Wednesday, June 3, 2015
HG E22, 10:30 - 10:50

Off-Limits Modeling for Biological Systems, Valery Weber (IBM Research, Switzerland)

Co-authors: Teodoro Laino (IBM Research, Switzerland); Alessandro Curioni (IBM Research, Switzerland)

Reliable atomistic modeling of complex life-science systems has so far been limited by the sizes and time scales accessible by molecular simulations. In this talk, we will present a radical and innovative approach to enable the application of quantum simulations to biological domains typical of classical Hamiltonians. Our approach will merge the extensive knowledge accumulated in the field of semi-empirical quantum simulation and the latest development in low-complexity and scalable algorithms, allowing us to exploit modern supercomputers efficiently and to achieve high scalability and low time to solution. Details of the methodology and efficiency will be discussed.

Wednesday, June 3, 2015
HG E22, 10:50 - 11:10

Modelling and Simulation of Branching Morphogenesis, Roberto Croce (ETH Zurich, Switzerland)

Co-authors: Dzianis Menshykau (ETH Zurich, Switzerland); Tamas Kurics (ETH Zurich, Switzerland); Dagmar Iber (ETH Zurich, Switzerland)

Organogenesis is a dynamic, self-organizing process. Many of the individual regulatory components, e.g. signalling molecules and their regulatory interactions, have been identified in experiments. However, an integrative mechanistic understanding of the regulatory processes is missing. Computational modelling provides a formalism to formulate and test hypotheses. We present and discuss an according Turing model for the simulation of branching morphogenesis and focus on its numerical challenges. Finally, we show a quantitative comparison between simulated- and real branching morphogenesis in vitro, acquired at the D-BSSE Single Cell Facility.

Wednesday, June 3, 2015
HG E22, 11:10 - 11:30

Experiment-Based Simulations of Interacting Swimmers, Siddhartha Verma (ETH Zurich, Switzerland)

Co-authors: Sergey Ivannikov (ETH Zurich, Switzerland); Petros Koumoutsakos (ETH Zurich, Switzerland)

Large groups of fish in the ocean often swim in recognizable patterns. One line of thought identifies 'schooling' as an evolutionary means to dissuade attacks from predators. There is also speculation that such behavior may bestow a hydrodynamic advantage to swimmers. The mechanism of reduction in the required energy input may arise from interactions between the leaders' wake, and the undulatory motion of the following-swimmers. The goal of this study is to probe this possibility, by numerically re-creating swimming behavior observed in experiments. In preliminary studies, both the leader as well as the follower have been observed to experience an increase in swimming efficiency.

Poster Session, Monday, June 1, 2015
17:30 - 20:00

LS-01
A Parallel Block Preconditioner for Fluid-Structure Interaction Problems in Hemodynamics, Davide Forti (EPFL, Switzerland)

Co-authors: Simone Deparis (EPFL, Switzerland); Gwenol Grandperrin (EPFL, Switzerland); Alfio Quarteroni ( EPFL, Switzerland)

Modeling blood flow in large arteries is based on fluid-structure coupled problems. Because of the strong added mass effect, the continuity between kinematic and dynamic variables needs to be enforced at every time iteration, ideally using fully-implicit monolithic algorithms. To deal with the computational complexity induced by monolithic schemes, a parallel solution framework is mandatory. We present a parallel block preconditioner that exploits each of the physics involved in the FSI problem. We show the scalability of our solver implemented in LifeV applied to patient-specific femoropopliteal bypasses.

Poster Session, Monday, June 1, 2015
17:30 - 20:00

LS-02
Agent-based Modeling of Hunter-gatherer Populations, Natalie Tkachenko (University of Zurich, Switzerland)

Co-authors: Simone Callegari (University of Zurich, Switzerland); John David Weissmann (University of Zurich, Switzerland); George Lake (University of Zurich, Switzerland); Christoph P. E. Zollikofer (University of Zurich, Switzerland)

Agent-based models (ABMs) are bottom-up computational models of ecological systems and populations built from individuals. In the context of the PASC project HPC-ABGEM, we develop an ABM of human population dynamics in space and time, including life history traits of modern hunter-gatherers such as individual survival probability as a function of age and sex, daily energy requirements, fertility rates, etc. We present preliminarily simulation results and compare the emerging large-scale characteristics of the simulated population with observational data and classical (continuum) models.

Poster Session, Monday, June 1, 2015
17:30 - 20:00

LS-03
Backbone Hydration Determines the Folding Signature of Amino Acid Residues, Olivier Bignucolo (University of Basel, Switzerland)

Co-authors: Hoi Tik Alvin Leung (University of Basel, Switzerland); Stephan Grzesiek (University of Basel, Switzerland); Simon Bernèche (Swiss Institute of Bioinformatics, Switzerland)

The relation between the sequence of a protein and its structural propensities remains largely unknown. In order to elucidate the side-chain dependent process, we studied peptides of the sequence EGAAXAASS (X = Gly, Ile, Tyr, Trp) through precise comparison of molecular dynamics trajectories and NMR residual dipolar coupling measurements. We show that the formation of internal hydrogen bonds underlying a helical-turn is key to reproduce the experimental values. The computer simulations reveal that the driving force arises from the lack of hydration of the peptide chain on either side of the bulky side-chain, which can act as a nucleation point initiating the folding process.

Poster Session, Monday, June 1, 2015
17:30 - 20:00

LS-04
FEM/FD Immersed Boundary FSI Simulations, Barna Becsek (Universiy of Bern, Switzerland)

Co-authors: Lea Conen (Università della Svizzera italiana, Switzerland); Rolf Krause (Università della Svizzera italiana, Switzerland); Dominik Obrist (University of Bern, Switzerland)

Immersed boundary simulations have been under development for physiological flows, allowing for elegant handling of fluid-structure interaction modelling with large deformations due to retained domain-specific meshing. We couple a structural system in Lagrangian representation that is formulated in a weak form with a Navier-Stokes system discretized through a finite differences scheme. We build upon a proven highly scalable imcompressible flow solver that we extend to handle FSI. We aim at applying our method to investigating the hemodynamics of Aortic Valves. The code is going to be extended to conform to the new hybrid-node supercomputers.

Poster Session, Monday, June 1, 2015
17:30 - 20:00

LS-05
HPC-ABGEM: Simulating Population Dynamics and Genetics of the Worldwide Human Dispersal, Simone Callegari (University of Zurich, Switzerland)

Co-authors: John D. Weissmann (University of Zurich, Switzerland); Natalie Tkachenko (University of Zurich, Switzerland); G. Lake (University of Zurich, Switzerland); Ch. P. E. Zollikofer (University of Zurich, Switzerland)

Paleoanthropological and genetic evidence point to an African origin and subsequent worldwide dispersal of Homo sapiens, who interbred during this range expansion with other human populations (e.g. Neanderthals). Understanding this phenomenon requires modelling the underlying population dynamics and genetics as well as the influence of geography and climate. Within the PASC project HPC-ABGEM, we developed a high-performance agent-based simulation framework able to tackle such issues. We will present simulations of this large-scale process, reconstruct the genetic history of our agents, as well as discuss some properties of discrete-time stochastic individual-based models.

Poster Session, Monday, June 1, 2015
17:30 - 20:00

LS-06
Image-Based Computation of in Vivo Bone Loading History in Patients, Patrik Christen (ETH Zurich, Switzerland)

Co-authors: Ralph Müller (ETH Zurich, Switzerland)

We have recently developed and implemented a novel image-based computational method to derive a bones loading history from its microstructure as assessed by high-resolution computed tomography. Bone strives for uniform tissue loading, thus the loading history is found by scaling a set of physiologically realistic forces until their summed resulting tissue loading is most homogeneous. Using micro-finite element analysis to calculate tissue loading, this approach provided estimates in agreement with in vivo force measurements in mouse, dog, and human bone. Since clinical image resolution is limited in patients, we here present our new method and its resolution dependency and reproducibility.

Poster Session, Monday, June 1, 2015
17:30 - 20:00

LS-07
Investigation of the Effect of Ca2+ binding on Tissue Transglutaminase, Lukas Braun (ETH Zurich, Switzerland)

Co-authors: Florian Herzog(ETH Zurich, Switzerland); Viola Vogel (ETH Zurich, Switzerland)

Tissue transglutaminase (tTG) is a Ca2+ activated cross-linking enzyme that is involved in apoptosis, wound healing and extracellular-matrix remodeling. To date no crystal structure of the active state is published. Molecular dynamics simulations based on the structure of the inactive form were performed in order to determine the native mode of calcium binding and its impact on the enzymes conformation. The study was based on five putative binding sites (S1 to S5) characterized by Kiraly et al. MD simulations revealed the opening of a potential substrate channel near the active site, as well as a mechanism that may explain the experimentally observed cooperativity between two sites.

Poster Session, Monday, June 1, 2015
17:30 - 20:00

LS-08
Needle in a Bloody Haystack, Diego Rossinelli (ETH Zurich, Switzerland)

Co-authors: Dmitry Alexeev (ETH Zurich, Switzerland); Kirill Lykov (Università della Svizzera italiana, Switzerland); Igor Pivkin (Università della Svizzera italiana, Switzerland); Petros Koumoutsakos (ETH Zurich, Switzerland)

We present petascale simulations of microfluidics involving 100,000 of Red Blood Cells (RBCs) and a Circulating Tumor Cell (CTC) in a complex microscale  geometry. The simulations assess the effectiveness of the channel geometry in isolating a single CTC in a 'haystack' of RBCs. The simulation software harnesses the compute power of K20X-accelerated supercomputers reaching up to 60% of their nominal peak in terms of Instructions-Per-Cycle over 10,000s of compute nodes. With the present software we aim to unravel the key requirements for designing effective microfluidics devices and arm manufacturers and cancer researchers with a ground breaking in-silico prototyping tool.

Poster Session, Monday, June 1, 2015
17:30 - 20:00

LS-09
Novel Semi-Implicit Approach and Platform for Personalized Fluid-Structure Interaction Modeling, Frederico Teixeira (ETH Zurich, Switzerland)

Co-authors: Phillipp Wissmann (ETH Zurich, Switzerland); Esra Neufeld (ETH Zurich, Switzerland); Dominik Szczerba (ETH Zurich, Switzerland); Niels Kuster (ETH Zurich, Switzerland)

A semi-implicit method is developed to avoid the complexity of monolithic ones and interface degradation issues of common semi-implicit methods. It adapts the fluid mesh at every nonlinear iteration, instead of once per time-step, keeping the monolithic robustness while reducing complexity. It is implemented in a PETSc-based framework which supports HPC and mixed elements (tet/prism/hex/...). The platform incorporates a novel vasculature segmentation technique with tunable interactivity and adaptive surface generation methods to create realistic models from medical image data, as well as modeling, scripting, analysis, and visualization functionality. The methods are applied to real aneurysm.

Poster Session, Monday, June 1, 2015
17:30 - 20:00

LS-10
Standardization of Efficient Genomic Data Representation and Processing, Daniel Zerzion (Swiss Institute of Bioinformatics, Switzerland)

Co-authors: Yann Thoma (HEIG-VD, Switzerland); Enrico Petraglio (HEIG-VD, Switzerland); Claudio Alberti (EPFL, Switzerland); Marco Mattavelli (EPFL, Switzerland); Pascal Kahlem (Swiss Institute of Bioinformatics, Switzerland); Dmitry Kuznetsov (Swiss Institute of Bioinformatics, Switzerland); Nicolas Guex (Swiss Institute of Bioinformatics, Switzerland); Christian Iseli (Swiss Institute of Bioinformatics, Switzerland); Heinz Stockinger (Swiss Institute of Bioinformatics, Switzerland); Daniel Zerzion (Swiss Institute of Bioinformatics, Switzerland); Ioannis Xenarios (Swiss Institute of Bioinformatics, Switzerland)

The PoSeNoGap project focuses on the design and implementation of efficient genomic data formats and tools for genome analysis applications to scale to large datasets. The proposed solutions shall exploit the available parallelism of the platforms operated by PASC partners. The project promotes investigations on current issues in genomic data representation, compression and transmission within MPEG, an ISO/IEC working group specialized in digital media representation and compression. This activity has led to the definition of reference genomic datasets used to assess the performance of existing bioinformatic tools and to identify requirements for the standard representation of genome data.

Poster Session, Monday, June 1, 2015
17:30 - 20:00

LS-11
Structural Insights into Phosphoinositide 3-kinase Alpha (PI3Ks) Regulation using Molecular Dynamics Simulations, Ilias Patmanidis (University of Geneva, Switzerland)

Co-authors: Chiriano Gianpaolo (University of Geneva, Switzerland); Vadas Oscar (University of Geneva, Switzerland); Scapozza Leonardo (University of Geneva, Switzerland);

Phosphoinositide 3-kinases (PI3Ks) are cytosolic lipid kinases phosphorylating the 3 inositol ring of inositol-phospholipids (PtdIns) which act as lipid second messengers regulating key cellular functions. We focused on the isoform of class I PI3Ks and different mutants (G106V, N345K, E545K, H1047R) associated with cancer and increased enzymatic activity. Our work aimed at understanding the dynamical behavior of PI3Ks by Molecular Dynamics (MD). The MD results shed light on the conformational changes and fluctuations upon activation of WT PI3Ks and mutants, complementing the experimental observations by X-ray crystallography and Hydrogen/Deuterium exchange coupled to mass spectrometry.

Poster Session, Monday, June 1, 2015
17:30 - 20:00

LS-12
Tumor Induced Brain Deformations, Jana Lipkova (Technische Universität München, Germany)

Co-authors: Bjoern Menze (Technische Universität München, Germany); Petros Koumoutsakos (ETH Zurich, Switzerland); John Lowengrub (University of California, USA)

Increased intracranial pressure is the most critical symptom of brain cancer, leading to brain deformation, tissue and nerve compression. We present novel approach for modelling tumour progression together with corresponding brain deformations in patient individual anatomies obtained from medical images. We use the diffuse domain approach to implicitly capture complex brain anatomy. The governing equations are then appropriately modified and extended to a larger, regular domain. This approach helps to reduce errors caused by anatomy missegmentation and allows the use of efficient numerical methods that would not be applicable to the original problem formulation.

Poster Session, Monday, June 1, 2015
17:30 - 20:00

LS-13
Optimal Deployment of Multiscale Applications on a HPC Infrastructure, Bastien Chopard (Universiy of Geneva, Switzerland)

Co-authors: C. Bonadonna (University of Geneva, Switzerland); P. Albuquerque(University of Applied Sciences Western, Switzerland); J.-L. Falcone (University of Geneva, Switzerland); M. Ben Belgacem (University of Geneva, Switzerland); P. Künzli (University of Geneva, Switzerland); F. Brogi (University of Geneva, Switzerland); E. Rossi (University of Geneva, Switzerland); M. Bagheri (University of Geneva, Switzerland)

The goal of our project is to deploy a general framework for multiscale, multi-science applications on a distributed HPC resource. The framework, defined and tested within the European project MAPPER, includes tools and provides a methodology to design, implement and run a multiscale model. We are currently deploying this framework on the Swiss HPC infrastructure, and augmenting it with a performance prediction tool which will allow an optimal placement on the distributed HPC resource. As a test application, we are developing a model for the transport of volcanic ashes that combines models for plume dynamics, advection-diffusion-sedimentation transport and aggregation of fine airborne particles. All these phenomena are produced by different physical processes and take place at different spatial and temporal scales. The corresponding numerical codes have different requirements, some needing HPC resources, but are all tightly coupled.