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Kumar, Amit

Publications and source records attributed to Kumar, Amit.

At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Necromass responses to warming: A faster microbial turnover in favor of soil carbon stabilisation

Microbial byproducts and residues (hereafter ‘necromass’) potentially play the most critical role in soil organic carbon (SOC) sequestration. However, little is known about the influence of climate warming on necromass accumulation in the agroecosystem and the underlying mechanisms associated with microbial life strategies. Here, in order to address these knowledge gaps, we used amino sugars as biomarkers of microbial necromass, and investigated their variation through an 8-year trial in an agroecosystem with two warming levels (+1.6 and + 3.2 °C) compared to ambient temperature. The results showed that the lower warming level had no impact on total microbial necromass carbon. Conversely, warming the soil 3.2 °C above ambient increased total microbial necromass by 17 % and its contribution to SOC by 21.3 %, mainly by increasing fungal necromass (+19.8 %), whereas +3.2 °C warming had no impact on bacterial necromass. At the phylum level, compared with the ambient control, +3.2 °C warming induced an increase in the abundance of Proteobacteria and a decrease in both Acidobacteria and Actinobacteria, whereas in the fungal community, Ascomycota increased and Mortierellomycota decreased. This indicates that r-strategists outcompete K-strategists in warmer climates, which led to increased microbial necromass production and accumulation, as supported by the positive correlation between r-strategists and microbial necromass. Stronger microbial competition for resources also resulted in a higher biomass turnover rate, greater cell death, and greater production of microbial necromass. This was supported by the lower bacterial and fungal network complexity and trophic links under warming conditions. In addition, the necromass generated from accelerated microbial turnover further offsets warming-induced deceases in microbial biomass. Consequently, bulk SOC did not change, despite microbial necromass having a much greater response to warming than the soil C pool. Therefore, future climate warming may influence the composition and persistence of SOC during microbial degradation.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Predictions for the sPHENIX physics program

sPHENIX is a next-generation detector experiment at the Relativistic Heavy Ion Collider, designed for a broad set of jet and heavy-flavor probes of the Quark-Gluon Plasma created in heavy ion collisions. In anticipation of the commissioning and first data-taking of the detector in 2023, a RIKEN-BNL Research Center (RBRC) workshop was organized to collect theoretical input and identify compelling aspects of the physics program. Here this paper compiles theoretical predictions from the workshop participants for jet quenching, heavy flavor and quarkonia, cold QCD, and bulk physics measurements at sPHENIX.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

Targeted inhibition of MASTL kinase activity induces apoptosis in breast cancer

Microtubule-associated serine/threonine kinase-like (MASTL) (or Greatwall kinase (GWL)) is an important cell cycle regulating kinase that regulates the G2-M transition. Uncontrolled MASTL activity is implicated in breast cancer progression. To date, very few inhibitors have been reported against this protein. Here, structure-based computational modeling indicates that the natural product flavopiridol (FLV) binds strongly to MASTL and these results are validated using molecular dynamics simulation studies. Further, an in vitro kinase assay reveals an EC 50 (effective concentration) value of FLV to be 82.1 nM and a better IC 50 compared to the positive reference compound, staurosporine. FLV is found to inhibit MASTL kinase activity, arresting the cell growth in the G1 phase and inducing apoptosis in breast cancer cells. Consistent with these results differential gene expression obtained using RNA sequencing studies, and validated by RT PCR and immunoblot analysis, indicate that MASTL inhibition induces cell cycle arrest and apoptotic-related genes. Furthermore, metastasis- and inflammation- related genes are downregulated. Thus, the deregulation of MASTL signaling pathways on targeted inhibition of its kinase activity is revealed. This study lays a strong foundation for investigating FLV as a lead compound in breast cancer therapeutics.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Origin of magnetic ordering in half-Heusler RuMnGa

The half-Heusler alloy RuMnGa having valence electron count (VEC) 18 has recently been theoretically proposed to exhibit compensated ferrimagnetic (CFiM) character instead of the expected nonmagnetic ground state. On the other hand, a preliminary experimental study proposed ferromagnetic (FM) ordering. As no half-Heusler system with VEC 18 is known to exhibit magnetic ordering, we have investigated the details of crystal structure and magnetic properties of RuMnGa using a combination of experimental tools, viz., x-ray and neutron diffraction techniques, dc and ac susceptibility, isothermal magnetization, heat capacity, resistivity and neutron depolarisation measurements. Rietveld refinements of x-ray and neutron diffraction data suggest single phase nature of the compound with elemental composition RuMn 0.86 Ga 1.14 . We have shown that the system exhibits FM-type ordering owing to the inherent presence of this minor off-stoichiometry, showing very low magnetic moment. Further, the system also exhibits reentrant canonical spin-glass behavior, which is rarely observed in half-Heusler alloys. The temperature coefficient of resistivity changes its sign from negative to positive and further to negative as the temperature decreases.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

4 d element induced improvement of structural disorder and development of weakly reentrant spin-glass behavior in NiRuMnSn

The pursuit of efficient spin polarization in quaternary Heusler alloys with the general formula XX'YZ (where X, X', and Y are transition metals and Z is a p-block element) has been a subject of significant scientific interest. While previous studies showed that isoelectronic substitution of a 4d element in place of a 3d element in quaternary Heusler alloys improves the half-metallic ferromagnetic characteristics, our research here, on the quaternary Heusler alloy NiRuMnSn, reveals a strikingly different scenario. In this study, we present a detailed structural analysis of the material using x-ray absorption fine structure and neutron diffraction techniques which confirms the formation of a single-phase compound with 50:50 site disorder between Ni and Ru atoms at 4c and 4d sites. Contrary to expectations, our density functional theory calculations suggest a considerable decrease in spin polarization even in the ordered structure. Additionally, we report on the compound's exceptional behavior, displaying a rare reentrant spin-glass property below ~ 60 K, a unique and intriguing feature for quaternary Heusler-type compounds.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Experimental observation of spin glass state in the highly disordered quaternary Heusler alloy FeRuMnGa

The realization of the spin-glass (SG) state in Heusler alloys is very rare despite the presence of inherent structural and elemental disorder in those compounds. Although a few half- and full-Heusler alloys are known to exhibit the SG state, there is hardly any manifestation of the same in cases of quaternary Heusler compounds. Here we report the observation of a SG state in a highly disordered equiatomic quaternary Heusler compound: FeRuMnGa where the SG state is in between the canonical SG and the cluster glass. Different intricate features of the SG state including nonequilibrium magnetic dynamics at low temperatures in the compound are unveiled through our comprehensive magnetic, heat capacity, and neutron-diffraction studies. Further the structural disorder in the sample is neither conventional A2 - nor B2 -type whereas those two types are commonly observed for Heusler compounds. The presence of disorder also plays a significant role in electron transport properties of the alloy, which is reflected in its exhibition of semimetallic behavior and anomalous Hall effect at low temperatures.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Microbial necromass in cropland soils: A global meta-analysis of management effects

Microbial necromass is a large and persistent component of soil organic carbon (SOC), especially under croplands. The effects of cropland management on microbial necromass accumulation and its contribution to SOC have been measured in individual studies but have not yet been summarized on the global scale. For this study, we conducted a meta-analysis of 481-paired measurements from cropland soils to examine the management effects on microbial necromass and identify the optimal conditions for its accumulation. Nitrogen fertilization increased total microbial necromass C by 12%, cover crops by 14%, no or reduced tillage (NT/RT) by 20%, manure by 21%, and straw amendment by 21%. Microbial necromass accumulation was independent of biochar addition. NT/RT and straw amendment increased fungal necromass and its contribution to SOC more than bacterial necromass. Manure increased bacterial necromass higher than fungal, leading to decreased ratio of fungal-to-bacterial necromass. Greater microbial necromass increases after straw amendments were common under semi-arid and in cool climates in soils with pH <8, and were proportional to the amount of straw input. In contrast, NT/RT increased microbial necromass mainly under warm and humid climates. Manure application increased microbial necromass irrespective of soil properties and climate. Management effects were especially strong when applied during medium (3–10 years) to long (10+ years) periods to soils with larger initial SOC contents, but were absent in sandy soils. Close positive links between microbial biomass, necromass and SOC indicate the important role of stabilized microbial products for C accrual. Microbial necromass contribution to SOC increment (accumulation efficiency) under NT/RT, cover crops, manure and straw amendment ranged from 45% to 52%, which was 9%–16% larger than under N fertilization. In summary, long-term cropland management increases SOC by enhancing microbial necromass accumulation, and optimizing microbial necromass accumulation and its contribution to SOC sequestration requires site-specific management.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

A single, improbable B cell receptor mutation confers potent neutralization against cytomegalovirus

Cytomegalovirus (CMV) is a leading cause of infant hearing loss and neurodevelopmental delay, but there are no clinically licensed vaccines to prevent infection, in part due to challenges eliciting neutralizing antibodies. One of the most well-studied targets for CMV vaccines is the viral fusogen glycoprotein B (gB), which is required for viral entry into host cells. Within gB, antigenic domain 2 site 1 (AD-2S1) is a target of potently neutralizing antibodies, but gB-based candidate vaccines have yet to elicit robust responses against this region. We mapped the genealogy of B cells encoding potently neutralizing anti-gB AD-2S1 antibodies from their inferred unmutated common ancestor (UCA) and characterized the binding and function of early lineage ancestors. Surprisingly, we found that a single amino acid heavy chain mutation A33N, which was an improbable mutation rarely generated by somatic hypermutation machinery, conferred broad CMV neutralization to the non-neutralizing UCA antibody. Structural studies revealed that this mutation mediated key contacts with the gB AD-2S1 epitope. Collectively, these results provide insight into potently neutralizing gB-directed antibody evolution in a single donor and lay a foundation for using this B cell-lineage directed approach for the design of next-generation CMV vaccines.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Ferrielectricity in the Archetypal Antiferroelectric, PbZrO 3

Antiferroelectric materials, where the transition between antipolar and polar phase is controlled by external electric fields, offer exceptional energy storage capacity with high efficiencies, giant electrocaloric effect, and superb electromechanical response. PbZrO 3 is the first discovered and the archetypal antiferroelectric material. Nonetheless, substantial challenges in processing phase pure PbZrO 3 have limited studies of the undoped composition, hindering understanding of the phase transitions in this material or unraveling the controversial origins of a low-field ferroelectric phase observed in lead zirconate thin films. Here, leveraging highly oriented PbZrO 3 thin films, a room-temperature ferrielectric phase is observed in the absence of external electric fields, with modulations of amplitude and direction of the spontaneous polarization and large anisotropy for critical electric fields required for phase transition. The ferrielectric state observations are qualitatively consistent with theoretical predictions, and correlate with very high dielectric tunability, and ultrahigh strains (up to 1.1%). This work suggests a need for re-evaluation of the fundamental science of antiferroelectricity in this archetypal material.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Strengthening of enterococcal biofilms by Esp

Multidrug-resistant (MDR) Enterococcus faecalis are major causes of hospital-acquired infections. Numerous clinical strains of E . faecalis harbor a large pathogenicity island that encodes enterococcal surface protein (Esp), which is suggested to promote biofilm production and virulence, but this remains controversial. To resolve this issue, we characterized the Esp N-terminal region, the portion implicated in biofilm production. Small angle X-ray scattering indicated that the N-terminal region had a globular head, which consisted of two DEv-Ig domains as visualized by X-ray crystallography, followed by an extended tail. The N-terminal region was not required for biofilm production but instead significantly strengthened biofilms against mechanical or degradative disruption, greatly increasing retention of Enterococcus within biofilms. Biofilm strengthening required low pH, which resulted in Esp unfolding, aggregating, and forming amyloid-like structures. The pH threshold for biofilm strengthening depended on protein stability. A truncated fragment of the first DEv-Ig domain, plausibly generated by a host protease, was the least stable and sufficient to strengthen biofilms at pH ≤ 5.0, while the entire N-terminal region and intact Esp on the enterococcal surface was more stable and required a pH ≤ 4.3. These results suggested a virulence role of Esp in strengthening enterococcal biofilms in acidic abiotic or host environments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

The Signatures of Self-interacting Dark Matter and Subhalo Disruption on Cluster Substructure

The abundance, distribution, and inner structure of satellites of galaxy clusters can be sensitive probes of the properties of dark matter. We run 30 cosmological zoom-in simulations with self-interacting dark matter (SIDM), with a velocity-dependent cross section, to study the properties of subhalos within cluster-mass hosts. We find that the abundance of subhalos that survive in the SIDM simulations are suppressed relative to their cold dark matter (CDM) counterparts. Once the population of disrupted subhalos—which may host orphan galaxies—is taken into account, satellite galaxy populations in CDM and SIDM models can be reconciled. However, even in this case, the inner structures of subhalos are significantly different in the two dark matter models. We study the feasibility of using the weak-lensing signal from the subhalo density profiles to distinguish between the cold and self-interacting dark matter while accounting for the potential contribution of orphan galaxies. We find that the effects of self-interactions on the density profile of subhalos can appear degenerate with subhalo disruption in CDM, when orphans are accounted for. With current error bars from the Subaru Hyper Suprime-Cam Strategic Program, we find that subhalos in the outskirts of clusters (where disruption is less prevalent) can be used to constrain dark matter physics. In the future, the Vera C. Rubin Observatory Legacy Survey of Space and Time will give precise measurements of the weak-lensing profile and can be used to constrain σ $_{T}$/m at the ∼1 cm$^{2}$ g$^{−1}$ level at v ∼ 2000 km s$^{−1}$.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

What are mycorrhizal traits?

Traits are inherent properties of organisms, but how are they defined for organismal networks such as mycorrhizal symbioses? Mycorrhizal symbioses are complex and diverse belowground symbioses between plants and fungi that have proved challenging to fit into a unified and coherent trait framework. Here we propose an inclusive mycorrhizal trait framework that classifies traits as morphological, physiological, and phenological features that have functional implications for the symbiosis. We further classify mycorrhizal traits by location – plant, fungus, or the symbiosis – which highlights new questions in trait-based mycorrhizal ecology designed to charge and challenge the scientific community. This new framework is an opportunity for researchers to interrogate their data to identify novel insights and gaps in our understanding of mycorrhizal symbioses.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Revealing the Influence of Diverse Secondary Metal Cations on Redox-Active Palladium Complexes

Incorporation of redox-inactive metals into redox-active complexes and catalysts attracts attention for engendering new reactivity modes, but this strategy has not been extensively investigated beyond the first-row of the transition metals. In this report the isolation and characterization of the first series of heterobimetallic complexes of palladium with mono-, di-, and tri-valent redox-inactive metal ions are reported. A Reinhoudt-type heteroditopic ligand with a salen-derived [N 2 ,O 2 ] binding site for Pd and a crown-ether-derived [O 6 ] site has been used to prepare isolable adducts of the Lewis acidic redox-inactive metal ions (M n+ ). Comprehensive data from single-crystal X-ray diffraction analysis reveal distinctive trends in the structural properties of the heterobimetallic species, including an uncommon dependence of the Pd … M distance on Lewis acidity. The reorganization energy associated with reduction of the heterobimetallic species is strongly modulated by Lewis acidity, with the slowest heterogeneous electron transfer kinetics associated with the strongest incorporated Lewis acids. This hitherto unexplored reorganization energy penalty for electron transfer contrasts with prior thermodynamic studies, revealing that kinetic parameters should be considered in studies of reactivity involving heterobimetallic species.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Promotion and Tuning of the Electrochemical Reduction of Hetero‐ and Homobimetallic Zinc Complexes**

Abstract Compounds containing multiple metals attract significant interest due to the useful redox and reactivity properties of such species. Here, the electrochemical properties of a family of macrocyclic complexes that feature a zinc(II) center paired with a secondary redox‐inactive metal cation in heterobimetallic (Na + , Ca 2+ , Nd 3+ , Y 3+ ) motifs or homobimetallic (Zn 2+ ) motifs have been investigated. The new complexes were prepared via a divergent strategy, isolated, and structurally characterized with single‐crystal X‐ray diffraction (XRD) analysis. XRD results show that the structures of the complexes are modulated by the identity of the incorporated secondary metal ions. Cyclic voltammetry data reveal that ligand‐centered reduction is promoted in the bimetallic complexes and that the paired metal ions synergistically influence the redox properties of the complexes. Similar to prior work from our group and others, the bimetallic complexes containing stronger Lewis acids undergo more significant reduction potential shifts; contrasting with prior work on complexes containing redox‐active metals, however, the zinc(II) complexes studied here display faster electron transfer (as judged by lower reorganization energies, λ) when incorporating di‐ or tri‐valent Lewis acids in contrast to monovalent (and more weakly acidic) sodium. The quantified trends in these data offer insights that could help distinguish metal‐ versus ligand‐centered reduction of bimetallic complexes.

Kelsey, Shaun R.↗