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Description
The  Abdus  Salam  International  Cente  for  Theoretical  Physics  (ICTP),  Trieste, Italy is  organizing  a  Conference  on  Atomistic  Simulations  of  Biomolecules: towards a Quantitative  Understanding  of  Life  Machinery  to  be  held  in  Trieste,  Italy from  6 -10 March 2017.

ORGANIZERS:
Ali HASSANALI (ICTP, Trieste, Italy)
Lucy KIRURI (Kenyatta University, Nairobi, Kenya)
Alessandro LAIO (SISSA, Trieste, Italy)
Carmen Nina PASTOR COLON (UAEM, Mexico)

In the last decades accurate atomistic simulations have become a key tool for studying biomolecules and is an essential part of quantitative life sciences. Thanks to specialized hardware, distributed computing and enhanced sampling techniques, the timescales that can be reached by simulations and the shortest timescales that can be probed experimentally are now overlapping. Besides providing more benchmarks with which theoretical models can be validated, atomistic simulations give valuable information on microscopic details that help in the interpretation of experiments. It can be foreseen that in the near future, the scientific community will start trusting simulations as a genuinely predictive tool, whose outcome is valid even without direct experimental support. In the next years, simulations are likely to play a crucial role in understanding how life machinery works.

The scope of this conference is bringing together experts working in the field of atomistic simulations of biomolecules, with particular attention to exposing scientists working in developing countries to the state of the art methods and applications possible in the field. It will also serve to link together both students and faculty, to encourage involvement for exchange and collaboration.


Topics will include:
1) Simulation of nucleic acids;
2) Protein folding and aggregation;
3) Molecular recognition;
4) The role of water in bio-molecular processes;
5) Algorithm development for enhanced sampling and multiscale simulations;
6) Force-fields for bio-molecular simulations.


TENTATIVE LIST OF SPEAKERS:

Robert BEST  (NIH, Washington, U.S.A.)
Julio CABALLERO  (Universidad de Talca, Chile)
Pilar COSSIO TEJADA  (MPI, Frankfurt, Germany)
Gerhard HUMMER  (MPI, Frankfurt, Germany)
Lucy KIRURI (Kenyatta University, Nairobi, Kenya)
Vanessa LEONE-ALVAREZ  (NINDS/NIH, Bethesda, U.S.A.)
Kersten LINDORFF-LARSEN  (University of Copenhagen, Denmark)
George Ochieng OMOLLOH  (Kenyatta University, Kenya)
Juliana PALMA  (UNQ, Buenos Aires, Argentina)
Sergio PANTANO GUTIERREZ  (lnstitut Pasteur, Montevideo, Uruguay)
Carmen Nina PASTOR COLON (UAEM, Mexico)
Sergiy PEREPELYTSYA  (BITP, Kiev, Ukraine)
Simon POBLETE FUENTES  (SISSA, Trieste, Italy)
Peter POHL  (JKUL, Linz, Austria)
Meher PRAKASH  (JNCASR, Bangalore, India)
Fabio STERPONE  (IBPC-LBT, Paris, France)
FakhrEldin O. SULIMAN MOHAMED  (SQU, Muscat, Oman)
Hugo VERLI  (UFRGS, Porto Alegre, Brazil)

Material

Conference on Atomistic Simulations of Biomolecules: towards a Quantitative Understanding of Life Machinery | (smr 2828)
Go to day
  • Monday, 6 March 2017
    • 08:30 - 10:15 Session 1
      • 08:30 REGISTRATION & ADMINISTRATIVE FORMALITIES 1h30' 
        All visitors are requested to Register from 8.30 - 10.00 am 
in the reception area of the Leonardo da Vinci Building

(subsequently, outside the above hours, with the 
Secretariat in office no. 135, first floor (near the Library)
      • 10:00 OPENING/WELCOME REMARKS 15'
        Speaker: Ali HASSANALI (ICTP, Trieste, Italy)
    • 10:15 - 14:00 Session 2 
      DNA/RNA
      • 10:15 Introduction - Chair: Sergio PANTANO GUTIERREZ 5'
      • 10:20 Dynamics of ordered counterions in the ion-hydrate shell of DNA double helix 40'
        Speaker: Sergiy PEREPELYTSYA (Bogolyubov Institute for Theoretical Physics, Kiev, Ukraine)
        Material: Abstract Slides
      • 11:00 Introducing atomistic details into a base-centered representation of RNA 40'
        Speaker: Simon POBLETE (SISSA, Trieste, Italy)
        Material: Abstract Slides
      • 11:40 Adenine-thymine base-pair step four-body non-additivity contribution to B-DNA: a quantum monte carlo study 30'
        Speaker: Namarome C. BAKASA (University of Eldoret, Kenya)
        Material: Slides
      • 12:10 Lunch break 1h50' ( LB Cafeteria - terrace level )
    • 14:00 - 17:15 Session 3 
      QM/MM, CATALYSIS
      • 14:00 Introduction - Chair: Meher PRAKASH 5'
      • 14:05 Moving domain QM/MM methods for interactions of human estrogen receptor alpha with endocrine disruptive chemicals 40'
        Speaker: George Ochieng OMOLLOH (Kenyatta University, Nairobi, Kenya)
        Material: Abstract
      • 14:45 An overview of environmentally persistent free radicals (EPFRs) 40'
        Speaker: Lucy KIRURI (Kenyatta University, Nairobi, Kenya)
      • 15:25 Coffee break 30' ( )
      • 15:55 The Catalytic Mechanism of Pfk-2: first computational approximation 40'
        Speaker: Julio CABALLERO (Universidad de Talca, Chile)
      • 16:35 Insights into N-glycosylation machinery 40'
        Speaker: Hugo VERLI (UFRGS, Porto Alegre, Brazil)
  • Tuesday, 7 March 2017
    • 09:00 - 14:00 Session 4 
      AGGREGATES AND MOLECULAR SWITCHES
      • 09:00 Introduction - Chair: Alessandro LAIO 5'
      • 09:05 Caffeine self-association in Aqueous solution: from the supramolecular to atomic scale clustering 40'
        Speaker: Letizia TAVAGNACCO (Universita' di Sapienza, Rome, Italy)
        Material: Abstract Slides
      • 09:45 Stability of Biopolymers in Aqueous Solution. GMPC Approach 40'
        Speaker: Arevik ASATRYAN (Yerevan State University, Armenia)
        Material: Abstract Slides
      • 10:25 On the development of a Novel Bio-Molecular NanoSwitch: A Theoretical Investigation 30'
        Speaker: Hadeer ELEL SAYED EL HABASHY (The American University, Cario, Egypt)
        Material: Abstract
      • 10:55 Coffee break 30' ( )
      • 11:25 Interaction of antimicrobial peptides with POPC lipid structures modeled by molecular dynamics simulations 30'
        Speaker: Galo E. BALATTI (University of Buenos Aires, Argentina)
        Material: Slides
      • 11:55 Role of the subunit interactions in the conformational transitions in adult human hemoglobin: an explicit solvent molecular dynamics study 30'
        Speaker: Olaniyi Kamil YUSUFF (University of Iorin, Nigeria)
      • 12:25 Lunch break 1h35' ( LB Cafeteria - terrace level )
    • 14:00 - 17:15 Session 5 
      MULTISCALE MODELING
      • 14:00 Introduction - Chair: Robert BEST 5'
      • 14:05 Molecular simulations of membrane dynamics, remodeling and sensing 40'
        Speaker: Gerhard HUMMER (MPI, Frankfurt, Germany)
        Material: Abstract
      • 14:45 Structure and mechanism of the ATP synthase membrane motor inferred from quantitative integrative modeling 40'
        Speaker: Vanessa LEONE ALVREZ (NINDS, Bethesda, U.S.A.)
        Material: Abstract Slides
      • 15:25 Coffee break 30' ( )
      • 15:55 Affordable multiscale methods for simulating virus like particles 40'
        Speaker: Sergio Fabian PANTANO GUTIERREZ (Institut Pasteur de Montevideo, Uruguay)
        Material: Abstract
      • 16:35 Protein in cell. Toward microscopic simulations of cell-like environments 40'
        Speaker: Fabio STERPONE (UPR/CNRS, Paris, France)
        Material: Slides
    • 18:30 - 21:00 Session 6 
      POSTER SESSION & Welcome Reception

Arevik ASATRYAN (Yerevan State University, Armenia)
Stability of biopolymers in Aqueous solution. GMPC approach

Namarome BAKASA (University of Eldoret, Kenya)
Adenine-thymine base-pair step four-body non-additivity contribution to B-DNA:
A quantum monte carlo study

Galo BALATTI (University of Buenos Aires, Argentina)
Interactiion of antimicrobial peptides with POPC lipid structures modeled by molecular dynamics simulations

Hadeer ELSAYED (British University in Egypt / University of Cairo, Egypt)
On the development of a novel bio-molecular nanoswitch:  A theoretical investigation

Wilson GEH (University of Dschang, Cameroon)
Investigation of structural, electronic, optical, and thermodynamics properties of the molecules 1,2,3- trihydroxy-9, 10-anthraquinone; 1-(Methylamino)anthraquinone; 1-Bromonaphthalene and 9,10-phenanthrenequinone: A DFT Approach.

Luca GRISANTI (SISSA, Trieste, Italy)
Structure-related fluorescence and proton delocalization in amyloid proteins

Fabio PICHIERRI (Tohoku University, Japan)
Protein dynamics and electronic structure

Neda RAFIEIOLHOSSEINI (Institute for Research in Fundamental Sciences, Iran)
A molecular dynamics approach to find thermal conductivity of Macromolecules

Ali RAJABPOUR (Imam Khomeini International University of Qazvin, Iran)
Interfacial thermal conductance between a protein and water: Molecular dynamics study  

Jose SANTIAGO TERRONES (Universidad Autonoma del Estado de Morelos, Mexico)
Structural characterization of the TATA binding protein molecular surface from eukaryotic parasites, identification of druggable binding pockets

Parul SHARMA (All India Institute of Medical Sciences, India)
Conformational profile assessment of Human cathelicidin (II-37) and it's function as neutrophil apoptosis via the activation of FPRL1, explained using molecular dynamics simulations

Letizia TAVAGNACCO (University of Trieste, Italy)
Caffeine self-association in Aqueous solution: From the supramolecular to atomic scale clustering

Nidhi TIWARI (Centre of Biomedical Research, India)
Role of water in bone microstructure

Monika WISMAN ACHARIGE (University of Colombo, Sri Lanka)
Molecular simulations of the dynamics of water in model cartilage

Darren WRAGG (Cardiff University, U.K.)
Molecular dynamics studies of H202 permeation via Aquaporin-3

Olaniyi YUSUFF (University of Iorin, Nigeria)
Role of the subunit interactions in the conformational transitions in adult human hemoglobin: an explicit solvent molecular dynamics study
      Location: Poster Gallery (reception area, behind Budinich lecture hall)
  • Wednesday, 8 March 2017
    • 09:00 - 10:55 Session 7 
      DISORDERED PROTEINS
      • 09:00 Introduction - Chair: Nina PASTOR COLON 5'
      • 09:05 Separating the wheat from the chaff: tips on how to identify and characterize essential movements in frantically shaking proteins 40'
        Speaker: Juliana PALMA (Universidad Nacional de Quilmes, Buenos Aires, Argentina)
        Material: Abstract Slides
      • 09:45 Atomistic simulations of intrinsically disordered proteins 40'
        Speaker: Robert BEST (NIH, Bethesda, U.S.A.)
        Material: Abstract Slides
      • 10:25 Coffee break 30' ( )
    • 10:55 - 14:00 Session 8 
      WATER IN BIOLOGICAL SYSTEMS
      • 10:55 Introduction - Chair: Ali HASSANALI 5'
      • 11:00 Role of water in bone microstructure 30'
        Speaker: Nidhi TIWARI (Centre of Biomedical Research, Lucknow, India)
        Material: Abstract
      • 11:30 Molecular simulations of the dynamics of water in model cartilage 30'
        Speaker: Monika Madhavi WISMAN ACHARIGE (University of Colombo, Sri Lanka)
        Material: Slides
      • 12:00 Molecular dynamic studies of H202 permeation via Aquaporin-3 30'
        Speaker: Darren D. WRAGG (Cardiff University, U.K.)
        Material: Slides
      • 12:30 Lunch break 1h30' ( LB Cafeteria - terrace level )
    • 14:00 - 16:30 Session 9 
      STRUCTURAL EMSEMBLES/"?"
      • 14:00 Introduction - Chair: Fabio STERPONE 5'
      • 14:05 Linking structural ensembles from simulations to the analysis of individual cryo-EM images 40'
        Speaker: Pilar COSSIO TEJADA (MPI, Frankfurt, Germany)
        Material: Abstract Slides
      • 14:45 From unfolding intermediates to amyloid protofibrils: the beginning of light chain amyloidosis 40'
        Speaker: Carmen Nina PASTOR COLON (UAEM, Cuernavaca, Mexico)
        Material: Abstract
      • 15:25 Group Photo - Coffee Break 1h5' ( )
    • 16:30 - 17:30 Session 10 
      ICTP COLLOQUIUM

Followed by refreshments
      • 16:30 Shoot first, ask questions later: from molecular simulations to protein function 1h0'
        Speaker: Gerhard HUMMER (MPI, Frankfurt, Germany)
        Material: Abstract
  • Thursday, 9 March 2017
    • 09:00 - 14:00 Session 11 
      DRUGS AND OTHER INTERACTIONS
      • 09:00 Introduction - Chair: Sergio PANTANO GUTIERREZ 5'
      • 09:05 Designing drugs bacteria can not resist 40'
        Speaker: Meher PRAKASH (JNCASR, Bangalore, India)
      • 09:45 Applications of molecular modeling methods to host-guest supramolecular chemistry 40'
        Speaker: FakhEldin SULIMAN (Sultan Qaboos University, Muscat, Oman)
        Material: Abstract Slides
      • 10:25 Coffee break 30' ( )
      • 10:55 Conformational profile assessment of Human cathelicidin (ll-37) and it's function as neutrophil apoptosis via the activation of FPRL1, explained using molecular dynamics simulations 30'
        Speaker: Parul SHARMA (AIIMS, New Delhi, India)
        Material: Abstract Slides
      • 11:25 Structural characterization of the TATA binding protein molecular surface from eukaryotic parasites, identification of druggable binding pockets 30'
        Speaker: Jose Angel SANTIAGO TERRONES (UAEM, Mexico)
        Material: Slides
      • 11:55 Lunch break 2h5' ( LB Cafeteria - terrace level )
    • 14:00 - 18:00 Session 12 
      Excursion to GROTTA GIGANTE CAVES

Meeting Point:  reception area
      Location: Trieste
  • Friday, 10 March 2017
    • 09:00 - 12:15 Session 13 
      WHERE EXPERIMENTS MEET THEORY:
      • 09:00 Introduction - Chair: Gerhard HUMMER 5'
      • 09:05 Molecular dynamics and RNA: A perfect match? 40'
        Speaker: Sandro BOTTARO (University of Copenhagen, Denmark (talk presented on behalf of Kresten Lindorff-Larsen))
      • 09:45 Protons at the membrane water interface 40'
        Speaker: Peter POHL (Johannes Kepler University of Linz, Austria)
        Material: Abstract
      • 10:25 Coffee break 30' ( )
      • 10:55 Open panel discussion 1h5'
      • 12:00 CLOSING REMARKS 15'
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