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1. Unraveling the Role of Interfaces on the Spall Failure of Cu/Ta Multilayered Systems

   https://doi.org/10.1038/s41598-019-57048-9  

   Chen, Jie ; Mathaudhu, Suveen N. ; Thadhani, Naresh ; Dongare, Avinash M. ( January 2020 , Scientific Reports)

   Molecular dynamics (MD) simulations are carried out to investigate the effects of the type and spacing of FCC/BCC interfaces on the deformation and spall behavior. The simulations are carried out using model Cu/Ta multilayers with six different types of interfaces. The results suggest that interface type can significantly affect the structure and intensity of the incoming shock wave, change the activated slip systems, alter dislocation slip and twinning behavior, affect where and how voids are nucleated during spallation and the resulting spall strength. Moreover, the above aspects are significantly affected by the interface spacing. A transition from homogeneous to heterogeneous dislocation nucleation occurs as the interface spacing is decreased to 6 nm. Depending on interface type and spacing, damage (voids) nucleation and spall failure is observed to occur not only at the Cu/Ta interfaces, but also in the weaker Cu layer interior, or even in the stronger Ta layer interior, although different mechanisms underlie each of these three distinct failure modes. These findings point to the fact that, depending on the combination of interface type and spacing, interfaces can lead to both strengthening and weakening of the Cu/Ta multilayered microstructures.

    

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2. Tailoring compositionally graded interface of 316L stainless steel to Al12Si aluminum alloy bimetallic structures via Additive Manufacturing

   https://doi.org/doi.org/10.1021/acsami.0c21478  

   Zhang, Yanning ; Bandyopadhyay, Amit ( February 2021 , ACS applied materials interfaces)

   null (Ed.)

   316L stainless steel (SS) to Al12Si aluminum alloy structures were processed, tailoring the compositionally graded interface on a SS 316 substrate using a directed energy deposition (DED)-based additive manufacturing (AM) process. Applying such a compositionally graded transition on bimetallic materials, especially joining two dissimilar metals, could avoid the mechanical property mismatch. This study's objective was to understand the processing parameters that influence the properties of AM processed SS 316L to Al12Si bimetallic structures. Two different approaches fabricated these bimetallic structures. The results showed no visible defects on the as-fabricated samples using 4 layers of Al-rich mixed composition as the transition section. The microstructural characterization showed a unique morphology in each section. Both cooling rate and compositional variations caused microstructural variation. FeAl, Fe2Al5, and FeAl3 intermetallic phases were formed at the compositionally graded transition section. After stress relief heat-treatment of SS 316L/Al12Si bimetallic samples, diffused intermetallic phases were seen at the compositionally graded transition. At the interface, as processed, bimetallic structures had a microhardness value of 834.2 ± 107.1 HV0.1, which is a result of the FeAl3 phase at the compositionally graded transition area. After heat-treatment, the microhardness value reduced to 578.7 ± 154.1 HV0.1 due to more Fe dominated FexAly phase formation. The compression test results showed that the non-HT and HT SS 316L/Al12Si bimetallic structures had a similar maximum compressive strength of 299.4 ± 22.1 MPa and 270.1 ± 27.1 MPa, respectively. 

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3. A threonine zipper that mediates protein–protein interactions: Structure and prediction

   https://doi.org/10.1002/pro.3505  

   Oi, Curran ; Treado, John D. ; Levine, Zachary A. ; Lim, Christopher S. ; Knecht, Kirsten M. ; Xiong, Yong ; O'Hern, Corey S. ; Regan, Lynne ( October 2018 , Protein Science)

   We present the structure of an engineered protein–protein interface between two beta barrel proteins, which is mediated by interactions between threonine (Thr) residues. This Thr zipper structure suggests that the protein interface is stabilized by close‐packing of the Thr residues, with only one intermonomer hydrogen bond (H‐bond) between two of the Thr residues. This Thr‐rich interface provides a unique opportunity to study the behavior of Thr in the context of many other Thr residues. In previous work, we have shown that the side chain (χ₁) dihedral angles of interface and core Thr residues can be predicted with high accuracy using a hard sphere plus stereochemical constraint (HS) model. Here, we demonstrate that in the Thr‐rich local environment of the Thr zipper structure, we are able to predict theχ₁dihedral angles of most of the Thr residues. Some, however, are not well predicted by the HS model. We therefore employed explicitly solvated molecular dynamics (MD) simulations to further investigate the side chain conformations of these residues. The MD simulations illustrate the role that transient H‐bonding to water, in combination with steric constraints, plays in determining the behavior of these Thr side chains.

   Broader Audience Statement: Protein–protein interactions are critical to life and the search for ways to disrupt adverse protein–protein interactions involved in disease is an ongoing area of drug discovery. We must better understand protein–protein interfaces, both to be able to disrupt existing ones and to engineer new ones for a variety of biotechnological applications. We have discovered and characterized an artificial Thr‐rich protein–protein interface. This novel interface demonstrates a heretofore unknown property of Thr‐rich surfaces: mediating protein–protein interactions.

    

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4. Insights into the thermomechanical and interfacial behaviors of polymer‐clay nanocomposites via coarse‐grained molecular dynamics simulations

   https://doi.org/10.1002/pc.28357  

   Nie, Wenjian ; Liao, Yangchao ; Ghazanfari, Sarah ; Wang, Yang ; Wang, Xingyu ; Huang, Ying ; Xia, Wenjie ( March 2024 , Polymer Composites)

   Polymer‐clay nanocomposites (PCNs) are commonly applied as multi‐functional structural materials with exceptional thermomechanical properties, while maintaining the characteristics of lightweight and optical clarity. In this study, building upon previously developed coarse‐grained (CG) models for nanoclay and poly (methyl methacrylate) (PMMA), we employ molecular dynamics (MD) simulations to systematically investigate the thermomechanical properties of PCNs when arranged in stacked configurations. Incorporating stacked clay nanofillers into a polymer matrix, we systematically conduct shear and tensile simulations to investigate the influences of variations in weight percentage, system temperature, and nanoclay size on the thermomechanical properties of PCNs at a fundamental level. The weight percentage of nanoclay in nanocomposites proves to have a significant influence on both the shear and Young's modulus (e.g., the addition of 10 Wt% nanoclay leads to an increase of 32.6% in the Young's modulus), with each exhibiting greater mechanical strength in the in‐plane direction compared to the out‐of‐plane direction, and the disparity between these two directions further widens with an increase in the weight percentage of nanoclay. Furthermore, the increase in the size of nanoclay contributes to an overall modulus enhancement in the composite while the growth reaches a saturation point after a certain threshold of about 10 nm. Our simulation results indicate that the overall dynamics of PMMA are suppressed due to the strong interactions between nanoclay and PMMA, where the confinement effect on local segmental dynamics of PMMA decays from the nanoclay‐polymer interface to the polymer matrix. Our findings provide valuable molecular‐level insights into microstructural and dynamical features of PCNs under deformation, emphasizing the pivotal role of clay‐polymer interface in influencing the thermomechanical properties of the composite materials.

   CG modeling is performed to explore the thermomechanical behavior of PCN.

   Effects of nanoclay weight percentage and size on modulus are studied.

   Interface leads to nanoconfinement effect onT_gand molecular stiffness.

   Correlations between molecular stiffness and modulus are identified.

   Simulations show spatial variation of dynamical heterogeneity.

    

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5. Florida mangrove saltmarsh reference surface soils

   https://doi.org/10.6073/pasta/0e08cbe07c84488cb7b9dd16669946d0  

   Lewis, David Bruce ( January 2021 , Environmental Data Initiative)

   Site description. This data package consists of data obtained from sampling surface soil (the 0-7.6 cm depth profile) in black mangrove (Avicennia germinans) dominated forest and black needlerush (Juncus roemerianus) saltmarsh along the Gulf of Mexico coastline in peninsular west-central Florida, USA. This location has a subtropical climate with mean daily temperatures ranging from 15.4 °C in January to 27.8 °C in August, and annual precipitation of 1336 mm. Precipitation falls as rain primarily between June and September. Tides are semi-diurnal, with 0.57 m median amplitudes during the year preceding sampling (U.S. NOAA National Ocean Service, Clearwater Beach, Florida, station 8726724). Sea-level rise is 4.0 ± 0.6 mm per year (1973-2020 trend, mean ± 95 % confidence interval, NOAA NOS Clearwater Beach station). The A. germinans mangrove zone is either adjacent to water or fringed on the seaward side by a narrow band of red mangrove (Rhizophora mangle). A near-monoculture of J. roemerianus is often adjacent to and immediately landward of the A. germinans zone. The transition from the mangrove to the J. roemerianus zone is variable in our study area. An abrupt edge between closed-canopy mangrove and J. roemerianus monoculture may extend for up to several hundred meters in some locations, while other stretches of ecotone present a gradual transition where smaller, widely spaced trees are interspersed into the herbaceous marsh. Juncus roemerianus then extends landward to a high marsh patchwork of succulent halophytes (including Salicornia bigellovi, Sesuvium sp., and Batis maritima), scattered dwarf mangrove, and salt pans, followed in turn by upland vegetation that includes Pinus sp. and Serenoa repens. Field design and sample collection. We established three study sites spaced at approximately 5 km intervals along the western coastline of the central Florida peninsula. The sites consisted of the Salt Springs (28.3298°, -82.7274°), Energy Marine Center (28.2903°, -82.7278°), and Green Key (28.2530°, -82.7496°) sites on the Gulf of Mexico coastline in Pasco County, Florida, USA. At each site, we established three plot pairs, each consisting of one saltmarsh plot and one mangrove plot. Plots were 50 m^2 in size. Plots pairs within a site were separated by 230-1070 m, and the mangrove and saltmarsh plots composing a pair were 70-170 m apart. All plot pairs consisted of directly adjacent patches of mangrove forest and J. roemerianus saltmarsh, with the mangrove forests exhibiting a closed canopy and a tree architecture (height 4-6 m, crown width 1.5-3 m). Mangrove plots were located at approximately the midpoint between the seaward edge (water-mangrove interface) and landward edge (mangrove-marsh interface) of the mangrove zone. Saltmarsh plots were located 20-25 m away from any mangrove trees and into the J. roemerianus zone (i.e., landward from the mangrove-marsh interface). Plot pairs were coarsely similar in geomorphic setting, as all were located on the Gulf of Mexico coastline, rather than within major sheltering formations like Tampa Bay, and all plot pairs fit the tide-dominated domain of the Woodroffe classification (Woodroffe, 2002, "Coasts: Form, Process and Evolution", Cambridge University Press), given their conspicuous semi-diurnal tides. There was nevertheless some geomorphic variation, as some plot pairs were directly open to the Gulf of Mexico while others sat behind keys and spits or along small tidal creeks. Our use of a plot-pair approach is intended to control for this geomorphic variation. Plot center elevations (cm above mean sea level, NAVD 88) were estimated by overlaying the plot locations determined with a global positioning system (Garmin GPS 60, Olathe, KS, USA) on a LiDAR-derived bare-earth digital elevation model (Dewberry, Inc., 2019). The digital elevation model had a vertical accuracy of ± 10 cm (95 % CI) and a horizontal accuracy of ± 116 cm (95 % CI). Soil samples were collected via coring at low tide in June 2011. From each plot, we collected a composite soil sample consisting of three discrete 5.1 cm diameter soil cores taken at equidistant points to 7.6 cm depth. Cores were taken by tapping a sleeve into the soil until its top was flush with the soil surface, sliding a hand under the core, and lifting it up. Cores were then capped and transferred on ice to our laboratory at the University of South Florida (Tampa, Florida, USA), where they were combined in plastic zipper bags, and homogenized by hand into plot-level composite samples on the day they were collected. A damp soil subsample was immediately taken from each composite sample to initiate 1 y incubations for determination of active C and N (see below). The remainder of each composite sample was then placed in a drying oven (60 °C) for 1 week with frequent mixing of the soil to prevent aggregation and liberate water. Organic wetland soils are sometimes dried at 70 °C, however high drying temperatures can volatilize non-water liquids and oxidize and decompose organic matter, so 50 °C is also a common drying temperature for organic soils (Gardner 1986, "Methods of Soil Analysis: Part 1", Soil Science Society of America); we accordingly chose 60 °C as a compromise between sufficient water removal and avoidance of non-water mass loss. Bulk density was determined as soil dry mass per core volume (adding back the dry mass equivalent of the damp subsample removed prior to drying). Dried subsamples were obtained for determination of soil organic matter (SOM), mineral texture composition, and extractable and total carbon (C) and nitrogen (N) within the following week. Sample analyses. A dried subsample was apportioned from each composite sample to determine SOM as mass loss on ignition at 550 °C for 4 h. After organic matter was removed from soil via ignition, mineral particle size composition was determined using a combination of wet sieving and density separation in 49 mM (3 %) sodium hexametaphosphate ((NaPO_3)_6) following procedures in Kettler et al. (2001, Soil Science Society of America Journal 65, 849-852). The percentage of dry soil mass composed of silt and clay particles (hereafter, fines) was calculated as the mass lost from dispersed mineral soil after sieving (0.053 mm mesh sieve). Fines could have been slightly underestimated if any clay particles were burned off during the preceding ignition of soil. An additional subsample was taken from each composite sample to determine extractable N and organic C concentrations via 0.5 M potassium sulfate (K_2SO_4) extractions. We combined soil and extractant (ratio of 1 g dry soil:5 mL extractant) in plastic bottles, reciprocally shook the slurry for 1 h at 120 rpm, and then gravity filtered it through Fisher G6 (1.6 μm pore size) glass fiber filters, followed by colorimetric detection of nitrite (NO_2^-) + nitrate (NO_3^-) and ammonium (NH_4^+) in the filtrate (Hood Nowotny et al., 2010,Soil Science Society of America Journal 74, 1018-1027) using a microplate spectrophotometer (Biotek Epoch, Winooski, VT, USA). Filtrate was also analyzed for dissolved organic C (referred to hereafter as extractable organic C) and total dissolved N via combustion and oxidation followed by detection of the evolved CO_2 and N oxide gases on a Formacs HT TOC/TN analyzer (Skalar, Breda, The Netherlands). Extractable organic N was then computed as total dissolved N in filtrate minus extractable mineral N (itself the sum of extractable NH_4-N and NO_2-N + NO_3-N). We determined soil total C and N from dried, milled subsamples subjected to elemental analysis (ECS 4010, Costech, Inc., Valencia, CA, USA) at the University of South Florida Stable Isotope Laboratory. Median concentration of inorganic C in unvegetated surface soil at our sites is 0.5 % of soil mass (Anderson, 2019, Univ. of South Florida M.S. thesis via methods in Wang et al., 2011, Environmental Monitoring and Assessment 174, 241-257). Inorganic C concentrations are likely even lower in our samples from under vegetation, where organic matter would dilute the contribution of inorganic C to soil mass. Nevertheless, the presence of a small inorganic C pool in our soils may be counted in the total C values we report. Extractable organic C is necessarily of organic C origin given the method (sparging with HCl) used in detection. Active C and N represent the fractions of organic C and N that are mineralizable by soil microorganisms under aerobic conditions in long-term soil incubations. To quantify active C and N, 60 g of field-moist soil were apportioned from each composite sample, placed in a filtration apparatus, and incubated in the dark at 25 °C and field capacity moisture for 365 d (as in Lewis et al., 2014, Ecosphere 5, art59). Moisture levels were maintained by frequently weighing incubated soil and wetting them up to target mass. Daily CO_2 flux was quantified on 29 occasions at 0.5-3 week intervals during the incubation period (with shorter intervals earlier in the incubation), and these per day flux rates were integrated over the 365 d period to compute an estimate of active C. Observations of per day flux were made by sealing samples overnight in airtight chambers fitted with septa and quantifying headspace CO_2 accumulation by injecting headspace samples (obtained through the septa via needle and syringe) into an infrared gas analyzer (PP Systems EGM 4, Amesbury, MA, USA). To estimate active N, each incubated sample was leached with a C and N free, 35 psu solution containing micronutrients (Nadelhoffer, 1990, Soil Science Society of America Journal 54, 411-415) on 19 occasions at increasing 1-6 week intervals during the 365 d incubation, and then extracted in 0.5 M K_2SO_4 at the end of the incubation in order to remove any residual mineral N. Active N was then quantified as the total mass of mineral N leached and extracted. Mineral N in leached and extracted solutions was detected as NH_4-N and NO_2-N + NO_3-N via colorimetry as above. This incubation technique precludes new C and N inputs and persistently leaches mineral N, forcing microorganisms to meet demand by mineralizing existing pools, and thereby directly assays the potential activity of soil organic C and N pools present at the time of soil sampling. Because this analysis commences with disrupting soil physical structure, it is biased toward higher estimates of active fractions. Calculations. Non-mobile C and N fractions were computed as total C and N concentrations minus the extractable and active fractions of each element. This data package reports surface-soil constituents (moisture, fines, SOM, and C and N pools and fractions) in both gravimetric units (mass constituent / mass soil) and areal units (mass constituent / soil surface area integrated through 7.6 cm soil depth, the depth of sampling). Areal concentrations were computed as X × D × 7.6, where X is the gravimetric concentration of a soil constituent, D is soil bulk density (g dry soil / cm^3), and 7.6 is the sampling depth in cm. 

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