A self-assembling protein template for constrained synthesis and patterning of nanoparticle arrays
No abstract available
Alloys/chemistry↗
SEARCH · Engineering Papers
Results for “molecular templating”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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Understanding Hydrogenation Chemistry at MgB 2 Reactive Edges from Ab Initio Molecular Dynamics
Solid-state hydrogen storage materials often operate via transient, multistep chemical reactions at complex interfaces that are difficult to capture. Here, we use direct ab initio molecular dynamics simulations at accelerated temperatures and hydrogen pressures to probe the hydrogenation chemistry of the candidate material MgB 2 without a priori assumption of reaction pathways. Focusing on highly reactive ($10\overline{1}0$) edge planes where initial hydrogen attack is likely to occur, we track mechanistic steps toward the formation of hydrogen-saturated BH 4 – units and key chemical intermediates, involving H 2 dissociation, generation of functionalities and molecular complexes containing BH 2 and BH 3 motifs, and B–B bond breaking. Further, the genesis of higher-order boron clustering is also observed. Different charge states and chemical environments at the B-rich and Mg-rich edge planes are found to produce different chemical pathways and preferred speciation, with implications for overall hydrogenation kinetics. The reaction processes rely on B–H bond polarization and fluctuations between ionic and covalent character, which are critically enabled by the presence of Mg 2+ cations in the nearby interphase region. Our results provide guidance for devising kinetic improvement strategies for MgB 2 -based hydrogen storage materials, while also providing a template for exploring chemical pathways in other solid-state energy storage reactions.
08 HYDROGEN↗
Commodity Thermoplastic Elastomer-Enabled Templated Synthesis of Large-Pore Ordered Mesoporous Materials
Fabrication of ordered mesoporous materials (OMMs) has predominantly relied on templating-based methods. However, these methods are constrained by several limitations, especially the limited pore sizes attainable with commercially available surfactants used as structure-directing agents. To unlock the full potential of the OMMs, it is essential to develop synthetic strategies that facilitate the production of large-pore OMMs using scalable processes and cost-effective precursors. This work demonstrates the use of thermoplastic elastomer (TPE)-derived carbon replicas for synthesizing ordered mesoporous silica (OMS) and metal oxides (OMMOs) via precursor infiltration and template removal. The nanostructural evolution of the resulting inorganic materials was systematically investigated. Specifically, using tetraethyl orthosilicate (TEOS) as a silica precursor, this method can produce an OMS with relatively large pores. To establish the generalizability of this process, the fabrication approach was extended to other commercially available TPEs with varied chemical compositions and molecular weights while consistently resulting in ordered structures. Additionally, this synthetic strategy can be successfully applied to the production of OMMOs, including tin and titanium oxide matrix chemistries, yielding pore sizes of 16.0 and 19.2 nm, respectively. By developing a general method and using low-cost precursors, this work presents a scalable approach for fabricating large-pore OMMs with tunable pore textures and matrix chemistries.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Polarization-induced 2D hole gases in pseudomorphic undoped GaN/AlN heterostructures on single-crystal AlN substrates
A high-conductivity two-dimensional (2D) hole gas is the enabler of wide-bandgap p-channel transistors. Compared to commonly used AlN template substrates with high dislocation densities, the recently available single-crystal AlN substrates are promising to boost the speed and power handling capability of p-channel transistors based on GaN/AlN 2D hole gases (2DHGs) thanks to the much lower dislocation densities and the absence of thermal boundary resistance. Using plasma-assisted molecular beam epitaxy, we report the observation of polarization-induced high-density 2DHGs in undoped pseudomorphic GaN/AlN heterostructures on the single-crystal AlN substrates with high structural quality and atomic steps on the surface. The high-density 2DHG persists down to cryogenic temperatures with a record high mobility exceeding 280 cm 2 /V s and a density of 2.2 × 10 13 /cm 2 at 10 K. These results shed light on aspects of improving 2D hole mobilities and indicate significant potential of GaN/AlN 2DHG grown on bulk AlN substrates for future high performance wide-bandgap p-channel transistors.
36 MATERIALS SCIENCE↗
Studies of surface adsorbate electronic structure and femtochemistry at the fundamental length and time scales. Final report
The electronic structure and ultrafast (10-15 s-femtosecond timescale) electron dynamics were investigated for clean and atom/molecule covered metal surfaces. The studies were performed by scanning tunneling microscopy (STM) to measure the structure of adsorbed atoms and molecules on metal surfaces, and to investigate their electronic properties. The electronic structure of the observed molecular networks was calculated by electronic structure theory in collaboration with Prof. Jin Zhao, who is a long-time collaborator, a Professor at the University of Science and Technology of China, and holds an Adjunct Professorship at the University of Pittsburgh. We also investigated the electronic properties of C60 molecules when they are templated by corrugated black phosphorous surfaces. We found unexpected charge delocalization that is enabled by the templating. This research was done in collaboration with Professor Min Feng at the Wuhan University, and who also holds an Adjunct Professorship at the University of Pittsburgh. Moreover, the electronic structure and electron dynamics in metal surfaces were investigated by time-resolved photoemission electron spectroscopy. The focus of ultrafast spectroscopy has been on the plasmonic response of silver surfaces. One direction has been to develop multidimensional (energy, momentum, and time) photoelectron spectroscopy of the coherent response of solid surfaces. This method was applied to study the collective electron excitations known generally as plasmons, which screen optical fields from penetration into metals. Although this collective response has been known for more than 60 years and is used extensively to deposit optical energy into metals, how this happens is poorly known. We investigated the plasmonic response of silver at the point where the dielectric response passes through zero and bulk plasmon is excited by light. We discovered that the plasmon excitation decays by exciting electrons from the Fermi level of a metal, which is contrary to what is believed in the plasmonic science community. This research has been performed in collaboration with Dr. Marcel Reutzel, who was a postdoctoral fellow working on this research at the University of Pittsburgh, and now has a faculty position at the University of Göttingen in Germany. Prof. Branko Gumhalter from the Institute of Physics in Zagreb contributed on the theory of plasmonic decay processes. Furthermore, we investigated the Floquet engineering of electronic bands in metals leading to multiphoton photoemission and above threshold photoemission. Finally, we demonstrated that it is possible to change the electronic structure of metals by application of optical fields. Our studies indicated that this happens on subfemtosecond time scale and could potentially be used in ultrafast information processing and quantum computation. Related document information
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Product and rate determinations with chemically activated nucleotides in the presence of various prebiotic materials, including other mono- and polynucleotides
We are investigating the reactions of ImpN's in the presence of a number of prebiotically plausible materials, such as metal ions, phosphate, amines and other nucleotides and hope to learn more about the stability/reactivity of ImpN's in a prebiotic aqueous environment. We find that, in the presence of phosphate, ImpN's form substantial amounts of diphosphate nucleotides. These diphosphate nucleotides are not very good substrates for template directed reactions, but are chemically activated and are known to revert to the phosphoimidazolides in the presence of imidazole under solid state conditions. With respect to our studies of the oligomerization reaction, the determination of the dimerization rate constant of a specific ImpN (guanosine 5'-phospho 2 methylimidazolide) both in the absence and the presence of the template leads to the conclusion that at 37 C the dimerization is not template directed, although the subsequent polymerization steps are. In other words, this specific polynucleotide synthesizing system favors the elongation of oligonucleotides as compared with the formation of dimers and trimers. This favoring of the synthesis of long as opposed to short oligonucleotides may be regarded as a rudimentary example of natural selection at the molecular level.
Kanavarioti, A.↗
Substitution of Ribonucleotides in the T7 RNA Polymerase Promoter Element
A systematic analysis was carried out to examine the effects of ribonucleotide substitution at various locations within the promoter element for T7 RNA polymerase. Ribonucleotides could be introduced at most positions without significantly decreasing transcription efficiency. A critical window of residues that were intolerant of RNA substitution was defined for both the non-template and template strands of the promoter. These residues are involved in important contacts with the AT-rich recognition loop, specificity loop, and P-intercalating hairpin of the polymerase. These results highlight the malleability of T7 RNA polymerase in recognizing its promoter element and suggest that promoters with altered backbone conformations may be used in molecular biology applications that employ T7 RNA polymerase for in vitro transcription.
McGinness, Kathleen E.↗
Topology-Informed Design Rules for Deconstructable Thermoset Copolymer Networks
Existing models of thermoset deconstruction facilitated by incorporating cleavable comonomers rely on a mean-field reverse gel point paradigm, which predicts network dissolution once cleavable bonds reach a critical stoichiometric threshold, but does not account for where those bonds reside within the network architecture. Using reactive coarse-grained molecular dynamics simulations coupled with graph-theoretic analysis, we extend this stoichiometric picture to show that deconstructability is governed by the curing-imprinted network topology rather than stoichiometry alone. This topological organization is hierarchical: at the local scale, the elastic effectiveness of cross-link junctions determines which cross-links constitute the load-bearing scaffold; at the mesoscale, the cross-linking rate kinetically templates that scaffold into topologically modular communities─densely cross-linked clusters connected by sparse bridging strands that sustain network connectivity. Using betweenness centrality to identify nodes that disproportionately lie on intercommunity shortest paths, we demonstrate that effective deconstruction of the network into macromolecular fragments requires cleavable comonomers to intercept these high-centrality bridging strands. We further find that under uniform, disassortative comonomer incorporation, this topological requirement provides a mechanistic basis for extending the reverse gel point to incorporate network topology. We also show that modularity imposes a fundamental limit on fragment uniformity that persists even when the centrality requirement is met. Finally, we demonstrate that chain stiffness provides a nearly independent lever to suppress mechanically redundant cross-links and raise the glass transition temperature without significantly altering the deconstruction outcome. Together, these findings reframe the thermoset design space around network topology and provide actionable guidelines for engineering thermoset copolymers with predictable deconstructability and targeted thermomechanical performance.
coarse-grained molecular dynamics↗
Enzymatic synthesis of polymers containing nicotinamide mononucleotide
Nicotinamide mononucleoside 5'-diphosphate in its reduced form is an excellent substrate for polynucleotide phosphorylase from Micrococcus luteus both in de novo polymerization reactions and in primer extension reactions. The oxidized form of the diphosphate is a much less efficient substrate; it can be used to extend primers but does not oligomerize in the absence of a primer. The cyanide adduct of the oxidized substrate, like the reduced substrate, polymerizes efficiently. Loss of cyanide yields high molecular weight polymers of the oxidized form. Terminal transferase from calf thymus accepts nicotinamide mononucleoside 5'-triphosphate as a substrate and efficiently adds one residue to the 3'-end of an oligodeoxynucleotide. T4 polynucleotide kinase accepts oligomers of nicotinamide mononucleotide as substrates. However, RNA polymerases do not incorporate nicotinamide mononucleoside 5'-triphosphate into products on any of the templates that we used.
Liu, Rihe↗
Enzymatic Synthesis of Polymers Containing Nicotinamide Mononucleotide
Nicotinamide mononucleoside 5'-diphosphate in its reduced form is an excellent substrate for polynucleotide phosphorylase from Micrococcus luteus both in de novo polymerization reactions and in primer extension reactions. The oxidized form of the diphosphate is a much less efficient substrate; it can be used to extend primers but does not oligomerize in the absence of a primer. The cyanide adduct of the oxidized substrate, like the reduced substrate, polymerizes efficiently. Loss of cyanide yields high molecular weight polymers of the oxidized form. Terminal transferase from calf thymus accepts nicotinamide mononucleoside 5'-triphosphate as a substrate and efficiently adds one residue to the 3'-end of an oligodeoxynucleotide. T4 polynucleotide kinase accepts oligomers of nicotinamide mononucleotide as substrates. However, RNA polymerases do not incorporate nicotinamide mononucleoside 5'-triphosphate into products on any of the templates that we used.
Liu, Rihe↗
Accelerating Biomimetic Solar - Energy Harvesting: Mapping the Interaction Landscape of Plasmonic-Excitonic Hybrid Nanosystems (Final Report)
In general, excitonic and plasmonic nanoscale materials in close proximity show high potential for significant breakthroughs in energy related materials research. The interactions between these two kinds of materials result in coupled optical transitions (plexcitons), distinct from those of both the individual exciton and plasmon as well as from those of the sum of their constituents (synergistic effects). By linking together materials-research and physical-research approaches, this project contributes to a concerted approach on nanomaterials energy research. The project’s overall goal is to accelerate the development of well-defined plexcitonic model systems consisting of carefully engineered plasmonic and excitonic nanomaterial— essential for both gaining a fundamental understanding of plexcitonic nanomaterials and the development of novel design principles for biomimetic solar energy harvesting. During the 3-year project period and the terminal renewal with limited support for a 12-month period, we successfully synthesized and characterized (1) a robust excitonic nanomaterial and (2) a library of plasmonic nanoparticles as well as developed (3) a microfluidic platform for homogenous nanosynthesis as summarized below: (1) Robust Excitonic Nanomaterial. Supramolecular assemblies are Nature’s most successful material system for solar energy harvesting. However, photovoltaic devices based on artificial supramolecular assemblies continue to be stymied by disappointing efficiencies and poor stability. The conceptual failure may lie in current solar cell architectures, which rely on solidifying supramolecular assemblies as an ensemble into a solid matrix, neglecting the intrinsic fragility of the assemblies’ internal structure, thus disrupting or even destroying their delicate optoelectronic properties, that is, delicate Frenkel excitonic properties. Supramolecular assemblies may finally serve as usable light harvesting material systems for solar energy conversion technologies, only if they meet the following criteria: (a) Stability, that is, the fragile structure including its delicate Frenkel excitonic character needs to be stable, (b) Robustness, that is, resistant against elevated and fluctuating temperatures, and (c) Viability for device integration, that is, capable of being immobilized onto solid substrates. Here, by developing a nanocomposite via a tunable, cage-like scaffold design, we successfully provided stable supramolecular nanocomposites, that inhabit robust Frenkel excitons despite harming environmental conditions such as extreme heat stress. (2) Library of Plasmonic Nanoparticles. Naturally, current models describing plasmonic hybrid quantum states—plasmonic hybridizations—parallel those developed for molecular orbitals, equating individual plasmonic nanostructures with “atoms” and the plasmonic nanoassemblies with “molecules.” In analogy to organic synthesis, a suitably robust fabrication method would allow for “atom-like” manipulation of “molecule-like” plasmonic nanoassemblies; of high value for next-generation energy nanotechnologies. Despite this frequent comparison, current plasmonic nanoassembly fabrication methods favor top-down templating over wet-chemical synthesis, however, achieving precise control over nanostructure’s geometry and surface characteristics remain an art and a scientific challenge. The conceptual failure may lie in the current wet-chemical synthesis paradigm, as it relies on the accessibility of a multi-dimensional synthesis parameter space through limited, rather one-dimensional synthesis procedures by employing step-by-step approaches. Solution-based nanoarchitectonics for rational design of precisely built plasmonic nanoassemblies via solution-based fabrication may finally be possible only if multi-dimensional syntheses approaches are available that allow for comprehensive control over the plasmonic nanomaterials’ (a) Structural Properties and (b) Surface Properties. Here, by developing an innovative multidimensional 1,3-propanediol based polyol synthesis, we successfully provided control over the plasmonic building-block’s geometry (size and shape) together with its surface characteristics. Our results present a critical step toward the vision of a “periodic table-like” system for plasmonic materials based on straightforward wet-chemical syntheses for energy nanotechnologies. Developing deliberate modifications on this synthesis, we generated a library of plasmonic nanostructures covering the vast parameter space—opening the door for fundamental investigation of plexcitonic model systems. (3) Microfluidic Platform for Homogenous Nanosynthesis. Control over structural properties of plexcitonic nanocomposites remains a challenge due to current limitations in nanosynthesis techniques. Slight variations in nanostructure’s geometry impact their optoelectronic properties, demanding precise synthesis beyond the capabilities of solution-based (batch) synthesis processes. In contrast, the small, confined liquid volumes used in microfluidics—a reaction technique where the manipulation of fluids takes place in channels with dimensions of tens of micrometers—allows for homogenous synthesis conditions, providing excellent control of the reaction and, as a result, of the materials’ geopmetry and composition. However, thus far, the majority of plexcitonic systems has been developed via batch synthesis. Here, by successfully developing a two-channel microreactor, our microfluidic-supported synthesis approach combines the advantages of both microfluidics and batch platforms, allowing for precise spatio-temporal control over all synthesis parameters opening the possibility for homogenous nanosythnesis of well-defined plexcitonic model systems.
14 SOLAR ENERGY↗
Spontaneous assembly of hierarchical phases
We report the grand promise of self-assembly is the creation of target nanostructures through spontaneous molecular organization, a process that is — in principle — simpler and more scalable than laborious top-down nanofabrication methods. Yet self-assembly faces a fundamental challenge: the structures that form thermodynamically tend to minimize surface area and maximize symmetry; the most readily-accessible structures are thus quite simple. Block copolymer (BCP) self-assembly, for example, takes advantage of the chemical incompatibility along a polymer backbone to drive local phase separation; frustrated assembly leads to a nanoscale morphology whose unit cell is dictated by chain architecture. Canonical BCPs (linear chains with two blocks) form alternating lamellae and hexagonally-packed cylinders in a straightforward manner; but more exotic phases require additional control, for example directing the assembly using external forces, such as shear or chemical templates. An elegant alternative is to use synthetic methods to design more sophisticated chain architectures, which may give rise to new morphologies. An outstanding challenge is to achieve morphological control without undue synthetic burden. Sun et al. now report in Nature Nanotechnology the design and synthesis of novel triblock copolymers that give rise to structural order at multiple length scales, thereby forming complex and hierarchical nanoscale phases.
77 NANOSCIENCE AND NANOTECHNOLOGY↗
Metastable doubly threaded [3]rotaxanes with a large macrocycle
Ring size is a critically important parameter in many interlocked molecules as it directly impacts many of the unique molecular motions that they exhibit. Reported herein are studies using one of the largest macrocycles reported to date to synthesize doubly threaded [3]rotaxanes. A large ditopic 46 atom macrocycle containing two 2,6-bis(N-alkyl-benzimidazolyl)pyridine ligands has been used to synthesize several metastable doubly threaded [3]rotaxanes in high yield (65–75% isolated) via metal templating. Macrocycle and linear thread components were synthesized and self-assembled upon addition of iron(II) ions to form the doubly threaded pseudo[3]rotaxanes that could be subsequently stoppered using azide–alkyne cycloaddition chemistry. Following demetallation with base, these doubly threaded [3]rotaxanes were fully characterized utilizing a variety of NMR spectroscopy, mass spectrometry, size-exclusion chromatography, and all-atom simulation techniques. Critical to the success of accessing a metastable [3]rotaxane with such a large macrocycle was the nature of the stopper group employed. By varying the size of the stopper group it was possible to access metastable [3]rotaxanes with stabilities in deuterated chloroform ranging from a half-life of <1 minute to ca. 6 months at room temperature potentially opening the door to interlocked materials with controllable degradation rates.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
A synthetic RNA-mediated evolution system in yeast
Laboratory evolution is a powerful approach to search for genetic adaptations to new or improved phenotypes, yet either relies on labour-intensive human-guided iterative rounds of mutagenesis and selection, or prolonged adaptation regimes based on naturally evolving cell populations. Here we present CRISPR- and RNA-assisted in vivo directed evolution (CRAIDE) of genomic loci using evolving chimeric donor gRNAs continuously delivered from an error-prone T7 RNA polymerase, and directly introduced as RNA repair donors into genomic targets under either Cas9 or dCas9 guidance. We validate CRAIDE by evolving novel functional variants of an auxotrophic marker gene, and by conferring resistance to a toxic amino acid analogue in baker's yeast Saccharomyces cerevisiae with a mutation rate >3,000-fold higher compared to spontaneous native rate, thus enabling the first demonstrations of in vivo delivery and information transfer from long evolving RNA donor templates into genomic context without the use of in vitro supplied and pre-programmed repair donors.
59 BASIC BIOLOGICAL SCIENCES↗
Orienting an Organic Semiconductor into DNA 3D Arrays by Covalent Bonds
Abstract A quasi‐one‐dimensional organic semiconductor, hepta(p‐phenylene vinylene) (HPV), was incorporated into a DNA tensegrity triangle motif using a covalent strategy. 3D arrays were self‐assembled from an HPV‐DNA pseudo‐rhombohedron edge by rational design and characterized by X‐ray diffraction. Templated by the DNA motif, HPV molecules exist as single‐molecule fluorescence emitters at the concentration of 8 mM within the crystal lattice. The anisotropic fluorescence emission from HPV‐DNA crystals indicates HPV molecules are well aligned in the macroscopic 3D DNA lattices. Sophisticated nanodevices and functional materials constructed from DNA can be developed from this strategy by addressing functional components with molecular accuracy.
Wang, Xiao↗
Self‐Assembly of Helical Nanofibrous Chiral Covalent Organic Frameworks
Abstract Despite significant progress on the design and synthesis of covalent organic frameworks (COFs), precise control over microstructures of such materials remains challenging. Herein, two chiral COFs with well‐defined one‐handed double‐helical nanofibrous morphologies were constructed via an unprecedented template‐free method, capitalizing on the diastereoselective formation of aminal linkages. Detailed time‐dependent experiments reveal the spontaneous transformation of initial rod‐like aggregates into the double‐helical microstructures. We have further demonstrated that the helical chirality and circular dichroism signal can be facilely inversed by simply adjusting the amount of acetic acid during synthesis. Moreover, by transferring chirality to achiral fluorescent molecular adsorbents, the helical COF nanostructures can effectively induce circularly polarized luminescence with the highest luminescent asymmetric factor ( g lum ) up to ≈0.01.
Tang, Xihao↗
Properties of Polycyclic Aromatic Hydrocarbons in the Northwest Photon Dominated Region of NGC 7023. I. PAH Size, Charge, Composition, and Structure Distribution
Polycyclic aromatic hydrocarbon (PAH) emission in the Spitzer Infrared Spectrograph spectral map of the northwest photon dominated region (PDR) in NGC 7023 was analyzed exclusively using PAH spectra from the NASA Ames PAH IR Spectroscopic Database (www.astrochem.org/pahdb). The 5-15 micron spectrum at each pixel is fitted using a non-negative-least-squares fitting approach. The fits are of good quality, allowing decomposition of the PAH emission into four subclasses: size, charge, composition, and hydrogen adjacency (structure). Maps tracing PAH subclass distributions across the region paint a coherent astrophysical picture. Once past some 20 seconds of arc from HD 200775, the emission is dominated by the more stable, large, symmetric, compact PAH cations with smaller, neutral PAHs taking over along the lines-of-sight toward the more distant molecular cloud. The boundary between the PDR and the denser cloud material shows up as a distinct discontinuity in the breakdown maps. Noteworthy is the requirement for PANH cations to fit the bulk of the 6.2 and 11.0 micron features and the indication of PAH photo-dehydrogenation and fragmentation close to HD 200775. Decomposition of the spectral maps into "principal" subclass template spectra provides additional insight into the behavior of each subclass. However, the general applicability of this computationally more efficient approach is presently undetermined. This is the first time the spectra of individual PAHs are exclusively used to fit the 5-15 micron region and analyze the spatial behavior of the aromatic infrared bands, providing fundamental, new information about astronomical PAH subpopulations including their dependence on, and response to, changes in local conditions.
northwest photon↗
Structural basis of transcription recognition of a hydrophobic unnatural base pair by T7 RNA polymerase
Bacteriophage T7 RNA polymerase (T7 RNAP) is widely used for synthesizing RNA molecules with synthetic modifications and unnatural base pairs (UBPs) for a variety of biotechnical and therapeutic applications. However, the molecular basis of transcription recognition of UBPs by T7 RNAP remains poorly understood. Here we focused on a representative UBP, 7-(2-thienyl)-imidazo[4,5-b]pyridine (Ds) and pyrrole 2-carbaldehyde (Pa), and investigated how the hydrophobic Ds–Pa pair is recognized by T7 RNAP. Our kinetic assays revealed that T7 RNAP selectively recognizes the Ds or Pa base in the templates and preferentially incorporates their cognate unnatural base nucleotide substrate (PaTP or DsTP) over natural NTPs. Our structural studies reveal that T7 RNAP recognizes the unnatural substrates at the pre-insertion state in a distinct manner compared to natural substrates. These results provide mechanistic insights into transcription recognition of UBP by T7 RNAP and provide valuable information for designing the next generation of UBPs.
59 BASIC BIOLOGICAL SCIENCES↗