Scientific Highlights 2021

Rupture risk assessment is a key to devising patient-specific treatment plans for cerebral aneurysms.

In situ visualization on high-performance computing systems allows us to analyze simulation results that would otherwise be impossible, given the size of the simulation data sets and offline post-processing execution time.

The study of electronic transitions within a molecule connected to the absorption or emission of light is a common task in the process of the design of new materials.

In this work, we quantified GROMACS parallel performance using different configurations, HPC systems, and FFT libraries (FFTW, Intel MKL FFT, and FFT PACK).

Simulations of flow over a smooth bump are being conducted by R. Stanley under the supervision of Drs. Mukha, Schlatter, and Markidis. Currently, numerical tripping is used to trigger transition of the incoming boundary layer to turbulence.

Recent developments in large-eddy simulation of thermally stratified atmospheric boundary layers (ABLs) are achieved in collaboration by Drs. Mohanan, Mukha, Brethouwer, Schlatter, Henningson and Svensson.

We investigated a communication-bound solver at the core of many high-performance applications, namely the Conjugate Gradient (CG)  method.

In most molecular dynamics simulations the 3D fast Fourier transform used for calculating the long-range electrostatic interactions is what limits parallelization.

This study is one of the first AI-based computational pathology studies that focus on precision diagnostics, i.e. extracting novel information that can be used to risk stratify patients beyond current clinical routine.

We completed the KARISMA trial (PI Per Hall) and show for the first time in a 6-armed controlled randomized trial (n=1440) that low-dose Tamoxifen induces noninferior magnitude of breast density decrease at a 2.5 mg dose, but fewer side effects compared with the standard dose of 20 mg [4].

We finished the STHLM3-MRI trial and wrote the first two publications from the trial, published in the New England Journal of Medicine (impact factor 91) and the Lancet Oncology (impact factor 54) (Eklund et al 2021, Nordström et al 2021).

We provided important evidence to policy makers on prostate cancer screening and testing.

Topological and geometric segmentation methods provide powerful concepts for analysis and visualization of density fields.

Point defects in semiconductors is an active field in quantum applications. These defects are used as sensors and qubits.

Since thermal fluctuations become more important as dimensions shrink, it is expected that low-dimensional magnets are more sensitive to atomic displacement and phonons than bulk systems are.

The bi-thiophene-vinylene-benzothiazole (bTVBT4) ligand developed for Alzheimer’s disease (AD) specific detection of amyloid tau has been studied by a combination of several theoretical methods and experimental spectroscopies.

In collaboration between theory, visualization and experiment we predicted and confirmed experimentally a possibility to synthesize new layered compound with atomic-thick BeN4 layers interconnected via weak van der Waals bonds consisting of polyacetylene-like nitrogen chains with conjugated π-systems and Be atoms in square-planar coordination.

Milda Pocevičiūtė, Gabriel Eilertsen, Claes Lundström, “Unsupervised anomaly detection in digital pathology using GANs”, IEEE International Symposium on Biomedical Imaging, 2021.

Ruibo Tu, Kun Zhang, Hedvig Kjellström, and Cheng Zhang. Optimal transport for causal discovery.

Guastoni, Ghadirzadeh, Rabault, Schlatter, Azizpour, Vinuesa, “Deep Reinforcement Learning for Active Drag Reduction in Wall Turbulence”, American Physics Society, 2021.

Figure legend: Building on the proposed indexing theory offering a unifying framework for explaining the interactions between short- and long-term memory networks underlying working memory function, we further explored the dynamics of associative binding between networks.

Figure legend:  Continuing the major effort in developing a brain-like neural network architecture for holistic pattern recognition the focus has been on evaluating its capability to learn input representations.

Figure legend: We have built a biochemical model of protein kinase A (PKA) activation by cAMP and its inhibition by calcium activated phosphatases such as calcineurin (CN) using our workflow for modeling and data-driven calibration and analyses of systems biology models.

Figure legend: The oscillator model dynamics for the Control and ADHD subgroups.

Figure Legend: Schematic figure that summarizes the key steps for the proposed model. A) The calculation of the parameter q int is illustrated for the case of a pair of brain areas in the left and right motor cortex.