New brochure "High-Performance Computing and Data Science in the MPG"

Contribution by Jan Huertas, Hans Schöler and Vlad Cojocaru of the MPI for Molecular Biomedicine

August 11, 2021

Anyone who still remembers 'floppy disks' with 1.44 MB storage capacity will realize how quickly computer technology has advanced. In science, too, the amounts of data to be processed have become ever larger. The Max Planck Society (MPG) has very early on recognized the importance of this technology for its scientists and started building up its own computing centre in 1961 in Garching. Today, 60 years later, the Max Planck Computing and Data Facility (MPCDF) is a cross-institutional competence centre of the Max Planck Society to support computational and data sciences. The article of Jan Huertas and his mentor Vlad Cojocaru, Project Group Leader of Computational Structural Biology at the Max Planck Institute for Molecular Biomedicine and Group Leader at the Hubrecht Institute in in Utrecht, The Netherlands, is one of the 28 articles that make up the anniversary issue of the brochure on "High-Performance Computing and Data Science in the Max Planck Society".

The link leads directly to the article by Huertas, Schöler and Cojocaru (pages 56-57) more

Jan Huertas and Vlad Cojocaru used the so-called “computational nanoscope” to visualize structural rearrangements of chromatin, which is composed of genomic DNA that is wrapped around histone proteins in nucleosomes. Chromatin is a highly dynamic structure that encodes gene regulatory programs. The computational nanoscope is a term that refers to a collection of molecular modeling and simulation methods that enable the visualization of bio-molecular dynamics at atomistic and sub- atomistic resolution.

Over the past years, simulations of atomistic molecular dynamics have become so accurate that one can observe the molecules moving on the computer as if one is observing them under a very high-resolution nanoscope.

Using resources available at the Max Planck Computing and Data Facility (MPCDF), Jan Huertas and Vlad Cojocaru were now able to generate a trajectory for single nucleosomes of one microsecond in one to two months of computing time. With findings from simulations of multiple atomistic molecular dynamics, over 25 microseconds in total, of three nucleosomes, the scientists discovered the correlation between nucleosome breathing and histone tail dynamics. Furthermore, their findings revealed the structural features and dynamics involved in binding of the transcription factor Oct4 to different locations on the nucleosome. These data are important for understanding chromatin dynamics and the function of pioneer transcription factors.

The brochure provides examples of science that is currently being supported by the MPCDF services. The by-no-means comprehensive selection includes 28 articles from astrophysics, brain research, materials and bio science, high-energy physics, plasma physics and fusion research, turbulence research, demographics, contributed by various Max Planck Institutes.

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