University of Orléans