Background: Cardiac pacemaking remains an unsolved matter from many perspectives. Extensive experimental and computational studies have been performed to describe the sinoatrial physiology across different scales, from the molecular to clinical levels. Nevertheless, the mechanism by which a heartbeat is generated inside the sinoatrial node and propagated to the working myocardium is not fully understood at present. This work aims to provide quantitative information about this fascinating phenomenon, especially regarding the contributions of cellular heterogeneity and fibroblasts to sinoatrial node automaticity and atrial driving. Methods: We developed a bidimensional computational model of the human right atrial tissue, including the sinoatrial node. State-of-the-art knowledge of the anatomical and physiological aspects was adopted during the design of the baseline tissue model. The novelty of this study is the consideration of cellular heterogeneity and fibroblasts inside the sinoatrial node for investigating the manner by which they tune the robustness of stimulus formation and conduction under different conditions (baseline, ionic current blocks, autonomic modulation, and external high-frequency pacing). Results: The simulations show that both heterogeneity and fibroblasts significantly increase the safety factor for conduction by more than 10% in almost all the conditions tested and shorten the sinus node recovery time after overdrive suppression by up to 60%. In the human model, especially under challenging conditions, the fibroblasts help the heterogeneous myocytes to synchronise their rate (e.g. -82% in σ C L under 25 nM of acetylcholine administration) and capture the atrium (with 25% L-type calcium current block). However, the anatomical and gap junctional coupling aspects remain the most important model parameters that allow effective atrial excitations. Conclusion: Despite the limitations to the proposed model, this work suggests a quantitative explanation to the astonishing overall heterogeneity shown by the sinoatrial node.

Presented and discussed here is the implementation of a software solution that provides prompt X-ray diffraction data analysis during fast dynamic compression experiments conducted within the dynamic diamond anvil cell technique. It includes efficient data collection, streaming of data and metadata to a high-performance cluster (HPC), fast azimuthal data integration on the cluster, and tools for controlling the data processing steps and visualizing the data using the DIOPTAS software package. This data processing pipeline is invaluable for a great number of studies. The potential of the pipeline is illustrated with two examples of data collected on ammonia-water mixtures and multiphase mineral assemblies under high pressure. The pipeline is designed to be generic in nature and could be readily adapted to provide rapid feedback for many other X-ray diffraction techniques, e.g. large-volume press studies, in situ stress/strain studies, phase transformation studies, chemical reactions studied with high-resolution diffraction etc.

Every year, more than 19 million cancer cases are diagnosed, and this number continues to increase annually. Since standard treatment options have varying success rates for different types of cancer, understanding the biology of an individual\'s tumour becomes crucial, especially for cases that are difficult to treat. Personalised high-throughput profiling, using next-generation sequencing, allows for a comprehensive examination of biopsy specimens. Furthermore, the widespread use of this technology has generated a wealth of information on cancer-specific gene alterations. However, there exists a significant gap between identified alterations and their proven impact on protein function. Here, we present a bioinformatics pipeline that enables fast analysis of a missense mutation\'s effect on stability and function in known oncogenic proteins. This pipeline is coupled with a predictor that summarises the outputs of different tools used throughout the pipeline, providing a single probability score, achieving a balanced accuracy above 86%. The pipeline incorporates a virtual screening method to suggest potential FDA/EMA-approved drugs to be considered for treatment. We showcase three case studies to demonstrate the timely utility of this pipeline. To facilitate access and analysis of cancer-related mutations, we have packaged the pipeline as a web server, which is freely available at https://loschmidt.chemi.muni.cz/predictonco/ .Scientific contributionThis work presents a novel bioinformatics pipeline that integrates multiple computational tools to predict the effects of missense mutations on proteins of oncological interest. The pipeline uniquely combines fast protein modelling, stability prediction, and evolutionary analysis with virtual drug screening, while offering actionable insights for precision oncology. This comprehensive approach surpasses existing tools by automating the interpretation of mutations and suggesting potential treatments, thereby striving to bridge the gap between sequencing data and clinical application.

This article introduces a suite of mini-applications (mini-apps) designed to optimise computational kernels in ab initio electronic structure codes. The suite is developed from flagship applications participating in the NOMAD Center of Excellence, such as the ELPA eigensolver library and the GW implementations of the exciting, Abinit, and FHI-aims codes. The mini-apps were identified by targeting functions that significantly contribute to the total execution time in the parent applications. This strategic selection allows for concentrated optimisation efforts. The suite is designed for easy deployment on various High-Performance Computing (HPC) systems, supported by an integrated CMake build system for straightforward compilation and execution. The aim is to harness the capabilities of emerging (post)exascale systems, which necessitate concurrent hardware and software development - a concept known as co-design. The mini-app suite serves as a tool for profiling and benchmarking, providing insights that can guide both software optimisation and hardware design. Ultimately, these developments will enable more accurate and efficient simulations of novel materials, leveraging the full potential of exascale computing in material science research.

Physical mechanisms that contribute to the generation of fracture waves in condensed media under intensive dynamic impacts have not been fully studied. One of the hypotheses is that this process is associated with the blocky structure of a material. As the loading wave passes, the compliant interlayers between blocks are fractured, releasing the energy of self-balanced initial stresses in the blocks, which supports the motion of the fracture wave. We propose a new efficient numerical method for the analysis of the wave nature of the propagation of a system of cracks in thin interlayers of a blocky medium with complex rheological properties. The method is based on a variational formulation of the constitutive relations for the deformation of elastic-plastic materials, as well as the conditions for contact interaction of blocks through interlayers. We have developed a parallel computational algorithm that implements this method for supercomputers with cluster architecture. The results of the numerical simulation of the fracture wave propagation in tempered glass under the action of distributed pulse disturbances are presented. This article is part of the theme issue \'Non-smooth variational problems with applications in mechanics\'.

The expansive scientific software ecosystem, characterized by millions of titles across various platforms and formats, poses significant challenges in maintaining reproducibility and provenance in scientific research. The diversity of independently developed applications, evolving versions and heterogeneous components highlights the need for rigorous methodologies to navigate these complexities. In response to these challenges, the SBGrid team builds, installs and configures over 530 specialized software applications for use in the on-premises and cloud-based computing environments of SBGrid Consortium members. To address the intricacies of supporting this diverse application collection, the team has developed the Capsule Software Execution Environment, generally referred to as Capsules. Capsules rely on a collection of programmatically generated bash scripts that work together to isolate the runtime environment of one application from all other applications, thereby providing a transparent cross-platform solution without requiring specialized tools or elevated account privileges for researchers. Capsules facilitate modular, secure software distribution while maintaining a centralized, conflict-free environment. The SBGrid platform, which combines Capsules with the SBGrid collection of structural biology applications, aligns with FAIR goals by enhancing the findability, accessibility, interoperability and reusability of scientific software, ensuring seamless functionality across diverse computing environments. Its adaptability enables application beyond structural biology into other scientific fields.

Ultracold atoms provide a platform for analog quantum computer capable of simulating the quantum turbulence that underlies puzzling phenomena like pulsar glitches in rapidly spinning neutron stars. Unlike other platforms like liquid helium, ultracold atoms have a viable theoretical framework for dynamics, but simulations push the edge of current classical computers. We present the largest simulations of fermionic quantum turbulence to date and explain the computing technology needed, especially improvements in the Eigenvalue soLvers for Petaflop Applications library that enable us to diagonalize matrices of record size (millions by millions). We quantify how dissipation and thermalization proceed in fermionic quantum turbulence by using the internal structure of vortices as a new probe of the local effective temperature. All simulation data and source codes are made available to facilitate rapid scientific progress in the field of ultracold Fermi gases.

DNA-based identification is vital for classifying biological specimens, yet methods to quantify the uncertainty of sequence-based taxonomic assignments are scarce. Challenges arise from noisy reference databases, including mislabelled entries and missing taxa. PROTAX addresses these issues with a probabilistic approach to taxonomic classification, advancing on methods that rely solely on sequence similarity. It provides calibrated probabilistic assignments to a partially populated taxonomic hierarchy, accounting for taxa that lack references and incorrect taxonomic annotation. While effective on smaller scales, global application of PROTAX necessitates substantially larger reference libraries, a goal previously hindered by computational barriers. We introduce PROTAX-GPU, a scalable algorithm capable of leveraging the global Barcode of Life Data System (>14 million specimens) as a reference database. Using graphics processing units (GPU) to accelerate similarity and nearest-neighbour operations and the JAX library for Python integration, we achieve over a 1000 × speedup compared with the central processing unit (CPU)-based implementation without compromising PROTAX\'s key benefits. PROTAX-GPU marks a significant stride towards real-time DNA barcoding, enabling quicker and more efficient species identification in environmental assessments. This capability opens up new avenues for real-time monitoring and analysis of biodiversity, advancing our ability to understand and respond to ecological dynamics. This article is part of the theme issue \'Towards a toolkit for global insect biodiversity monitoring\'.

Two-photon lithography (TPL) is a laser-based additive manufacturing technique that enables the printing of arbitrarily complex cm-scale polymeric 3D structures with sub-micron features. Although various approaches have been investigated to enable the printing of fine features in TPL, it is still challenging to achieve rapid sub-100 nm 3D printing. A key limitation is that the physical phenomena that govern the theoretical and practical limits of the minimum feature size are not well known. Here, we investigate these limits in the projection TPL (P-PTL) process, which is a high-throughput variant of TPL, wherein entire 2D layers are printed at once. We quantify the effects of the projected feature size, optical power, exposure time, and photoinitiator concentration on the printed feature size through finite element modeling of photopolymerization. Simulations are performed rapidly over a vast parameter set exceeding 10,000 combinations through a dynamic programming scheme, which is implemented on high-performance computing resources. We demonstrate that there is no physics-based limit to the minimum feature sizes achievable with a precise and well-calibrated P-TPL system, despite the discrete nature of illumination. However, the practically achievable minimum feature size is limited by the increased sensitivity of the degree of polymer conversion to the processing parameters in the sub-100 nm regime. The insights generated here can serve as a roadmap towards fast, precise, and predictable sub-100 nm 3D printing.

The computational performance requirements of space payloads are constantly increasing, and the redevelopment of space-grade processors requires a significant amount of time and is costly. This study investigates performance evaluation benchmarks for processors designed for various application scenarios. It also constructs benchmark modules and typical space application benchmarks specifically tailored for the space domain. Furthermore, the study systematically evaluates and analyzes the performance of NVIDIA Jetson AGX Xavier platform and Loongson platforms to identify processors that are suitable for space missions. The experimental results of the evaluation demonstrate that Jetson AGX Xavier performs exceptionally well and consumes less power during dense computations. The Loongson platform can achieve 80% of Xavier\'s performance in certain parallel optimized computations, surpassing Xavier\'s performance at the expense of higher power consumption.