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At least 1,729 records · Page 96

Biochemical, Mechanistic, and Spectroscopic Characterization of Metallo-β-lactamase VIM-2

Our study examines metal binding to metallo-β-lactamase VIM-2, demonstrating the first successful preparation of a Co(II)-substituted VIM-2 analogue. Spectroscopic studies of the half- and fully metal loaded enzymes show that both Zn(II) and Co(II) bind cooperatively, where the major species present, regardless of stoichiometry, are apo- and di-Zn (or di-Co) enzymes. We also determined the di-Zn VIM-2 structure to a resolution of 1.55 Å, and this structure supports results from spectroscopic studies. Kinetics, both steady-state and pre-steady-state, show that VIM-2 utilizes a mechanism that proceeds through a very short-lived anionic intermediate when chromacef is used as the substrate. Comparison with other B1 enzymes shows that those that bind Zn(II) cooperatively are better poised to protonate the intermediate on its formation, compared to those that bind Zn(II) non-cooperatively, which uniformly build up substantial amounts of the intermediate.

59 BASIC BIOLOGICAL SCIENCES↗

Molecular Dynamics Simulations of Aldol Condensation Catalyzed by Alkylamine-Functionalized Crystalline Silica Surfaces

Molecular dynamics simulations are performed to investigate the cooperatively catalyzed aldol condensation between acetone and 4-nitrobenzaldehyde on alkylamine (or alkylenamine)-grafted silica surfaces, focusing on the mechanism of the catalytic activation of the acetone and 4-nitrobenzaldehyde by the acidic surface silanols followed by the nucleophilic attack of the basic amine functional group toward the activated reactant. From the analysis of the correlations between the catalytically active acid-base sites and reactants, it is concluded that the catalytic cooperativity of the acid-base pair can be affected by two factors: 1) the competition between the silanol and the amine (or enamine) to form a hydrogen bond with a reactant and 2) the flexibility of the alkylamine (or alkylenamine) backbone. Increasing the flexibility of the alkylamine facilitates the nucleophilic attack of the amine on the reactants. From the molecular dynamics simulations, it is found that C 3 propylamine and C 4 butylamine linkers exhibit the highest probability of reaction, which is consistent with the experimental observation that the activity of the aldol reaction on mesoporous silica depends on the length of alkylamine grafted on the silica surface. Furthermore, this simulation work serves as a pioneering study demonstrating how the molecular simulation approach can be successfully employed to investigate the cooperative catalytic activity of such bifunctional acid-base catalysts.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

EF-Hand Battle Royale: Hetero-ion Complexation in Lanmodulin

The lanmodulin (LanM) protein has emerged as an effective means for rare earth element (REE) extraction and separation from complex feedstocks without the use of organic solvents. Whereas the binding of LanM to individual REEs has been well characterized, little is known about the thermodynamics of mixed metal binding complexes (i.e., heterogeneous ion complexes), which limits the ability to accurately predict separation performance for a given metal ion mixture. In this paper, we employ the law of mass action to establish a theory of perfect cooperativity for LanM-REE complexation at the two highest-affinity binding sites. The theory is then used to derive an equation that explains the nonintuitive REE binding behavior of LanM, where separation factors for binary pairs of ions vary widely based on the ratio of ions in the aqueous phase, a phenomenon that is distinct from single-ion-binding chemical chelators. We then experimentally validate this theory and perform the first quantitative characterization of LanM complexation with heterogeneous ion pairs using resin-immobilized LanM. Importantly, the resulting homogeneous and heterogeneous constants enable accurate prediction of the equilibrium state of LanM in the presence of mixtures of up to 10 REEs, confirming that the perfect cooperativity model is an accurate mechanistic description of REE complexation by LanM. We further employ the model to simulate separation performance over a range of homogeneous and heterogeneous binding constants, revealing important insights into how mixed binding differentially impacts REE separations based on the relative positioning of the ion pairs within the lanthanide series. In addition to informing REE separation process optimization, these results provide mathematical and experimental insight into competition dynamics in other ubiquitous and medically relevant, cooperative binding proteins, such as calmodulin.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Pairing in a dry Fermi sea

In the traditional Bardeen–Cooper–Schrieffer theory of superconductivity, the amplitude for the propagation of a pair of electrons with momentum k and -k has a log singularity as the temperature decreases. This so-called Cooper instability arises from the presence of an electron Fermi sea. It means that an attractive interaction, no matter how weak, will eventually lead to a pairing instability. However, in the pseudogap regime of the cuprate superconductors, where parts of the Fermi surface are destroyed, this log singularity is suppressed, raising the question of how pairing occurs in the absence of a Fermi sea. In this paper, we report Hubbard model numerical results and the analysis of angular-resolved photoemission experiments on a cuprate superconductor. Finally, in contrast to the traditional theory, we find that in the pseudogap regime the pairing instability arises from an increase in the strength of the spin–fluctuation pairing interaction as the temperature decreases rather than the Cooper log instability.

36 MATERIALS SCIENCE↗

Synergistic epistasis enhances the co-operativity of mutualistic interspecies interactions

Abstract Early evolution of mutualism is characterized by big and predictable adaptive changes, including the specialization of interacting partners, such as through deleterious mutations in genes not required for metabolic cross-feeding. We sought to investigate whether these early mutations improve cooperativity by manifesting in synergistic epistasis between genomes of the mutually interacting species. Specifically, we have characterized evolutionary trajectories of syntrophic interactions of Desulfovibrio vulgaris (Dv) with Methanococcus maripaludis (Mm) by longitudinally monitoring mutations accumulated over 1000 generations of nine independently evolved communities with analysis of the genotypic structure of one community down to the single-cell level. We discovered extensive parallelism across communities despite considerable variance in their evolutionary trajectories and the perseverance within many evolution lines of a rare lineage of Dv that retained sulfate-respiration (SR+) capability, which is not required for metabolic cross-feeding. An in-depth investigation revealed that synergistic epistasis across pairings of Dv and Mm genotypes had enhanced cooperativity within SR− and SR+ assemblages, enabling their coexistence within the same community. Thus, our findings demonstrate that cooperativity of a mutualism can improve through synergistic epistasis between genomes of the interacting species, enabling the coexistence of mutualistic assemblages of generalists and their specialized variants.

59 BASIC BIOLOGICAL SCIENCES↗

Unconventional supercurrent phase in Ising superconductor Josephson junction with atomically thin magnetic insulator

Abstract In two-dimensional (2D) NbSe 2 crystal, which lacks inversion symmetry, strong spin-orbit coupling aligns the spins of Cooper pairs to the orbital valleys, forming Ising Cooper pairs (ICPs). The unusual spin texture of ICPs can be further modulated by introducing magnetic exchange. Here, we report unconventional supercurrent phase in van der Waals heterostructure Josephson junctions (JJs) that couples NbSe 2 ICPs across an atomically thin magnetic insulator (MI) Cr 2 Ge 2 Te 6 . By constructing a superconducting quantum interference device (SQUID), we measure the phase of the transferred Cooper pairs in the MI JJ. We demonstrate a doubly degenerate nontrivial JJ phase ( ϕ ), formed by momentum-conserving tunneling of ICPs across magnetic domains in the barrier. The doubly degenerate ground states in MI JJs provide a two-level quantum system that can be utilized as a new dissipationless component for superconducting quantum devices. Our work boosts the study of various superconducting states with spin-orbit coupling, opening up an avenue to designing new superconducting phase-controlled quantum electronic devices.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Resilient water infrastructure partnerships in institutionally complex systems face challenging supply and financial risk tradeoffs

Abstract As regions around the world invest billions in new infrastructure to overcome increasing water scarcity, better guidance is needed to facilitate cooperative planning and investment in institutionally complex and interconnected water supply systems. This work combines detailed water resource system ensemble modeling with multiobjective intelligent search to explore infrastructure investment partnership design in the context of ongoing canal rehabilitation and groundwater banking in California. Here we demonstrate that severe tradeoffs can emerge between conflicting goals related to water supply deliveries, partnership size, and the underlying financial risks associated with cooperative infrastructure investments. We show how hydroclimatic variability and institutional complexity can create significant uncertainty in realized water supply benefits and heterogeneity in partners’ financial risks that threaten infrastructure investment partnership viability. We demonstrate how multiobjective intelligent search can design partnerships with substantially higher water supply benefits and a fraction of the financial risk compared to status quo planning processes. This work has important implications globally for efforts to use cooperative infrastructure investments to enhance the climate resilience and financial stability of water supply systems.

Science & Technology - Other Topics↗

Principles of paralog-specific targeted protein degradation engaging the C-degron E3 KLHDC2

Abstract PROTAC® (proteolysis-targeting chimera) molecules induce proximity between an E3 ligase and protein-of-interest (POI) to target the POI for ubiquitin-mediated degradation. Cooperative E3-PROTAC-POI complexes have potential to achieve neo-substrate selectivity beyond that established by POI binding to the ligand alone. Here, we extend the collection of ubiquitin ligases employable for cooperative ternary complex formation to include the C-degron E3 KLHDC2. Ligands were identified that engage the C-degron binding site in KLHDC2, subjected to structure-based improvement, and linked to JQ1 for BET-family neo-substrate recruitment. Consideration of the exit vector emanating from the ligand engaged in KLHDC2’s U-shaped degron-binding pocket enabled generation of SJ46421, which drives formation of a remarkably cooperative, paralog-selective ternary complex with BRD3 BD2 . Meanwhile, screening pro-drug variants enabled surmounting cell permeability limitations imposed by acidic moieties resembling the KLHDC2-binding C-degron. Selectivity for BRD3 compared to other BET-family members is further manifested in ubiquitylation in vitro, and prodrug version SJ46420-mediated degradation in cells. Selectivity is also achieved for the ubiquitin ligase, overcoming E3 auto-inhibition to engage KLHDC2, but not the related KLHDC1, KLHDC3, or KLHDC10 E3s. In sum, our study establishes neo-substrate-specific targeted protein degradation via KLHDC2, and provides a framework for developing selective PROTAC protein degraders employing C-degron E3 ligases.

Science & Technology - Other Topics↗

Non-equilibrium anti-Stokes Raman spectroscopy for investigating Higgs modes in superconductors

Abstract Even before its role in electroweak symmetry breaking, the Anderson-Higgs mechanism was introduced to explain the Meissner effect in superconductors. Spontaneous symmetry-breaking yields massless phase modes representing the low-energy excitations of the Mexican-Hat potential. Only in superconductors the phase mode is shifted towards higher energies owing to the gauge field of the charged condensate. This results in a low-energy excitation spectrum governed by the Higgs mode. Consequently, the Bardeen-Cooper-Schrieffer-like Meissner effect signifies a macroscopic quantum condensate in which a photon acquires mass, representing a one-to-one analogy to high-energy physics. We report on an innovative spectroscopic technique to study symmetries and energies of the Higgs modes in the high-temperature superconductor Bi 2 Sr 2 CaCu 2 O 8 after a soft quench of the Mexican-Hat potential. Population inversion induced by an initial laser pulse leads to an additional anti-Stokes Raman-scattering signal, which is consistent with polarization-dependent Higgs modes. Within Ginzburg-Landau theory, the Higgs-mode energy is connected to the Cooper-pair coherence length. Within a Bardeen-Cooper-Schrieffer weak-coupling model we develop a quantitative and coherent description of single-particle and two-particle channels. This opens the avenue for Higgs Spectroscopy in quantum condensates and provides a unique pathway to control and explore Higgs physics.

Science & Technology - Other Topics↗

Resonance from antiferromagnetic spin fluctuations for superconductivity in UTe 2

We report superconductivity originates from the formation of bound (Cooper) pairs of electrons that can move through the lattice without resistance below the superconducting transition temperature $T_c$. Electron Cooper pairs in most superconductors form anti-parallel spin singlets with total spin S = 0, although they can also form parallel spin-triplet Cooper pairs with S = 1 and an odd parity wavefunction. Spin-triplet pairing is important because it can host topological states and Majorana fermions relevant for quantum computation. Because spin-triplet pairing is usually mediated by ferromagnetic (FM) spin fluctuations3, uranium-based materials near an FM instability are considered to be ideal candidates for realizing spin-triplet superconductivity. Indeed, UTe 2 , which has a $T_c$ ≈ 1.6 K, has been identified as a candidate for a chiral spin-triplet topological superconductor near an FM instability, although it also has antiferromagnetic (AF) spin fluctuations. Here we use inelastic neutron scattering (INS) to show that superconductivity in UTe 2 is coupled to a sharp magnetic excitation, termed resonance, at the Brillouin zone boundary near AF order. Because the resonance has only been found in spin-singlet unconventional superconductors near an AF instability, its observation in UTe 2 suggests that AF spin fluctuations may also induce spin-triplet pairing or that electron pairing in UTe 2 has a spin-singlet component.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Evidence for Dirac flat band superconductivity enabled by quantum geometry

In a flat band superconductor, the charge carriers’ group velocity v F is extremely slow. Superconductivity therein is particularly intriguing, being related to the long-standing mysteries of high-temperature superconductors and heavy-fermion systems. Yet the emergence of superconductivity in flat bands would appear paradoxical, as a small v F in the conventional Bardeen–Cooper–Schrieffer theory implies vanishing coherence length, superfluid stiffness and critical current. Here, using twisted bilayer graphene, we explore the profound effect of vanishingly small velocity in a superconducting Dirac flat band system. Using Schwinger-limited non-linear transport studies we demonstrate an extremely slow normal state drift velocity v n ≈ 1,000 m s –1 for filling fraction ν between -1/2 and -3/4 of the moiré superlattice. In the superconducting state, the same velocity limit constitutes a new limiting mechanism for the critical current, analogous to a relativistic superfluid. Importantly, our measurement of superfluid stiffness, which controls the superconductor’s electrodynamic response, shows that it is not dominated by the kinetic energy but instead by the interaction-driven superconducting gap, consistent with recent theories on a quantum geometric contribution. Here we find evidence for small Cooper pairs, characteristic of the Bardeen–Cooper–Schrieffer to Bose–Einstein condensation crossover, with an unprecedented ratio of the superconducting transition temperature to the Fermi temperature exceeding unity and discuss how this arises for ultra-strong coupling superconductivity in ultra-flat Dirac bands.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Coupled electronic and magnetic excitations in the cuprates and their role in the superconducting transition

The formation of Cooper pairs, a bound state of two electrons of opposite spin and momenta by exchange of a phonon, is a defining feature of conventional superconductivity. In the cuprate high temperature superconductors, even though the superconducting state also consists of Cooper pairs, the pairing mechanism remains intensely debated. Here, we investigate superconducting pairing in the Bi 2 Sr 2 CaCu 2 O 8+δ (Bi2212) cuprate by employing spectral functions obtained from angle-resolved photoemission as input to the Bethe-Salpeter equation. Assuming Cooper pairing is driven by spin fluctuations, we construct the spin-fluctuation-mediated pairing interaction and use it to compute the eigenfunctions and eigenvalues of the Bethe-Salpeter equation for multiple Bi2212 samples. The leading d-wave eigenvalue increases as the temperature is decreased toward $T_c$, reaching a value of approximately 1 at the $T_c$ corresponding to each doping value. This suggests that spin fluctuations can approximately account for $T_c$ and mediate pairing in the cuprate superconductors.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Investigation of sensitizer ions tunable-distribution in fluoride nanoparticles for efficient accretive three-center energy transfer

Cooperative upconversion luminescence of Yb³⁺-Yb³⁺ couples and three-center energy transfer mechanisms have been deeply investigated in Yb³⁺ doped and Yb³⁺-Tb³⁺ co-doped β-PbF₂ nanoparticles. As sensitizer ions, the distribution of Yb³⁺ ions, which is a key factor that affects the cooperative upconversion luminescence and three-center energy transfer processes, can be tuned by the structure of nanoparticles. Based on the three-center distributions in tetragonal PbYb{sub x}Tb{sub 1–x}F₅ nanoparticles, two different energy transfer models, Cooperative Energy Transfer (CET) and Accretive Energy Transfer (AET) mechanisms were established. Especially, AET model is observed and verified in this work for the first time. Experimental results obtained from photoluminescence spectroscopy study are in agreement with the theoretical calculations by applying rate equations in these models, strongly supporting the proposed three-center energy transfer mechanisms. The sensitization between Yb³⁺ ions only existing in AET process can greatly improve the energy transfer rates, further to enhance the quantum efficiency. The results that the calculated luminescence quantum efficiency in AET quantum cutting process is much higher than that in CET process (134% and 104%, respectively), can benefit for further increasing the conversion efficiency of c-Si solar cells.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Probing the folded state and mechanical unfolding pathways of T4 lysozyme using all-atom and coarse-grained molecular simulation

The Bacteriophage T4 Lysozyme (T4L) is a prototype modular protein comprised of an N-terminal and a C-domain domain, which was extensively studied to understand the folding/unfolding mechanism of modular proteins. To offer detailed structural and dynamic insights to the folded-state stability and the mechanical unfolding behaviors of T4L, we have performed extensive equilibrium and steered molecular dynamics simulations of both the wild-type (WT) and a circular permutation (CP) variant of T4L using all-atom and coarse-grained force fields. Our all-atom and coarse-grained simulations of the folded state have consistently found greater stability of the C-domain than the N-domain in isolation, which is in agreement with past thermostatic studies of T4L. While the all-atom simulation cannot fully explain the mechanical unfolding behaviors of the WT and the CP variant observed in an optical tweezers study, the coarse-grained simulations based on the Go model or a modified elastic network model (mENM) are in qualitative agreement with the experimental finding of greater unfolding cooperativity in the WT than the CP variant. Interestingly, the two coarse-grained models predict different structural mechanisms for the observed change in cooperativity between the WT and the CP variant—while the Go model predicts minor modification of the unfolding pathways by circular permutation (i.e., preserving the general order that the N-domain unfolds before the C-domain), the mENM predicts a dramatic change in unfolding pathways (e.g., different order of N/C-domain unfolding in the WT and the CP variant). Based on our simulations, we have analyzed the limitations of and the key differences between these models and offered testable predictions for future experiments to resolve the structural mechanism for cooperative folding/unfolding of T4L.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Predicted strong coupling of solid-state spins via a single magnon mode

Abstract We propose an approach to realize a hybrid quantum system composed of a diamond nitrogen-vacancy (NV) center spin coupled to a magnon mode of the low-damping, low-moment organic ferrimagnet vanadium tetracyanoethylene. We derive an analytical expression for the spin-magnon cooperativity as a function of NV position under a micron-scale perpendicularly magnetized disk, and show that, surprisingly, the cooperativity will be higher using this magnetic material than in more conventional materials with larger magnetic moments, due to in part to the reduced demagnetization field. For reasonable experimental parameters, we predict that the spin-magnon-mode coupling strength is g ∼ 2π×10 kHz. For isotopically pure 12 C diamond we predict strong coupling of an NV spin to the unoccupied magnon mode, with cooperativity C λ = 15 for a wide range of NV spin locations within the diamond, well within the spatial precision of NV center implantation. Thus our proposal describes a practical pathway for single-spin-state-to-single-magnon-occupancy transduction and for entangling NV centers over micron length scales.

Candido, Denis R. (ORCID:0000000267083280)↗

Postquench gap dynamics of two-band superconductors

Recent experimental progress in the fields of cold quantum gases and ultrafast optical spectroscopy of quantum materials allows us to controllably induce and probe nonadiabatic dynamics of superconductors and superfluids. The time evolution of the gap function before relaxation with the lattice is determined by the superposition of coherently evolving individual Cooper pairs within the manifold of the Bardeen-Cooper-Schrieffer (BCS) wave function. While dynamics following an abrupt quench of the pairing interaction strength in the single-band BCS model has been exactly solved due to the integrability of the model, the dynamics of postquench multiband superconductors remain under scrutiny. Here, we develop a generalization of the Volkov-Kogan Laplace-space perturbative method that allows us to determine the nonadiabatic gap dynamics of two-band fully gapped superconductors for a wide range of quench amplitudes. Our approach expands the long-time dynamics around the steady-state asymptotic value of the gap, which is self-consistently determined, rather than around the equilibrium value of the gap. We explicitly demonstrate that this method recovers the exact solution of the long-time gap dynamics in the single-band case and perfectly agrees with a numerical solution of the two-band model. We discover that dephasing of Cooper pairs from different bands leads to faster collisionless relaxation of the gap oscillation with a power law of t –3/2 instead of the well-known t –1/2 behavior found in the single-band case. Moreover, the gap oscillations display beating patterns arising from the existence of two different asymptotic gap values. Our results have important implications to a variety of two-band superconductors driven out of equilibrium, such as iron-based superconductors, MgB 2 , and SrTiO 3 .

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Multidimensional coherent spectroscopy of light-driven states and their collective modes in multiband superconductors

We present a comprehensive theory of light-controlled multiband superconductivity, and apply it to predict distinctive signatures of light-driven superconducting (SC) states in terahertz multidimensional coherent spectroscopy (THz-MDCS) experiments. We first derive gauge-invariant Maxwell-Bloch equations for multiband BCS superconductors with spatial fluctuations. We consider driving electromagnetic fields determined self-consistently by Maxwell's equations. By calculating the THz-MDCS spectra measured experimentally in the clean SC limit, we identify unique signatures of finite-momentum Cooper-pairing states that live longer than the laser pulse. They are controlled by a pair of THz laser pulses with well-defined relative phase (pulse pair). The pseudospin oscillators that describe the properties of these SC states are parametrically driven by both finite-momentum Cooper pairing and by time oscillations of the order-parameter relative phase. We show that such strong parametric driving leads to drastic changes in the THz-MDCS spectral shape from the predictions of third-order nonlinear susceptibility calculations. These spectral changes strongly depend on the interband-to-intraband interaction ratio and on the collective modes of the light-driven state. For negligible interband interaction, the spectra show a transition with increasing field, from traditional pump-probe, four-wave-mixing, and third-harmonic generation peaks determined by the laser frequency to sidebands determined by the excitations of the driven system. These sidebands emerge from difference-frequency Raman processes in the nonequilibrium SC state. For interband couplings weaker than the intraband pairing, we show that the Leggett phase collective mode leads to harmonic sidebands around the traditional pump-probe peaks. Additional Higgs collective mode peaks result from light-induced inversion-symmetry breaking in a thin-film geometry. For strong interband coupling, we find a transition from a nonequilibrium finite Cooper-pair momentum state characterized by hybrid-Higgs amplitude mode peaks in THz-MDCS spectra to a driven state identified experimentally by the emergence of Floquet-type sidebands at bi-Higgs frequencies. Those dominant bi-Higgs-frequency satellites are manifestations of a new order parameter relative phase collective mode that characterizes the nonequilibrium SC state. The predicted interaction- and field-dependent transitions in the spectral profile allow us to propose THz-MDCS experiments for quantum tomography of light-driven superconductivity.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Estimating the energy threshold of phonon-mediated superconducting qubit detectors operated in an energy-relaxation sensing scheme

In recent years, the lack of a conclusive detection of weakly interacting massive particle dark matter at the 10 GeV/c 2 mass scale and above has encouraged development of low-threshold detector technology aimed at probing lighter dark matter candidates. Detectors based on Cooper-pair-breaking sensors have emerged as a promising avenue for this detection due to the low (meV-scale) energy required for breaking a Cooper pair in most superconductors. Among them, devices based on superconducting qubits are interesting candidates for sensing due to their observed sensitivity to broken Cooper pairs. Here, we have developed an end-to-end G 4 CMP -based simulation framework and have used it to evaluate performance metrics of qubit-based devices operating in a gate-based “energy relaxation” readout scheme, akin to those used in recent studies of qubit sensitivity to ionizing radiation. We find that for this readout scheme, the qubit acts as a phonon sensor with an energy threshold ranging down to ≃ 0.4 eV for near-term performance parameters.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗