Micromanagement in the gut : microenvironmental factors govern colon mucosal biofilm structure and functionality

The human gut microbiome provides us with functional features that we did not have to evolve ourselves and can be viewed as a structured microbial community that operates like a microbial organ within the human host. A minor but important part of this microbiome is the ability to colonise and thrive within the mucous layer that covers the colon epithelium. These mucosal microbes intimately interact with the intestinal tissue and seem to be important modulators of human health. Embedded in the host-secreted mucous matrix, they form a 'mucosal biofilm' with a distinct composition and functionality. In this review, we provide evidence that six specific (micro) environmental factors near the colon mucosa shape and determine mucosal biofilm formation and stability, that is, (1) mucous rigidity, (2) gradients of fluid shear, (3) radial oxygen gradients, (4) secretions of host defense molecules, (5) the presence of a rich but challenging nutrient platform and (6) the presence of niches at the colon epithelial surface. In addition, it appears that microbes actively participate in shaping their mucosal environment. Current insights into the interaction between mucosal microbes and their environment are rather limited, and many questions regarding the contribution of mucosal biofilm functionality and stability to human health remain to be answered. Yet, given the higher potency of mucosal microbes than their luminal counterparts to interact with the host, new insights can accelerate the development of novel disease-preventive or therapeutic strategies

MuMax: a new high-performance micromagnetic simulation tool

We present MuMax, a general-purpose micromagnetic simulation tool running on Graphical Processing Units (GPUs). MuMax is designed for high performance computations and specifically targets large simulations. In that case speedups of over a factor 100x can easily be obtained compared to the CPU-based OOMMF program developed at NIST. MuMax aims to be general and broadly applicable. It solves the classical Landau-Lifshitz equation taking into account the magnetostatic, exchange and anisotropy interactions, thermal effects and spin-transfer torque. Periodic boundary conditions can optionally be imposed. A spatial discretization using finite differences in 2 or 3 dimensions can be employed. MuMax is publicly available as open source software. It can thus be freely used and extended by community. Due to its high computational performance, MuMax should open up the possibility of running extensive simulations that would be nearly inaccessible with typical CPU-based simulators.Comment: To be published in JMM

The effect of disorder on transverse domain wall dynamics in magnetic nanostrips

We study the effect of disorder on the dynamics of a transverse domain wall in ferromagnetic nanostrips, driven either by magnetic fields or spin-polarized currents, by performing a large ensemble of GPU-accelerated micromagnetic simulations. Disorder is modeled by including small, randomly distributed non-magnetic voids in the system. Studying the domain wall velocity as a function of the applied field and current density reveals fundamental differences in the domain wall dynamics induced by these two modes of driving: For the field-driven case, we identify two different domain wall pinning mechanisms, operating below and above the Walker breakdown, respectively, whereas for the current-driven case pinning is absent above the Walker breakdown. Increasing the disorder strength induces a larger Walker breakdown field and current, and leads to decreased and increased domain wall velocities at the breakdown field and current, respectively. Furthermore, for adiabatic spin transfer torque, the intrinsic pinning mechanism is found to be suppressed by disorder. We explain these findings within the one-dimensional model in terms of an effective damping parameter $\alpha^*$ increasing with the disorder strength.Comment: 5 pages, 3 figure

Numerical study of magnetic processes: extending the Landau-Lifshitz-Gilbert approach from nanoscale to microscale

The micromagnetic theory describes the magnetic processes in magnetic materials on a microscopic time and space length. Therefore, micromagnetic models are since long employed in the design of for instants magnetic storage media as magnetic tapes and Random Access Memory elements, used in computers. The use of efficient numerical techniques and the availability of powerful computers now make it possible to apply the same micromagnetic models on larger and more complex material systems with the aim of increasing our insight in the experimentally observed magnetic phenomena. In this PhD research, an efficient numerical micromagnetic model is developed that enables the analysis of magnetic processes starting from the nanometer space scale up to the micrometer space scale. Therefore, efficient algorithms are presented on the one hand to simulate the ultra fast dynamics of the magnetic processes as described by the Landau-Lifshitz-Gilbert equation. On the other hand, powerful numerical techniques are developed to evaluate the magnetic fields, characteristic to the micromagnetic description, in a fast way. The developed micromagnetic model is validated extensively in comparative studies with other micromagnetic and macroscopic magnetic material models. Moreover, the model is successfully applied in different magnetic research domains: magnetic switching processes in classical samples with nanometer dimensions are analysed, magnetic domains are studied in structures with order micrometer dimensions and magnetic hysteresis properties are investigated