New Grand Challenge Projects selected

In CSC's last Grand Challenge Call 2018-1, in total 11 proposals were submitted requesting 109,2 million core hours and 635 terabytes of disk space. The Scientific Customer Panel selected 5 GC Projects to be run with 40 million core hours in total:

Frederick Gent, Aalto University: Interaction of small and large scale galactic dynamos (GDYNS)

Magnetic fields (MF) thread the galaxy and are argued to be critical to star formation processes. They fundamentally affect cosmic ray diffusion and the production of observable synchrotron emission. It is widely accepted that the observed, dynamically significant, MF could not persist over Giga year time scales without some dynamo amplification. In most, if not all, astrophysical systems the dynamo mechanism is poorly understood. A large-scale dynamo (LSD) mechanism, feeding on anisotropic turbulence embedded in rotating, density stratified shear flows, is theoretically expected and also verified numerically (e.g. our previous GC project SNDYN). Another dynamo instability, the small-scale dynamo (SSD), is also expected independently in all astrophysical objects to generate additional intense magnetic fluctuations.

Capturing SSD, and studying its interactions with LSD requires demanding high-resolution numerical modelling, that is only now becoming attainable with the latest computing resources. Debate over the nature of SSD-LSD interactions has raged since the 1990s and results to date remain controversial. With our improved Pencil Code interstellar medium (ISM) setup we shall investigate the SSD properties and effects on LSD, as function of the key system parameters, such as Mach number, magnetic Reynolds and Prandtl numbers, to further illuminate these important open questions.
 

Gerrit Groenhof, University of Jyväskylä: Manipulating chemistry with confined light (Manipulight)

Transition to solar energy requires means to steer photochemical reactions, but catalysts to control excited-state dynamics do not yet exist. The observation that photochemical reaction yields increase when the reactants are inside optical cavities, suggests that cavities may be promising catalysts for photochemistry. The confinement of light inside such cavities increases the interaction with photoactive molecules and leads to the formation of new hybrid light-matter states (polaritons) that are coherent superpositions of excitations of the molecules and of the cavity. The hybridization between light and matter not only delocalizes the excitation over many molecules, but also changes their potential energy surface, and thus could be used to control chemistry.

Manipulating photochemistry with cavities requires complete understanding of how the interaction with confined light affects reactivity. Therefore, we have developed a method for performing atomistic simulations of molecules strongly coupled to cavities. We will simulate cavity systems with thousands of molecules on thousands of processors to design cavities that bring about a desired change in the photochemistry of these molecules. The simulations will be the starting point for experimentally demonstrating that catalysis with confined light is possible, thereby opening up a new field in catalysis with implications for artificial light harvesting.
 

Minna Palmroth, University of Helsinki: From 2D to 3D: Towards Kinetic Understanding of Geospace (FRODO)

Space is an emerging megatrend, and increasing numbers of small satellites are being launched. A central factor affecting spacecraft health is the unpredictable radiation environment consisting of charged particles. Particles may be accelerated or lost from the system due to a number of mechanisms that are poorly understood. From the modelling perspective, the lack of understanding of the radiation environment results from two aspects: the global models are lacking in physical accuracy, while local models lack accurate driving. We propose to improve both aspects by this proposal.

While a global 3-dimensional (3D) model solving electron physics is out of reach computationally, it has become possible to take the first step towards this future goal. This goal requires two independent steps by which the future implementation strategy will become evident:

1. The first global survey of electron distribution functions in 2D within the near-Earth space, a task that has never been realized before, and

2. The first 3D description of the global hybrid-Vlasov ion regime, also never achieved before.

The project is intimately tied to with the success of an ERC Consolidator grant, a Finnish Centre of Excellence, and an Academy project.
 

Isaac Salazar-Ciudad, University of Helsinki: Computational investigation of short- and long- term evolution of development (Evo-Devo)

A central question in biology is how genotypes are translated to phenotypes. In metazoa, this translation happens through embryonic development, which involves coordinated action at several levels of organization – gene expression, protein interactions, cell behavior and tissue biophysics. These interactions make the map from genotypes to phenotypes highly nonlinear. Thus, even if mutations at the DNA level arise randomly, the resulting phenotypic variation is far from random. Because natural selection acts at the phenotypic level, understanding the genotype-phenotype map becomes key to understanding evolution.

Our main objective is to understand the interplay between evolutionary change and embryonic development, and includes three subprojects:

1. What is necessary for complex morphologies to develop and how this complexity affects phenotypic variation.

 2. Understanding the effects of long-term stabilizing selection on the genotype to phenotype map and the possible variation.

 3. How the topology of the genotype-phenotype map affects the predictability of evolutionary change

For all three projects, we will use software developed in the lab: EmbryoMaker and Toothmaker. These packages simulate development in 3D tissues, incorporating gene regulatory dynamics, various cell behaviors and physical interactions. Thus, they are particularly suited to study the evolution of development on various time scales.
 

Ilpo Vattulainen, University of Helsinki: Revealing the activation mechanism of the insulin receptor (AIR)

Imbalance in insulin receptor (IR) functionality is traditionally known to result in diabetes. Insulin binding induces a structural change in its receptor that is translated across the membrane to the intracellular domains, which then phosphorylate each other and thus initiate signaling cascades. Recent studies using single-particle electron microscopy (EM) have shed light on the conformational changes in the IR on insulin binding. However, high-resolution models describing the activation and deactivation mechanisms and their dynamics are still missing. The objective of this project is to provide atomistic-level understanding of the insulin-induced conformation changes in the IR using all-atom molecular dynamics (MD) simulations tightly linked to EM and cell biology experiments

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