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UID:submissions.pasc-conference.org_PASC24_sess167@linklings.com
SUMMARY:MS5H - Reaching More Relevant Time Scales with Molecular Dynamics 
 Simulations
DESCRIPTION:Minisymposium\n\nMolecular dynamics (MD) simulations are a too
 l used frequently in the life sciences to study processes of interest at v
 ery high resolution (from atomistic to mesoscopic). Because the experiment
 al characterization of many of the phenomena of interest usually lacks spa
 tial and/or temporal resolution, computer simulations are, in principle, a
 n attractive complement to experiment. One challenge in studying these sys
 tems with computational models is that the time scales of the processes of
  interest are large and heterogeneous, ranging from picoseconds to seconds
  or longer.\nThis minisymposium will bring together different perspectives
  on how to address this overarching challenge. Because MD simulations tend
  to be limited by basic latency issues, rather than by the total amount of
  computing power available, no universal solutions are currently on the ho
 rizon. The session will feature talks from experts on pushing the boundari
 es by hardware/software co-design, by sacrificing some spatiotemporal reso
 lution (coarse-graining), by modifying directly the computational models t
 o optimize dynamical properties, and by using parallel (swarm-like) sampli
 ng methodologies coupled with dedicated data analysis tools.\n\nProbing th
 e Slow Dissociation of Protein-RNA-Complexes with Adaptive Sampling\n\nMos
 t processes of life are the result of polyvalent interactions between macr
 omolecules. Due to their size, the times these interactions require to for
 m and break are often prohibitively long for interrogation using molecular
  dynamics. Additionally, the heterogeneous composition of biological syste
 m...\n\n\nJulian Widmer, Andreas Vitalis, and Amedeo Caflisch (University 
 of Zurich)\n---------------------\nFrom Atomistic to Coarse-Grained Models
  of Complex Systems: Physics-Based or Data-Driven Approaches?\n\nThe compu
 tational study of complex polymeric materials is a very challenging field,
  due to the broad spectrum of the underlying length and time scales. Here,
  we present a hierarchical multi-scale methodology for predicting the macr
 oscopic properties of polymer-based nanostructured systems, which inv...\n
 \n\nVagelis Harmandaris (The Cyprus Institute, University of Crete)\n-----
 ----------------\nMolecular Dynamics Algorithms and Parallelization in the
  Exascale Era\n\nBio-molecular simulations are successfully harnessing exa
 scale computing resources to solve challenging life science problems despi
 te the challenges of the fast-changing changing post-Dennard scaling compu
 ting landscape, characterized by increasing amount of hardware parallelism
  and increasing hardw...\n\n\nSzilárd Páll (KTH Royal Institute of Technol
 ogy, PDC Center for High Performance Computing)\n---------------------\nMu
 ltiscale Simulations of Molecular Recognition by Phase Separated MUT-16: A
  Scaffolding Protein of Mutator Foci\n\nPhase-separated condensates play a
  pivotal role in organizing biomolecular interactions within cells. In the
  context of the RNA silencing pathway, crucial for gene expression regulat
 ion and defense against foreign nucleic acids in organisms like C. elegans
 , Mutator foci serve as perinuclear germ gra...\n\n\nKumar Gaurav (Johanne
 s Gutenberg University Mainz; Institue of Molecular Biology, Mainz)\n\nDom
 ain: Chemistry and Materials, Life Sciences, Physics\n\nSession Chair: And
 reas Vitalis (University of Zurich)
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