Controlling antiferromagnetic domains in patterned La0.7Sr0.3FeO3 thin films

Transition metal oxide thin films and heterostructures are promising platforms to achieve full control of the antiferromagnetic (AFM) domain structure in patterned features as needed for AFM spintronic devices. In this work, soft x-ray photoemission electron microscopy was utilized to image AFM domains in micromagnets patterned into La0.7Sr0.3FeO3 (LSFO) thin films and La0.7Sr0.3MnO3 (LSMO)/LSFO superlattices. A delicate balance exists between magnetocrystalline anisotropy, shape anisotropy, and exchange interactions such that the AFM domain structure can be controlled using parameters such as LSFO and LSMO layer thickness, micromagnet shape, and temperature. In LSFO thin films, shape anisotropy gains importance only in micromagnets where at least one extended edge is aligned parallel to an AFM easy axis. In contrast, in the limit of ultrathin LSFO layers in the LSMO/LSFO superlattice, shape anisotropy effects dominate such that the AFM spin axes at micromagnet edges can be aligned along any in-plane crystallographic direction

A microfluidics and agent-based modeling framework for investigating spatial organization in bacterial colonies: The case of Pseudomonas Aeruginosa amd H1-type VI secretion interactions

The factors leading to changes in the organization of microbial assemblages at fine spatial scales are not well characterized or understood. However, they are expected to guide the succession of community development and function toward specific outcomes that could impact human health and the environment. In this study, we put forward a combined experimental and agent-based modeling framework and use it to interpret unique spatial organization patterns of H1-Type VI secretion system (T6SS) mutants of P. aeruginosa under spatial confinement. We find that key parameters, such as T6SS-mediated cell contact and lysis, spatial localization, relative species abundance, cell density and local concentrations of growth substrates and metabolites are influenced by spatial confinement. The model, written in the accessible programming language NetLogo, can be adapted to a variety of biological systems of interest and used to simulate experiments across a broad parameter space. It was implemented and run in a high-throughput mode by deploying it across multiple CPUs, with each simulation representing an individual well within a high-throughput microwell array experimental platform. The microfluidics and agent-based modeling framework we present in this paper provides an effective means by which to connect experimental studies in microbiology to model development. The work demonstrates progress in coupling experimental results to simulation while also highlighting potential sources of discrepancies between real-world experiments and idealized models

Microstructural and Rheological Transitions in Bacterial Biofilms

Abstract Biofilms are aggregated bacterial communities structured within an extracellular matrix (ECM). ECM controls biofilm architecture and confers mechanical resistance against shear forces. From a physical perspective, biofilms can be described as colloidal gels, where bacterial cells are analogous to colloidal particles distributed in the polymeric ECM. However, the influence of the ECM in altering the cellular packing fraction (ϕ) and the resulting viscoelastic behavior of biofilm remains unexplored. Using biofilms of Pantoea sp. (WT) and its mutant (ΔUDP), the correlation between biofilm structure and its viscoelastic response is investigated. Experiments show that the reduction of exopolysaccharide production in ΔUDP biofilms corresponds with a seven‐fold increase in ϕ, resulting in a colloidal glass‐like structure. Consequently, the rheological signatures become altered, with the WT behaving like a weak gel, whilst the ΔUDP displayed a glass‐like rheological signature. By co‐culturing the two strains, biofilm ϕ is modulated which allows us to explore the structural changes and capture a change in viscoelastic response from a weak to a strong gel, and to a colloidal glass‐like state. The results reveal the role of exopolysaccharide in mediating a structural transition in biofilms and demonstrate a correlation between biofilm structure and viscoelastic response

Controlling the switching field in nanomagnets by means of domain-engineered antiferromagnets

Using soft x-ray spectromicroscopy, we investigate the magnetic domain structure in embedded nanomagnets defined in La$_{0.7}$Sr$_{0.3}$MnO$_3$ thin films and LaFeO$_3$/La$_{0.7}$Sr$_{0.3}$MnO$_3$ bilayers. We find that shape-controlled antiferromagnetic domain states give rise to a significant reduction of the switching field of the rectangular nanomagnets. This is discussed in the framework of competition between an intrinsic spin-flop coupling and shape anisotropy. The data demonstrates that shape effects in antiferromagnets may be used to control the magnetic properties in nanomagnets

Nanostructured complex oxides as a route towards thermal behavior in artificial spin ice systems

We have used soft x-ray photoemission electron microscopy to image the magnetization of single domain La$_{0.7}$Sr$_{0.3}$MnO$_{3}$ nano-islands arranged in geometrically frustrated configurations such as square ice and kagome ice geometries. Upon thermal randomization, ensembles of nano-islands with strong inter-island magnetic coupling relax towards low-energy configurations. Statistical analysis shows that the likelihood of ensembles falling into low-energy configurations depends strongly on the annealing temperature. Annealing to just below the Curie temperature of the ferromagnetic film (T$_{C}$ = 338 K) allows for a much greater probability of achieving low energy configurations as compared to annealing above the Curie temperature. At this thermally active temperature of 325 K, the ensemble of ferromagnetic nano-islands explore their energy landscape over time and eventually transition to lower energy states as compared to the frozen-in configurations obtained upon cooling from above the Curie temperature. Thus, this materials system allows for a facile method to systematically study thermal evolution of artificial spin ice arrays of nano-islands at temperatures modestly above room temperature.Comment: 4 figures and 9 supplemental figure

Spin-Flop Coupling and Exchange Bias in Embedded Complex Oxide Micromagnets

The magnetic domains of embedded micromagnets with 2  μm×2  μm dimensions defined in epitaxial La0.7Sr0.3MnO3 (LSMO) thin films and LaFeO3/LSMO bilayers were investigated using soft x-ray magnetic microscopy. Square micromagnets aligned with their edges parallel to the easy axes of LSMO provide an ideal experimental geometry for probing the influence of interface exchange coupling on the magnetic domain patterns. The observation of unique domain patterns not reported for ferromagnetic metal microstructures, namely divergent antiferromagnetic vortex domains and "Z"-type domains, suggests the simultaneous presence of spin-flop coupling and local exchange bias in this system

Nanotools for Neuroscience and Brain Activity Mapping

Neuroscience is at a crossroads. Great effort is being invested into deciphering specific neural interactions and circuits. At the same time, there exist few general theories or principles that explain brain function. We attribute this disparity, in part, to limitations in current methodologies. Traditional neurophysiological approaches record the activities of one neuron or a few neurons at a time. Neurochemical approaches focus on single neurotransmitters. Yet, there is an increasing realization that neural circuits operate at emergent levels, where the interactions between hundreds or thousands of neurons, utilizing multiple chemical transmitters, generate functional states. Brains function at the nanoscale, so tools to study brains must ultimately operate at this scale, as well. Nanoscience and nanotechnology are poised to provide a rich toolkit of novel methods to explore brain function by enabling simultaneous measurement and manipulation of activity of thousands or even millions of neurons. We and others refer to this goal as the Brain Activity Mapping Project. In this Nano Focus, we discuss how recent developments in nanoscale analysis tools and in the design and synthesis of nanomaterials have generated optical, electrical, and chemical methods that can readily be adapted for use in neuroscience. These approaches represent exciting areas of technical development and research. Moreover, unique opportunities exist for nanoscientists, nanotechnologists, and other physical scientists and engineers to contribute to tackling the challenging problems involved in understanding the fundamentals of brain function

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Enzyme reactions in nanoporous, picoliter volume containers

Advancements in nanoscale fabrication allow creation of small-volume reaction containers that can facilitate the screening and characterization of enzymes. A porous, ∼19 pL volume vessel has been used in this work to carry out enzyme reactions under varying substrate concentrations. Assessment of small-molecule and green fluorescent protein diffusion from the vessels indicates that pore sizes on the order of 10 nm can be obtained, allowing capture of proteins and diffusive exchange of small molecules. Glucose oxidase and horseradish peroxidase can be contained in these structures and diffusively fed with a solution containing glucose and the fluorogenic substrate amplex red through the engineered nanoscale pore structure. Fluorescent microscopy was used to monitor the reaction, which was carried out under microfluidic control. Kinetic characteristics of the enzyme (K m and V max) were evaluated and compared with results from conventional scale reactions. These picoliter, nanoporous containers can facilitate quick determination of enzyme kinetics in microfluidic systems without the requirement of surface tethering and can be used for applications in drug discovery, clinical diagnostics, and high-throughput screening

Analysis of Factors Limiting Bacterial Growth in PDMS Mother Machine Devices

The microfluidic mother machine platform has attracted much interest for its potential in studies of bacterial physiology, cellular organization, and cell mechanics. Despite numerous experiments and development of dedicated analysis software, differences in bacterial growth and morphology in narrow mother machine channels compared to typical liquid media conditions have not been systematically characterized. Here we determine changes in E. coli growth rates and cell dimensions in different sized dead-end microfluidic channels using high resolution optical microscopy. We find that E. coli adapt to the confined channel environment by becoming narrower and longer compared to the same strain grown in liquid culture. Cell dimensions decrease as the channel length increases and width decreases. These changes are accompanied by increases in doubling times in agreement with the universal growth law. In channels 100 μm and longer, cell doublings can completely stop as a result of frictional forces that oppose cell elongation. Before complete cessation of elongation, mechanical stresses lead to substantial deformation of cells and changes in their morphology. Our work shows that mechanical forces rather than nutrient limitation are the main growth limiting factor for bacterial growth in long and narrow channels