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Peptide design by optimization on a data-parameterized protein interaction landscape
Many applications in protein engineering require optimizing multiple protein properties simultaneously, such as binding one target but not others or binding a target while maintaining stability. Such multistate design problems require navigating a high-dimensional space to find proteins with desired characteristics. A model that relates protein sequence to functional attributes can guide design to solutions that would be hard to discover via screening. In this work, we measured thousands of protein–peptide binding affinities with the high-throughput interaction assay amped SORTCERY and used the data to parameterize a model of the alpha-helical peptide-binding landscape for three members of the Bcl-2 family of proteins: Bcl-x L , Mcl-1, and Bfl-1. We applied optimization protocols to explore extremes in this landscape to discover peptides with desired interaction profiles. Computational design generated 36 peptides, all of which bound with high affinity and specificity to just one of Bcl-x L , Mcl-1, or Bfl-1, as intended. We designed additional peptides that bound selectively to two out of three of these proteins. The designed peptides were dissimilar to known Bcl-2–binding peptides, and high-resolution crystal structures confirmed that they engaged their targets as expected. Excellent results on this challenging problem demonstrate the power of a landscape modeling approach, and the designed peptides have potential uses as diagnostic tools or cancer therapeutics.
Simultaneous optimal system and controller design for multibody systems with joint friction using direct sensitivities
Abstract Real-world multibody systems are often subject to phenomena like friction, joint clearances, and external events. These phenomena can significantly impact the optimal design of the system and its controller. This work addresses the gradient-based optimization methodology for multibody dynamic systems with joint friction using a direct sensitivity approach. The Brown–McPhee model has been used to characterize the joint friction in the system. This model is suitable for the study due to its accuracy for dynamic simulation and its compatibility with sensitivity analysis. This novel methodology supports codesign of the multibody system and its controller, which is especially relevant for applications like robotics and servo-mechanical systems, where the actuation and design are highly dependent on each other. Numerical results are obtained using a software package written in Julia with state-of-the-art libraries for automatic differentiation and differential equations. Three case studies are provided to demonstrate the attractive properties of simultaneous optimal design and control approach for certain applications.
Three-dimensional imaging of grain boundaries via quantitative fluorescence X-ray tomography analysis
Abstract Three-dimensional visualization of material composition within multiple grains and across complex networks of grain boundaries at nanoscales can provide new insight into the structure evolution and emerging functional properties of the material for diverse applications. Here, using nanoscale scanning X-ray fluorescence tomography, coupled with an advanced self-absorption correction algorithm developed in this work, we analyze the three-dimensional gain distributions and compositions in a Ce 0.8 Gd 0.2 O 2-δ -CoFe 2 O 4 mixed ionic-electronic conductor system with high accuracy and statistical significance. Our systematic investigation reveals an additional emergent phase and uncovers highly intriguing composition stability ranges for the multiple material phases within this system. The presented visualization of composition variations across complex interfaces, supported by our quantitative composition analysis, discloses mechanistic pathways of the diverse phase transformations occurring in the material synthesis, providing insights for the optimization of transport properties in the mixed ionic-electronic conductor system.
Co-Optimization of Fuels & Engines: Fuel Blendstocks with the Potential to Optimize Future Gasoline Engine Performance; Identification of Five Chemical Families for Detailed Evaluation
The U.S. Department of Energy's (DOE's) Co-Optimization of Fuels & Engines (Co-Optima) initiative is conducting the early-stage research needed to accelerate the market introduction of advanced fuel and engine technologies. The research includes both spark-ignition (SI) and compression-ignition (CI) combustion approaches, targeting applications that impact the entire on-road fleet (light-, medium-, and heavy-duty vehicles). The initiative's major goals include significant improvements in vehicle fuel economy, lower-cost pathways to reduce emissions, and leveraging diverse U.S. fuel resources. A key objective of Co-Optima's research is to identify new blendstocks that enhance current petroleum blending components, increase blendstock diversity, and provide refiners with increased flexibility to blend fuels with the key properties required to optimize advanced internal combustion engines. This report identifies eight representative blendstocks from five chemical families that have demonstrated the potential to increase boosted SI engine efficiency, meet key fuel quality requirements, and be viable for production at commercial scale by 2025-2030.
Nanographene Aerogels: Size Effect of the Precursor Graphene Oxide on Gelation Process and Electrochemical Properties
Improving the electrochemical properties of graphene aerogels (GAs) without doping or making composites is an attractive synthetic strategy. Here in this work we report on the effects of graphene sheet dimensions on the properties of GAs. Nanographene aerogels (nG-AGs) were synthesized using nanographene oxide (nGO) powder with a mean platelet diameter of 90 nm. In-situ Fourier transform infrared spectroscopy (FTIR) during gelation revealed a longer fast-gelation regime for nG-AGs than for stdG-AGs. The surface-area-normalized capacitance of nG-AGs calculated from cyclic voltammetry is 16% higher than that of stdG-AGs, and the onset of hydrogen evolution is observed at a lower over-potential. These observations can be attributed to increased density of edge sites and defects in nanographene sheets. Our results imply that the diameter of the precursor graphene sheets can be used as a parameter to optimize the electrochemical properties of graphene AGs depending on the application.
Heterogeneities dominate mechanical performance of additively manufactured metal lattice struts
Architected structural metamaterials, also known as lattice, truss, or acoustic materials, provide opportunities to produce tailored effective properties that are not achievable in bulk monolithic materials. These topologies are typically designed under the assumption of uniform, isotropic base material properties taken from reference databases and without consideration for sub-optimal as-printed properties or off-nominal dimensional heterogeneities. However, manufacturing imperfections such as surface roughness are present throughout the lattices and their constituent struts create significant variability in mechanical properties and part performance. Here, this study utilized a customized tensile bar with a gauge section consisting of five parallel struts loaded in a stretch (tensile) orientation to examine the impact of manufacturing heterogeneities on quasi-static deformation of the struts, with a focus on ultimate tensile strength and ductility.
Multiamorphous Phases in Diketopyrrolopyrrole-Based Conjugated Polymers: From Bulk to Ultrathin Films
The glass transition temperature (T g ) of conjugated polymers is a crucial physical parameter that governs their mechanical and electrical properties for applications from sensor technology to skin-like electronics. Despite some well-developed methods that exist for detecting T g of conjugated polymers, there is still a need for the combination of advanced calorimetric methodologies to characterize T g in a broad range of temperatures and scales from bulk to nanometer-thin films. In this work, alternating current (ac) chip calorimetry and flash differential scanning calorimetry (flash DSC) are applied to successfully identify the Tgs and segmental relaxations of conjugated polymers. The detected relaxations were interpreted, in agreement with existing observations in similar systems, as a side-chain relaxation (low temperature), mobile amorphous fractions (MAF), and rigid amorphous fractions (RAF). T g s of MAF and RAF increase and decrease with increasing size of fused thiophene units in the backbone, respectively. The T g s of diketopyrrolopyrrole-based conjugated polymer thin films are also identified by the same method, with both T g s showing a decreased value compared to those of bulk samples. Furthermore, the weight fractions of MAF and RAF with various film thicknesses are qualitatively analyzed based on the heat capacity step of each amorphous fraction during the glass transition. This facile method gives insights into the physical nature of amorphous phases in conjugated polymers for better revealing their structure-property relationships, which will guide the designs of new materials with optimized electrical and mechanical properties in the future.
Influence of processing factors on the physical metallurgy of LENS deposited 316L stainless steel.
Directed energy deposition (DED) is a type of additive manufacturing (AM) process; Laser Engineered Net Shaping (LENS) is a commercial DED process. We are developing LENS technology for printing 316L stainless steel components for structural applications. It is widely known that material properties of AM components are process dependent, attributed to different molten metal incorporation and thermal transport mechanisms. This investigation focuses on process-structure-property relationships for LENS deposits for enabling the process development and optimization to control material property. We observed interactions among powder melting, directional molten metal flow, and the molten metal solidification. The resultant LENS induced microstructure found to be dictated by the process-related characteristics, i.e., interpass boundaries from multi-layer deposition, molten metal flow lines, and solidification dendrite cells. Each characteristic bears the signature of the unique localized thermal history during deposition. Correlation observed between localized thermal transport, resultant microstructure, and its subsequent impact on the mechanical behavior of the current 316L is discussed. We also discuss how the structures of interpass boundaries are susceptible to localized recrystallization, grain growth and/or defect formation, and therefore, heterogeneous mechanical properties due to the adverse presence of unmelted powder inclusions.
Antibacterial Minerals: A geochemical approach to combating antibiotic resistance
The rapid rise of antibiotic resistant bacteria is seriously threatening our ability to treat lifethreatening infections. As a result, our approach to medicine and agriculture will require significant changes if we are to successfully maintain current levels of healthcare and food security. Certain naturally occurring clays have been shown to harbor antimicrobial properties and kill antibiotic resistant bacteria. These clays have been proposed as a new paradigm for fighting the potentially devastating effects of the post antibiotic era. However, natural samples, by their inherent properties, exhibit variable antibacterial effectiveness and the synthesis of minerals with reproducible antibacterial activity is needed. Our project focused on 3 specific aims; 1) develop synthetic versions of naturally occurring bactericidal minerals to control the chemical purity and antibacterial potency, 2) determine how effective these mineral formulations are at killing antibiotic resistant bacteria and 3) investigate the response of human skin cell cultures to these antibacterial minerals. Utilizing hydrothermal based methods our team was able to reproduce the antibacterial activity observed in natural antibacterial minerals, while eliminating unwanted elemental impurities. Importantly, we were able to create a mineral based bactericide that has reproducible reactivity that could provide a consistent dose response. These antibacterial mineral formulations are effective at killing common hospital acquired antibiotic resistant bacteria while providing minimal toxicity to human fibroblasts. Our research has optimized the antibacterial properties of antibacterial minerals to allow greater efficacy from a public health perspective.
Particle size effect of Ni-rich cathode materials on lithium ion battery performance
Graphical abstract: The preparation condition of Ni-rich cathode materials was investigated. When the retention time was short, a poor cathode performance was observed. For long retention time condition, cathode performance displayed a best result at pH 12. Highlights: Black-Right-Pointing-Pointer Ni-rich cathode materials (LiNi{sub 0.8}Co{sub 0.15}Al{sub 0.05}O{sub 2}) were prepared by co-precipitation method using separate addition of Al salt. Black-Right-Pointing-Pointer Particle size of Ni-rich cathode materials became larger with increase of retention time and solution pH. Black-Right-Pointing-Pointer Cathode performance was poor for low retention time. Black-Right-Pointing-Pointer Optimal pH for co-precipitation was 12. -- Abstract: Herein, Ni-rich cathode materials (LiNi{sub 0.8}Co{sub 0.15}Al{sub 0.05}O{sub 2}) in lithium ion batteries are prepared by a separate addition of Ni/Co salt and Al sol solution using a continuously stirred tank reactor. Retention time and solution pH were controlled in order to obtain high performance cathode material. Particle size increase was observed with a higher retention time of the reactants. Also, primary and secondary particles became smaller according to an increase of solution pH, which was probably due to a decrease of growth rate. From the cathode application, a high discharge capacity (175 mAh g{sup -1}), a high initial efficiency (90%) and a good cycleability were observed in the cathode material prepared under pH 12 condition, which was attributed to its well-developed layered property and the optimal particle size. However, rate capability was inversely proportional to the particle size, which was clarified by a decrease of charge-transfer resistance measured in the electrochemical impedance spectroscopy.
Thermal and Reliability Characterization of an Epoxy Resin-Based Double-Side Cooled Power Module
Wide-Band Gap (WBG) power devices have become a promising option for high-power applications due to the superior material properties over traditional Silicon. To not limit WBG devices’ mother nature, a rugged and high-performance power device packaging solution is necessary. This study proposes a Double-Side Cooled (DSC) 1.2 kV half-bridge power module having dual epoxy resin insulated metal substrate (eIMS) for solving convectional power module challenges and providing a cost-effective solution. The thermal performance outperforms traditional Alumina (Al2O3) Direct Bonded Copper (DBC) DSC power module due to moderate thermal conductivity (10 W/mK) and thin (120 mm) epoxy resin composite dielectric working as the IMS insulation layer. This novel organic dielectric can withstand high voltage (5 kVAC @ 120 μm) and has a Glass Transition Temperature (Tg) of 300°C, which is suitable for high-power applications. In the thermal-mechanical modeling, the organic DSC power module can pass the thermal cycling test over 1,000 cycles by optimizing the mechanical properties of the encapsulant material. In conclusion, this article not only proposes a competitive organic-based power module but also a methodology of evaluation for thermal and mechanical performance.
Structural evolution, sintering behavior and microwave dielectric properties of (1−x)Li{sub 2}TiO{sub 3} + xLiF ceramics
Graphical abstract: - Highlights: • Structure, sinterability and dielectric properties of LiF-doped Li{sub 2}TiO{sub 3} were studied. • Li{sub 2}TiO{sub 3} can be densitied (TD 98%) at lower sintering temperature by LiF additions. • Excellent microwave dielectric properties could be obtained. - Abstract: Structural evolution, sintering behavior, and microwave dielectric properties of (1−x)Li{sub 2}TiO{sub 3} + xLiF (0.05 ≤ x ≤ 0.70) ceramics have been studied by X-ray diffraction (XRD), Scanning Electron Microscopy (SEM), Raman spectra, thermal dilatometry and microwave resonant measurement at the frequency of about 7–11 GHz. The results show that Li{sub 2}TiO{sub 3} can form limited solid solution with LiF (x ≤ 0.4) and LiF second phase appeared when x{sup 3}0.5. The structure of the solid solution transformed from ordered monoclinic phase (β-Li{sub 2}TiO{sub 3} (ss)) to disordered cubic rock salt (α-Li{sub 2}TiO{sub 3} (ss)) when x{sup 3}0.15. The presence of short range ordering was confirmed for the cubic phase. The sinterability was considerably improved by doping with LiF. Densified ceramics with about 95–98% theoretical density could be obtained for the doped compositions after sintering at 900–1150 °C/2 h. An optimized microwave dielectric properties with ε{sub r} of ∼23.6, Q × f of ∼108,000 GHz and τ{sub f} of ∼4.2 ppm/°C could be obtained for the x = 0.1 composition after sintering at 1100 °C/2 h.
Metal ion dopant-induced famatinite to chalcostibite phase transformation of copper antimony sulphide colloidal nanostructures: effect on photophysical and pseudocapacitance properties
Here, the strategic doping of transition metal ions into copper antimony sulphide (CAS) semiconducting nanostructures can significantly influence their photophysical and pseudocapacitive properties, for which there are few reports and therefore is the focus of this study. Accordingly, highly crystalline metal ion (Mn 2+ , Fe 2+ , Co 2+ , Ni 2+ and Zn 2+ ) doped off-stoichiometric copper rich/poor, antimony-rich/poor, and sulphur-poor CAS nanostructures (10–23 nm) were grown via colloidal (hot-injection) synthesis using metal diethyldithiocarbamate precursors. Importantly, metal ion doping significantly influences the structure and composition of the off-stoichiometric CAS nanostructures. Data from powder X-ray diffraction, Raman spectroscopy, high-resolution scanning/transmission electron microscopy, and energy dispersive X-ray spectroscopy confirm that the heavier metal ion dopants induce a novel phase transformation from famatinite (fCAS) to chalcostibite (cCAS) nanostructures. The influence of the metal ion dopants is also observed in the optical properties of as-synthesized nanostructures. This involves blue-shifted ultraviolet-visible absorption, reduced Urbach tailing, and tunable bandgaps between 2.17 and 2.38 eV. Also, the doped nanostructures display broad visible-near infrared photoluminescence via a triple radiative pathway with relatively short decay lifetimes between 0.2 and 6.1 ns. This is mediated by electronic transitions involving intrinsic (copper/antimony/sulphur interstitial) and extrinsic (metal ion interstitial) defect states. Additionally, electrodes prepared from Mn 2+ -doped fCAS nanostructures show enhanced pseudocapacitance via Na+ surface adsorption and intercalation relative to undoped fCAS electrodes, while Zn 2+ -doped cCAS electrodes exhibit pseudocapacitance via a combination of Na+ surface adsorption, intercalation, and redox reactions. These electrodes exhibit reduced charge transfer resistance, improved electronic conductivity and notably enhanced specific capacitance (∼222 F g −1 ), and charge transport, as measured in 1 M Na 2 SO 4 electrolyte via cyclic voltammetry and electrochemical impedance spectroscopy. To this end, the discovery of the metal ion-induced phase transformation presents a new avenue for optimizing the functional properties of fCAS and cCAS nanostructures, highlighting the critical role of metal ion-related defects in controlling the optical and electrochemical properties, towards potential solar absorption and energy storage applications.
Crystalline Ceramic Waste Forms: Reference Formulation Report
The research conducted in this work package is aimed at taking advantage of the long term thermodynamic stability of crystalline ceramics to create more durable waste forms (as compared to high level waste glass) in order to reduce the reliance on engineered and natural barrier systems. Durable ceramic waste forms that incorporate a wide range of radionuclides have the potential to broaden the available disposal options and to lower the storage and disposal costs associated with advanced fuel cycles. Assemblages of several titanate phases have been successfully demonstrated to incorporate radioactive waste elements, and the multiphase nature of these materials allows them to accommodate variation in the waste composition. Recent work has shown that they can be successfully produced from a melting and crystallization process. The objective of this report is to explain the design of ceramic host systems culminating in a reference ceramic formulation for use in subsequent studies on process optimization and melt property data assessment in support of FY13 melter demonstration testing. The waste stream used as the basis for the development and testing is a combination of the projected Cs/Sr separated stream, the Trivalent Actinide - Lanthanide Separation by Phosphorous reagent Extraction from Aqueous Komplexes (TALSPEAK) waste stream consisting of lanthanide fission products, the transition metal fission product waste stream resulting from the transuranic extraction (TRUEX) process, and a high molybdenum concentration with relatively low noble metal concentrations. In addition to the combined CS/LN/TM High Mo waste stream, variants without Mo and without Mo and Zr were also evaluated. Based on the results of fabricating and characterizing several simulated ceramic waste forms, two reference ceramic waste form compositions are recommended in this report. The first composition targets the CS/LN/TM combined waste stream with and without Mo. The second composition targets with CS/LN/TM combined waste stream with Mo and Zr removed. Waste streams that contain Mo must be produced in reducing environments to avoid Cs-Mo oxide phase formation. Waste streams without Mo have the ability to be melt processed in air. A path forward for further optimizing the processing steps needed to form the targeted phase assemblages is outlined in this report. Processing modifications including melting in a reducing atmosphere, and controlled heat treatment schedules are anticipated to improve the targeted elemental partitioning.
Integrated Nano-Domains of Disordered and Ordered Spinel Phases in LiNi 0.5 Mn 1.5 O 4 for Li-Ion Batteries
Recent calculations and experimental data suggest that understanding the local ordering behavior of Ni/Mn will be critical to optimize the electrochemical properties of LiNi 0.5 Mn 1.5 O 4 (LNMO) high voltage spinel. In this study, we systematically controlled the evolution of Ni and Mn ordering in LNMO samples by annealing them at 700 °C in air for different dwelling times, followed by quenching to room temperature. The long- and short-range ordering behavior of Ni and Mn were analyzed by combining neutron powder diffraction, X-ray powder diffraction (XRD), transmission electron microscopy (TEM), and Fourier transform infrared spectroscopy (FT-IR) data. The results show that the fraction of ordered phase increases rapidly during initial annealing at 700 °C for 6 h, and accompanied by decreasing amounts of secondary phases. Annealing longer than 6 h led to the growth in size of ordered domains (i.e., increased segregation of ordered and disordered domains) along with a slow increase in the fraction of ordered phase. The dependence of open circuit voltages (OCVs) of the LNMO on the degree of ordering agrees well with recent calculations using the density functional theory. The increase in the degree of ordering increases the open circuit voltage (OCV) and the initial capacity but reduces cycle life and rate capability. The LNMO delivered optimal battery performances (capacity, cycle life, and rate capability) after annealing at 700 °C for 2 h. This partially ordered sample showed the respective advantages from both disordered and ordered spinels: better spinel-phase purity (thus, higher initial capacity) from the ordered LNMO and better cycle life and rate capability from the disordered LNMO.
Photoluminescence properties and crystallization of silicon quantum dots in hydrogenated amorphous Si-rich silicon carbide films
Silicon quantum dots (QDs) embedded in hydrogenated amorphous Si-rich silicon carbide (α-SiC:H) thin films were realized by plasma-enhanced chemical vapor deposition process and post-annealing. Fluorescence spectroscopy was used to characterize the room-temperature photoluminescence properties. X-ray photoelectron spectroscopy was used to analyze the element compositions and bonding configurations. Ultraviolet visible spectroscopy, Raman scattering, and high-resolution transmission electron microscopy were used to display the microstructural properties. Photoluminescence measurements reveal that there are six emission sub-bands, which behave in different ways. The peak wavelengths of sub-bands P1, P2, P3, and P6 are pinned at about 425.0, 437.3, 465.0, and 591.0 nm, respectively. Other two sub-bands, P4 is red-shifted from 494.6 to 512.4 nm and P5 from 570.2 to 587.8 nm with temperature increasing from 600 to 900 °C. But then are both blue-shifted, P4 to 500.2 nm and P5 to 573.8 nm from 900 to 1200 °C. The X-ray photoelectron spectroscopy analysis shows that the samples are in Si-rich nature, Si-O and Si-N bonds consumed some silicon atoms. The structure characterization displays that a separation between silicon phase and SiC phase happened; amorphous and crystalline silicon QDs synthesized with increasing the annealing temperature. P1, P2, P3, and P6 sub-bands are explained in terms of defect-related emission, while P4 and P5 sub-bands are explained in terms of quantum confinement effect. A correlation between the peak wavelength shift, as well as the integral intensity of the spectrum and crystallization of silicon QDs is supposed. These results help clarify the probable luminescence mechanisms and provide the possibility to optimize the optical properties of silicon QDs in Si-rich α-SiC: H materials.
An Integrated Approach To Offshore Wind Energy Assessment: Great Lakes 3D Wind Experiment
This grant supported fundamental research into the characterization of flow parameters of relevance to the wind energy industry focused on offshore and the coastal zone. A major focus of the project was application of the latest generation of remote sensing instrumentation and also integration of measurements and numerical modeling to optimize characterization of time-evolving atmospheric flow parameters in 3-D. Our research developed a new data-constrained Wind Atlas for the Great Lakes, and developed new insights into flow parameters in heterogeneous environments. Four experiments were conducted during the project: At a large operating onshore wind farm in May 2012; At the National Renewable Energy Laboratory National Wind Technology Center (NREL NWTC) during February 2013; At the shoreline of Lake Erie in May 2013; and At the Wind Energy Institute of Canada on Prince Edward Island in May 2015. The experiment we conducted in the coastal zone of Lake Erie indicated very complex flow fields and the frequent presence of upward momentum fluxes and resulting distortion of the wind speed profile at turbine relevant heights due to swells in the Great Lakes. Additionally, our data (and modeling) indicate the frequent presence of low level jets at 600 m height over the Lake and occasions when the wind speed profile across the rotor plane may be impacted by this phenomenon. Experimental data and modeling of the fourth experiment on Prince Edward Island showed that at 10-14 m escarpment adjacent to long-overseas fetch the zone of wind speed decrease before the terrain feature and the increase at (and slightly downwind of) the escarpment is ~3–5% at turbine hub-heights. Additionally, our measurements were used to improve methods to compute the uncertainty in lidar-derived flow properties and to optimize lidar-scanning strategies. For example, on the basis of the experimental data we collected plus those from one of our research partners we advanced a new methodology to estimate a priori the uncertainty in wind speed retrievals from arc scans based on site characteristics such as wind velocity, turbulence intensity and proposed scan geometry. Insights regarding use of remote sensing technologies deriving from project experiments were used to compile a best practice document http://doi.org/10.7298/X4QV3JGF for measuring wind speeds and turbulence offshore through in-situ and remote sensing technologies. A project-specific web-site was developed and is available at: http://www.geo.cornell.edu/eas/PeoplePlaces/Faculty/spryor/DoE_AIATOWEA/index.html