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Modeling and Simulations

 Across Molecular Sciences and Engineering

July 8 – 12, 2019


This course presents the theory, concepts, tools and techniques of modern modeling and computer simulations, and provides a very broad overview of their various fields of application across chemistry, biochemistry, biology, physics and engineering.

The course will span a broad spectrum of modeling, from electronic structure calculations of small molecules as well as the solid state, (bio)molecular docking and molecular dynamics simulations, multi-scale modeling of complex systems, to emerging technologies driven by machine learning and artificial intelligence.

Typical systems modeled include but are not restricted to organic molecules, peptides and proteins, nucleic acids, polymers and inorganics, with applications to process engineering, materials design, nanotechnology, drug discovery and quantum computing.

The course includes a significant practical component where students acquire hands-on experience with commonly used computer simulation software, from the desktop to state-of-the-art supercomputing infrastructures, and with simulation analysis, automation, scripting and the tools of efficient advanced research computing.

Learning Outcomes

Students will learn advanced research computing on state-of-the-art supercomputing infrastructure. Most importantly, the student experience will be unique in that they will learn both the basic foundation and practical know-how of modeling and simulation across fields, and they will be guided as to how to deepen and expand their expertise in any given field by lecturers and the academic team (selected for its multi-disciplinarity).

The thematic sessions generally include a scientific lecture given by an internationally recognized expert in the field from academia, research computing organizations and/or the private sector, followed by a computer lab tutorial session, The lecture will provide an overview of molecular modeling and simulations within the context of the thematic session and highlight the current state-of-the-art in the field. The key concepts freshly acquired will then immediately be illustrated by hands-on applications in the computer lab tutorial with frequent and less formal interactions with the instructor(s). Late-afternoon poster and informal discussion sessions will provide an informal opportunity for participants to discuss and review course material as well as socialize, providing the foundation of a lasting network.

Armed with proper training, students will make a tremendous asset of the vast amount of available online resources mentioned earlier to advance research in a smart way in their or other fields. This may change the way they do research and lead to innovations in e.g. drug discovery or smart materials design, opening a window to real-life applications and industrial partnerships.


Students and interdisciplinarity are at the core of the School.

Participants from different fields of science and engineering will get together, properly learn theory and techniques from guest lectures and apply them right away in the computer laboratory with appropriate software and guidance; for example, a biologist will learn not only the simulation tools pertaining to their domain but also those of materials engineering and some of their applications, which should facilitate cross-field communication between scientists and may well result in breakthroughs in a given field by adapting modeling methods borrowed from others.

Some participants will be primarily experimentalists seeking a molecular-level understanding of their findings, and teaching them the proper art of modeling may change the way they do research, conducting predictive simulations before undergoing convoluted experimentation.

The course will include the following sessions:

  1. Introductory Lectures (2 lectures)
  2. Advanced Research Computing (Lecture + Lab)
  3. Molecular Structure and Properties from First Principles (Lecture + Lab)
  4. Electron Densities and Reactivity of Molecules (Lecture + Lab)
  5. Modeling Solids and Materials from First Principles (Lecture + Lab)
  6. Molecular-Level Modeling for Engineering and Technology (Lecture + Lab)
  7. Modeling Organics, Proteins and Nucleic Acids (Lecture + Lab)
  8. Molecular Dynamics Simulations of Biological Systems (Lecture + Lab)
  9. Modeling and Drug Discovery (Lecture + Lab)
  10. The Rise and Future of Multi-Scale Modeling, Machine Learning and Quantum Computing (2 lectures)

Financial Assistance

Fellowship financial assistance will be provided in the form of partial tuition fee waivers on a competitive basis. Selection criteria include academic standing, relevance of training to the student’s research project, potential for cross-collaborations and research trans-fertilization, and geographical location.


All out-of-town students will be offered free housing at the Grey Nuns' residences. For more detail, click the "Logistics" button below. Do let us know of any food allergies you may have when applying.

Readings and Evaluation

Student evaluation will be based on a poster presentation of the student current research project given on site, and a report due one week after the end of the summer school including 1) a short essay on knowledge and skills acquired during the summer school and 2) an account of a small molecular modeling research project to be selected in consultation with the academic team during the summer school. Proper references and suggested readings will be disseminated during the summer school.


Graduate students with an interest in modern modeling and computer simulations, preferably enrolled in an accredited graduate program in the molecular sciences (chemistry, biochemistry, biology, physics, materials or engineering), are invited to apply right away. Full applications include an up-to-date CV, statement of purpose (addressing past and current research area and project, relationship to training to be gained from the summer school; maximum 600 words) and all University degree transcripts, compiled in a single PDF file.

International applicants for whom some tuition fee remission would facilitate enrollment or would be required to attend the summer school should indicate so at the time of application by briefly addressing their financial need in their Statement of Purpose.

Please click the "Apply!" button below to proceed.


Application Deadline is May 15.

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