An Event-Driven Approach to Genotype Imputation on a Custom RISC-V Cluster.

This article proposes an event-driven solution to genotype imputation, a technique used to statistically infer missing genetic markers in DNA. The work implements the widely accepted Li and Stephens model, primary contributor to the computational complexity of modern x86 solutions, in an attempt to determine whether further investigation of the application is warranted in the event-driven domain. The model is implemented using graph-based Hidden Markov Modeling and executed as a customized forward/backward dynamic programming algorithm. The solution uses an event-driven paradigm to map the algorithm to thousands of concurrent cores, where events are small messages that carry both control and data within the algorithm. The design of a single processing element is discussed. This is then extended across multiple cores and executed on a custom RISC-V NoC cluster called POETS. Results demonstrate how the algorithm scales over increasing hardware resources and a multi-core run demonstrates a 270X reduction in wall-clock processing time when compared to a single-threaded x86 solution. Optimisation of the algorithm via linear interpolation is then introduced and tested, with results demonstrating a wall-clock reduction time of  âˆ¼ 5 orders of magnitude when compared to a similarly optimised x86 solution.

Coupling Bulk Phase Separation of Disordered Proteins to Membrane Domain Formation in Molecular Simulations on a Bespoke Compute Fabric.

Phospholipid membranes surround the cell and its internal organelles, and their multicomponent nature allows the formation of domains that are important in cellular signalling, the immune system, and bacterial infection. Cytoplasmic compartments are also created by the phase separation of intrinsically disordered proteins into biomolecular condensates. The ubiquity of lipid membranes and protein condensates raises the question of how three-dimensional droplets might interact with two-dimensional domains, and whether this coupling has physiological or pathological importance. Here, we explore the equilibrium morphologies of a dilute phase of a model disordered protein interacting with an ideal-mixing, two-component lipid membrane using coarse-grained molecular simulations. We find that the proteins can wet the membrane with and without domain formation, and form phase separated droplets bound to membrane domains. Results from much larger simulations performed on a novel non-von-Neumann compute architecture called POETS, which greatly accelerates their execution compared to conventional hardware, confirm the observations. Reducing the wall clock time for such simulations requires new architectures and computational techniques. We demonstrate here an inter-disciplinary approach that uses real-world biophysical questions to drive the development of new computing hardware and simulation algorithms.

Thermal stability and topological protection of skyrmions in nanotracks.

Magnetic skyrmions are hailed as a potential technology for data storage and other data processing devices. However, their stability against thermal fluctuations is an open question that must be answered before skyrmion-based devices can be designed. In this work, we study paths in the energy landscape via which the transition between the skyrmion and the uniform state can occur in interfacial Dzyaloshinskii-Moriya finite-sized systems. We find three mechanisms the system can take in the process of skyrmion nucleation or destruction and identify that the transition facilitated by the boundary has a significantly lower energy barrier than the other energy paths. This clearly demonstrates the lack of the skyrmion topological protection in finite-sized magnetic systems. Overall, the energy barriers of the system under investigation are too small for storage applications at room temperature, but research into device materials, geometry and design may be able to address this.

Ground state search, hysteretic behaviour, and reversal mechanism of skyrmionic textures in confined helimagnetic nanostructures.

Magnetic skyrmions have the potential to provide solutions for low-power, high-density data storage and processing. One of the major challenges in developing skyrmion-based devices is the skyrmions' magnetic stability in confined helimagnetic nanostructures. Through a systematic study of equilibrium states, using a full three-dimensional micromagnetic model including demagnetisation effects, we demonstrate that skyrmionic textures are the lowest energy states in helimagnetic thin film nanostructures at zero external magnetic field and in absence of magnetocrystalline anisotropy. We also report the regions of metastability for non-ground state equilibrium configurations. We show that bistable skyrmionic textures undergo hysteretic behaviour between two energetically equivalent skyrmionic states with different core orientation, even in absence of both magnetocrystalline and demagnetisation-based shape anisotropies, suggesting the existence of Dzyaloshinskii-Moriya-based shape anisotropy. Finally, we show that the skyrmionic texture core reversal dynamics is facilitated by the Bloch point occurrence and propagation.