Old projects

Numerical Analysis: Computational electromagnetics in complex environments

The Yee scheme is still the main workhorse for computational electromagnetics in industry. …

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Numerical Analysis: A fast summation method for fiber simulations

A numerical method for large scale simulations of fibers immersed in a Stokesian fluid has been developed. …

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Numerical Analysis: Coarse graining of stochastic differential equations with application to wireless channel modeling

Stochastic modeling is an essential tool for studying statistical properties of wireless channels. In Multipath Fading Channel (MFC) models the signal reception is modeled by a sum of wave path contributions, and and Clarke’s model [1] is an important example of such which has been widely accepted in many wireless applications. …

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Numerical Analysis: Adaptive multilevel Monte Carlo simulation

Stochastic Differential Equations (SDE) are non-deterministic processes used to model natural processes with uncertainty, such as micro scale particle dynamics and the evolution of financial assets. …

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Numerical Analysis: Fast interface tracking

A multiresolution description of interfaces are used to develop a fast algorithm for their propagation. …

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Numerical Analysis: Numerical treatment of surfactants in multiphase flow

In this project we have developed a numerical method for two-phase flow with insoluble surfactants and contact line dynamics in two dimensions. …

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Numerical Analysis: Fast Ewald summation for Stokesian particle suspensions

We have developed a numerical method for suspensions of spheroids of arbitrary aspect ratio which sediment under gravity. …

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Numerical Analysis: Fast methods for high frequency wave propagation problems

We design methods for wave propagation, whose cost grows slowly with the frequency for a fixed tolerance. …

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Numerical Analysis: Computational modeling of the mammalian cell

The project aims to develop realistic and computationally effective models of cellular metabolism. …

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Numerical Analysis: Calibration in mathematical finance

Figure 1. Local volatility surface corresponding to option prices on the OMXS30 index.

The calibration problem is posed as an optimization problem under pde-constraints, and solved using e.g. techinques from optimal control. …

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Numerical Analysis: Gaussian beam approximations

Development and analysis of Gaussian beam methods for high frequency waves. …

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Numerical Analysis: FEniCS-HPC

High Performance Adaptive Finite Element Methods for Turbulent Flow and Multiphysics with Applications to Aerodynamics, Aeroacoustics, Biomedicine and Geophysics. …

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Numerical Analysis: Iterative methods for nonlinear eigenvalue problems

This project involves the derivation and study algorithms for new types of nonlinear eigenvalue problems. …

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Numerical Analysis: An accurate integral equation method for simulating multi-phase Stokes flow

We have developed a numerical method based on an integral equation formulation for simulating drops in viscous fluids in the plane. …

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Numerical Analysis: Adaptive methods for subsurface flow

This project focuses on adaptive finite element approximations and a posteriori error estimates for PDE with random data. One would like to model subsurface fluid flow and transport to understand, test, and verify predictions for a variety of applications, including: the propagation of contaminants and pollutants in groundwater, carbon sequestration in deep saline aquifers, and flow in composite biological materials. …

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Numerical Analysis: Quadratic hedging

The classic financial theory that started with the arbitrage free pricing theory of Black, Scholes and Merton (1973) deals with markets that are complete in the sense that every financial contract in the market can be perfectly (“almost surely”) replicated by a dynamic portfolio of other contracts.

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NA: Reconstruction methods for very noisy Electron Tomography data

Development of numerical methods for inverse problems in structural biology. …

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Numerical Analysis: Radial basis function methods for partial differential equations

In this project radial basis functions are used to discretize and solve PDEs. …

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Numerical Analysis: Cut finite element methods

We develop finite element methods for PDEs where the domain is allowed to cut through a fixed background mesh in an arbitrary fashion without loosing accuracy and without problems with ill-conditioned linear systems. …

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PSDE: ScalaLife

The ScalaLife project intends to build a cross-disciplinary Competence Centre for life science software that should evolve to a “one-stop-shop” for users and developers of Life Science software alike. …

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PSDE: PRACE

The mission of the PRACE RI is to enable high impact European scientific discovery and engineering research and development across all disciplines to enhance European competitiveness for the benefit of society. The PRACE RI seeks to realize this mission through world class computing and data management resources and services open to all European public research through a peer review process. …

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PSDE: EGI-Inspire

The ultimate goal of EGI-InSPIRE is to provide European scientists and their international partners with a sustainable, reliable e-Infrastructure that can support their needs for large-scale data analysis. This is essential in order to solve the big questions facing science today, and in the decades to come. …

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PSDE: PEPPHER

The emergence of highly parallel, heterogeneous, many-core processors poses major challenges to the European software industry. It is imperative that future many-core architectures can be fully exploited without starting from scratch with each new design. In particular, there is an urgent need for techniques for efficient, productive and portable programming of heterogeneous many-core systems. …

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PSDE: ENCORE

The ENCORE project objective is to achieve a breakthrough on the usability, reliability, code portability, and performance scalability of multicore architectures. Design complexity and power density implications stopped the trend towards faster single-core processors. …

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PSDE: Venus-C

Cloud computing has the potential to transform scientific exploration, discovery and results by empowering research and SME communities in new ways. VENUS-C (Virtual Multidisciplinary EnviroNments USing Cloud Infrastructures) is pioneering project for the European Commission’s 7th Framework Programme that draws its strength from a joint co-operation between industry and scientific user communities. …

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PSDE: CRESTA

For the past thirty years, the need for ever greater supercomputer performance has driven the development of many computing technologies which have subsequently been exploited in the mass market. Delivering an exaflop (or a million million million calculations per second) by the end of this decade is the challenge that the supercomputing community worldwide has set itself. …

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PSDE: Vision Cloud

The goal of the VISION project is to advance the competitiveness of the EU economy by introducing a powerful ICT infrastructure for reliable and effective delivery of data-intensive storage services, facilitating the convergence of ICT, media and telecommunications. …

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PSDE: OPENPROD

OPENPROD is an ITEA2 European project that will provide an open, whole-product model-driven rapid systems development, modeling, and simulation environment integrating …

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PSDE: Large scale data management using iRODS

This project will investigate the use of iRODS as a framework for data management. …

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PSDE: Biobanking and biomedical research integration toward a global sharing of biobank resources

Biobanks are biospecimen repositories that collect, process and store biomaterials and generate the associated data and information. …

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FLOW and NA: Quadrature rules for boundary integral methods applied to Stokes flow

This project focuses on the design of accurate quadrature rules for functions with isolated singularities. …

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FLOW: Numerical treatment of surfactants in multiphase flow

In this project we have developed a numerical method for two-phase flow with insoluble surfactants and contact line dynamics in two dimensions. …

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FLOW: Simulations of quasi-geostrophic turbulence

Two codes have been developed and implemented for use on massively parallel super computers to simulate twodimensional and quasi-geostrophic turbulence. …

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FLOW: Wall-bounded turbulence: Re-visit using numerical experiments

In our everyday live, we are constantly surrounded by fluids, be it gaseous air or liquid water.

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FLOW: Spectral-element simulations of turbulent separation

Fluid flows are complicated and nonlinear, which calls for accurate numerical treatment. …

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FLOW: WALLPART – Inertial Particles in developing wall turbulence

Traditionally, direct numerical simulations (DNS) of turbulent flows are performed in simplified computational domains that are characterised by periodic boundary conditions in all three directions.

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FLOW: Large-scale simulations of turbulent flows, including transition and separation

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FLOW: Simulations of turbulent boundary layers with passive scalars

The study of turbulent boundary layers with passive scalar transport has been an important research topic for the last few decades, since such a problem involves two fundamental aspects: the development of turbulence in a thin region adjacent to a solid wall, and the transport and diffusion of passive species by turbulent motion. …

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FLOW: Rotating channel flow at high Reynolds number

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FLOW: Simulation and modelling of turbulent combustion

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FLOW: Development of subgrid models and application of large-eddy simulations

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FLOW: DNS of high-Reynolds number turbulent pipe flow

Fully developed incompressible turbulent flow through a smooth pipe is a canonical problem in fluid mechanics. …

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FLOW: Parallel adaptive FEM

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FLOW: Tools for Visualisations with Simson

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FLOW: Stratified wall-bounded flows

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FLOW: Arctic Sea ice in warm climates

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FLOW: Bifurcation and stability analysis of a jet in crossflow

This project builds on the work of Refs. [1] and [2], where the Direct Numerical Simulation (DNS) of a jet in crossflow was studied in detail and a stability analysis was performed. …

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FLOW: Studies of transition in Couette flow

Plane Couette flow, the flow between two parallel walls moving in opposite directions, is the simplest canonical example of the effect of shear on a viscous fluid. …

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FLOW: Adjoint-based linear and nonlinear optimisation in wall-bounded shear flow

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FLOW: Numerical simulation of generation of sound in separated internal flows

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FLOW: Numerical methods for fluid-structure interaction aero-acoustics

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FLOW: Simulation of free-boundary problems and phase change

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FLOW: Numerical simulation of swimming micro-organisms in suspensions

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FLOW: Particle-laden transitional flows; small and finite-size particles

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FLOW: An accurate integral equation method for simulating multi-phase Stokes flow

We have developed a numerical method based on an integral equation formulation for simulating drops in viscous fluids in the plane.

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FLOW: ASTRID – ”A STudy of Rotation In Developing boundary-layer flows”: Direct numerical simulations

The main aim of the work is to increase the knowledge of the flow over a rotating disk, also called the von Kármán flow.

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Sessi MCP: A Profiling Framework for the Microsecond Range

Scientific applications of Molecular Dynamics usually require strong scaling. For efficient MD codes, such at GROMACS, this leads to sub-millisecond iteration times, where important tasks take tens of milliseconds. …

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Sessi MCP: An optimized FFT library for 3D real-valued small-size data

The use of Fast Fourier Transform (FFT) is ubiquitous in computational science. Its usage varies from solving Partial Differential Equations, to calculating convolutions, to performing spectral analysis. …

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Sessi MCP: Low-Overhead Thread-Parallelization Library

Over the past decade OpenMP has become the most popular threading model for HPC applications. …

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Sessi MCP: Parallel Implementation of the Setup of an Algebraic Multigrid Solver

Numerical modelling of various physical phenomena is based on solving big systems of linear equations arising from the discretisation of PDE. …

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Sessi MCP: Code optimization for on-node performance: SIMD and LIBXSMM for small dense matrix-matrix multiplications, streaming stores for optimizing cache to memory operations

In the Nek5000 code, the tensor-product-based operator evaluation can be implemented as small dense matrix-matrix multiplications. …

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Sessi MCP: Refactoring of Nek5000

Nek5000 is a scalable open-source code for CFD modelling with a long development history starting in the 1970s. It is written in FORTRAN77 and C extensively using a number of Fortran features like implicit data typing, common blocks or equivalence. …

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Sessi MCP: Runtime Profiling and Automatisation of Projections

One of the important methods used by Nek5000 to speed up solution of linear problem Ax=b with the iterative solvers is the residual projection, in which solutions (x) and right hand sides (b) from previous time steps are used to built projection space for the current solution, right hand side pair. …

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Sessi MCP: Investigation of Communication Kernel in Nek5000

Important advantage of spectral element method is its meshing flexibility coming from spatial decomposition of simulation domain into a set of non-overlapping sub-domains. …

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Sessi MCP: Overcoming I/O limitations on exascale architectures

With larger systems and application scales, I/O is increasingly becoming a bottleneck. This is particularly true when global system states need to save regularly for checkpointing and analysis purposes, like in computational fluid dynamics applications. …

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Sessi MCP: OpenACC for Nek5000

Nek5000 is an open-source code for the simulation of incompressible flows. Nek5000 is widely used in a broad range of applications, including the study of thermal hydraulics in nuclear reactor cores, the modeling of ocean currents and the simulation of combustion in mechanical engines. …

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Sessi MCP: Algorithms for molecular dynamics on heterogeneous architectures

With molecular dynamics molecular processes can be followed in atomistic detail, something which is difficult or impossible to achieve with experimental techniques. But obtaining this information comes at a high computational cost. …

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Sessi MCP: Assembly level vectorization of compute intensive kernels in Nek5000

Nek5000 is a computational fluid dynamics solver for the Navier-Stokes equations based on the spectral element method. This method is a compromise between high accuracy and geometric flexibility. However, this flexibility has a price. …

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Visualization: Efficient Methods for Volumetric Illumination

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Visualization: Visualization of MR Diffusion Data

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Visualization: Lagrangian Analysis of Intracardiac Blood Flow using 4D Flow MRI

Cardiovascular disease is a serious health threat in developed countries, and remains the number one cause of death. …

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Visualization: Semi-Automatic Visualization and Quantification of Intra-Cardiac 4D Flow MRI Data for Large Patient Studies

Besides the long acquisition times, application of 4D flow is hindered by the complexity of the analysis of the comprehensive data sets. …

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Visualization: Volumetric Finite Element Visualization

The finite element (FE) method is an important computational technique in science, engineering and medicine for solving partial differential and integral equations. …

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Visualization: Cardiovascular blood flow analysis

This project analyses blood flow data from direct measurements (4D flow MRI). A clustering approach has been developed based on 2D coherence maps placed in the in- and outflow areas, which summarize the flow behavior of the 3D volume. …

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Visualization: Organic solar cells design

Organic solar cells, or other photovoltaic devices play an important role in many future technologies. …

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Visualization: OpenSpace – A tool for Space Research and Communication

OpenSpace is new open source interactive data visualization software designed to visualize the entire known universe and portray our ongoing efforts to investigate the cosmos. …

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Visualization: Interactive 3D Histology Visualization for Pathology

Histology, the medical analysis at microscopic level of tissue specimen from the human body, is a cornerstone in healthcare and medical research. …

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Visualization: FlowZoom: Feature-based, multi-resolution in-situ sampling of very large turbulence simulations

Turbulence simulations have become so large, that the sheer size is an obstacle for even saving the data in full spatio-temporal resolution. …

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Visualization: Multi-scale visualization of binding processes related to conformational changes of proteins for Alzheimer’s disease research

Conformational changes of proteins occur as effect of external stimuli and can lead to pathogenic states. E.g. proteins can aggregate into β sheet-rich fibrillar assemblies, known as amyloid fibrils, which cause Alzheimer’s disease. …

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Electronic: Spin molecular electronics

A very intriguing prospect is to generalize the thermoelectric concept to spin voltages and spin currents. This leads to the so-called spin Seebeck effect, discovered in 2008. The fact that thermoelectric effects are spin dependent has been known for a very long time but research in the area has been impeded due to experimental difficulties. …

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PSDE: OpCoReS – Optimized Component Runtime System

OpCoReS focuses on the use of task-oriented programming models, high-level equation-based object-oriented textual/graphical programming models and efficient compilation of such models to task-oriented and data-parallel code, the exploitation of multi-level parallelism in application development as well as during runtime and associated performance monitoring and analysis. …

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PSDE: Integration of data from Swedish Biobanks and Quality Registries

The project aims at developing standards, ontologies, and tools for simplifying data integration from biobanks and quality registries. …

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PSDE: Ontology engineering for management and integration of data

This project aims to develop methods and tools to improve and integrate ontologies for use in management and integration of data. …

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PSDE: E-Science in Medicine – Prediction, Prognosis, and Understanding of Complex Diseases

We develop and apply integrative experimental and computational tools to identify and enable quantitative understanding of molecular mechanisms of disease. …

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PSDE: Big Data Tools for Social Science

Social science has in recent decades become a data science. The use of more powerful statistical tools has enabled researchers to improve our understanding of human interactions through inferring causality in observational studies and finding hidden patterns, general relationships and unknown correlations between individuals and groups of individuals. …

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Molecular: Markov state models for simulation

Molecular dynamics simulation has evolved from a severely limited esoteric method into a cornerstone of many fields, in particular structural biology where it is now just as established NMR or X-ray crystallography. To achieve high performance, the simulations are typically run on massively parallel computers using domain decomposition of calculations, and for large enough systems (hundreds of millions of particles) this can scale to very large machines. …

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Molecular: Distributed computing simulation

The amount of compute resources has grown vastly in the recent years, however they are underutilized but there are many problems that can put them into good use. As an example within the field of molecular dynamics, adaptive sampling algorithms such as Markov State modeling or Free energy calculations constitute of many short(100-1000) simulations to gather statistics followed by iterations of adaptive sampling in order to guide simulations for the coming iteration. …

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Molecular: Algorithms for molecular dynamics on heterogeneous architectures

The amount of compute resources has grown vastly in the recent years, however they are underutilized but there are many problems that can put them into good use. As an example within the field of molecular dynamics, adaptive sampling algorithms such as Markov State modeling or Free energy calculations constitute of many short(100-1000) simulations to gather statistics followed by iterations of adaptive sampling in order to guide simulations for the coming iteration. Although it is a simple workflow to define, these type of problems can easily utilize thousands of cores and generate massive amounts of data and require something more than a queue. …

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Molecular: Algorithms for molecular dynamics on heterogeneous architectures

With molecular dynamics molecular processes can be followed in atomistic detail, something which is difficult or impossible to achieve with experimental techniques. But obtaining this information comes at a high computational cost. The equations of motion of hundreds of thousands of atoms need to be integrated for billions of time steps, which can mean months of simulation time. Gains in computational efficiency are therefore highly beneficial for molecular simulation community, not only within SeRC, but world wide. …

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Molecular: Efficient free energy calculations for biomolecular applications

Free energy calculations is an important task in molecular simulations, since it is probably the most obvious property that can be easily obtained directly in the lab, without several intermediate steps of interpreting raw data. Typical examples include solubility of small compounds in water, the binding energy of a drug to a protein, or how conformational transitions in macromolecules are affected by changes in the environment or ligand binding. …

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Molecular: Hierarchical Multiscale Modeling with a new class of force fields

We propose a novel methodology to produce a new class of force fields (FF) for predictive molecular simulations and computer modeling, based on large-scale ab initio computer simulations (with no empirical input), combined with mining from structural data bases such as CSD and PDB. The FFs are effective potentials, obtained in a by us developed inverse Newtonian scheme called the Inverse Monte Carlo (IMC). …

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Molecular: Molecular processes at the three-phase contact line

This project is about gaining fundamental understanding of the processes governing the dynamic wetting behavior of droplets on solid surfaces. The dynamics of wetting of a solid by a liquid plays a crucial role in many processes, both in nature and in industry. Despite significant efforts in this field, the exact mechanism of contact line advancement is still not clear. Volume wise, most processes can be described by continuum models (e.g. Navier Stokes). …

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Molecular: Parallel sampling of functional motions in proteins

Molecular dynamics can reveal molecular motion in atomistic detail, but this comes at a high computational cost. Billions of time steps of femtoseconds are required to reach biologically relevant time scales of microseconds. For particular scientific problems smarter sampling could accelerate sampling by orders of magnitude, thereby enabling new problems to be tackled. …

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Molecular: Spectrally accurate fast Ewald summation

The goal of this project is to develop spectrally accurate and fast Ewald summation methods ­­– suitable for parallel computations – for various problems in molecular dynamics and fluid mechanics.

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Molecular: Computational studies of membrane protein-ligand interactions

The goal of our research is to improve atomic-level understanding of receptor-ligand interactions using computational models. Using methods such as molecular dynamics simulations, molecular docking, and homology modeling we model how small molecules interact with proteins and thereby modulate their function. …

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Molecular: Novel approaches for the evaluation of long range electrostatic interactions in MD

The calculation of electrostatic interactions in molecular computer simulations is by far most time-consuming part due to their long-ranged nature. In the last few years some promising algorithm to treat long range interactions based on Non Uniform FFT has been proposed. …

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Molecular: New state of the art hardware technologies and computational techniques to boost molecular simulations

Recent hardware developments have led to an extensive availability of multi-core CPUs and dedicated accelerator processors such as graphical processing units (GPUs). Using these devices, a massive parallelism at appreciable low cost can be implemented, producing an acceleration in computational performance that can be very high for several applications. …

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Molecular: Systematic coarse grained modelling of DNA and proteins using the Newton Inversion method

The development of coarse-grained (CG) models of large biological molecules for efficient and accurate large scale molecular simulations is rapidly gaining increasing interest. Such simplified models allow studies across length and time scales not amenable at a detailed atomistic resolution. …

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MCP Brain-IT: Multiscale modeling using the MUSIC tool

To understand the brain, there is a need to study multiscale phenomena and to detail out how phenomena at one level of organization are affected by the ongoing brain activity at other levels. Computational modeling and simulations provide an important approach in these attempts. …

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Visualization: Uncertainty Visualization

This project targets the area of uncertainty analysis in medical imaging. While there is a steady and fast pace of technological advances in diagnostic radiology in general, the area of uncertainty analysis is underdeveloped despite clear needs. …

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Visualization: Clinically Applied Multivariate Volume Rendering

This project targets an area of medical imaging with great potential for health care benefits, but also constituting a great eScience challenge. The objective of this project is to develop novel medical visualization methods for multivariate Direct Volume Rendering (DVR) that enable new levels of clinical usefulness. …

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Visualization: A Signal Processing Approach to Direct Volume Rendering

In this project we explore the application of state-of-the-art signal processing techniques into volumetric visualization to extract additional information to provide more knowledge about the content inside the dataset. …

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Visualization: Assimilation of experimental and computational fluid dynamics

Traditionally, imaging has focused on (time-resolved) acquisition of morphological information. Using MRI, blood flow velocities can be measured in the cardiovascular system. Restrictions in measurement times have limited these scans to 2D, but recent advances in software and hardware allow for time-resolved 3D approaches (4D flow MRI). Analysis of this wealth of data is currently time-consuming and user-dependent.

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Visualization: Methods for High-Quality Illumination in Interactive Volume Rendering

In order to improve the visual quality and usefulness of direct volume rendering we need to utilize more advanced illumination techniques. The benefits of using more advanced illumination techniques come from improving depth perception as well as making it easier for the user to understand the data which is being visualized.

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Visualization: POrtable Diary Data Collector

Activity diaries are a powerful data source for studying the time use of individuals and entire populations and for creating awareness of individuals’ daily activity patterns. This project is concerned with the development and testing of a portable activity diary data collection tool, the PODD, implemented on a modern smart phone. …

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Visualization: Supporting collaborative view transformations of simulation-based data

Aims: 1. Create an experimental interactive infrastructure that supports direct simultaneous multi-user view transformations of pre-simulated visual structures in support of collaborative visual exploration in large visualization environments. 2. Evaluate the interactive infrastructures proposed in Aim 1 with domain experts and relevant data and tasks. 3. Produce a permanent support infrastructure that is integrated into real work practices of domain experts and which gives rise to long-lasting positive efficiency effects. …

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MCP eCPC: eCPC WP5: Prediction and screening models

This project will develop predictive and screening models for breast and prostate cancer on several levels. …

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MCP eCPC: eCPC WP4: Cancer systems biology

This project will develop models for eCPC based on a systems biology approach. …

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MCP eCPC: eCPC WP3: Cancer microsimulation

This project will develop a microsimulation engine with the initial endpoints breast and prostate cancer. …

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MCP eCPC: eCPC WP2: Managing sensitive data in distributed environments

We will develop a secure and scalable infrastructure to store and analyze sensitive and large scale data in the domain of life science, with a focus on providing resources for the eCPC project. …

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MCP eCPC: eCPC WP1: Platform and infrastructure development

This project will develop an extensible platform capable of integrating predictive models, data, and simulations developed in eCPC. …

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Electronic: Thermoelectric materials

Thermoelectric effects refer to the conversion of a temperature gradient to electric energy or vice versa. At the atomic scale, an applied temperature gradient causes charge carriers in the material to diffuse from the hot side to the cold side. As a result, a potential difference builds up. …

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Electronic: Method development in studies of charge transport in organic materials

Ab-initio and semi-classical calculations are perfomed to investigate electronic structure, molecular structure and charge transport in organic crystals, polymers, and in bulk-heterojunction systems.

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Electronic: Multilayer parallelization of DALTON quantum chemistry program

The main objective of this project is to enhance the performance of the DALTON quantum chemistry program on modern high performance computer systems with multicore CPUs, and enable efficient computations of electronic structure and molecular properties in massively parallel runs (beyond 500 CPUs).

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Electronic: Ab initio simulation of strongly correlated materials: methods and applications

During last several decades, the ab-initio approach to simulations of materials has proven to be very fruitful. This approach is based on the density functional theory (DFT) and has allowed for theoretical modeling of a wide range of properties of solid-state materials without use of any adjustable parameters.

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Electronic: Nucleation, stability and light-absorption of pollutant particles in the atmosphere and its climate implications

The impact of aerosols on climate can be categorized into direct and indirect effects. The direct effect includes scattering and absorption of radiation due to the presence of e.g. fossil fuel black carbon, while the indirect effect arises from modification of cloud properties such as albedo (reflectivity) induced by salts, inorganic acids and organic compounds that occur in atmosphere. …

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Electronic: Method development for multiscale computations

By using multi-scale modeling one goes through several characteristic length and time scales in which different physical models of varying levels of theoretical sophistication are applied and tied together in such a way that information is passed between the levels. …

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Electronic: Method development for calculation of transport and magnetic properties

Computing spin and charge transport properties from first principles is an increasingly important area of research aiming at finding solutions to the world’s increasing demand for clean energy and energy-efficient electronics. …

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Electronic: Atomistic spin dynamics

The project has the overall objective to study magnetization dynamics on atomic scale using a combination of electronic structure methods and atomistic simulations. Of particular interest are materials aimed for future applications in information technology, like memory devices using spin-transfer torque and nanomagnets for storage. …

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Electronic: Exploitation of heterogeneous processor-coprocessor (CPU/CCPU) environments for high level ab initio electronic structure calculations

This project aims to boost performance of quantum chemistry programs by developing a library for evaluation of various algorithms on Intel Xeon Phi coprocessors, and in this way exploit computational resources provided by heterogeneous processor/coprocessors (CPU/CCPU) systems.

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Electronic: QMMM in the complex TDDFT representation

Since the development of the first organic solar cell in 1983 with a power conversion efficiency lower than 1% this area, also called plastic electronics, has grown and is growing today by leaps and bounds.

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Electronic: Visualization tool for electronic structure calculations

Visualization tools are important not only for interpreting and presenting data, but also for analyzing problems and choosing strategy when approaching a complex problem. Together with Anders Ynnerman (Professor) at LiU, we aim at developing an electronic structure visualization table, in line with the by Ynnerman developed virtual autopsy table.

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Electronic: Morphology and electro-optical properties of materials in solar cell

The interest for conjugated systems, which particular photo-physics characteristics emanate from the existence of a cloud of π electrons delocalized, is coming among others from the possibility to incorporate them as active components in a large range of optoelectronic devices, such as organic light emitting diodes [1], solar cells or photovoltaics [2], field effect transistor [3], and (bio)chemical sensors. …

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Electronic: Multiscale Modeling Methods for Biomolecules

The main objective of this project is to develop novel hybrid quantum mechanics/molecular mechanics (QM/MM) methods for computation of various spectroscopic properties of the biomolecules.

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Climate: Ensemble single-column model system

The goal is to develop a user-friendly single-column model of the global climate model EC-Earth that can be run simultaneously at numerous locations through a web interface.

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Courtesy of ECMWF

Climate: Computational issues with interaction between the core and parameterized small-scale processes in climate models

Building e.g. the atmospheric part of a global climate model is done in two major steps. First the core is formulated, i.e. defining the equation system, choose numerical methods and calculation grid for the resolved flow. Then, standard idealized tests are performed to assess the performance of the core. …

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Climate: Direct numerical simulation of cloud turbulence and its interaction with cloud drops

The role played by the clouds is fundamental for the atmosphere and the water of the earth. Nowadays our knowledge in cloud dynamics is still so poor that it represents the cause of an amount of uncertainty in climate predictions and in atmospheric circulation models.

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Climate: Treating multiple sea-ice categories in EC-EARTH

EC-EARTH combines the atmosphere model IFS with the ocean model NEMO with the sea-ice model LIM3 being part of NEMO. An outstanding feature of LIM3 compared to LIM2 which was the sea-ice model in the previous EC-EARTH model version is the ability to represent multiple sea-ice thickness categories. …

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Bioinformatics: Study of Cardiovascular Diseases

Integrating physical interaction networks in the analysis of Complex Diseases

Improving the power of statistical tests for genetic interactions

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Bioinformatics: Using machine learning potentials in conformational sampling and selection of protein structures

Modeling of protein structure is a central challenge in structural bioinformatics, and holds the promise not only to identify classes of structure, but also to provide detailed information about the specific structure and biological function of molecules. This is critically important to guide and understand experimental studies: It enables prediction of binding, simulation, and design for a huge set of proteins whose structures have not yet been determined experimentally (or cannot be obtained), and it is a central part of contemporary drug development.

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Bioinformatics: Improved scaffolding for genome assembly

A crucial part of genomics is the ability to accurately assemble reads (often short) into larger pieces, so-called contigs. This is still considered difficult and recent results indicate that there is no single assembler that good for all data sets. An important step in genome assembly is scaffolding, in which information about read-pairing is used to connect contigs into larger units.

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Bioinformatics: Using predictions to improve predictions of membrane proteins

Machine learning methods have a long history within bioinformatics. Sequence based machine learning methods can roughly be divided into two classes, local and structural. The local methods are trained on information from a fixed length sequence window surrounding a residue. …

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Bioinformatics: Development of automated protein family classification using hidden Markov models for functional characterization of proteins

There is a great need to subdivide large protein families into smaller, homogeneous subfamilies, corresponding to functional entities. Hidden Markov models constitute a powerful technique for such subclassification.

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Bioinformatics: Inferring functional coupling of proteins using next gen sequencing data

Next generation sequencing experiments have a very high throughput producing gigabytes of raw data and setting a big challenge on analytic and processing ability, but in turn have the possibility to produce accurate and abundant data. The main goal of the project has been to try to utilize next generation sequencing data to infer functional coupling in protein interaction networks. The next gen data type used in this project was RNA-Seq.

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Bioinformatics: High throughput prediction of disease caused by SNPs

Many diseases are caused by single nuclear polymorphisms (SNPs) that cause an amino acid in a protein to be mutated. However, most SNPs do not cause a disease. Today SNPs are readily detected in large scale studies of individual genetic variation. Here, we want to develop methods for analysis of molecular consequences following these SNPs and thereby aid in the identification of what SNPs are most likely to be disease causing.

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Bioinformatics: Integrating physical interaction networks in the analysis of Complex Diseases

The traditional genome-wide association (GWA) studies have been largely unsuccessful for complex diseases, like cardiovascular disease. They often fail to replicate their results, and the DNA variants that have been found have a low effect on the disease. It is widely believed that this is due to non-additive genetic interactions, where the disease depends on the variance at two or more loci. Considering the vast number of possible genetic interactions, the traditional GWA methodology is not viable; as a consequence most studies ignore genetic interactions.

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Bioinformatics: Improving the power of statistical tests for genetic interactions

This project aims to improve statistical tests for genetic interactions without main effects. These types of interactions, coined epistatic interactions are hypothesized to account for most of the phenotypic variation, and are therefore important to study.

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Numerical Analysis: Multiscale methods in fluid dynamics

Multiscale problems appear in several areas of fluid dynamics. …

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Numerical Analysis: Spectrally accurate fast Ewald summation

The goal of this project is to develop spectrally accurate and fast Ewald summation methods – suitable for parallel computations – for various problems in molecular dynamics and fluid mechanics.  …

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Numerical Analysis: Numerical methods for molecular dynamics

The goal of this project is to develop numerical methods for deterministic and stochastic molecular dynamics simulations that include accurate error estimates. …

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FLOW: Constructing non-reflecting boundaries using multiple Penalty terms

For any difference method the boundary conditions must be implemented so the problem is stable, which can be done by adding a single penalty term at the first and/or last grid point for the onedimensional problem.  …

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Bioinformatics: Computational optimization of mass spectrometry-based proteomics experiments

Mass spectrometry (MS)-based proteomics is currently the most efficient method for large-scale analysis of protein content in biological mixtures. …

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Protein structure prediction — state-of-the-art methods proven in contests

SeRC faculty Björn Wallner and Arne Elofsson are experts on protein structure predictions and have developed several tools for prediction and assessment of protein structure models. Their web service Pcons.net is a popular and important tool…

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Improved model quality assessment using deep neural networks

Protein structure modeling is crucial for a detailed understanding of the biological function at the molecular level (Wallner&Elofsson, 2003; Wang et al, 2009). In 2003 we developed the first single-model quality estimation program…

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MCP Brain-IT: Computational modeling of intracellular signaling cascades in the basal ganglia

The striatum is the input layer of basal ganglia, a set of ancient brain nuclei involved in control of movements, action selection, reinforced learning and in pathologies like drug addiction and Parkinson disease. The striatum receives several chemical signals not only through projections from the cortex (glutamate) and midbrain (dopamine) but also from striatal interneurons like TAN (acetylcholine) and nNOS (NO).

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MCP Brain-IT: Parameter estimation, uncertainty analysis and global sensitivity analysis of intracellular neuronal models

Within this project we develop a workflow combining uncertainty analysis with global sensitivity analysis and apply this on intracellular models of synapses.

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MCP Brain-IT: ’Embedding’ – Investigate activation of receptor induced cascades in the context of an active neuronal network

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MCP Brain-IT: Comparative analysis (data/models) of the dynamics of networks

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MCP Brain-IT: Implementing models in hardware

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FLOW: Methods for Lagrangian particles in complex geometries

Fluid flows comprise a wide variety of complex phenomena which, among others, depend on the geometrical configuration of the problem flow phases, as well as on the Reynolds number of the flow (Re). …

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Bioinformatics: Computational methods to assess and remedy mapping bias in allele-specific expression and genomic cis-element analysis

Assessing allele-specific expression (ASE) and allele-specific cis-element (ASC) binding or modification from massively parallel sequencing read data is a straightforward way to home in on transcriptional and cis-regulatory variation at the level of single individuals.

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FLOW: Numerical experiments in a virtual wind tunnel

Being at the forefront of computational science in the coming years means effectively utilizing millions of processors for simulations of physical phenomena. Such capabilities will allow accurate large scale numerical simulations to take a role analogous to that of physical experiments. This paradigm shift has tremendous implications for many areas, including computation of aeronautical flows.

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Bioinformatics: VMCMC: a graphical and statistical analysis tool for Markov chain Monte Carlo traces

Analysing the output from Markov chain Monte Carlo (MCMC) computations is a crucial step in many scientific investigations today, and in particular in evolutionary studies where MCMC has proved to be a strong and flexible framework. VMCMC is a convenient tool with two aims: to make phylogenetic MCMC trace analysis of multiple experiments convenient, especially in a HPC environment, and to simplify visualisation of single traces.

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Bioinformatics: Deep learning in protein structure predictions

Protein structure prediction is fundamental for our understanding of molecular functions in cells. Fundamental for this is the prediction of contact between interacting residues and the evaluation of the quality of protein models. We are developing novel deep learning approaches for both these problems.

 

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