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At least 379 records · Page 21

Microcanonical Kinetics of Water-Mediated Proton Transfer in 4ABAH + ·(H 2 O) n = 4–6 Clusters (ABA = Aminobenzoic Acid): A Model System for Size-Dependent Relaxation to Ergodic Behavior

Here, we leverage the unique properties of the 4ABAH + · (H 2 O) n clusters (ABA = 4-aminobenzoic acid, n = 4−6) to quantitatively address how a finite, isolated system evolves into an ergodic condition starting from localized arrangements in configuration space. This system adopts two distinct structural isomers in which water molecules cluster around the cationic centers of its two protomers with widely separated positive charge centers. These isomers arise from excess proton attachment to either the acid (O) or amino (N) group on opposite sides of the benzene ring. Both forms are captured and kinetically trapped using cryogenic ion methods and then selectively vibrationally excited through their mutually exclusive IR bands involving NH and OH stretching fundamentals. Because the IR excitation lies below the water binding energy, the system can evolve to explore slow, rare events that lead to the interconversion between the two isomers. The rates of these intracluster reactions are determined by using a pump−probe scheme involving ∼5 ns IR pump and UV probe lasers. The rates occur on the microsecond time scale, leading to steady state populations of the isomers, thus revealing the cluster size-dependent fractionation between the two species at microcanonical equilibrium. The steady state distributions are correlated with the expected trend in the cluster size-dependent reaction energetics, which are in turn consistent with changes in the relative densities of states of the two species. These results thus provide an unusually clear example in which complex, protic-solvent-mediated chemical transformations are captured within a finite system at a precisely determined internal energy.

Rana, Abhijit [Yale Univ., New Haven, CT (United S↗

Facile One-Pot Block Copolymer-Mediated Solvothermal Approach for Synthesis of High-Entropy Alloy with Enhanced OER Activity

Herein, we introduce a straightforward synthesis approach for highly active dendritic multimetallic high-entropy alloy (DMHEA@PtIrPdAgRu) nanoparticles with sufficient entropic mixing, featuring uniform distribution of five noble group metals (Pt, Ir, Pd, Ag, and Ru) via a block copolymer-mediated one-pot solvothermal reduction method for oxygen evolution reaction (OER). In this synthesis, N,N -dimethylformamide (DMF) is used as a reductant as well as solvent and core–shell-corona-type (poly(styrene)- block -poly(vinylpyridine)- block -poly(ethylene oxide)) (PS-PVP-PEO) block copolymer as a structure directing agent. The cooperative effect between the copolymer architecture and the reducing environment of DMF promoted a confined nucleation mechanism for forming a single-phase dendritic structure HEA with high compositional uniformity, thereby mitigating phase segregation, a common challenge in the synthesis of multimetallic nanoparticles. This prepared DMHEA@PtIrPdAgRu catalyst exhibits a low overpotential of 490 mV to attain a high current density of 100 mA cm –2 with a Tafel slope of 442 mV dec –1 for oxygen evolution. The superior OER performance is attributed to the synergistic cooperation among its active and coordinated metal centers as well as the incorporation of corrosion-resistant metal like platinum.

block copolymer↗

Molecular bridge-mediated ultralow-power gas sensing

Abstract We report the electrical detection of captured gases through measurement of the quantum tunneling characteristics of gas-mediated molecular junctions formed across nanogaps. The gas-sensing nanogap device consists of a pair of vertically stacked gold electrodes separated by an insulating 6 nm spacer (~1.5 nm of sputtered α-Si and ~4.5 nm ALD SiO 2 ), which is notched ~10 nm into the stack between the gold electrodes. The exposed gold surface is functionalized with a self-assembled monolayer (SAM) of conjugated thiol linker molecules. When the device is exposed to a target gas (1,5-diaminopentane), the SAM layer electrostatically captures the target gas molecules, forming a molecular bridge across the nanogap. The gas capture lowers the barrier potential for electron tunneling across the notched edge region, from ~5 eV to ~0.9 eV and establishes additional conducting paths for charge transport between the gold electrodes, leading to a substantial decrease in junction resistance. We demonstrated an output resistance change of >10 8 times upon exposure to 80 ppm diamine target gas as well as ultralow standby power consumption of <15 pW, confirming electron tunneling through molecular bridges for ultralow-power gas sensing.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

An integrated multi-omics approach identifies the landscape of interferon-α-mediated responses of human pancreatic beta cells

Proinflammatory cytokines are important mediators of pancreatic beta cell dysfunction and demise in the early stages of type 1 diabetes (T1D). Interferon-a (IFNa), a type I interferon member, is expressed in the islets of T1D individuals and it is expression and signaling is regulated by both genetic (T1D risk variants) and environmental factors (viral infections) associated to T1D. We presently characterized human beta cells responses to IFNa by combining ATAC-seq, RNA-seq and proteomics assays. The initial beta cell response to IFNa was characterized by major chromatin remodeling, followed by marked changes in transcriptional and translational regulation. IFNa-induced changes in alternative splicing (AS) and first exon usage increased the diversity of transcripts expressed by beta cells. This, combined with changes observed on protein modification/degradation, ER stress and MHC class I, may significantly expand the peptide repertoire presented by beta cells to the immune system. On the other hand, beta cells up-regulated checkpoint proteins, such as PDL1 and HLA-E, that may protect them against the autoimmune assault. Data mining of the present multi-omics analysis led to the identification of two compound classes that revert IFNa effects on human beta cells and may be translated to clinical trials.

60 APPLIED LIFE SCIENCES↗

KRAS interaction with RAF1 RAS-binding domain and cysteine-rich domain provides insights into RAS-mediated RAF activation

The first step of RAF activation involves binding to active RAS, resulting in the recruitment of RAF to the plasma membrane. To understand the molecular details of RAS-RAF interaction, we present crystal structures of wild-type and oncogenic mutants of KRAS complexed with the RAS-binding domain (RBD) and the membrane-interacting cysteine-rich domain (CRD) from the N-terminal regulatory region of RAF1. Our structures reveal that RBD and CRD interact with each other to form one structural entity in which both RBD and CRD interact extensively with KRAS. Mutations at the KRAS-CRD interface result in a significant reduction in RAF1 activation despite only a modest decrease in binding affinity. Combining our structures and published data, we provide a model of RAS-RAF complexation at the membrane, and molecular insights into RAS-RAF interaction during the process of RAS-mediated RAF activation.

60 APPLIED LIFE SCIENCES↗

Directed evolution of and structural insights into antibody-mediated disruption of a stable receptor-ligand complex

Antibody drugs exert therapeutic effects via a range of mechanisms, including competitive inhibition, allosteric modulation, and immune effector mechanisms. Facilitated dissociation is an additional mechanism where antibody-mediated “disruption” of stable high-affinity macromolecular complexes can potentially enhance therapeutic efficacy. However, this mechanism is not well understood or utilized therapeutically. Here, we investigate and engineer the weak disruptive activity of an existing therapeutic antibody, omalizumab, which targets IgE antibodies to block the allergic response. We develop a yeast display approach to select for and engineer antibody disruptive efficiency and generate potent omalizumab variants that dissociate receptor-bound IgE. We determine a low resolution cryo-EM structure of a transient disruption intermediate containing the IgE-Fc, its partially dissociated receptor and an antibody inhibitor. Our results provide a conceptual framework for engineering disruptive inhibitors for other targets, insights into the failure in clinical trials of the previous high affinity omalizumab HAE variant and anti-IgE antibodies that safely and rapidly disarm allergic effector cells.

59 BASIC BIOLOGICAL SCIENCES↗

Chemistry-mediated Ostwald ripening in carbon-rich C/O systems at extreme conditions

Abstract There is significant interest in establishing a capability for tailored synthesis of next-generation carbon-based nanomaterials due to their broad range of applications and high degree of tunability. High pressure (e.g., shockwave-driven) synthesis holds promise as an effective discovery method, but experimental challenges preclude elucidating the processes governing nanocarbon production from carbon-rich precursors that could otherwise guide efforts through the prohibitively expansive design space. Here we report findings from large scale atomistically-resolved simulations of carbon condensation from C/O mixtures subjected to extreme pressures and temperatures, made possible by machine-learned reactive interatomic potentials. We find that liquid nanocarbon formation follows classical growth kinetics driven by Ostwald ripening (i.e., growth of large clusters at the expense of shrinking small ones) and obeys dynamical scaling in a process mediated by carbon chemistry in the surrounding reactive fluid. The results provide direct insight into carbon condensation in a representative system and pave the way for its exploration in higher complexity organic materials. They also suggest that simulations using machine-learned interatomic potentials could eventually be employed as in-silico design tools for new nanomaterials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Molecular insights into antibody-mediated protection against the prototypic simian immunodeficiency virus

SIVmac239 infection of macaques is a favored model of human HIV infection. However, the SIVmac239 envelope (Env) trimer structure, glycan occupancy, and the targets and ability of neutralizing antibodies (nAbs) to protect against SIVmac239 remain unknown. Here, we report the isolation of SIVmac239 nAbs that recognize a glycan hole and the V1/V4 loop. A high-resolution structure of a SIVmac239 Env trimer-nAb complex shows many similarities to HIV and SIVcpz Envs, but with distinct V4 features and an extended V1 loop. Moreover, SIVmac239 Env has a higher glycan shield density than HIV Env that may contribute to poor or delayed nAb responses in SIVmac239-infected macaques. Passive transfer of a nAb protects macaques from repeated intravenous SIVmac239 challenge at serum titers comparable to those described for protection of humans against HIV infection. Our results provide structural insights for vaccine design and shed light on antibody-mediated protection in the SIV model.

60 APPLIED LIFE SCIENCES↗

Shining light on the microscopic resonant mechanism responsible for cavity-mediated chemical reactivity

Strong light–matter interaction in cavity environments is emerging as a promising approach to control chemical reactions in a non-intrusive and efficient manner. The underlying mechanism that distinguishes between steering, accelerating, or decelerating a chemical reaction has, however, remained unclear, hampering progress in this frontier area of research. We leverage quantum-electrodynamical density-functional theory to unveil the microscopic mechanism behind the experimentally observed reduced reaction rate under cavity induced resonant vibrational strong light-matter coupling. We observe multiple resonances and obtain the thus far theoretically elusive but experimentally critical resonant feature for a single strongly coupled molecule undergoing the reaction. While we describe only a single mode and do not explicitly account for collective coupling or intermolecular interactions, the qualitative agreement with experimental measurements suggests that our conclusions can be largely abstracted towards the experimental realization. Specifically, we find that the cavity mode acts as mediator between different vibrational modes. In effect, vibrational energy localized in single bonds that are critical for the reaction is redistributed differently which ultimately inhibits the reaction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Superior zero thermal expansion dual-phase alloy via boron-migration mediated solid-state reaction

Rapid progress in modern technologies demands zero thermal expansion (ZTE) materials with multi-property profiles to withstand harsh service conditions. Thus far, the majority of documented ZTE materials have shortcomings in different aspects that limit their practical utilization. Here, we report on a superior isotropic ZTE alloy with collective properties regarding wide operating temperature windows, high strength-stiffness, and cyclic thermal stability. A boron-migration-mediated solid-state reaction (BMSR) constructs a salient “plum pudding” structure in a dual-phase Er-Fe-B alloy, where the precursor ErFe 10 phase reacts with the migrated boron and transforms into the target Er 2 Fe 14 B (pudding) and α-Fe phases (plum). The formation of such microstructure helps to eliminate apparent crystallographic texture, tailor and form isotropic ZTE, and simultaneously enhance the strength and toughness of the alloy. These findings suggest a promising design paradigm for comprehensive performance ZTE alloys.

36 MATERIALS SCIENCE↗

Theory predicts UV/vis-to-IR photonic down conversion mediated by excited state vibrational polaritons

This work proposes a photophysical phenomenon whereby ultraviolet/visible (UV/vis) excitation of a molecule involving a Franck-Condon (FC) active vibration yields infrared (IR) emission by strong coupling to an optical cavity. The resulting UV/vis-to-IR photonic down conversion process is mediated by vibrational polaritons in the electronic excited state potential. It is shown that the formation of excited state vibrational polaritons (ESVP) via UV/vis excitation only involve vibrational modes with both a non-zero FC activity and IR activity in the excited state. Density functional theory calculations are used to identify 1-Pyreneacetic acid as a molecule with this property and the dynamics of ESVP are modeled. Overall, this work introduces an avenue of polariton chemistry where excited state dynamics are influenced by the formation of vibrational polaritons. Along with this, the UV/vis-to-IR photonic down conversion is potentially useful in both sensing excited state vibrations and quantum transduction schemes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Deep mutational scanning reveals the molecular determinants of RNA polymerase-mediated adaptation and tradeoffs

RNA polymerase (RNAP) is emblematic of complex biological systems that control multiple traits involving trade-offs such as growth versus maintenance. Laboratory evolution has revealed that mutations in RNAP subunits, including RpoB, are frequently selected. However, we lack a systems view of how mutations alter the RNAP molecular functions to promote adaptation. We, therefore, measured the fitness of thousands of mutations within a region of rpoB under multiple conditions and genetic backgrounds, to find that adaptive mutations cluster in two modules. Mutations in one module favor growth over maintenance through a partial loss of an interaction associated with faster elongation. Mutations in the other favor maintenance over growth through a destabilized RNAP-DNA complex. The two molecular handles capture the versatile RNAP-mediated adaptations. Combining both interaction losses simultaneously improved maintenance and growth, challenging the idea that growth-maintenance tradeoff resorts only from limited resources, and revealing how compensatory evolution operates within RNAP.

59 BASIC BIOLOGICAL SCIENCES↗

Two DOT1 enzymes cooperatively mediate efficient ubiquitin-independent histone H3 lysine 76 tri-methylation in kinetoplastids

In higher eukaryotes, a single DOT1 histone H3 lysine 79 (H3K79) methyltransferase processively produces H3K79me2/me3 through histone H2B mono-ubiquitin interaction, while the kinetoplastid Trypanosoma brucei di-methyltransferase DOT1A and tri-methyltransferase DOT1B efficiently methylate the homologous H3K76 without H2B mono-ubiquitination. Based on structural and biochemical analyses of DOT1A, we identify key residues in the methyltransferase motifs VI and X for efficient ubiquitin-independent H3K76 methylation in kinetoplastids. Substitution of a basic to an acidic residue within motif VI (Gx 6 K ) is essential to stabilize the DOT1A enzyme-substrate complex, while substitution of the motif X sequence VYGE by CAKS renders a rigid active-site loop flexible, implying a distinct mechanism of substrate recognition. We further reveal distinct methylation kinetics and substrate preferences of DOT1A (H3K76me0) and DOT1B (DOT1A products H3K76me1/me2) in vitro, determined by a Ser and Ala residue within motif IV, respectively, enabling DOT1A and DOT1B to mediate efficient H3K76 tri-methylation non-processively but cooperatively, and suggesting why kinetoplastids have evolved two DOT1 enzymes.

59 BASIC BIOLOGICAL SCIENCES↗

Multi-layered heterochromatin interaction as a switch for DIM2-mediated DNA methylation

Functional crosstalk between DNA methylation, histone H3 lysine-9 trimethylation (H3K9me3) and heterochromatin protein 1 (HP1) is essential for proper heterochromatin assembly and genome stability. However, how repressive chromatin cues guide DNA methyltransferases for region-specific DNA methylation remains largely unknown. Here, we report structure-function characterizations of DNA methyltransferase Defective-In-Methylation-2 (DIM2) in Neurospora . The DNA methylation activity of DIM2 requires the presence of both H3K9me3 and HP1. Our structural study reveals a bipartite DIM2-HP1 interaction, leading to a disorder-to-order transition of the DIM2 target-recognition domain that is essential for substrate binding. Furthermore, the structure of DIM2-HP1-H3K9me3-DNA complex reveals a substrate-binding mechanism distinct from that for its mammalian orthologue DNMT1. In addition, the dual recognition of H3K9me3 peptide by the DIM2 RFTS and BAH1 domains allosterically impacts the DIM2-substrate binding, thereby controlling DIM2-mediated DNA methylation. Together, this study uncovers how multiple heterochromatin factors coordinately orchestrate an activity-switching mechanism for region-specific DNA methylation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Interfacial dynamics mediate surface binding events on supramolecular nanostructures

The dynamic behavior of biological materials is central to their functionality, suggesting that interfacial dynamics could also mediate the activity of chemical events at the surfaces of synthetic materials. Here, we investigate the influence of surface flexibility and hydration on heavy metal remediation by nanostructures self-assembled from small molecules that are decorated with surface-bound chelators in water. We find that incorporating short oligo(ethylene glycol) spacers between the surface and interior domain of self-assembled nanostructures can drastically increase the conformational mobility of surface-bound lead-chelating moieties and promote interaction with surrounding water. In turn, we find the binding affinities of chelators tethered to the most flexible surfaces are more than ten times greater than the least flexible surfaces. Accordingly, nanostructures composed of amphiphiles that give rise to the most dynamic surfaces are capable of remediating thousands of liters of 50 ppb Pb 2+ -contaminated water with single grams of material. These findings establish interfacial dynamics as a critical design parameter for functional self-assembled nanostructures.

42 ENGINEERING↗

High-fidelity remote entanglement of trapped atoms mediated by time-bin photons

Abstract Photonic interconnects between quantum processing nodes are likely the only way to achieve large-scale quantum computers and networks. The bottleneck in such an architecture is the interface between well-isolated quantum memories and flying photons. We establish high-fidelity entanglement between remotely separated trapped atomic qubit memories, mediated by photonic qubits stored in the timing of their pulses. Such time-bin encoding removes sensitivity to polarization errors, enables long-distance quantum communication, and is extensible to quantum memories with more than two states. Using a measurement-based error detection process and suppressing a fundamental source of error due to atomic recoil, we achieve an entanglement fidelity of 97% and show that fundamental limits due to atomic recoil still allow fidelities in excess of 99.9%.

Science & Technology - Other Topics↗

Electrochemically mediated disproportionation for selective formaldehyde upcycling in acid

Formaldehyde (FA) electrolysis is attractive for paired production of value‑added chemicals. However, conventional electrolysis adopts alkaline electrolytes, which triggers FA self-disproportionation and severe feed loss. Here we introduce a sustainable and selective strategy for valorizing FA through electrochemically mediated disproportionation in acidic electrolytes. By leveraging a dual-electrode system consisting of a hydrophobic copper tetraminophthalocyanine layer (CuTAPc-layer) cathode and a Pt 2 Ru bimetallic anode, we efficiently convert FA into methanol and formic acid at high Faradaic efficiencies of 93.2% and 91.3%, respectively. Compared with alkaline FA oxidation, which can lose up to 76% FA and complicate downstream separation, the acidic system suppresses side reactions to ensure high product purity. Mechanism studies reveal that the hydrophobic microenvironment of CuTAPc-layer suppresses hydrogen evolution, while the stronger oxophilicity of Pt 2 Ru enhances FA activation and lowers the key deprotonation barrier for FA oxidation. The integrated device demonstrates application potential in polyoxymethylene upgrading, delivering 374.2 mA at 4 V with ~90% single-pass conversion, establishing a scalable and eco-friendly electrochemical pathway for chemical upcycling.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Influence of the broadly neutralizing antibody VRC01 on HIV breakthrough virus populations in antibody-mediated prevention trials

In the antibody mediated prevention (AMP) trials, the broadly neutralizing antibody (bNAb) VRC01 demonstrated protective efficacy against susceptible HIV strains. To understand how VRC01 shaped breakthrough infections, deep sequencing was performed on 172 participants (>100,000 gag-Δpol and rev-env-Δnef sequences), at diagnosis and over time, in the placebo and treatment arms of the African (HVTN703/HPTN081; NCT02568215) and Americas/Europe (HVTN704/HPTN085; NCT02716675) cohorts. A high frequency of multilineage infections was detected (38%), including co-infection with both VRC01 sensitive and resistant viruses. This high frequency is largely accounted for by low-abundance lineages. Although VRC01 does not significantly affect the genetic transmission bottleneck compared to placebo, higher VRC01 doses trend towards greater VRC01 neutralization differences among co-infecting lineages. Two-thirds of multilineage infections showed evidence of recombination at the diagnostic timepoint. In the treatment group there is evidence of recombinant viruses preferentially inheriting resistance-associated mutations. This study provides critical insights into viral genetic and antigenic diversity that needs to be targeted to achieve protection, and highlights the role of recombination in facilitating escape.

59 BASIC BIOLOGICAL SCIENCES↗