In all known genetic polymers, molecular recognition via hydrogen bonding between complementary subunits underpins their ability to encode and transmit information, to form sequence-defined duplexes, ...and to fold into catalytically active forms. Reversible covalent interactions between complementary subunits provide a different way to encode information, and potentially function, in sequence-defined oligomers. Here, we examine six oligoarylacetylene trimers composed of aniline and benzaldehyde subunits. Four of these trimers self-pair to form two-rung duplex structures, and two form macrocyclic 1,3-folded structures. The equilibrium proportions of these structures can be driven to favor each of the observed structures almost entirely depending upon the concentration of trimers and an acid catalyst. Quenching the acidic trimer solutions with an organic base kinetically traps all species such that they can be isolated and characterized. Mixtures of complementary trimers form exclusively sequence-specific 3-rung duplexes. Our results suggest that reversible covalent bonds could in principle guide the formation of more complex folded conformations of longer oligomers.
Genetic biopolymers utilize defined sequences and monomer-specific molecular recognition to store and transfer information. Synthetic polymers that mimic these attributes using reversible covalent ...chemistry for base-pairing pose unique synthetic challenges. Here, we describe a solid-phase synthesis methodology for the efficient construction of ethynyl benzene oligomers with specific sequences of aniline and benzaldehyde subunits. Handling these oligomers is complicated by the fact that they often exhibit multiple conformations because of intra- or intermolecular pairing. We describe conditions that allow the dynamic behavior of these oligomers to be controlled so that they may be manipulated and characterized without needing to mask the recognition units with protecting groups.
The ability of the biopolymers RNA and DNA to store and transfer information is essential to life. Herein, we demonstrate template-directed replication in a set of dimer duplexes that use reversible ...covalent bonds to form base-pairing interactions. Binary sequence information was encoded as a sequence of aniline and benzaldehyde subunits linked together by a diethynyl benzene backbone. These dimers formed sequence-specific, imine-linked duplexes, which could be separated and used as templates for the synthesis of daughter duplexes with identical sequences.
Surface and groundwater interact in the hyporheic zone beneath and adjacent to rivers in the presence of a diverse microbial community. Heterotrophic bacteria mediate a range of environmentally ...important reactions, yet few studies have quantified bacterial growth and death dynamics in the hyporheic zone, and none have systematically analyzed their response to variations in hydraulic or chemical conditions. We used MODFLOW and SEAM3D to simulate hydraulics; dissolved oxygen (DO) and dissolved organic carbon (DOC) transport; and aerobic microbial metabolism, growth, and death in hyporheic zones induced by riverbed dunes. We ran simulations both with and without growth/death processes, and varied hydraulic parameters and DO/DOC boundary concentrations. Microbial biomass reached steady state (t = 3 days) in every simulation, at which time there was greater biomass and DOC biodegradation rates in the hyporheic flowcell (300 % and 85 % higher for the base case, respectively) when accounting for microbial growth dynamics. This occurred as microbial biomass tailored its spatial distribution to the availability of DO and DOC, demonstrating the importance of simulating growth/death processes. Biomass generally increased with hyporheic flow cell area as upwelling groundwater decreased. When varying surface water DO and DOC source concentrations relative to the base case, the greatest effect on biomass occurred when increasing DOC and decreasing DO. We determined minimum DO and DOC steady-state concentrations required for microbial growth, but the minimums were not absolute or related by stoichiometry. Increasing DOC created a smaller area of microbes with higher concentrations relative to the base case. Increasing DO slightly increased the area occupied by microbes while keeping the total biomass nearly constant. Overall, microbial growth and death dynamics depend on DO and DOC availability in the hyporheic zone, which is dependent on DOC/DO boundary concentrations and hyporheic flow paths, and in turn the hydraulic interaction between surface water and groundwater.
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•Microbial populations that mediate hyporheic zone reactions grow and shrink with varying conditions•We simulated population growth and death, compared to simulating static populations, and conducted sensitivity analyses•Microbes adjusted to spatial patterns of DOC sources and increased efficiency of DOC consumption•Microbial biomass and oxygen/carbon consumption scaled with hydraulic and chemical boundary conditions•Results with dynamic populations much different that results with static populations
The flocculation properties of a natural silt–clay mud taken from the San Jacinto estuary near Houston, TX were investigated over a range of suspended sediment concentrations, salinities, and ...turbulent shear rates. The study was conducted in a laboratory using a paddle mixer to create a turbulent shear field for driving the flocculation process; floc settling velocity and size attributes were measured in a settling column with a camera system and image analysis. In general, maximum floc sizes were observed at turbulent shear rates less than 30
s
−1. For turbulent shear rates less than 50
s
−1, flocs originating in saline water at 10 and 15
ppt were larger and more loosely packed than those created in freshwater at identical turbulent shear rates and suspended sediment concentrations. At turbulent shear rates of 50
s
−1, floc properties of size, submerged specific gravity and fractal dimension were approximately equal for all conditions. Two ranges of behavior were observed in regards to the fractal dimension of flocs at a constant turbulent shear rate. In the first region, for floc sizes less than
200
μ
m
, a variable fractal dimension was needed to describe the submerged specific gravity as a function of floc size. It is suggested that this variability in fractal dimension may physically be the result of ploysized primary particles. In the second region, for floc sizes greater than
200
μ
m
, a constant fractal dimension was found to suffice in describing the submerged specific gravity. The constant fractal dimension for this second region was
n
f
=2.3 for freshwater flocs and
n
f
=1.95 for saltwater flocs. Based on the observation of the two-region behavior, a new variable fractal dimension model is presented using a simple exponential decay which asymptotically approaches a constant fractal dimension at a specified floc size. The model itself is based on the uniform-size primary particle formulation of the relationship between floc size and fractal dimension, but the equation was able to model the average shift from variable to constant fractal dimension, which was thought to primarily be due to polysized primary particles.
The ability of genetic biopolymers to store and transfer information provides the mechanism for the evolution of function from a population of sequences. Synthetic polymers with the ability to ...transmit information are exceedingly rare. This work demonstrates template‐directed information transfer in oligoarylacetylene trimers that use reversible covalent bonds to form base pairing interactions. Information was encoded as a sequence of aniline and benzaldehyde subunits linked together by a diethynylbenzene backbone. Trimers formed sequence‐specific, imine‐linked monomer‐template complexes, which could be oligomerized using palladium mediated Sonogashira coupling to generate daughter trimers with complementary sequences.
Information transfer via template oligomerization. Monomers attached to sequence‐defined trimers through imine bonds were oligomerized using Sonogashira cross‐coupling. The resulting three‐rung duplexes were chain terminated with triisopropylsilylacetylene and hydrolyzed to the starting template and newly formed complementary daughter.
•Instream plants emerge as a strategical tool in regulating eco-morphological dynamics in rivers.•Experiments were conducted at reach-scale in a partly vegetated flume with and without sediments.•The ...objective of the tests was to understand the sediment capturing ability of a vegetated channel.•Morphology of deposited sediments, sediment sorting, and water surface slopes were examined.•The findings revealed the role of instream plants in depositing suspended sediment in a reach.
Instream plants, which act as biological processors, have emerged as potentially advantageous eco-morphologic tools to be used in river management and restoration. Most of the study on the geomorphic role of vegetation as it interacts with flow and sediment has focused on local patch-scale dynamics. In this study, we present flume experiments aimed at improving our understanding of how vegetation patches link together to impact reach-scale hydraulics and suspended sediment transport and disposition. On the hydraulics side, we investigate a) the relationship between the imposed instream vegetation configuration and water surface slopes, b) the secondary flow patterns which arise because of the imposed vegetative obstructions, and c) the role of vegetative resistance on residence time within reach. We also examine how different vegetation arrangements determine the patterns, quantity, and caliber of suspended sediment deposited in the flume. A key result of vegetation within the channel is the overall non-uniformity in flow conditions it imposes upstream, within, and downstream of the vegetated reach. At steady-state, vegetated patches locally increase the resistance, leading to a backwater condition upstream of the patch and high water-surface slopes within the patch. In general, this leads to enhanced deposition of suspended sediment upstream of the patch and reduced deposition within the patch relative to a case with no vegetation at all.
Muddy sediment constitutes a major fraction of the suspended sediment mass carried by the Mississippi River. Thus, adequate knowledge of the transport dynamics of suspended mud in this region is ...critical in devising efficient management plans for coastal Louisiana. We conducted laboratory tank experiments on the sediment suspended in the lower reaches of the Mississippi River to provide insight into the flocculation behavior of the mud. In particular, we measure how the floc size distribution responds to changing environmental factors of turbulent energy, sediment concentration, and changes in base water composition and salinity during summer and winter. We also compare observations from the tank experiments to in situ observations. Turbulence shear rate, a measure of river hydrodynamic energy, was found to be the most influential factor in determining mud floc size. All flocs produced at a given shear rate could be kept in suspension down to shear rates of approximately 20 s −1 . At this shear rate, flocs on the order of 150–200 μm and larger can settle out. Equilibrium floc size was not found to depend on sediment concentration; flocs larger than 100 μm formed in sediment concentrations as low as 20 mgL −1 . An increase in salinity generated by adding salts to river water suspensions did not increase the flocculation rate or equilibrium size. However, the addition of water collected from the Gulf of Mexico to river-water suspensions did enhance the flocculation rate and the equilibrium sizes. We speculate that the effects of Gulf of Mexico water originate from its biomatter content rather than its ion composition. Floc sizes in the mixing tanks were comparable to those from the field for similar estimated turbulent energy. Flocs were found to break within minutes under increased turbulence but can take hours to grow under conditions of reduced shear in freshwater settings. Growth was faster with the addition of Gulf of Mexico water. Overall, the experiments provide information on how suspended mud in the lower reaches of the Mississippi might respond to changes in turbulence and salinity moving from the fluvial to marine setting through natural distributary channels or man-made diversions.
Pulses of fine sediment composed of sand, silt, and clay can be introduced to gravel bed rivers through runoff from burn‐impacted hillslopes, landslides, bank failure, or the introduction of ...reservoir sediment as a result of sluicing or dam decommissioning. Here we present a study aimed at quantifying exchange between suspensions of clay and gravel beds. The questions that motivate the work are: how do bed roughness and pore space characteristics, shear velocity (
u∗), and initial concentration (C0) affect clay deposition on or within gravel beds? Where does deposition within these beds occur, and can deposited clay be resuspended while the gravel is immobile? We examine these questions in a laboratory flume using acrylic, open‐framework gravel, and armored sand‐gravel beds under conditions of varying
u∗ and C0. Deposition of clay occurred to all beds (even with Rouse numbers ∼ 0.01). We attribute deposition under full suspension conditions to be an outcome of localized protected zones where clay can settle and available pore space in the bed. For smooth wall cases, protection came from the viscous wall region and the development of bed forms; for the rough beds, protection came from separation zones and low‐velocity pore spaces. Bed porosity was the strongest influencer of nondimensional deposition rate; deposition increased with porosity. Deposition was inversely related to
u∗ for the acrylic bed runs; no influence of
u∗ was found for the porous bed runs. Increases in discharge resulted in resuspension of clay from acrylic beds; no resuspension was observed in the porous bed runs.
Key Points
Suspended clay deposited to both the surface and substrate of gravel beds even though Rouse numbers were on the order of 0.01
Scaled deposition rate was a function of the surface roughness characteristics and substrate porosity, but not shear velocity
Little to no deposited clay was reentrained without mobilizing the surface layer due to sheltering, pore space accommodation, and cohesion
A field study was conducted to examine the turbulent properties of the flow around a naturally formed cluster bedform. This was carried out on a mountain river using a 3D acoustic Doppler velocimeter ...(ADV). Concurrent with this objective, the ability of the ADV to make measurements in a shallow flow over a cobble bed
(
ho
∕
d84
=1.75)
was examined. ADV measurements in natural clear-water shallow flows around obstacles are inherently difficult to obtain due to (1) signal interference between the acoustic reflections from the boundary and the ADV sample volume; (2) regions of high turbulent intensity, such as in local detached shear layers; and (3) low concentrations of suspended particles passing through the ADV sampling volume. These processes result in velocity time series that contain a significant amount of spikes, lower-than-average signal-to-noise ratios, and lower than average correlation values. A filtering process that optimized the removal of bad points while retaining a sufficient number of points to describe the velocity time series histogram was developed. In general, flow over the study section can be described by an inner roughness layer dominated by large roughness and detached flow, and an outer flow that exhibits a form of log scaling. It was found that the cluster acts to locally modify this structure by shifting the elevation of the roughness layer and the zone of primary production and dissipation of turbulent energy up towards the center of the water column. Mean and turbulent statistics, energy distributions, spectral properties, and a quadrant analysis are presented to characterize the flow around the cluster.
Celotno besedilo
Dostopno za:
DOBA, FGGLJ, IZUM, KILJ, NUK, PILJ, PNG, SAZU, UILJ, UKNU, UL, UM, UPUK
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