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DOE OSTI2017

Global transcriptional regulatory network for Escherichia coli robustly connects gene expression to transcription factor activities

Significance While the transcriptional regulatory network (TRN) of Escherichia coli has expanded considerably in recent years through new chromatin immunoprecipitation (ChIP) data, an open question remains: Does the global TRN, reconstructed by combining ChIP data for individual transcriptions factors, consistently explain observed differential gene expression? We have reconstructed a high-confidence TRN, determined its consistency with transcriptomics and predictive capabilities across multiple conditions, extracted 10 functional regulatory modules, and characterized this network at the sequence and structural levels. Our multiomics algorithmic pipeline is expected to facilitate rigorous validation and prioritization of experiments to elucidate TRNs in other bacteria.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2019

A Novel TDC Scheme: Combinatorial Gray Code Oscillator Based TDC for Low Power and Low Resource Usage Applications

In common digital electronics design practice, combinatorial loop is less preferable, especially in the multi-bit cases. An exception of multi-bit feedback system that is allowed to be implemented in combinatorial loop is the Gray code sequence generator. The Gray code sequence generator runs by itself without being driven by an external clock. It steps through Gray code sequence significantly faster than the Gray code counter under the same silicon technology. In high energy physics experiments, it is necessary to find a low resource usage and low power TDC (Time-to-Digital-Converter) scheme for high channel count detectors. A Gray code oscillator based TDC is a good candidate for such a scheme. In this paper, we describe our work of design and implementation of a TDC based on combinatorial Gray code oscillator in a Xilinx Kintex-7 FPGA (Field-Programmable Gate Array). The implementation and test results are presented. The test result shows that the TDC using only 8 logic elements is able to reach a RMS precision of 160 ps for time difference measurements of a single pulse. The single pulse measurement precision can be further improved to 51 ps with the weighted average scheme using data from the same TDC channels captured by 4 consecutive system clock edges.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2020

Distributed Intrusion Detection System using Semantic-based Rules for SCADA in Smart Grid

Cyber-physical system (CPS) security for the smart grid enables secure communication for the SCADA and wide-area measurement system data. Power utilities world-wide use various SCADA protocols, namely DNP3, Modbus, and IEC 61850, for the data exchanges across substation field devices, remote terminal units (RTUs), and control center applications. Adversaries may exploit compromised SCADA protocols for the reconnaissance, data exfiltration, vulnerability assessment, and injection of stealthy cyberattacks to affect power system operation. In this paper, we propose an efficient algorithm to generate robust rule sets. We integrate the rule sets into an intrusion detection system (IDS), which continuously monitors the DNP3 data traffic at a substation network and detects intrusions and anomalies in real-time. To enable CPS-aware wide-area situational awareness, we integrated the methodology into an open-source distributed-IDS (D-IDS) framework. The D-IDS facilitates central monitoring of the detected anomalies from the geographically distributed substations and to the control center. The proposed algorithm provides an optimal solution to detect network intrusions and abnormal behavior. Different types of IDS rules based on packet payload, packet flow, and time threshold are generated. Further, IDS testing and evaluation is performed with a set of rules in different sequences. The detection time is measured for different IDS rules, and the results are plotted. All the experiments are conducted at Power Cyber Lab, Iowa State University, for multiple power grid models. After successful testing and evaluation, knowledge and implementation are transferred to field deployment.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2022

Phylogenetic conservatism of mycoparasitism and its contribution to pathogen antagonism

Abstract Closely related species are expected to have similar functional traits due to shared ancestry and phylogenetic inertia. However, few tests of this hypothesis are available for plant‐associated fungal symbionts. Fungal leaf endophytes occur in all land plants and can protect their host plant from disease by a variety of mechanisms, including by parasitizing pathogens (e.g., mycoparasitism). Here, we tested whether phylogenetic relatedness among species of Cladosporium , a widespread genus that includes mycoparasitic species, predicts the effect of this endophyte on the severity of leaf rust disease. First, we used congruence among different marker sequences (i.e., genealogical concordance phylogenetic species recognition criterion) to delimit species of Cladosporium . Next, in a controlled experiment, we quantified both mycoparasitism and disease modification for the selected Cladosporium species. We identified 17 species of Cladosporium ; all the species reduced rust disease severity in our experiment. Cladosporium phylogeny was a significant predictor of mycoparasitism. However, we did not observe a phylogenetic effect on disease severity overall, indicating that other mechanism/s operating independently of shared ancestry also contributed to endophyte effects on disease severity. Indeed, a second experiment showed that Cladosporium endophyte exudates (no live organism) from divergent species groups equally reduced disease severity. Our results reveal that multiple mechanisms contribute to the protective effects of an endophyte against a plant pathogen, but not all traits underlying these mechanisms are phylogenetically conserved.

Barge, Edward G.↗

DOE OSTI2020

Aerial Crosspolarized NQR-NMR: Buried Explosive Detection From a Safe Distance

Nuclear quadrupole resonance is a non-destructive detection and inspection technique with potential as a non-destructive test (NDT) tool. Establishment of the capability opens the door to its use in furthering the mission of the labs. There are many possible uses of the capability: explosive detection and stress/strain detection in epoxies are two of the more obvious and are the main results of this work. Enhancement of the signal-to-noise ratio (SNR) and improvements in the acquisition time of the experiment were key focuses of this work. These were achieved by combing special spin-lock pulse sequences with cross-polarization (CP) schemes to improve the signals with shorter acquisition times. A novel rotating magnetic field device was created to facilitate CP in the field. Implementation of these schemes provided a significant reduction in SNR/time.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

DOE OSTI2022

Nondestructive Evaluation (NDE) of Cable Anomalies using Frequency Domain Reflectometry (FDR) and Spread Spectrum Time Domain Reflectometry (SSTDR)

This report presents a comparative assessment of the performance of frequency domain reflectometry (FDR) and spread spectrum time domain reflectometry (SSTDR) in detecting a wide range of electrical cable anomalies. All tests and results reported herein were performed at the PNNL Accelerated and Real-Time Environmental Nodal Assessment (ARENA) cable and motor test bed. The primary objective of this work was to evaluate the effectiveness of SSTDR, a fledgling cable monitoring technique that shows promise for application in online monitoring of energized cable systems, against FDR, an offline technique widely employed in the nuclear power plant (NPP) industry. FDR tests are becoming more widely used in nuclear power plant cable aging management and test programs – particularly for low voltage cables. FDR capabilities for these kinds of tests have been reported by PNNL and others. The FDR test is performed on de-energized cables by connecting the FDR instrument to two of the cable conductors, or one conductor and the shield. A broad band low voltage (< 5 V) chirp is introduced in the cable, and any reflected response is captured in the frequency domain. The captured reflection is then processed by performing an inverse Fourier transform to a time domain response which can then be converted to a distance response based on the cable velocity of propagation (VoP). SSTDR measurements are functionally similar to FDR measurements in that a broad-band voltage signal composed of a square or sine wave modulated pseudo-random sequence of chips (< 5 volts), is injected onto one of the cable conductors. The injected signal will experience partial energy reflection and transmission at each impedance discontinuity along the transmission line. Any reflected response is detected by computing a cross-correlation between the reflected signals and a delayed copy of the incident SSTDR signal. the time delay for the reflected signal to experience the best matched correlation with the incident signal, indicates the travel time for the signal to reach a change in impedance. By knowing this time delay and velocity of propagation (VoP) of the signal, one can compute the physical distance. A big advantage that SSTDR measurements have over other methods is the ability to be connected to energized or live wires (currently up to 1kV) thereby enabling online monitoring of cables. SSTDR has been used successfully in several applications, e.g., aircraft, rail, and photovoltaic systems. In this work FDR and SSTDR cable assessment techniques were used to characterize a variety of cable anomalies and faults including: (1) Presence or absence of a motor; (2) Ground faults and short circuit faults; (3) Moist environments and water ingress faults; (4) Accelerated thermal aging. Both shielded and non-shielded cables were evaluated in this report. Offline measurements were made using FDR and online measurements were made by SSTDR for a range of test scenarios. Based on the results across all cable anomalies evaluated in this study, FDR displayed high sensitivity towards cable condition assessment, while SSTDR showed promise for future application in monitoring NPP cable systems. However, further developments are suggested to improve the resolution and sensitivity of SSTDR towards faults and anomalies in low voltage cables.rt presents a comparative

42 ENGINEERING↗

DOE OSTI2019

In Situ Loading and Delivery of Short Single- and Double-Stranded DNA by Supramolecular Organic Frameworks

Short DNA represents an important class of biomacromolecules that are widely applied in gene therapy, editing, and modulation. However, the development of simple and reliable methods for their intracellular delivery remains a challenge. Herein, we describe that seven water-soluble, homogeneous supramolecular organic frameworks (SOFs) with a well-defined pore size and high stability in water that can accomplish in situ inclusion of single-stranded (ss) and double-stranded (ds) DNA (21, 23, and 58 nt) and effective intracellular delivery (including two noncancerous and six cancerous cell lines). Fluorescence quenching experiments for single and double end-labeled ss- and ds-DNA support that the DNA sequences can be completely enveloped by the SOFs. Confocal laser scanning microscopy and flow cytometry reveal that five of the SOFs exhibit excellent delivery efficiencies that, in most of the studied cases, outperform the commercial standard Lipo2000, even at low SOF–nucleic acid ratios. In addition to high delivery efficiencies, the water-soluble, self-assembled SOF carriers have a variety of advantages, including convenient preparation, high stability, and in situ DNA inclusion, which are all critical for practical applications in nucleic acid delivery.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Application of wideband pulsed high-frequency EPR to molecular quantum spin science

This presentation provides an overview of a range of new applications in the area of molecular quantum spin science that are now possible at the US National High Magnetic Field Laboratory as a result of the development of a wideband, high-power 94 GHz pulsed EPR spectrometer. Here, this instrument allows true Fourier-transform detected experiments spanning a 1 GHz instantaneous bandwidth, akin to what has been possible in NMR for several decades. The presentation will begin by describing experiments on a nitroxide radical using chirped pulses, enabling acquisition of the full spectrum in a single sequence, thus providing a very efficient and convenient means to measure the field orientation dependence of the spin-lattice relaxation time, T 1 . This will be followed by a discussion of a coherent population transfer protocol involving the 2S + 1 = 8 Zeeman levels associated with the spin S = 7/2 Gd 3+ ion, potentially paving the way towards implementation of well-known quantum search algorithms. It will also be shown how the use of chirped pulses provides a route to achieving highly non-thermal spin populations, suggesting novel initialization schemes.

47 OTHER INSTRUMENTATION↗

DOE OSTI2021

Expanding standards in viromics: in silico evaluation of dsDNA viral genome identification, classification, and auxiliary metabolic gene curation

Viruses influence global patterns of microbial diversity and nutrient cycles. Though viral metagenomics (viromics), specifically targeting dsDNA viruses, has been critical for revealing viral roles across diverse ecosystems, its analyses differ in many ways from those used for microbes. To date, viromics benchmarking has covered read pre-processing, assembly, relative abundance, read mapping thresholds and diversity estimation, but other steps would benefit from benchmarking and standardization. Here we use in silico-generated datasets and an extensive literature survey to evaluate and highlight how dataset composition (i.e., viromes vs bulk metagenomes) and assembly fragmentation impact (i) viral contig identification tool, (ii) virus taxonomic classification, and (iii) identification and curation of auxiliary metabolic genes (AMGs). The in silico benchmarking of five commonly used virus identification tools show that gene-content-based tools consistently performed well for long (≥3 kbp) contigs, while k -mer- and blast-based tools were uniquely able to detect viruses from short (≤3 kbp) contigs. Notably, however, the performance increase of k -mer- and blast-based tools for short contigs was obtained at the cost of increased false positives (sometimes up to ~5% for virome and ~75% bulk samples), particularly when eukaryotic or mobile genetic element sequences were included in the test datasets. Furthermore, for viral classification, variously sized genome fragments were assessed using gene-sharing network analytics to quantify drop-offs in taxonomic assignments, which revealed correct assignations ranging from ~95% (whole genomes) down to ~80% (3 kbp sized genome fragments). A similar trend was also observed for other viral classification tools such as VPF-class, ViPTree and VIRIDIC, suggesting that caution is warranted when classifying short genome fragments and not full genomes. Finally, we highlight how fragmented assemblies can lead to erroneous identification of AMGs and outline a best-practices workflow to curate candidate AMGs in viral genomes assembled from metagenomes. Together, these benchmarking experiments and annotation guidelines should aid researchers seeking to best detect, classify, and characterize the myriad viruses ‘hidden’ in diverse sequence datasets.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Enhancing strontium clock atom interferometry using quantum optimal control

Strontium clock atom interferometry is a promising new technology, with multiple experiments under development around the world to explore its potential for dark matter and gravitational wave detection. In these detectors, large momentum transfer using sequences of many laser pulses is necessary, and thus high-fidelity pulses are important since small errors become magnified. Quantum optimal control (QOC) is a framework for developing control pulse waveforms that achieve high fidelity and are robust against experimental imperfections. Resonant single-photon transitions using the narrow clock transition of strontium involve significantly different quantum dynamics than more established atom interferometry methods based on far-detuned two-photon Raman or Bragg transitions, which leads to new opportunities and challenges when applying QOC. Here, we study in simulation QOC pulses for strontium clock interferometry and demonstrate their advantage over basic square pulses (primitive pulses) and composite pulses in terms of robustness against multiple noise channels. In conclusion, this could improve the scale of large momentum transfer in Sr clock interferometers, paving the way to achieving these scientific goals.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2017

Systems level insights into alternate methane cycling modes phase II: deciphering mechanistic details of interspecies cooperation through manipulation of model microbial communities. Final Technical Report

Activities from this DOE sponsored project can be divided into three broad areas: (1) Isolation, characterization and sequencing of genomes of novel model organisms representing species active in methane oxidation, as judged from prior functional metagenomics-based experiments; (2) Manipulation of natural communities consuming methane, followed by observation on community dynamics and species succession, under specific environmental pressures such as variable O 2 and methane concentrations; and (3) Development of synthetic community models, from simple to complex, followed by observations on community dynamics and transcript and metabolite patterns. From these efforts, we have established several dozen novel model organisms representing different types of methane-utilizing species, different types of methylotrophic non-methane-utilizing guilds, as well as non-methylotrophic heterotrophs of different types, all with sequenced and manually curated genome annotations. From manipulation of natural sediment communities under controlled environmental conditions, we have deduced prominent species dynamics patterns and identified most important players in methane metabolism. We have also observed specific patterns in functional partnerships. Based on the discoveries from natural community manipulations, we have established model synthetic communities, ranging from simple, two-species, to complex, 50-species synthetic communities. The patterns from manipulation of synthetic communities were compared to the ones from natural communities. Synthetic communities were also characterized in terms of differential gene expression in response to community living, highlighting the role of alternative methanol dehydrogenases in community function. These observations were further validated through targeted metabolomics, identifying methanol as one major metabolite shared among community members.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Kinetic and X-ray Absorption Spectroscopic Analysis of Catalytic Redox Cycles over Highly Uniform Polymetal Oxo Clusters

Metal–organic framework materials (MOFs) offer an opportunity for investigating catalytic properties of polymetal oxo clusters that are highly well defined and uniform in nature, in contrast to other classes of catalysts that may exhibit a propensity toward active site heterogeneity. We report herein a kinetic and X-ray absorption spectroscopy (XAS) analysis of the two-electron oxidation of CO over divalent metal sites in MIL-100(M = Fe, Cr) (MIL = Materials of Institut Lavoisier) materials carrying μ 3 -oxo bridged trimers, and connect observations about the kinetic relevance of redox steps to density functional theory (DFT) predictions published previously. The high degree of uniformity evident from in situ titration measurements leads to a congruence in mechanistic inferences made from steady-state catalytic, transient stoichiometric, isotopic exchange, and isotopic tracer data that all point to a sequential mechanism comprised of separate oxidation and reduction half-cycle steps conjoined by an active oxygen intermediate. In situ XAS data reinforce mechanistic conclusions derived from kinetic analysis, and suggest that the active oxygen intermediate may be more appropriately characterized as an iron-oxyl (Fe 3+ –O – ) rather than an iron-oxo (Fe 4+ =O 2– ) species. The Cr analogue of MIL-100 exhibits contrasting rate features that can be rationalized using an identical sequence of steps as MIL-100(Fe), but with a highly dissimilar set of kinetic parameters that can also be validated using transient stoichiometric experiments. The larger coverages of active oxygen intermediates on MIL-100(Cr) are consistent with predictions from prior DFT studies that suggest more stable and less reactive active oxygen species for metals with lower d-electron counts, and point to metal identity as a lever for precisely controlling the kinetic relevance of oxidation and reduction half-cycles in catalytic redox sequences over polymetal oxo clusters. Importantly, the results presented point to the utility of developing broadly applicable structure–catalytic property relationships over MOF nodes specifically, and highly uniform catalysts more generally.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Reduced Late Bombardment on Rocky Exoplanets around M Dwarfs

Ocean-vaporizing impacts of chemically reduced planetesimals onto the early Earth have been suggested to catalyze atmospheric production of reduced nitrogen compounds and trigger prebiotic synthesis despite an oxidized lithosphere. While geochemical evidence supports a dry, highly reduced late veneer on Earth, the composition of late-impacting debris around lower-mass stars is subject to variable volatile loss as a result of their hosts' extended pre-main-sequence phase. We perform simulations of late-stage planet formation across the M-dwarf mass spectrum to derive upper limits on reducing bombardment epochs in Hadean-analog environments. We contrast the solar system scenario with varying initial volatile distributions due to extended primordial runaway greenhouse phases on protoplanets and the desiccation of smaller planetesimals by internal radiogenic heating. We find a decreasing rate of late-accreting reducing impacts with decreasing stellar mass. Young planets around stars ≤0.4 M ⊙ experience no impacts of sufficient mass to generate prebiotically relevant concentrations of reduced atmospheric compounds once their stars have reached the main sequence. For M-dwarf planets to not exceed Earth-like concentrations of volatiles, both planetesimals, and larger protoplanets must undergo extensive devolatilization processes and can typically emerge from long-lived magma ocean phases with sufficient atmophile content to outgas secondary atmospheres. Our results suggest that transiently reducing surface conditions on young rocky exoplanets are favored around FGK stellar types relative to M dwarfs.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2024

Pebble Tanker Model for Nuclear Criticality Safety Needs

This report documents a study performed to investigate the requirements for criticality safety benchmark experiments for high-assay, low-enriched uranium (HALEU) fuel in transportation applications. In this work, an exploratory application model, the “Pebble Tanker,” was developed to represent TRISO fuel in a transportation scenario for an analysis of the validation basis in industrial quantities. An aspect of the criticality validation process involves assessing the “similarity” between application and experimental benchmark systems through an integral index parameter evaluation. Here, this includes propagating nuclear data uncertainties and calculating a correlation coefficient (hereinafter referred to as “c k ”) to evaluate the similarity of benchmark experiments compared with the application Pebble Tanker model. Finding sufficient critical benchmark experiments allows for the evaluation of bias and bias uncertainty, thus determining the upper subcritical limit (USL) of the transportation package. A target k eff of ~0.94 was used in this work to establish appropriate modeling conditions, reflecting a reasonable estimate for a USL. Two container models were investigated: one with the Hermes-type pebble and one with the Pebble Bed Modular Reactor (PBMR)–type pebble. The models were simplified, considering only fuel, containment structure, and either water or air. This allows a focus on the underlying physics of applications involving TRISO fuel pebbles using the Pebble Tanker model. A crucial consideration is the transport package's ability to safely hold pebbles while flooded, maintaining subcritical conditions. Tools available in the SCALE 6.3.1 suite—the CSAS6-Shift, TSUNAMI-3D-Shift, and TSUNAMI-IP sequences—were employed for neutronics and sensitivity and uncertainty (S/U) analysis of the Pebble Tanker. Findings demonstrated sufficient available critical experiment benchmarks to perform a validation of the Pebble Tanker in the most reactive state, i.e., when the Tanker is flooded.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2025

Design of Experiments for Dynamic Test Runs in Solvent-Based CO 2 Capture Pilot Plants

Test runs in the pilot plants consume significant resources, and therefore, the learning from test runs should be maximized. Test runs conducted in the pilot plants are often steady state. It takes several hours for reaching steady-state in the pilot plants, and thus, the duration of the test runs needs to be long even for collecting few steady-state data points. On the other hand, a large number of measurements can be collected through dynamic test runs in a short span of time. This paper presents a systematic design of dynamic experiments (DoDEs) for identifiability of model parameters, which is achieved by persistently exciting the inputs signals. A pseudorandom binary sequence (PRBS) is designed as the input signal for DoDE due to its efficiency in obtaining sufficient spectral content. However, due to the long sequence size of the PRBS signal, a Schroeder-phase input signal, which is a multisine signal, is also designed. Tests for both types of signals are run in the Pilot Solvent Test Unit (PSTU) at the National Carbon Capture Center in Wilsonville, Alabama. The transient data are used to solve dynamic data reconciliation and parameter estimation problem. The estimated parameters are found to be not only superior to those estimated from using data collected from hundreds of steady-state test runs in a nonreactive (air–water) system, but the parameters could be estimated by using the dynamic data collected for about 24 h from the pilot plant for the MEA-H 2 O–CO 2 system.

CO2 capture↗

DOE OSTI2019

India National Gas Hydrate Program Expedition 02 Summary of Scientific Results: Numerical Simulation of Reservoir Response to Depressurization

The India National Gas Hydrate Program Expedition 02 (NGHP-02) discovered gas hydrate at high saturation in sand reservoirs at several sites in the deepwater Bay of Bengal. To assess the potential response of those deposits to scientific depressurization experiments, comprehensive geologic models were constructed to enable numerical simulation for two sites. Both sites (NGHP-02-09 and NGHP-02-16) feature thick sequences of thinly-interbedded reservoir and non-reservoir facies at sub-seafloor depths less than 300m and sub-sea depths of 2400m or more. These settings pose significant challenges to current modeling capabilities. First, the thinly-interbedded reservoir architecture complicates the determination of basic reservoir parameters from both log and core data due to measurement resolution issues. Secondly, the fine scale variation in sediment properties imparts great contrasts in key parameters over very short distances, creating high gradients at multiple scales and varying orientations that necessitate careful design of high-definition simulation grids. Thirdly, the deposits include internal sources of water, as well as a range of complex boundary conditions, including variable permeability within the overlying mud-rich “seals,” that complicate reservoir depressurization. Lastly, because of the unique combination of great water depth and relatively shallow sub-seafloor depth: models designed to maximize the dissociation rate impose large pressure drawdowns on relatively low-strength sediments. This condition renders the proper evaluation and integration of the geomechanical response to hydrate dissociation critical. In this report, we review the history of gas hydrate reservoir simulation, discuss methods for creating geologic input models, and summarize the key findings and implications of the collaborative NGHP-02 numerical simulation effort. Together, the studies confirm the viability of the modeled accumulations for scientific testing and identify key challenges related to the selection of specific test sites and the design of test wells.

Boswell, Ray↗

DOE OSTI2025

Short-term warming increased soil heterotrophic respiration due to enhanced active microbial community

Soil microbes, particularly active microbes, play a crucial role in conserving soil carbon under climate change, especially in forest ecosystems, constituting over 50% of global soil organic carbon. Nevertheless, the response mechanisms of active microbial community to climate warming and their subsequent impacts on soil heterotrophic respiration (Rh) remain insufficiently understood. To resolve this mechanistic uncertainty, we implemented a 3-year soil translocation experiment to investigate soil warming effects on active microbial community and Rh. We used 16S rRNA gene amplicon sequencing, Metatranscriptomics sequencing, coupled with correlation analyses to explore the linkages between warming-induced shifts in Rh and the active microbial community. Our results demonstrated that warming of soil induced a 55% enhancement in Rh. Concurrently, the Shannon index and Richness of active microbial community increased by 20% and 117%, respectively. Warming significantly altered active microbial community composition, inducing a compositional shift characterized by 0.5-to 2-fold increases in the abundances of Proteobacteria, Chloroflexi, and Actinobacteria. Our study also revealed 92–100% increases in the abundance of C-degradation functional genes encoding starch, cellulose, and lignin decomposition pathways within active microbial community under warming. Statistical analyses identified significant positive correlations between Rh and the abundance of Proteobacteria and Actinobacteria, as well as expression levels of functional genes associated with lignin and cellulose decomposition pathways. Furthermore, our results suggested that short-term warming increased Rh through altering diversity, species composition, and C degradation functional genes of active microbial community providing insights into the influence of microbial communities on soil C-climate feedbacks under climate warming.

Active microbial community↗

DOE OSTI2019

Many-Body Effects Determine the Local Hydration Structure of Cs+ in Solution

A systematic analysis of the hydration structure of Cs+ ions in solution is derived from simulations carried out using a series of molecular models built upon a hierarchy of approximate representations of many-body effects in ion-water interactions. It is found that a pairwise-additive model, commonly used in biomolecular simulations, provides poor agreement with experimental X-ray spectra, indicating an incorrect description of the underlying hydration structure. Although the agreement with experiment improves in simulations with a polarizable model, the predicted hydration structure is found to lack the correct sequence of water shells. Progressive inclusion of explicit many- body effects in the representation of Cs+-water interactions as well as account for nuclear quantum effects is shown to be necessary for quantitatively reproducing the experimental spectra. Besides emphasizing the importance of many-body effects, these results suggests that molecular models rigorously derived from many-body expansions hold promise for realistic simulations of aqueous solutions. Work by J.L.F. and G.K.S. was supported by the U.S. Department of Energy (DOE), Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for DOE by Battelle.

Zhuang, Debbie↗