SEARCH · Search NASA
Results for “deterministic assembly”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
Balanced stochastic versus deterministic assembly processes benefit diverse yet uneven ecosystem functions in representative agroecosystems
Ecological assembly processes, by influencing community composition, determine ecosystem functions of microbiomes. However, debate remains on how stochastic versus deterministic assembly processes influence ecosystem functions such as carbon and nutrient cycling. Towards a better understanding, we investigated three types of agroecosystems (the upland, paddy, and flooded) that represent a gradient of stochastic versus deterministic assembly processes. Carbon and nutrient cycling multifunctionality, characterized by nine enzymes associated with soil carbon, nitrogen, phosphorous and sulfur cycling, was evaluated and then associated with microbial assembly processes and cooccurrence patterns of vital ecological groups. Our results suggest that strong deterministic processes favour microorganisms with convergent functions (as in the upland agroecosystem), while stochasticity-dominated processes lead to divergent functions (as in the flooded agroecosystem). To benefit agroecosystems services, we speculate that it is critical for a system to maintain balance between its stochastic and deterministic assembly processes (as in the paddy agroecosystem). By doing so, the system can preserve a diverse array of functional traits and also allow for particular traits to flourish. To further confirm this speculation, it is necessary to develop a systematic knowledge beyond merely characterizing general patterns towards the associations among community assembly, composition, and ecosystem functions.
Data and scripts associated with the manuscript "Organic Molecules are Deterministically Assembled in River Sediments"
This data package is associated with the publication "Organic Molecules are Deterministically Assembled in River Sediments" submitted to Scientific Reports (Stegen et al., 2024). The study applies community ecology methods to dissolved organic matter (DOM) chemistry from variably inundated riverbed sediments to uncover principles governing DOM composition at a reach-scale. This data package documents the workflow used to process and generate the main findings in the manuscript. The R scripts reference the raw, unprocessed Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) data from another data package, available on ESS-DIVE at https://data.ess-dive.lbl.gov/view/doi:10.15485/1834208. The scripts then process the raw FTICR-MS data and generate the findings and figures presented in the associated manuscript. In brief, this study demonstrates that DOM assemblages in variably inundated sediments are primarily governed by deterministic variable selection, including sediment moisture effecting the degree of deterministic assembly. See the manuscript for more details pertaining to interpretation and implications of the findings. This data package is associated with the GitHub repository found at https://github.com/WHONDRS-Hub/ECA_2020_Sed.This data package is comprised of 6 scripts and 7 folders. The file-level metadata file (file ending in "flmd.csv") lists all files contained in this data package and descriptions for each. The data dictionary (file ending in "dd.csv) describes all tabular data columns and their respective definitions and units. The FTICR_Processing_Scripts produce the outputs found in the "Processed_Data" folder. The remaining scripts (located in the parent directory) produce the outputs found in the following four folders: (1) "MCD_Dendrograms", "MCD_Randomizations", "MCD_bNTI_Outcomes", and "OM_Null_Modeling". The fifth script additionally takes the three comma-separated values (CSV) files found in the parent directory as input ("VGC_texture.csv", "merged_weights.csv", and "ECA2_FTICR_BetaDisp.csv"). The outputs of each of the five scripts serve as the input to the following script, with the final outputs stored in the folder "OM_Null_Modeling".
Deterministic influences exceed dispersal effects on hydrologically-connected microbiomes: Deterministic assembly of hyporheic microbiomes
Subsurface zones of groundwater and surface water mixing (hyporheic zones) are regions of enhanced rates of biogeochemical cycling, yet ecological processes governing hyporheic microbiome composition and function through space and time remain unknown. We sampled attached and planktonic microbiomes in the Columbia River hyporheic zone across seasonal hydrologic change, and employed statistical null models to infer mechanisms generating temporal changes in microbiomes within three hydrologically-connected, physicochemically-distinct geographic zones (inland, nearshore, river). We reveal that microbiomes remain dissimilar through time across all zones and habitat types (attached vs. planktonic) and that deterministic assembly processes regulate microbiome composition in all data subsets. The consistent presence of heterotrophic taxa and members of the Planctomycetes-Verrucomicrobia-Chlamydiae (PVC) superphylum nonetheless suggests common selective pressures for physiologies represented in these groups. Further, co-occurrence networks were used to provide insight into taxa most affected by deterministic assembly processes. We identified network clusters to represent groups of organisms that correlated with seasonal and physicochemical change. Extended network analyses identified keystone taxa within each cluster that we propose are central in microbiome composition and function. Finally, the abundance of one network cluster of nearshore organisms exhibited a seasonal shift from heterotrophic to autotrophic metabolisms and correlated with microbial metabolism, possibly indicating an ecological role for these organisms as foundational species in driving biogeochemical reactions within the hyporheic zone. Taken together, our research demonstrates a predominant role for deterministic assembly across highly-connected environments and provides insight into niche dynamics associated with seasonal changes in hyporheic microbiome composition and metabolism.
Deterministic assembly of releasable single crystal silicon-metal oxide field-effect devices formed from bulk wafers
Deterministic assembly of ultrathin metal oxide-semiconductor field-effect transistors released from the surfaces of bulk wafers with (111) orientation provides a route to high quality electronics on nearly any type of substrate. Device parameters and bias stability characteristics from transistors on sheets of plastic confirm the effectiveness of the approach and the critical roles of thermally grown layers of silicon dioxide for the gate dielectrics and passivation layers. Here, systematic studies of the anisotropic etching processes used to release the devices illustrate capabilities into the sub-micron thickness regime, with beneficial effects on the bending stiffness and degree of bendability.
Active, Programmable Elastomeric Surfaces with Tunable Adhesion for Deterministic Assembly by Transfer Printing
Active, programmable control of interfacial adhesion is an important, desired feature of many existing and envisioned systems, including medical tapes, releasable joints, and stamps for transfer printing. Here a design for an elastomeric surface that offers switchable adhesion strength through a combination of peel-rate dependent effects and actuation of sub-surface fluid chambers is presented. Microchannels and open reservoirs positioned under a thin surface membrane can be pressurized in a controlled manner to induce various levels of surface deformation via inflation. These pressurized structures demonstrate utility in controllably decreasing the strength of adhesion of flat, solid objects to the elastomeric surface, particularly in the limit of low peel-rates. Experimental and theoretical studies of these systems reveal the key mechanisms, and guide optimized geometries for broad control over adhesion, in a programmable and reversible manner. Implementing these concepts in stamps for transfer printing enables new modes for deterministic assembly of micro- and nanoscale materials onto diverse types of substrates. Furthermore, collections of silicon plates delivered onto plastic, paper and other surfaces with single or multiply addressable stamps illustrate some of the capabilities.
Soil pH mediates the balance between stochastic and deterministic assembly of bacteria
Little is known about the factors affecting the relative influence of stochastic and deterministic processes that governs the assembly of microbial communities in successional soils. Here, we conducted a meta-analysis of bacterial communities using six different successional soils data sets, scattered across different regions, with different pH conditions in early and late successional soils. We found that soil pH was the best predictor of bacterial community assembly and the relative importance of stochastic and deterministic processes along successional soils. Extreme acidic or alkaline pH conditions lead to assembly of phylogenetically more clustered bacterial communities through deterministic processes, whereas pH conditions close to neutral lead to phylogenetically less clustered bacterial communities with more stochasticity. We suggest that the influence of pH, rather than successional age, is the main driving force in producing trends in phylogenetic assembly of bacteria, and that pH also influences the relative balance of stochastic and deterministic processes along successional soils. Given that pH had a much stronger association with community assembly than did successional age, we evaluated whether the inferred influence of pH was maintained when studying globally-distributed samples collected without regard for successional age. This dataset confirmed the strong influence of pH, suggesting that the influence of soil pH on community assembly processes occurs globally. Extreme pH conditions likely exert more stringent limits on survival and fitness, imposing strong selective pressures through ecological and evolutionary time. Taken together, these findings suggest that the degree to which stochastic vs. deterministic processes shape soil bacterial community assembly is a consequence of soil pH rather than successional age.
Organic molecules are deterministically assembled in variably inundated river sediments, but drivers remain unclear
Dissolved organic matter (DOM) is central to ecosystem function. A fundamental challenge is understanding the processes leading to variation in the chemistry of organic molecules that comprise DOM. Here we study these processes in variably inundated riverbed sediments, as an understudied, yet ubiquitous component of rivers. Using null-model approaches adopted from community ecology, we found that within-site variation in environmental conditions caused non-random (i.e., deterministic) shifts in DOM chemistry. Deterministic shifts were observed across diverse biomes, though the strength of determinism varied substantially. We found that the strength of determinism decreased with increasing sediment moisture, but in the form of a constraint space. Many systems fell below the upper constraint boundary, however. We propose a conceptual model based on our results and other publications in which DOM assemblages are hypothesized to be increasingly deterministic across the continuum from the river water column to saturated sediment pore spaces to unsaturated and dry soils/sediments.
Deterministic assembly of complex, three-dimensional architectures by compressive buckling
Origami- and Kirigami-inspired assembly of predetermined three-dimensional forms is presented in comprehensive theoretical and experimental studies, with examples of a broad range of topologies and material compositions. The resulting engineering options in the construction of functional 3D structures have important implications for advanced microsystem technologies.
Transfer Printing Techniques for Materials Assembly and Micro/Nanodevice Fabrication
Transfer printing represents a set of techniques for deterministic assembly of micro-and nanomaterials into spatially organized, functional arrangements with two and three-dimensional layouts. Such processes provide versatile routes not only to test structures and vehicles for scientific studies but also to high-performance, heterogeneously integrated functional systems, including those in flexible electronics, three-dimensional and/or curvilinear optoelectronics, and bio-integrated sensing and therapeutic devices. This article summarizes recent advances in a variety of transfer printing techniques, ranging from the mechanics and materials aspects that govern their operation to engineering features of their use in systems with varying levels of complexity. Here, a concluding section presents perspectives on opportunities for basic and applied research, and on emerging use of these methods in high throughput, industrial-scale manufacturing.
Long-Term Stochasticity Combines With Short-Term Variability in Assembly Processes to Underlie Rice Paddy Sustainability
Revealing temporal patterns of community assembly processes is important for understanding how microorganisms underlie the sustainability of agroecosystem. The ancient terraced rice paddies at Longji provide an ideal platform to study temporal dynamics of agroecosystem sustainability due to their chronosequential records of soil physicochemistry and well-archived microbial information along 630-year rice cultivation. We used statistical null models to evaluate microbial assembly processes along the soil chronosequences of Longji rice paddies through time. Stochastic and deterministic assembly processes jointly governed microbial community composition within successional eras (less than 250 years), and within-era determinism was mainly driven by soil fertility and redox conditions alone or in combination. Conversely, across successional eras (i.e., over 300 years), stochasticity linearly increased with increasing duration between eras and was eventually predominant for the whole 630 years. We suggest that the impact of stochasticity vs. determinism on assembly is timescale-dependent, and we propose that the importance of stochastic assembly of microbial community at longer timescales is due to the gradual changes in soil properties under long-term rice cultivation, which in turn contribute to the sustainability of paddy ecosystem by maintaining a diverse community of microorganisms with multi-functional traits. In total, our results indicate that knowledge on the timescales at which assembly processes govern microbial community composition is key to understanding the ecological mechanisms generating agroecosystem sustainability.
Disturbance triggers non-linear microbe–environment feedbacks
Abstract. Conceptual frameworks linking microbial community membership, properties, and processes with the environment and emergent function have been proposed but remain untested. Here we refine and test a recent conceptual framework using hyporheic zone sediments exposed to wetting–drying transitions. Our refined framework includes relationships between cumulative properties of a microbial community (e.g., microbial membership, community assembly properties, and biogeochemical rates), environmental features (e.g., organic matter thermodynamics), and emergent ecosystem function. Our primary aim was to evaluate the hypothesized relationships that comprise the conceptual framework and contrast outcomes from the whole and putatively active bacterial and archaeal communities. Throughout the system we found threshold-like responses to the duration of desiccation. Membership of the putatively active community – but not the whole bacterial and archaeal community – responded due to enhanced deterministic selection (an emergent community property). Concurrently, the thermodynamic properties of organic matter (OM) became less favorable for oxidation (an environmental component), and respiration decreased (a microbial process). While these responses were step functions of desiccation, we found that in deterministically assembled active communities, respiration was lower and thermodynamic properties of OM were less favorable. Placing the results in context of our conceptual framework points to previously unrecognized internal feedbacks that are initiated by disturbance and mediated by thermodynamics and that cause the impacts of disturbance to be dependent on the history of disturbance.
Using metacommunity ecology to understand environmental metabolomes
Abstract Environmental metabolomes are fundamentally coupled to microbially-linked biogeochemical processes within ecosystems. However, significant gaps exist in our understanding of their spatiotemporal organization, limiting our ability to uncover transferrable principles and predict ecosystem function. We propose that a theoretical paradigm, which integrates concepts from metacommunity ecology, is necessary to reveal underlying mechanisms governing metabolomes. We call this synthesis between ecology and metabolomics ‘meta-metabolome ecology’ and demonstrate its utility using a mass spectrometry dataset. We developed three relational metabolite dendrograms using molecular properties and putative biochemical transformations and performed ecological null modeling. Based upon null modeling results, we show that stochastic processes drove molecular properties while biochemical transformations were structured deterministically. We further suggest that potentially biochemically active metabolites were more deterministically assembled than less active metabolites. Understanding variation in the influences of stochasticity and determinism provides a way to focus attention on which meta-metabolomes and which parts of meta-metabolomes are most likely to be important to consider in mechanistic models. We propose that this paradigm will allow researchers to study the connections between ecological systems and their molecular processes in previously inaccessible detail.
Van der Waals heterostructures
The integration of dissimilar materials into heterostructures has become a powerful tool for engineering interfaces and electronic structure. The advent of two-dimensional (2D) materials brought unprecedented opportunities for novel heterostructures in the form of van der Waals stacks, laterally stitched 2D layers, and more complex layered and 3D architectures. This Primer provides an overview of state-of-the-art methodologies for producing such van der Waals heterostructures, focusing on the two fundamentally different strategies, top-down deterministic assembly and bottom-up synthesis. For both approaches, successful techniques, advantages, and limitations are discussed. As important as the fabrication itself is the characterization of the resulting engineered materials, for which a range of analysis techniques covering structure, composition, and emerging functionality are highlighted. Examples of the properties of artificial van der Waals structures include optoelectronics and plasmonics, twistronics, and unique functionality arising from the generalization of van der Waals assembly from 2D- to 3D-crystalline components. Lastly, current issues of reproducibility, limitations, and opportunities for future breakthroughs in terms of enhanced homogeneity, interfacial purity, feature control, and ultimately orders of magnitude increased complexity of van der Waals heterostructures are discussed.
Ultrafast quantum photonics enabled by coupling plasmonic nanocavities to strongly radiative antennas
Quantum emitters coupled to plasmonic nanostructures can act as exceptionally bright sources of single photons, operating at room temperature. Plasmonic mode volumes supported by these nanostructures can be several orders of magnitude smaller than the cubic wavelength, which leads to dramatically enhanced light–matter interactions and drastically increased photon production rates. However, when increasing the light localization further, these deeply subwavelength modes may in turn hinder the fast outcoupling of photons into free space. Plasmonic hybrid nanostructures combining a highly confined cavity mode and a larger antenna mode circumvent this issue. We establish the fundamental limits for quantum emission enhancement in such systems and find that the best performance is achieved when the cavity and antenna modes differ significantly in size. We experimentally support this idea by photomodifying a nanopatch antenna deterministically assembled around a nanodiamond known to contain a single nitrogen–vacancy (NV) center. As a result, the cavity mode shrinks, further shortening the NV fluorescence lifetime and increasing the single-photon brightness. Our analytical and numerical simulation results provide intuitive insight into the operation of these emitter–cavity–antenna systems and show that this approach could lead to single-photon sources with emission rates up to hundreds of THz and efficiencies close to unity.
Dispersal-Based Microbial Community Assembly Decreases Biogeochemical Function
Ecological mechanisms influence relationships among microbial communities, which in turn impact biogeochemistry. In particular, microbial communities are assembled by deterministic (e.g., selection) and stochastic (e.g., dispersal) processes, and the relative balance of these two process types is hypothesized to alter the influence of microbial communities over biogeochemical function. We used an ecological simulation model to evaluate this hypothesis, defining biogeochemical function generically to represent any biogeochemical reaction of interest. We assembled receiving communities under different levels of dispersal from a source community that was assembled purely by selection. The dispersal scenarios ranged from no dispersal (i.e., selection-only) to dispersal rates high enough to overwhelm selection (i.e., homogenizing dispersal). We used an aggregate measure of community fitness to infer a given community’s biogeochemical function relative to other communities. We also used ecological null models to further link the relative influence of deterministic assembly to function. We found that increasing rates of dispersal decrease biogeochemical function by increasing the proportion of maladapted taxa in a local community. Niche breadth was also a key determinant of biogeochemical function, suggesting a tradeoff between the function of generalist and specialist species. Finally, we show that microbial assembly processes exert greater influence over biogeochemical function when there is variation in the relative contributions of dispersal and selection among communities. Taken together, our results highlight the influence of spatial processes on biogeochemical function and indicate the need to account for such effects in models that aim to predict biogeochemical function under future environmental scenarios.
Bilayer self-assembly on a hydrophilic, deterministically nano-patterned surface
We present measurements of the in-situ, microscopic architecture of a self-assembled bilayer at the interface between a regularly nano-patterned surface and an aqueous sub-phase using neutron reflectometry. The substrate is patterned with a rectangular array of nano-scaled holes. Because of the high quality of the pattern, using neutron reflectometry, we are able to map the surface-normal density distribution of the patterned silicon, the penetration of water into the pattern, and the distribution of a deposited film inside and outside of the etched holes. In this study, 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC) single bilayers were deposited on the hydrophilic patterned surface. For bilayers deposited either by vesicle fusion (VF) or by the Langmuir Schaefer (L-S) technique, the most consistent model found to fit the data shows that the lipids form bilayer coatings on top of the substrate as well as the bottoms of the holes in an essentially conformal fashion. However, while there is a single bilayer on the unetched silicon surface, the lipids coating the bottoms of the holes form a complex bimodal structure consistent with a rough surface produced by the etching process. This study provides insight into film transfer both outside and inside regular nano-patterned features.
Position-Dependency of Fuel Assembly Homogenization in a Pressurized Water Reactor
2-step nuclear reactor core analysis has long been established as the conventional calculational procedure for the pressurized water reactor (PWR) due to its efficiency. This is because the procedure significantly avoids the potentially huge computational burden arising from an explicit geometrical modeling and consideration of over ∼ 500 energy groups. It instead approaches the problem with spatial homogenization and group condensation: a 2-D lattice transport calculation to homogenize the fuel assembly cross-sections and a 3-D whole core nodal diffusion. One notes that the few-group constant generation using deterministic method could be complicated due to its limited flexibilities in geometrical modeling and inherent drawbacks of the multi-group approximation. Furthermore, accuracy of the deterministic few-group constant generation can especially be compromised during the resonance treatment calculation. As such, an alternative lattice calculation using the Monte Carlo (MC) approach, in place of the deterministic fuel assembly homogenization (few-group constant generation), has previously been proposed. During the assembly homogenization, directions and magnitudes of the current at boundaries are unknowns. Therefore, zero net current boundary conditions (infinite lattice) are instead used as the assembly node. The assumption is quite reasonable considering heterogeneities inside the node are more dominant than heterogeneities due to nodal location in the core. In fact, this approximation has successfully been applied to many LWR core analyses to reasonable accuracy. It should nonetheless be noted that the net current zero boundary assumption effectively ignores position-dependency of the fuel assembly homogenization in the general 2-step method. As such, there are a number of well-known researches on the extended assembly homogenization techniques, which introduce correction factors to compensate effects of the assembly environment, such as Generalized Equivalence Theory (GET), Super-homogenization method (SPH), and color set calculation method. Even though the assembly environment effect has long been acknowledged, its effect has not properly been investigated due to the limited computing power in the past and due to the reasonable accuracy of the extended assembly homogenization techniques. Nonetheless, quantification of position-dependency of the assembly homogenization in the core could still potentially offer additional value in terms of calculation accuracy to the 2-step reactor analysis. It is upon this motivation that the paper is prepared. In this research, position-dependent few-group constants were calculated and compared against those of infinite lattices. All calculations were completed using the MC Serpent2 code with ENDF/B7.0 nuclear data library. In this study, position-dependency of the fuel assembly homogenized cross sections in a PWR core has been investigated through comparison of the conventional 2-step reactor analysis with the reference high fidelity Monte Carlo simulation. It was found that the homogenized two-group constants are clearly position-dependent as the discrepancies between infinite lattice and whole-core calculations are quite significant especially in a rodded assembly. As such, the corresponding correction required due to the assembly environment effect is not negligible compared to the correction required due to assembly heterogeneity itself. It is therefore quite clear that position-dependency of the group cross sections should be considered in the 2-step procedure for a more accurate PWR core analysis. (authors)