Virtual micromagnetics: a framework for accessible and reproducible micromagnetic simulation

Computational micromagnetics requires numerical solution of partial differential equations to resolve complex interactions in magnetic nanomaterials. The Virtual Micromagnetics project described here provides virtual machine simulation environments to run open-source micromagnetic simulation packages [1]. These environments allow easy access to simulation packages that are often difficult to compile and install, and enable simulations and their data to be shared and stored in a single virtual hard disk file, which encourages reproducible research. Virtual Micromagnetics can be extended to automate the installation of micromagnetic simulation packages on non-virtual machines, and to support closed-source and new open-source simulation packages, including packages from disciplines other than micromagnetics, encouraging reuse. Virtual Micromagnetics is stored in a public GitHub repository under a three-clause Berkeley Software Distribution (BSD) license

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

Hysteresis of nanocylinders with Dzyaloshinskii-Moriya interaction

The potential for application of magnetic skyrmions in high density storage devices provides a strong drive to investigate and exploit their stability and manipulability. Through a three-dimensional micromagnetic hysteresis study, we investigate the question of existence of skyrmions in cylindrical nanostructures of variable thickness. We quantify the applied field and thickness dependence of skyrmion states, and show that these states can be accessed through relevant practical hysteresis loop measurement protocols. As skyrmionic states have yet to be observed experimentally in confined helimagnetic geometries, our work opens prospects for developing viable hysteresis process-based methodologies to access and observe skyrmionic states.Comment: 4 pages, 2 figure

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.Comment: manuscript: 14 pages, 7 figures; supplementary information: 8 pages, 7 figure

Skyrmions in thin films with easy-plane magnetocrystalline anisotropy

We demonstrate that chiral skyrmionic magnetization configurations can be found as the minimum energy state in B20 thin film materials with easy-plane magnetocrystalline anisotropy with an applied magnetic field perpendicular to the film plane. Our observations contradict results from prior analytical work, but are compatible with recent experimental investigations. The size of the observed skyrmions increases with the easy-plane magnetocrystalline anisotropy. We use a full micromagnetic model including demagnetization and a three-dimensional geometry to find local energy minimum (metastable) magnetization configurations using numerical damped time integration. We explore the phase space of the system and start simulations from a variety of initial magnetization configurations to present a systematic overview of anisotropy and magnetic field parameters for which skyrmions are metastable and global energy minimum (stable) states.Comment: 5 pages, 3 figure

iRFP is a real time marker for transformation based assays in high content screening

Anchorage independent growth is one of the hallmarks of oncogenic transformation. Here we show that infrared fluorescent protein (iRFP) based assays allow accurate and unbiased determination of colony formation and anchorage independent growth over time. This protocol is particularly compatible with high throughput systems, in contrast to traditional methods which are often labor-intensive, subjective to bias and do not allow further analysis using the same cells. Transformation in a single layer soft agar assay could be documented as early as 2 to 3 days in a 96 well format, which can be easily combined with standard transfection, infection and compound screening setups to allow for high throughput screening to identify therapeutic targets

A hardware/application overlay model for large-scale neuromorphic simulation

Neuromorphic computing is gaining momentum as an alternative hardware platform for large-scale neural simulation. However, with several major devices and systems available and planned, often with very different characteristics, it is not always clear which platform is suitable for which application. Simulating the platform on conventional computers is typically too slow to be of use, but an alternative approach is to implement an ‘emulation’ of the hardware in FPGAs which can execute at near-hardware speeds but does not commit to a specific hardware architecture. We present an overlay model - a method which superimposes bespoke features on top of a standard template - in both hardware and software to implement neuromorphic architectures using the POETS (Partially Ordered Event Triggered Systems) system. This combination of overlays permits very large-scale simulations to be performed in real time for hardware exploration or application verification, while retaining the flexibility to redefine either the hardware or software layer, if results indicate potential to improve performance, or significant design problems. Using this system we simulate up to 500,000 neurons on a single-box system, that can be scaled to ∼4,000,000 neurons in an 8-box configuration. Results indicate the crucial constraint for real-time simulation: peak input spike rate per neuron; and help to optimise both hardware and software around neural application requirements. The preliminary architecture demonstrates the feasibility of an overlay model, while indicating directions for future neuromorphic systems. With POETS, we introduce a platform that can help to shape and investigate the neuromorphic architectures of the future

RAG-induced DNA double-strand breaks signal through Pim2 to promote pre-B cell survival and limit proliferation

Interleukin 7 (IL-7) promotes pre–B cell survival and proliferation by activating the Pim1 and Akt kinases. These signals must be attenuated to induce G1 cell cycle arrest and expression of the RAG endonuclease, which are both required for IgL chain gene rearrangement. As lost IL-7 signals would limit pre–B cell survival, how cells survive during IgL chain gene rearrangement remains unclear. We show that RAG-induced DNA double-strand breaks (DSBs) generated during IgL chain gene assembly paradoxically promote pre–B cell survival. This occurs through the ATM-dependent induction of Pim2 kinase expression. Similar to Pim1, Pim2 phosphorylates BAD, which antagonizes the pro-apoptotic function of BAX. However, unlike IL-7 induction of Pim1, RAG DSB-mediated induction of Pim2 does not drive proliferation. Rather, Pim2 has antiproliferative functions that prevent the transit of pre–B cells harboring RAG DSBs from G1 into S phase, where these DNA breaks could be aberrantly repaired. Thus, signals from IL-7 and RAG DSBs activate distinct Pim kinase family members that have context-dependent activities in regulating pre–B cell proliferation and survival

Dynamics of skyrmionic states in confined helimagnetic nanostructures

In confined helimagnetic nanostructures, skyrmionic states in the form of incomplete and isolated skyrmion states can emerge as the ground state in absence of both external magnetic field and magnetocrystalline anisotropy. In this work, we study the dynamic properties (resonance frequencies and corresponding eigenmodes) of skyrmionic states in thin film FeGe disk samples. We employ two different methods in finite-element based micromagnetic simulation: eigenvalue and ringdown method. The eigenvalue method allows us to identify all resonance frequencies and corresponding eigenmodes that can exist in the simulated system. However, using a particular experimentally feasible excitation can excite only a limited set of eigenmodes. Because of that, we perform ringdown simulations that resemble the experimental setup using both in-plane and out-of-plane excitations. In addition, we report the nonlinear dependence of resonance frequencies on the external magnetic bias field and disk sample diameter and discuss the possible reversal mode of skyrmionic states. We compare the power spectral densities of incomplete skyrmion and isolated skyrmion states and observe several key differences that can contribute to the experimental identification of the state present in the sample. We measure the FeGe Gilbert damping, and using its value we determine what eigenmodes can be expected to be observed in experiments. Finally, we show that neglecting the demagnetization energy contribution or ignoring the magnetization variation in the out-of-film direction—although not changing the eigenmode's magnetization dynamics significantly—changes their resonance frequencies substantially. Apart from contributing to the understanding of skyrmionic states physics, this systematic work can be used as a guide for the experimental identification of skyrmionic states in confined helimagnetic nanostructures

Effects of rhythm on memory for spoken sequences : a model and tests of its stimulus-driven mechanism

Immediate memory for spoken sequences depends on their rhythm – different levels of accuracy and patterns of error are seen according to the way in which items are spaced in time. Current models address these phenomena only partially or not at all. We investigate the idea that temporal grouping effects are an emergent property of a general serial ordering mechanism based on a population of oscillators locally-sensitive to amplitude modulations on different temporal scales. Two experiments show that the effects of temporal grouping are independent of the predictability of the grouping pattern, consistent with this model’s stimulus-driven mechanism and inconsistent with alternative accounts in terms of top-down processes. The second experiment reports detailed and systematic differences in the recall of irregularly grouped sequences that are broadly consistent with predictions of the new model. We suggest that the bottom-up multi-scale population oscillator (or BUMP) mechanism is a useful starting point for a general account of serial order in language processing more widely