Advances in Molecular Modeling Workshop

9 Dec 2024, 01:45 → 10 Dec 2024, 16:20 Europe/Copenhagen

Auditorium A (Niels Bohr Institute, University of Copenhagen )

Weria Pezeshkian (Niels Bohr International Academy, Niels Bohr Institute, University of Copenhagen)

The Niels Bohr International Academy is launching a new annual workshop series 
Current Themes in Biological and Soft Matter.

The 2024 workshop focuses on
Advances in Molecular Modelling. 

Date: 9 - 10th December 2024. 

Registration is free. The number of seats is limited, and registration will be closed as soon as the limit is reached.

Talks:

• Siewert Jan Marrink (University of Groningen)
• Franca Fraternali (University College London)
• Dmitry Fedosov (Research Center Jülich)
• Cecilia Clementi (Freie Universität Berlin)

 

Workshops:

• Edina Rosta (University College London)
• Kresten Lindorff-Larsen (University of Copenhagen)
• Paulo Cesar Telles de Souza (CNRS, Lyon)
• Weria Pezeshkian (University of Copenhagen)

 

Venue

The Niels Bohr Institute is of historical and scientific importance. Please see here for some history.

Ad_final.pdf

Monday 9 December

08:30 → 09:00 Registration

09:00 → 09:15 Introduction

09:15 → 10:00 Uncovering antibody sequences and structures, their assembly and their conformational flexibility

Speaker: Prof. Franca Fraternali (University College London London, England)

10:00 → 10:15 Structural modeling of antibody variant epitope specificity with complementary experimental and computational techniques

Speaker: Eva Smorodina (University of Oslo)

10:15 → 10:45 Coffee break

10:45 → 12:00 Workshop: Combining experiments and simulations: theory and practical examples for disordered proteins

Speaker: Prof. Kresten Lindorff-Larsen (Department of Biology, University of Copenhagen, Copenhagen, Denmark)

12:00 → 13:00 Lunch Break

13:00 → 13:45 Simulating entire cells with Martini

Speaker: Prof. Siewert Jan Marrink (Faculty of Science and Engineering Engineering, University of Groningen Groningen, The Netherlands.)

13:45 → 15:15 Workshop: Mastering Parametrization in Martini 3: Tips and Tricks for Small Molecules and Lipids

https://github.com/Martini-Force-Field-Initiative/CopenhagenWorkshop2024

Speaker: Dr Paulo Cesar Telles de Souza (ENS de Lyon, CNRS CNRS, Franc)

15:15 → 15:45 Coffee Break

15:45 → 16:00 An integrative MD model reveals protein complexes and protein distribution in mitochondria

Speaker: Fabian Schuhmann (Niels Bohr Institute, University of Copenhagen)

16:00 → 16:15 Investigating the role of cholesterol in regulating the SLC7 family of amino acid transporters

Speaker: Dimitrios Kolokouris (University of Copenhagen)

16:15 → 16:30 PINning down the elevator-type mechanism of auxin transport

Speaker: Lorena Zuzic (Aarhus University)

16:30 → 16:45 Advanced Sampling Methodology for Investigating Early-Stage Amyloid Aggregation Structures

Speaker: Ali Asghar Hakami Zanjani (University of Southern Denmark)

16:45 → 17:00 Pore formation in complex biological membranes

Speaker: Leonhard Starke (Aarhus University)

17:00 → 18:00 Poster Session

18:00 → 21:00 Social Dinner

Tuesday 10 December

09:00 → 09:45 Navigating protein landscapes with a machine learned transferable coarse-grained model

Speaker: Prof. Cecilia Clementi (Free University of Berlin Berlin, Germany)

09:45 → 10:00 Role of the sequnce length in the coil-to-globule transition of elastin-like polypeptides

Speaker: Tatiana Morozova (CNRS/Institut Pasteur)

10:00 → 10:15 Group picture of attendees in front of NBI

10:15 → 10:45 Coffee Break

10:45 → 12:00 Workshop: Enhanced Sampling Simulation Methods for Thermodynamics, Kinetics, and Pathways

https://github.com/rostaresearch/enhanced-sampling-workshop-2022/

Speaker: Prof. Edina Rosta (University College London London, England)

12:00 → 13:00 Lunch Break

13:00 → 13:45 Simulations of active vesicles

Speaker: Dr Dmitry Fedosov (Forschungszentrum Jülich GmbH Wilhelm Johnen StraßeStraße, Jülich Germany)

13:45 → 14:00 On the sampling of simulations of membrane shape

Speaker: Adria Bravo Vidal (Niels Bohr Institute, University of Copenhagen)

14:00 → 15:00 Workshop: Mesoscale simulation of biomembranes with FreeDTS

https://github.com/weria-pezeshkian/FreeDTS/wiki/Workshop-2024

Speaker: Dr Weria Pezeshkian (Niels Bohr Institute, University of Copenhagen, Denmark)

15:00 → 16:00 Coffee break and GoodBye