Flow-driven branching in a frangible porous medium

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Derr, N. J., Fronk, D. C., Weber, C. A., Mahadevan, A., Rycroft, C. H., & Mahadevan, L. Flow-driven branching in a frangible porous medium. Physical Review Letters, 125(15), (2020): 158002, doi:10.1103/PhysRevLett.125.158002.Channel formation and branching is widely seen in physical systems where movement of fluid through a porous structure causes the spatiotemporal evolution of the medium. We provide a simple theoretical framework that embodies this feedback mechanism in a multiphase model for flow through a frangible porous medium with a dynamic permeability. Numerical simulations of the model show the emergence of branched networks whose topology is determined by the geometry of external flow forcing. This allows us to delineate the conditions under which splitting and/or coalescing branched network formation is favored, with potential implications for both understanding and controlling branching in soft frangible media.N. D. was partially supported by the NSF-Simons Center for Mathematical and Statistical Analysis of Biology at Harvard, Grant No. 1764269, and the Harvard Quantitative Biology Initiative. C. H. R. and N. D. were partially supported by the National Science Foundation under Grant No. DMS-1753203. C. H. R. was partially supported by the Applied Mathematics Program of the U.S. DOE Office of Science Advanced Scientific Computing Research under Contract No. DE-AC02-05CH11231. L. M. was partially supported by the National Science Foundation under Grants No. DMR-2011754 and No. DMR-1922321

Flow-driven branching in a frangible porous medium

Channel formation and branching is widely seen in physical systems where movement of fluid through a porous structure causes the spatiotemporal evolution of the medium in response to the flow, in turn causing flow pathways to evolve. We provide a simple theoretical framework that embodies this feedback mechanism in a multi-phase model for flow through a fragile porous medium with a dynamic permeability. Numerical simulations of the model show the emergence of branched networks whose topology is determined by the geometry of external flow forcing. This allows us to delineate the conditions under which splitting and/or coalescing branched network formation is favored, with potential implications for both understanding and controlling branching in soft frangible media.Comment: 5 pages, 4 figures, submitted to Physical Review Letter

Field Reentrance of the Hidden Order State of URu2Si2 under Pressure

Combination of neutron scattering and thermal expansion measurements under pressure shows that the so-called hidden order phase of URu2Si2 reenters in magnetic field when antiferromagnetism (AF) collapses at H_AF (T). Macroscopic pressure studies of the HO-AF boundaries were realized at different pressures via thermal expansion measurements under magnetic field using a strain gauge. Microscopic proof at a given pressure is the reappearance of the resonance at Q_0=(1,0,0) under field which is correlated with the collapse of the AF Bragg reflections at Q_0.Comment: 5 pages, 6 figures, accepted for publication in J. Phys. Soc. Jp

Precise study of the resonance at Q0=(1,0,0) in URu2Si2

New inelastic neutron scattering experiments have been performed on URu2Si2 with special focus on the response at Q0=(1,0,0), which is a clear signature of the hidden order (HO) phase of the compound. With polarized inelastic neutron experiments, it is clearly shown that below the HO temperature (T0 = 17.8 K) a collective excitation (the magnetic resonance at E0 \approx 1.7 meV) as well as a magnetic continuum co-exist. Careful measurements of the temperature dependence of the resonance lead to the observation that its position shifts abruptly in temperature with an activation law governed by the partial gap opening and that its integrated intensity has a BCS-type temperature dependence. Discussion with respect to recent theoretical development is made

STEM through Authentic Research and Training Program (START) for Underrepresented Communities: Adapting to the COVID-19 Pandemic

The STEM Through Authentic Research and Training (START) Program is a new program integrating academic, social, and professional experiences, in the theme of exomedicine, to build a pipeline into college for first generation and traditionally underrepresented students by providing year-round authentic opportunities and professional development for high school students and teachers. In response to the COVID-19 pandemic, the START Program has worked with the local Fayette County public school and community partners to provide content to over 300 students through: virtual laboratory tours with community partner Space Tango, meet a scientist discussions, and online near-peer student demonstrations aimed at making the practice of STEM disciplines approachable. Furthermore, the START Program has partnered with Higher Orbits to provide at-home, space-themed learning kits for students to develop teamwork, communication, and STEM principles while engaging in online content with teachers, professionals, and astronauts. Finally, the START Program has moved its training platforms online, including receiving College Reading and Learning Association (CRLA) Peer Educator accreditation for our near-peer mentoring and coaching training. As a result, the START Program is better positioned to address this critical need in STEM education, while reaching more students in the community than possible with face-to-face interactions alone

Retrotransposon vectors for gene delivery in plants

<p>Abstract</p> <p>Background</p> <p>Retrotransposons are abundant components of plant genomes, and although some plant retrotransposons have been used as insertional mutagens, these mobile genetic elements have not been widely exploited for plant genome manipulation. In vertebrates and yeast, retrotransposons and retroviruses are routinely altered to carry additional genes that are copied into complementary (c)DNA through reverse transcription. Integration of cDNA results in gene delivery; recombination of cDNA with homologous chromosomal sequences can create targeted gene modifications. Plant retrotransposon-based vectors, therefore, may provide new opportunities for plant genome engineering.</p> <p>Results</p> <p>A retrotransposon vector system was developed for gene delivery in plants based on the Tnt1 element from <it>Nicotiana tabacum</it>. Mini-Tnt1 transfer vectors were constructed that lack coding sequences yet retain the 5' and 3' long terminal repeats (LTRs) and adjacent <it>cis </it>sequences required for reverse transcription. The internal coding region of Tnt1 was replaced with a neomycin phosphotransferase gene to monitor replication by reverse transcription. Two different mini-Tnt1 s were developed: one with the native 5' LTR and the other with a chimeric 5' LTR that had the first 233 bp replaced by the CaMV 35 S promoter. After transfer into tobacco protoplasts, both vectors undergo retrotransposition using GAG and POL proteins provided in <it>trans </it>by endogenous Tnt1 elements. The transposition frequencies of mini-Tnt1 vectors are comparable with native Tnt1 elements, and like the native elements, insertion sites are within or near coding sequences. In this paper, we provide evidence that template switching occurs during mini-Tnt1 reverse transcription, indicating that multiple copies of Tnt1 mRNA are packaged into virus-like particles.</p> <p>Conclusions</p> <p>Our data demonstrate that mini-Tnt1 vectors can replicate efficiently in tobacco cells using GAG and POL proteins provided in <it>trans </it>by native Tnt1 elements. This suggests that helper Tnt1 constructs can be developed to enable a Tnt1-based two-component vector system that could be used in other plant species. Such a vector system may prove useful for gene delivery or the production of cDNA that can serve as a donor molecule for gene modification through homologous recombination.</p

A new multicompartmental reaction-diffusion modeling method links transient membrane attachment of E. coli MinE to E-ring formation

Many important cellular processes are regulated by reaction-diffusion (RD) of molecules that takes place both in the cytoplasm and on the membrane. To model and analyze such multicompartmental processes, we developed a lattice-based Monte Carlo method, Spatiocyte that supports RD in volume and surface compartments at single molecule resolution. Stochasticity in RD and the excluded volume effect brought by intracellular molecular crowding, both of which can significantly affect RD and thus, cellular processes, are also supported. We verified the method by comparing simulation results of diffusion, irreversible and reversible reactions with the predicted analytical and best available numerical solutions. Moreover, to directly compare the localization patterns of molecules in fluorescence microscopy images with simulation, we devised a visualization method that mimics the microphotography process by showing the trajectory of simulated molecules averaged according to the camera exposure time. In the rod-shaped bacterium _Escherichia coli_, the division site is suppressed at the cell poles by periodic pole-to-pole oscillations of the Min proteins (MinC, MinD and MinE) arising from carefully orchestrated RD in both cytoplasm and membrane compartments. Using Spatiocyte we could model and reproduce the _in vivo_ MinDE localization dynamics by accounting for the established properties of MinE. Our results suggest that the MinE ring, which is essential in preventing polar septation, is largely composed of MinE that is transiently attached to the membrane independently after recruited by MinD. Overall, Spatiocyte allows simulation and visualization of complex spatial and reaction-diffusion mediated cellular processes in volumes and surfaces. As we showed, it can potentially provide mechanistic insights otherwise difficult to obtain experimentally

Small-Scale Extrusion of Corn Masa By-Products

Corn masa by-product streams are high in fiber and are amenable for utilization in livestock feed rations. This approach is a potentially viable alternative to landfilling, the traditional disposal method for these processing residues. Suspended solids were separated from a masa processing waste stream, blended with soybean meal at four levels (0, 10, 20, and 30% wb), and extruded in a laboratory-scale extruder at speeds of 50 rpm (5.24 rad/sec) and 100 rpm (10.47 rad/sec) with temperature profiles of 80-90-100°C and 100-110-120°C. Processing conditions, including dough and die temperatures, drive torque, specific mechanical energy consumption, product and feed material throughput rates, dough apparent viscosity, and dough density, were monitored during extrusion. The resulting products were subjected to physical and nutritional characterization to determine the effects of processing conditions for these blends. Extrudate analysis included moisture content, water activity, crude protein, in vitro protein digestibility, crude fat, ash, product diameter, expansion ratios, unit and true density, color, water absorption and solubility, and durability. All blends were suitable for extrusion at the processing conditions used. Blend ratio had little effect on either processing parameters or extrudate properties; extrusion temperature and screw speed, on the other hand, significantly affected both processing and product properties

Regional expression of HOXA4 along the aorta and its potential role in human abdominal aortic aneurysms

<p>Abstract</p> <p>Background</p> <p>The infrarenal abdominal aorta exhibits increased disease susceptibility relative to other aortic regions. Allograft studies exchanging thoracic and abdominal segments showed that regional susceptibility is maintained regardless of location, suggesting substantial roles for embryological origin, tissue composition and site-specific gene expression.</p> <p>Results</p> <p>We analyzed gene expression with microarrays in baboon aortas, and found that members of the HOX gene family exhibited spatial expression differences. <it>HOXA4 </it>was chosen for further study, since it had decreased expression in the abdominal compared to the thoracic aorta. Western blot analysis from 24 human aortas demonstrated significantly higher HOXA4 protein levels in thoracic compared to abdominal tissues (<it>P </it>< 0.001). Immunohistochemical staining for HOXA4 showed nuclear and perinuclear staining in endothelial and smooth muscle cells in aorta. The <it>HOXA4 </it>transcript levels were significantly decreased in human abdominal aortic aneurysms (AAAs) compared to age-matched non-aneurysmal controls (<it>P </it>< 0.00004). Cultured human aortic endothelial and smooth muscle cells stimulated with INF-γ (an important inflammatory cytokine in AAA pathogenesis) showed decreased levels of HOXA4 protein (<it>P </it>< 0.0007).</p> <p>Conclusions</p> <p>Our results demonstrated spatial variation in expression of HOXA4 in human aortas that persisted into adulthood and that downregulation of <it>HOXA4 </it>expression was associated with AAAs, an important aortic disease of the ageing population.</p