Archived Highlights

NA Highlight: Spectrally accurate fast Ewald summation

A new highly accurate method for the evaluation of forces resulting from electrostatic interactions has been developed.

Read more

PSDE Highlight: Pediatric systems medicine: evaluating needs and opportunities using congenital heart block as a case study

Executing a systems medicine programme in pediatrics creates potential for collaboration between clinicians and families who are keen to prevent and predict diseases and nurture wellness in the families’ children. …

Read more

PSDE Highlight: Metabolite profiling identifies a key role for glycine in rapid cancer cell proliferation

Glycine consumption and expression of the mitochondrial glycine biosynthetic pathway seem to be strongly correlated with rates of growth across cancer cells. …

Read more

PSDE Highlight: An atlas of combinatorial transcriptional regulation in mice and man

Availability of large TF combinatorial networks in both humans and mice will provide many opportunities to study gene regulation, tissue differentiation, and mammalian evolution. …

Read more

PSDE Highlight: Enabling efficient and future-proof HPC applications: High-level component-based programming frameworks for heterogeneous parallel systems

Recent disruptive changes in computer hardware (in particular, the transition to multi-/manycore and heterogeneous architectures) have led to a crisis on the application software side: efficient programming for modern parallel and heterogeneous systems has become more tedious, error-prone and hardware specific than ever. In particular, this holds for GPU-based systems that are increasingly popular in high performance computing, with GPU architecture evolving quickly – but which application writer has the time to rewrite and/or re-optimize his/her code for each new hardware generation? …

Read more

PSDE Highlight: Object-Oriented Modeling and Simulation with Modelica

The modeling language Modelica is bringing about a revolution in the area of simulating complex cyber-physical systems for e.g. robotics, aircrafts, satellites or power plants. …

Read more

PSDE Highlight: Decentralized Graph Partitioning for Social Networks and Classification Systems

SeRC researchers have developed a novel decentralized method for partitioning of graphs, with applications in areas such as social networks and classification systems, that was awarded with best paper in the IEEE International Conference on Self-Adaptive and Self-Organizing Systems, 2013.

Read more

PSDE Highlight: Scalable Performance Monitoring

Understanding how parallel applications behave is crucial for using HPC resources efficiently. Particularly, exascale systems will be composed by heterogeneous architectures with multiple levels of concurrency and energy constraints. In such complex scenarios, performance monitoring and runtime systems will play a major role to obtain good application performance and scalability. SeRC researchers have developed techniques for online access to performance data and efficient data formats for performance data.

Read more

PSDE Highlight: World Record Hadoop Performance

Led by Dr Jim Dowling, in 2016, SeRC researchers from the PSDE community announced world-record performance for the Hadoop platform, with their next-generation distribution of Apache Hadoop File System, HopsFS. …

Read more

Visualization Highlight: ERC Starting Grant: HEART4FLOW

The objective of the HEART4FLOW project is to develop the next generation of methods for the non-invasive quantitative assessment of cardiac diseases and therapies. …

Read more

Visualization Highlight: Vinnova Framework Grant: Digital Pathology

Within pathology there is an urgent need for substantially increased efficiency in parallel with continued improvements in quality of care. …

Read more

Visualization Highlight: KAW Research Grant: Seeing Organ Function

More recent medical imaging modalities support acquisition of patient-specific functional data embedded in a high-resolution spatial context. …

Read more

Visualization Highlight: Cover story: Interactive Visualization of 3D Scanned Mummies at Public Venues

By combining visualization techniques with interactive multi-touch tables and intuitive user interfaces, visitors to museums and science centers can conduct self-guided tours of large volumetric image data. …

Read more

Molecular Highlight: Accurate predictions of GPCR-drug complexes

SeRC researchers have developed methods that enable accurate prediction of receptor-drug interactions at the atomic level. …

Read more

Molecular Highlight: The world’s fastest software for Molecular Dynamics on CPUs & GPUs

The increase in computing power allows part of (bio) molecular experimental work to be replaced by simulations. However, designing software that leverages the full power of modern (super) computing is becoming more and more challenging due to the fact that hardware is continuously becoming more parallel and heterogeneous. …

Read more

Molecular Highlight: Unraveling the strokes of ion transporters in computers

As highlighted by the 2013 Nobel Prize for chemistry, life science and biomolecular modeling are some of the most important applications for molecular simulation. By simulating the motions of membrane protein transporters in close connection with experiments, we have been able to explain fundamental mechanisms of nerve signal propagation both inside and between cells. …

Read more

Molecular Highlight: Accelerating cryo electron microscopy refinement

Over the past years cryo electron microscopy has become a dominant technique for determining the structure of large biomolecules. …

Read more

FLOW Highlight: Universal Scaling Laws or Dense Particle Suspensions in Turbulent Wall-Bounded Flows

We examine by means of large-scale interface-resolved numerical simulations the macroscopic behavior of dense suspensions of neutrally-buoyant spheres in turbulent plane channel flow. …

Read more

FLOW Highlight: Natural Laminar Flow

Direct numerical simulations of flow over wings for understanding the physics of modern methods of transition control. …

Read more

FLOW Highlight: TRITOS: Transitions and Turbulence Of complex Suspensions

Investigating the mechanisms by which the system microstructure determines the macroscopic flow properties provides valuable insight into the nature of flowing suspensions, and also leads to new ways of modelling and controlling it.

Read more

FLOW Highlight: Recurring intense bursts of turbulence in rotating channel flow simulations

Carrying out extensive simulations and observing for the first time intense recurrent bursts of turbulence in rotating channel flow. Rotating channel flow is therefore suggested as a prototype for future studies. …

Read more

FLOW Highlight: Simulations of turbulent boundary layers at high Reynolds numbers

The study of simplified canonical flows allows for deducing important properties of the physics. Therefore, a number of canonical flow cases have emerged as standard model problems to study wall-bounded turbulence. …

Read more

FLOW Highlight: Fully resolved simulations of fibers with a significant size in turbulent flows

The interaction between fibers and carrier fluid is modeled through an external boundary force method. …

Read more

Electronic Highlight: On the Influence of Water on the Electronic Structure of Firefly Oxyluciferin Anions

Combining molecular dynamics simulations and time-dependent density functional theory calculations indicate that the preferred binding site for the water molecule is the phenolate oxygen of the anion. …

Read more

Electronic Highlight: Hyperfine Splitting and Room-Temperature Ferromagnetism of Ni at Multimegabar Pressure

Observed magnetic hyperfine splitting confirms the ferromagnetic state of Ni up to 260 GPa, the highest pressure where magnetism in any material has been observed so far. …

Read more

Electronic Highlight: Development of the Dalton program

Two powerful molecular electronic structure programs, Dalton and lsDalton, provide an extensive functionality for the calculation of molecular properties. …

Read more

Electronic Highlight: Machine Learning Energies of 2 Million Elpasolite (ABC2D6) Crystals

Elpasolite is a common crystal structure. We have developed and trained a machine learning model to predict formation energies of all 2M pristine ABC2D6 elpasolite crystals that can be made up from main-group elements (up to bismuth). …

Read more

NA Highlight: Spectrally accurate fast Ewald summation

A new highly accurate method for the evaluation of forces resulting from electrostatic interactions has been developed. …

Read more

NA Highlight: Numerical methods for molecular dynamics

Langevin dynamics has been derived from the more fundamental Ehrenfest dynamics. …

Read more

NA Highlight: Multi-scale methods for wave propagation

A new type of multi-scale numerical method for simulation of wave problems has been developed and analyzed. …

Read more

NA Highlight: Structured iterative methods for waveguide eigenvalue problems

In the field of electromagnetics, certain types of wave propagation can be modeled with waveguides, and can be analyzed by discretizing an associated partial differential equation. …

Read more

Brain-IT Highlight: D1R-Golf signaling modules segregate into compartments

The development of a large signaling model that takes into consideration the existence of at least two D1R-Golf signaling compartments explains the data pattern. …

Read more

Brain-IT Highlight: Workflows for the estimation of model parameters

When modeling subcellular signaling pathways, experimental data are integrated into a precise and structured framework from which it is possible to make predictions that could be tested experimentally. …

Read more

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

Several scientists in the Bioinformatics community study and develop methods for protein structure prediction.

Read more

Bioinformatics Highlight: Assessing protein mass spectrometry data using Percolator – how to weed out valuable information from the noise

Mass spectrometry (MS) is currently the most effective way to analyze protein on a large scale, and hence one of the most important tools for answering those questions. There are still however difficult challenges in analysing the wealth of data MS-based experiments produce.

Read more

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…

Read more

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…

Read more

Brain-IT Highlight: D1R-Golf signaling modules segregate into compartments

The development of a large signaling model that takes into consideration the existence of at least two D1R-Golf signaling compartments explains the data pattern. …

 

Read more