PRACE-ICEI – Call #2 Awarded Projects

On this page you will find the projects that were awarded under PRACE-ICEI Calls For Proposals – Call #2.

Awarded Projects

Project Title: Studying protein dimerization with the MARTINI coarse-grained force field in aqueous solution and in the membrane

Project Leader: Dr. Zoe Cournia, Biomedical Research Foundation, Academy of Athens, Greece

Resource Awarded
The following resources were awarded – hosted by ETH Zurich/CSCS, Switzerland:

  • 3 TB of storage

Research Field: Computational Biology

Abstract:
Protein-protein complex assembly is one of the major drivers of biologic response. Understanding the mechanisms of protein oligomerization/dimerization would allow to elucidate how these complexes participate in biological actions and could ultimately lead to new approaches in designing new therapeutic agents. However, determining the exact association pathways and structures of such complexes remains a challenge. Here, we evaluate the Martini 2.2P and Martini open-beta 3 (Martini 3) force fields to reproduce the dimerization process of several membrane and aqueous proteins in order to assess whether it is feasible to study protein dimerization in reasonable accuracy and throughput. We find that Martini 2.2P systematically overestimates the free energy of association estimating large barriers in distinct areas, which likely leads to over-aggregation when multiple monomers are present. In comparison, the less viscous Martini 3 results to a systematic underestimation of the free energy of association. In all cases the near-native dimer complexes are identified as minima in the free energy surface, albeit not always as the lowest minima. In the case of Martini 3 we expect that the fictitious supramolecular protein aggregation present in Martini 2.2P multimer simulations will be alleviated and thus this force field may be more suitable for the study of protein oligomerization. We apply for archival of the data produced in this study to make it available to the wider community.

Project Title: Neutrinoless double beta decay of 100Mo

Project Leader: Dr. Giovanni De Gregorio, Universitá degli studi della campania “Luigi Vanvitelli”, Italy

Resource Awarded
The following resources were awarded – hosted by CINECA, Italy:

  • 50 000 node hours of scalable computing
  • 2 TB active storage
  • 100 TB archive storage

Research Field: Nuclear physics

Abstract:
The neutrino oscillation experiments have provided the evidence that neutrinos have non zero masses.
However, the nature of these particles is still unknown, i.e. if they are Dirac or Majorana particles.
Therefore, one has to study phenomena in which it plays an important role. This is the case of the Neutrinoless Double Beta Decay. One of the possible candidates is the 100Mo and the prediction of its half-life would help to design the new experiments that will look for this decay.

We plan to study this nucleus using the nuclear shell model. It is based on the assumption that the nucleus is composed of a closed-shell inert core with additional valence nucleons interacting through an effective potential.

We will derive this potential by way of many body perturbation theory starting from a realistic two-body potential. With the increasing number of nucleons in the model space the dimension of Hamiltonian to be diagonalized increases dramatically. For example, for the 0+ subspace, with a 78Ni core, the dimension range from 104 for 92Mo to 1011 of 100Mo, which is very close to the current limit of shell model codes, therefore, the use of the HPC systems is of crucial importance.

Project Title: Computational characterization of the supramolecular reorganization of alkanes upon cooling

Project Leader: Prof. Dr. Anela Ivanova, University of Sofia, Faculty of Chemistry and Pharmacy, Bulgaria

Resource Awarded
The following resources were awarded – hosted by ETH Zurich/CSCS, Switzerland:

  • 12 500 node hours per quarter on Piz Daint
  • 1 TB of storage

Collaborators

  • Prof. Dr. Nikolai Denkov, University of Sofia, Faculty of Chemistry and Pharmacy, Bulgaria
  • Prof. Dr. Slavka Tcholakova, University of Sofia, Faculty of Chemistry and Pharmacy, Bulgaria
  • Dr. Sonya Tsibranska-Gyoreva, University of Sofia, Faculty of Chemistry and Pharmacy, Bulgaria
  • Stoyan Iliev, University of Sofia, Faculty of Chemistry and Pharmacy, Bulgaria

Research Field: Physical chemistry

Abstract:
Recently, we discovered that micrometer drops from alkanes and surfactants exhibit a spectacular series of shape transformations upon cooling (Figure-1A).1,2 The shapes encompass spheres, icosahedra, prisms, and even fibers or drops bursting into nanoparticles.3-5 The method is very efficient and scalable.6 Theoretical analysis suggested that the shapes are caused by freezing layers of long-chain surfactants, adsorbed at alkane-water interface, acting as 2D template for ordering of neighboring alkane molecules into thin surface multilayers.7,8 The drop dynamics shows: (1) the alkane multilayers resemble “intermediate rotator phases”9 and (2) all phenomena depend strongly on the interfacial curvature. The research has been funded by an excellence VIHREN grant of the Bulgarian Ministry of Education and Science (Project ROTA-Active). The aim of this study is to start molecular simulations of the freezing of the surfactant adsorption layers and of the formation of multilayer alkane rotator phase, with focus on the role of curvature. The outcome will outline the molecular mechanism in the initial stages of freezing and will allow quantitative assessment of the curvature effect. Realistic models require at least several molecular layers or diameters of min. 5 nm of the curved surfaces. This renders the use of ICEI sclable computational resources indispensable.

Project Title: BioExcel biomolecular simulation workflows

Project Leader: Dr. Adam Hospital, Institute for Research in Biomedicine (IRB-Barcelona), Spain

Resource Awarded
The following resources were awarded – hosted by GCS at JSC, Germany:

  • 5 000 node hours on JUSUF-HPC

Research Field: Life Sciences, Biomolecular simulation, Structural Bioinformatics, Molecular Dynamics, Free energy, Docking

Abstract:
BioExcel Center of Excellence (BioExcel CoE) is the European central hub for biomolecular modelling and simulations. Started as an H2020 EU-funded project in 2015, it has now become a reference for the Life Science biomolecular simulation field. Partners involved in the project are the main developers of the most popular software tools in the field (over 20,000 users worldwide), including GROMACS (MD simulations), HADDOCK (Docking), pmx (free energy) and CP2K (QM, QM/MM). In order to increase researchers’ productivity and shorten the time to solution, these tools are integrated in scientific pipelines (biomolecular workflows) to tackle real scientific projects. Making these workflows reproducible, portable and in general more usable has been highly requested by the user communities and is one of the principal objectives of BioExcel. Following this target, a software library called BioExcel Building Blocks (biobb) has been developed, in collaboration with the ELIXIR European project. Using this library, a collection of biomolecular simulation workflows have been presented, which are now being used to showcase their power to the scientific community. These workflows can be easily installed in different infrastructures, and easily executed from GUIs such as Jupyter Notebooks. The primary objective of this proposal is to deploy BioExcel workflows in the varied ICEI/FENIX resources, from VMs to supercomputers, offer them as services to the wider community, and possibly start a long-term engagement with FENIX as an external resource provider of BioExcel.

Project Title: Strain-Induced Effects of Deformed Monolayer Graphene

Project Leader: Dr. Estelina Lora da Silva, University of Porto, Portugal

Resource Awarded
The following resources were awarded – hosted by ETH Zurich/CSCS, Switzerland:

  • 7 095 node hours per quarter on Piz Daint
  • 1 TB of storage

Research Field: Materials Science

Abstract:
The flexibility of manipulating monolayer graphene allows one to engineer the electronic and optical properties by inducing local deformations to control the strain distribution of this atom-thick material (straintronics).[1] In fact, structural corrugations and ripples have been observed in suspended graphene, exhibiting an unique out-of-plane motion.[2] The origin of these nanometer-sized ripples is still not understood and hence the proposed calculations can aid to deepen the understanding regarding the stabilization of such topological effects.

Another interesting fact is that strained geometric curvatures in graphene can give raise to an uniform pseudo-magnetic field, with intensities greater than 300 tesla,[3] which lead to observable phenomena, such as pseudo-quantum Hall effect and Landau levels.[4] Moreover, by applying large enough strain on graphene, variations of the frequency modes are evidenced, possessing features comparable to a 3D system.[5] Such features are of interest since potential applications may be used to produce interference devices within the domain of quantum optics, e.g Aharonov-Bohm type apparatus.[6]

[1]J. Phys. Condens. Matter 26, 18 (2014). Science 329, 544 (2010).
[2]arXiv:2002.09947.
[3]Nature Phys. 7, 810 (2011).
[4]Phys. Scr. 90, 045702 (2015).
[5]Phys. Rev. Lett. 123, 135501 (2019).
[6]Phys. Rev. A 76, 041801(R) (2007). J. Phys. A 32, 5367 (1999).