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University of Toronto Woodsworth College Science Abroad (CHM396y0) 11th Annual European Molecular Computational Summer School for Life Science Studen...
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University of Toronto Woodsworth College Science Abroad (CHM396y0)

11th Annual European Molecular Computational Summer School for Life Science Students

University of Miskolc, Miskolc, Hungary, EU 16 May - 1 July 2016

11th Annual European Molecular Computational Summer School for Life Science Students

University of Miskolc, Miskolc, Hungary, EU, 16 May-1 July 2016

11th Annual European Molecular Computational Summer School for Life Science Students

Historic Predicament (I. G. Csizmadia)

Similar to the Industrial Revolution marked by the establishment of the first safe and successful steam power plant over 300 years ago, the invention of digital computers has led to a new Scientific Revolution within in our present lifetime. The significance of the computer is visible in all aspects of today's society, however the field of chemistry and pharmaceutical industry in particular, are experiencing the most dramatic change at present as a result. This change implies that within the present Scientific Revolution which is still in the midst of unfolding, there is a significant dominance of a Molecular Revolution which will change drug discovery research just as dramatically. Some time ago, the situation was illustrated by the following schematic figure.

The above figure demonstrates the fact that most of the potential drug molecules are located somewhere else where we do our research. The innacuracy of such a figure, however, lies in the unexplored area, labelled as Universe of Organic Molecules, which is considerably larger than illustrated. University of Miskolc, Miskolc, Hungary, EU, 16 May-1 July 2016

11th Annual European Molecular Computational Summer School for Life Science Students

The following schematic figure, however, demonstrates this misproportion more accurately and illustates the number of drug-sized molecules left unknown today, more accurately 63 orders of magnitude larger (1070 / 107 = 1063) than the currently known drug database. Because only ten million (107) drug-sized organic molecules were discovered by the human race in the past two centuries, it isn’t unreasonable to suggest that it would require an significantly long time to discover the other 1063 molecules by traditional drug discovery techniques and strategies.

Fortunately, with computational methods, this process of drug discovery may be achieved faster with the use of High Performance Computers (HPC) and big-data storage facilities. Such in silico research would lead to the discovery of "lead-structures" which could then be synthesized and subjected to in vitro and in vivo testing for use in pharmaceutical research. Another research topic of interest for students studying the Life Sciences may be folded and misfolded polypeptides. Misfolded peptides are the causes of multiple neurodegenerative diseases. These include Alzheimer’s disease, Parkinson’s disease, Amyloidosis, and ALS.

University of Miskolc, Miskolc, Hungary, EU, 16 May-1 July 2016

11th Annual European Molecular Computational Summer School for Life Science Students

Each amino acid residue within these misfolded polypeptide sequences can be represented as a potential energy surface.

The purpose of the CHM396Y1 Science Abroad program is to expose undergraduate students to this novel way of thinking in terms of drug research design, as well as allow them the opportunity to develop the computational skills required to the carry out similar research projects in their future scientific careers.

University of Miskolc, Miskolc, Hungary, EU, 16 May-1 July 2016

11th Annual European Molecular Computational Summer School for Life Science Students

Participating lecturers

# 1 2

Lecturer Anita Rágyanszki Béla Fiser

University/Institute University of Miskolc, Miskolc, Hungary University of the Basque Country, San Sebastián, Spain

3 4 5 6 7 8 9

Béla Viskolcz Eszter P. Faragó György Ferenczy Imre G. Csizmadia Imre Jákli János J. Szórád John J. Villar

10 11 12 13

Klára Z. Gerlei Michael C. Owen Michelle Sahai Natalie J. Galant

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Ödön Farkas Svend K. Jensen Szilárd Fejér Zoltán Mucsi

University of Miskolc, Miskolc, Hungary TEVA Pharmaceutical Ltd., Debrecen Hungary Hungarian Academy of Sciences, Budapest, Hungary University of Toronto, Toronto Canada Eötvös Loránd University, Budapest, Hungary University of Szeged, Szeged, Hungary University of the Philippines Diliman, Quezon City, Philippines The University of Edinburgh Forschungszentrum Jülich, Jülich, Germany University of Roehampton, London, UK Faculty of Medicine, University of Toronto, Toronto Canada Eötvös Loránd University, Budapest, Hungary Aarhus University, Aarhus, Denmark University of Szeged, Szeged, Hungary Budapest University of Technology and Economics, Budapest, Hungary

University of Miskolc, Miskolc, Hungary, EU, 16 May-1 July 2016

11th Annual European Molecular Computational Summer School for Life Science Students

Program

Sunday 15 May Monday 16 May Date Tuesday 17 May Wednesday 18 May Thursday 19 May

Arrival & Accommodations Sight-Seeing Tour Lecturer Béla Viskolcz Imre G. Csizmadia Imre G. Csizmadia Imre G. Csizmadia

Lecture (starting at 10 a.m.) Opening ceremonies (starting at 9 a.m.) Introduction to organic chemistry Introduction to physical chemistry Introduction to isomerization

Friday 20 May

Imre G. Csizmadia

Quantum chemical background

Monday 23 May

Imre G. Csizmadia

Introduction to quantum chemistry

Tuesday 24 May

Béla Viskolcz

Wednesday 25 May

Ödön Farkas

Thursday 26 May

János J. Szórád

Friday 27 May Monday 30 May Tuesday 31 May Wednesday 1 June Thusrday 2 June Friday 3 June

Seminar (starting at 2 p.m.) PC/MacBook Set-Up

Gaussian Workshop MolGen Workshop Practical introduction to ChemOffice software Project selection, Practical introduction to Origin software

Optimization, potential energy surfaces Strategies of Geometry Optimizations Introduction to literature search and report writing

Method dependence of the PES

Natalie J. Galant

TBA

Project work

Klára Z. Gerlei

TBA

Project work

Anita Rágyanszki John J. Villar Béla Fiser Béla Fiser

Mathematical representation of PES Mathematical analysis of PES Introduction to Force Fields Introduction to Molecular Dynamics

Study of the Basis set effect

Introduction to literature searches

Project work Optimizations with AMBER force field Force Field Calculations Force Field Calculations

University of Miskolc, Miskolc, Hungary, EU, 16 May-1 July 2016

11th Annual European Molecular Computational Summer School for Life Science Students

Monday 6 June

Eszter P. Faragó

Tuesday 7 June

Szilárd Fejér

Wednesday 8 June

Szilárd Fejér

Thursday 9 June Firday 10 June Monday 13 June Tuesday 14 June Wednesday 15 June Thursday 16 June Friday 17 June Monday 20 June Tuesday 21 June Wednesday 22 June Thursday 23 June Friday 24 June Monday 27 June Tuesday 28 June Wednesday 29 June Thursday 30 June Friday 1 July

TBA

Preparation for Poster Presentation

Energy Landscapes of Self-assembling Systems Computational Modelling of Viruses

Michael Owen

TBA

Project work

Project work Project work

Deadline to finish Project Posters Imre Jákli

TBA

Project work

Svend K. Jensen

Determination of transition states and activation energies

Project work

6th Visegrad Symposium on Structural Systems Biology 6th Visegrad Symposium on Structural Systems Biology 6th Visegrad Symposium on Structural Systems Biology Zoltán Mucsi

“System chemistry”

Zoltán Mucsi

Introduction to Pharmaceuticals Introduction to Pharmaceutical Synthesis

Zoltán Mucsi

Project work Project work Project work

Michelle Sahai

TBA

Project work

György Ferenczy

TBA

Project work

Béla Viskolcz

Molecular Aging

Project work

Final Report Preparation Final Report Preparation Final Report Preparation Deadline to submit final report; Farewell Party

University of Miskolc, Miskolc, Hungary, EU, 16 May-1 July 2016

11th Annual European Molecular Computational Summer School for Life Science Students

University of Miskolc, Miskolc, Hungary, EU, 16 May-1 July 2016

11th Annual European Molecular Computational Summer School for Life Science Students

Map

University of Miskolc, Miskolc, Hungary, EU, 16 May-1 July 2016

11th Annual European Molecular Computational Summer School for Life Science Students

“The fundamental laws necessary for the mathematical treatment of a large part of physics and the whole chemistry are thus completely known, and the difficulty lies only in the fact that application of these laws leads to equations that are too complex to be solved”

University of Miskolc, Miskolc, Hungary, EU, 16 May-1 July 2016