Biomolecular Simulations at the Mesoscale
Location: University of Trento, Italy - Palazzo Consolati, Via S. Maria Maddalena 1, Trento
Organisers
Recent major breakthroughs in experimental biophysics include single molecule force-spectroscopy, super-resolution microscopy and the cryo-EM/ET revolution [1,2]. These experiments probe the biological mesoscale (length scale of 10 nm to 1 µm, and timescales of milliseconds to seconds) on which many critical biological processes operate. Complementary theoretical methods at these scales are conceptually more challenging and practically significantly less well developed than atomistic scale modelling [3], because they fall in between the realms of discrete particle- and field-based continuum descriptions.
A first objective of the workshop is to explore the technical basis of mesoscale modeling. In particular, we propose to compare the merits of two recent attempts (i) to introduce thermal fluctuations into three-dimensional finite-element representations of macromolecules [4] and (ii) to use soft meshes and a Molecular Dynamics engine to simulate the dynamics of fluid bilayer vesicles [5], to situate them with respect to existing schemes for the systematic elimination of microscopic degrees of freedom [6] and concurrent multi-scale modeling [7,8] as well as the potential of coupling them to the simulation methods of fluctuating and active hydrodynamics [9-14].
The second objective of the workshop is to discuss challenges on the mesoscale in the framework of the integrative modelling of biological systems, when disparate data-sets are combined into physics-based models to form a coherent picture [15] and where the theoretical challenges inherent in mesocale modelling risk to become a roadblock to future progress. Our vision is to inspire international collaborations and to define a roadmap for inventing and sharing the theoretical framework and computational toolkit to enable integrative biological workflows for these nascent biophysical tools. This will enable experimental results and theoretical modelling to be used synergistically to obtain a mechanistic understanding of mesoscale biological processes, such as the function of molecular motors [16], DNA packaging [17], cell-virus interactions [18], cell motility and division [19]. This requires input from mesoscale experimental biophysicists, biomolecular simulators and theoretical soft matter physicists. In mature areas of physics such as particle physics and condensed matter, the use of theory and computational models to obtain maximum insight from experimental results is embedded in the research culture, and our aim is to initiate an equivalent approach in (supra)molecular biology.
References
Ralf Everaers (École Normale Supérieure de Lyon) - Organiser
Italy
Gianluca Lattanzi (University of Trento) - Organiser
Angelo Rosa (Scuola Internazionale Superiore di Studi Avanzati (SISSA)) - Organiser
United Kingdom
Sarah Harris (University of Leeds) - Organiser
United States
Rommie Amaro (University of California, San Diego) - Organiser
Garegin Papoian (University of Maryland) - Organiser