Turbulent shear layers in confining channels

We present a simple model for the development of shear layers between parallel flows in confining channels. Such flows are important across a wide range of topics from diffusers, nozzles and ducts to urban air flow and geophysical fluid dynamics. The model approximates the flow in the shear layer as a linear profile separating uniform-velocity streams. Both the channel geometry and wall drag affect the development of the flow. The model shows good agreement with both particle-image-velocimetry experiments and computational turbulence modelling. The low computational cost of the model allows it to be used for design purposes, which we demonstrate by investigating optimal pressure recovery in diffusers with non-uniform inflow

Integral Mass Balance (IMB) Method for Measuring Multicomponent Gas Adsorption Equilibria in Nanoporous Materials

© 2020 American Chemical Society. To assess the performance of an adsorbent for a particular gas separation, and for process design, it is necessary to determine multicomponent gas adsorption equilibria, either experimentally or from predictions based on models or theory. The experimental techniques commonly used for this purpose, however, are time-consuming and typically require large samples. In this article, we describe a new approach, called the Integral Mass Balance (IMB) method, which combines the controlled flow of a gas mixture with in situ gravimetric measurement and gas composition analysis using quadrupole mass spectrometry. The IMB method allows very rapid equilibrium multicomponent gas adsorption measurements to be performed on samples weighing only a few grams. The method is demonstrated and validated by performing binary O2/N2 adsorption measurements on a commercial 5A zeolite, at ambient temperature and a total pressure of 0.915 MPa. Excellent agreement with previously published data was found, using a 3.5 g sample, with a measurement time of only 4 h for a 20 point isotherm. In contrast, other techniques of equivalent accuracy would require around 20 days of experimental effort to collect a comparable amount of data. Selectivities were also calculated and shown to agree with previously published results. In principle, the technique could readily be extended to measure gas adsorption from ternary or higher mixtures

Optimization of water use for field crop production in the upper Midwest

This project investigated combinations of both irrigation and drainage treatments in order to determine the best water management practices for field crop production in claypan soils in the upper Midwest. Four years of corn and one year of soybean yield data from forty field plots are presented. The irrigation treatments were sprinkler, furrow, and no irrigation; the drainage treatments were surface, subsurface, surface plus subsurface, and no drainage. The plots were located on a claypan soil in south-central Illinois. Sprinkler irrigation was provided by a solid set system. Furrow irrigation was done with gated pipes. The plots with surface drainage had a slope of 0.5%; the others were graded level. Subsurface drainage was provided by plastic tubing on 20-ft centers. Drainage water from the plots and surrounding areas was stored in ponds and recycled as irrigation water. The data indicate average corn yield increases of 13 and 50 bu/acre due to drainage and irrigation, respectively. Together, they act synergistically to produce an average yield increase of 92 bu/acre. This synergistic yield increase provides economic impetus to combining irrigation and drainage systems and storing drainage water in ponds or lakes for later use in irrigation. This combination will have the added effect of conserving water resources, of improving water use efficiency and downstream water quality, and of lessening downstream flooding.U.S. Geological SurveyU.S. Department of the InteriorOpe

A stitch in time: Efficient computation of genomic DNA melting bubbles

Background: It is of biological interest to make genome-wide predictions of the locations of DNA melting bubbles using statistical mechanics models. Computationally, this poses the challenge that a generic search through all combinations of bubble starts and ends is quadratic. Results: An efficient algorithm is described, which shows that the time complexity of the task is O(NlogN) rather than quadratic. The algorithm exploits that bubble lengths may be limited, but without a prior assumption of a maximal bubble length. No approximations, such as windowing, have been introduced to reduce the time complexity. More than just finding the bubbles, the algorithm produces a stitch profile, which is a probabilistic graphical model of bubbles and helical regions. The algorithm applies a probability peak finding method based on a hierarchical analysis of the energy barriers in the Poland-Scheraga model. Conclusions: Exact and fast computation of genomic stitch profiles is thus feasible. Sequences of several megabases have been computed, only limited by computer memory. Possible applications are the genome-wide comparisons of bubbles with promotors, TSS, viral integration sites, and other melting-related regions.Comment: 16 pages, 10 figure

Comparison of Best Management Practice Adoption Between Virginia\u27s Chesapeake Bay Basin and Southern Rivers Watersheds

Producers in two regions of Virginia (Chesapeake Bay basin and Southern Rivers region) were surveyed to compare farming practices and agricultural best management practice (BMP) adoption. Objectives were to assess farming operations and determine the extent of cost-share and non-cost-share BMP implementation and gain insight into the impact of selected socioeconomic factors on the BMP adoption. Although farming characteristics and producer attitudes toward pollution and water quality were similar, BMP implementation differed between the two regions. Differences in BMP implementation may be due to a more focused, longer-term NPS pollution control educational effort in the Bay basin

Ronin Governs Early Heart Development by Controlling Core Gene Expression Programs.

Ronin (THAP11), a DNA-binding protein that evolved from a primordial DNA transposon by molecular domestication, recognizes a hyperconserved promoter sequence to control developmentally and metabolically essential genes in pluripotent stem cells. However, it remains unclear whether Ronin or related THAP proteins perform similar functions in development. Here, we present evidence that Ronin functions within the nascent heart as it arises from the mesoderm and forms a four-chambered organ. We show that Ronin is vital for cardiogenesis during midgestation by controlling a set of critical genes. The activity of Ronin coincided with the recruitment of its cofactor, Hcf-1, and the elevation of H3K4me3 levels at specific target genes, suggesting the involvement of an epigenetic mechanism. On the strength of these findings, we propose that Ronin activity during cardiogenesis offers a template to understand how important gene programs are sustained across different cell types within a developing organ such as the heart

Theoretical Analysis of the Stress Induced B-Z Transition in Superhelical DNA

We present a method to calculate the propensities of regions within a DNA molecule to transition from B-form to Z-form under negative superhelical stresses. We use statistical mechanics to analyze the competition that occurs among all susceptible Z-forming regions at thermodynamic equilibrium in a superhelically stressed DNA of specified sequence. This method, which we call SIBZ, is similar to the SIDD algorithm that was previously developed to analyze superhelical duplex destabilization. A state of the system is determined by assigning to each base pair either the B- or the Z-conformation, accounting for the dinucleotide repeat unit of Z-DNA. The free energy of a state is comprised of the nucleation energy, the sequence-dependent B-Z transition energy, and the energy associated with the residual superhelicity remaining after the change of twist due to transition. Using this information, SIBZ calculates the equilibrium B-Z transition probability of each base pair in the sequence. This can be done at any physiologically reasonable level of negative superhelicity. We use SIBZ to analyze a variety of representative genomic DNA sequences. We show that the dominant Z-DNA forming regions in a sequence can compete in highly complex ways as the superhelicity level changes. Despite having no tunable parameters, the predictions of SIBZ agree precisely with experimental results, both for the onset of transition in plasmids containing introduced Z-forming sequences and for the locations of Z-forming regions in genomic sequences. We calculate the transition profiles of 5 kb regions taken from each of 12,841 mouse genes and centered on the transcription start site (TSS). We find a substantial increase in the frequency of Z-forming regions immediately upstream from the TSS. The approach developed here has the potential to illuminate the occurrence of Z-form regions in vivo, and the possible roles this transition may play in biological processes

Theoretical Analysis of Competing Conformational Transitions in Superhelical DNA

We develop a statistical mechanical model to analyze the competitive behavior of transitions to multiple alternate conformations in a negatively supercoiled DNA molecule of kilobase length and specified base sequence. Since DNA superhelicity topologically couples together the transition behaviors of all base pairs, a unified model is required to analyze all the transitions to which the DNA sequence is susceptible. Here we present a first model of this type. Our numerical approach generalizes the strategy of previously developed algorithms, which studied superhelical transitions to a single alternate conformation. We apply our multi-state model to study the competition between strand separation and B-Z transitions in superhelical DNA. We show this competition to be highly sensitive to temperature and to the imposed level of supercoiling. Comparison of our results with experimental data shows that, when the energetics appropriate to the experimental conditions are used, the competition between these two transitions is accurately captured by our algorithm. We analyze the superhelical competition between B-Z transitions and denaturation around the c-myc oncogene, where both transitions are known to occur when this gene is transcribing. We apply our model to explore the correlation between stress-induced transitions and transcriptional activity in various organisms. In higher eukaryotes we find a strong enhancement of Z-forming regions immediately 5′ to their transcription start sites (TSS), and a depletion of strand separating sites in a broad region around the TSS. The opposite patterns occur around transcript end locations. We also show that susceptibility to each type of transition is different in eukaryotes and prokaryotes. By analyzing a set of untranscribed pseudogenes we show that the Z-susceptibility just downstream of the TSS is not preserved, suggesting it may be under selection pressure

A developmentally regulated chaperone complex for the endoplasmic reticulum of male haploid germ cells

Glycoprotein folding is mediated by lectin-like chaperones and protein disulfide isomerases (PDIs) in the endoplasmic reticulum (ER). Calnexin and the PDI homologue ERp57 work together to help fold nascent polypeptides with glycans located toward the N-terminus of a protein, whereas PDI and BiP may engage proteins that lack glycans or have sugars toward the C-terminus. In this study, we show that the PDI homologue PDILT is expressed exclusively in post-meiotic male germ cells, in contrast to the ubiquitous expression of many other PDI family members in the testis. PDILT is induced during puberty and represents the first example of a PDI family member under developmental control. We find that PDILT is not active as an oxido-reductase, but interacts with the model peptide -somatostatin and nonnative BPTI in vitro, indicative of chaperone activity. In vivo, PDILT forms a tissue-specific chaperone complex with the calnexin homologue calmegin. The identification of a redox-inactive chaperone partnership defines a new system of testis-specific protein folding with implications for male fertility