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At least 415 records · Page 23

Diastereoselectivity Controlled by the Hydrogenation Mechanisms during the Electrochemical Reduction of a Carbonyl Group

Stereocontrol is of critical importance in organic synthesis. In this study, we demonstrate how heterogeneous electrochemical hydrogenation enables diastereocontrol simply by tuning electrochemical hydrogenation mechanisms without altering the adsorption conformation of a reactant on the electrode. We use 4-hydroxy-1-tetralone (4-OH-tetralone) as a model reactant, where diastereomers can be produced during the hydrogenation of the carbonyl group. In traditional thermocatalytic hydrogenation, H 2 first dissociates on the catalyst surface to form surface-adsorbed hydrogen (H*), and therefore, H* is always added to the organic reactant from the catalyst side via hydrogen atom transfer (HAT). Thus, in order to flip the diastereoselectivity, the adsorbed reactant itself must be physically flipped. In contrast, electrochemical hydrogenation can occur either via HAT, where H is added from the electrode surface, or via proton-coupled electron transfer (PCET), where H is added from the solution side of the adsorbed reactant. Thus, without changing the adsorption conformation of the reactant, opposite diastereomers can be obtained by switching the hydrogenation mechanism (HAT vs PCET). In this work, using a combination of experimental and computational studies, we demonstrate two examples of flipping diastereoselectivity by different electrochemical hydrogenation mechanisms. In the first case, we achieve opposite diastereoselectivities using metals that adopt different hydrogenation mechanisms (HAT vs PCET). In the second case, we flip the diastereoselectivity by varying the applied potential, which switches one hydrogenation mechanism to the other on the same metal electrode. In each case, our results offer an atomic-level understanding of the preferred hydrogenation mechanism that enables the corresponding diastereoselectivity.

adsorption↗

An immersed interface method for microstructure-scale electrochemical battery models: numerical formulation and performance portable implementation

We present the numerical formulation, verification, and performance portable implementation of an immersed interface method for microstructure scale electrochemical modeling of batteries. The innovation in this approach is the resolution of chemical species and electrostatic potential discontinuities at active interfaces without the use of interface conforming unstructured grids. A unified formulation on Cartesian grids for all domains (electrodes and electrolyte) is used with interfacial flux conditions applied using volume fraction or “color” function gradients. We have developed one dimensional and two dimensional test cases with analytic solutions for electrochemical modeling using which we verified the consistency and accuracy of our scheme. Our solver is also validated against solutions from a macroscale model and an unstructured multi-subdomain solver for a full lithium ion cell. We then demonstrated the utility of our solver on an image-based complex battery electrode microstructure at high charging rate. Our technique also exhibits good scalability on distributed memory architectures using central processing units (CPU), with problem sizes up to 1.8 billion degrees of freedom and with 5400 ranks. Initial performance studies of our open-source performance portable solver showed about 70 times speed up using a graphics processing unit (GPU) compared to single compute core for a problem with 4 million cells.

25 ENERGY STORAGE↗

Bootstrapping 2d ϕ 4 theory with Hamiltonian truncation data

We combine the methods of Hamiltonian Truncation and the recently proposed generalisation of the S-matrix bootstrap that includes local operators to determine the two-particle scattering amplitude and the two-particle form factor of the stress tensor at s > 0 in the 2d Φ 4 theory. We use the form factor of the stress tensor at s ≤ 0 and its spectral density computed using Lightcone Conformal Truncation (LCT), and inject them into the generalized S-matrix bootstrap set-up. The obtained results for the scattering amplitude and the form factor are fully reliable only in the elastic regime. We independently construct the “pure” S-matrix bootstrap bounds (bootstrap without including matrix elements of local operators), and find that the sinh-Gordon model and its analytic continuation the “staircase model” saturate these bounds. Surprisingly, the Φ 4 two-particle scattering amplitude also very nearly saturates these bounds, and moreover is extremely close to that of the sinh-Gordon/staircase model.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Gating interactions steer loop conformational changes in the active site of the L1 metallo-β-lactamase

β-Lactam antibiotics are the most important and widely used antibacterial agents across the world. However, the widespread dissemination of β-lactamases among pathogenic bacteria limits the efficacy of β-lactam antibiotics. This has created a major public health crisis. The use of β-lactamase inhibitors has proven useful in restoring the activity of β-lactam antibiotics, yet, effective clinically approved inhibitors against class B metallo-β-lactamases are not available. L1, a class B3 enzyme expressed by Stenotrophomonas maltophilia , is a significant contributor to the β-lactam resistance displayed by this opportunistic pathogen. Structurally, L1 is a tetramer with two elongated loops, α3-β7 and β12-α5, present around the active site of each monomer. Residues in these two loops influence substrate/inhibitor binding. To study how the conformational changes of the elongated loops affect the active site in each monomer, enhanced sampling molecular dynamics simulations were performed, Markov State Models were built, and convolutional variational autoencoder-based deep learning was applied. The key identified residues (D150a, H151, P225, Y227, and R236) were mutated and the activity of the generated L1 variants was evaluated in cell-based experiments. The results demonstrate that there are extremely significant gating interactions between α3-β7 and β12-α5 loops. Taken together, the gating interactions with the conformational changes of the key residues play an important role in the structural remodeling of the active site. These observations offer insights into the potential for novel drug development exploiting these gating interactions.

59 BASIC BIOLOGICAL SCIENCES↗

Model-dependence of minimal-twist OPEs in d > 2 holographic CFTs

Following recent work on heavy-light correlators in higher-dimensional conformal field theories (CFTs) with a large central charge C T , we clarify the properties of stress tensor composite primary operators of minimal twist, [ T m ], using arguments in both CFT and gravity. We provide an efficient proof that the three-point coupling $\left\langle {\mathcal{O}}_L{\mathcal{O}}_L\left[{T}^m\right]\right\rangle$, where ${\mathcal{O}}_L$ is any light primary operator, is independent of the purely gravitational action. Next, we consider corrections to this coupling due to additional interactions in AdS effective field theory and the corresponding dual CFT. When the CFT contains a non-zero three-point coupling $\left\langle TT{\mathcal{O}}_L\right\rangle$, the three-point coupling $\left\langle {\mathcal{O}}_L{\mathcal{O}}_L\left[{T}^2\right]\right\rangle$ is modified at large C T if $\left\langle TT{\mathcal{O}}_L\right\rangle \sim \sqrt{C_T}$. This scaling is obeyed by the dilaton, by Kaluza-Klein modes of prototypical supergravity compactifications, and by scalars in stress tensor multiplets of supersymmetric CFTs. Quartic derivative interactions involving the graviton and the light probe field dual to ${\mathcal{O}}_L $ can also modify the minimal-twist couplings; these local interactions may be generated by integrating out a spin- ℓ ≥ 2 bulk field at tree level, or any spin ℓ at loop level. These results show how the minimal-twist OPE coefficients can depend on the higher-spin gap scale, even perturbatively.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Conformational restriction shapes the inhibition of a multidrug efflux adaptor protein

Abstract Membrane efflux pumps play a major role in bacterial multidrug resistance. The tripartite multidrug efflux pump system from Escherichia coli , AcrAB-TolC, is a target for inhibition to lessen resistance development and restore antibiotic efficacy, with homologs in other ESKAPE pathogens. Here, we rationalize a mechanism of inhibition against the periplasmic adaptor protein, AcrA, using a combination of hydrogen/deuterium exchange mass spectrometry, cellular efflux assays, and molecular dynamics simulations. We define the structural dynamics of AcrA and find that an inhibitor can inflict long-range stabilisation across all four of its domains, whereas an interacting efflux substrate has minimal effect. Our results support a model where an inhibitor forms a molecular wedge within a cleft between the lipoyl and αβ barrel domains of AcrA, diminishing its conformational transmission of drug-evoked signals from AcrB to TolC. This work provides molecular insights into multidrug adaptor protein function which could be valuable for developing antimicrobial therapeutics.

59 BASIC BIOLOGICAL SCIENCES↗

Engineering Supramolecular Polymer Conformation for Efficient Carbon Nanotube Sorting

Supramolecular polymer sorting is a promising approach to separating single-walled carbon nanotubes (CNTs) by electronic type. Unlike conjugated polymers, they can be easily removed from the CNTs after sorting by breaking the supramolecular bonds, allowing for isolation of electronically pristine CNTs as well as facile recycling of the sorting polymer. However, little is understood about how supramolecular polymer properties affect CNT sorting. Herein, chain stoppers are used to engineer the conformation of a supramolecular sorting polymer, thereby elucidating the relationship between sorting efficacy and polymer conformation. Through NMR and UV–vis spectroscopy, small-angle X-ray scattering (SAXS), and thermodynamic modeling, it is shown that this supramolecular polymer exhibits ring–chain equilibrium, and that this equilibrium can be skewed toward chains by the addition of chain stoppers. Furthermore, by controlling the stopper–monomer ratio, the sorting yield can be doubled from 7% to 14% without compromising the semiconducting purity (>99%) or properties of sorted CNTs.

42 ENGINEERING↗

The role of SAXS and molecular simulations in 3D structure elucidation of a DNA aptamer against lung cancer

Aptamers are short, single-stranded DNA or RNA oligonucleotide molecules that function as synthetic analogs of antibodies and bind to a target molecule with high specificity. Aptamer affinity entirely depends on its tertiary structure and charge distribution. Therefore, length and structure optimization are essential for increasing aptamer specificity and affinity. Here, we present a general optimization procedure for finding the most populated atomistic structures of DNA aptamers. Based on the existed aptamer LC-18 for lung adenocarcinoma, a new truncated LC-18 (LC-18t) aptamer LC-18t was developed. A three-dimensional (3D) shape of LC-18t was reported based on small-angle X-ray scattering (SAXS) experiments and molecular modeling by fragment molecular orbital or molecular dynamic methods. Molecular simulations revealed an ensemble of possible aptamer conformations in solution that were in close agreement with measured SAXS data. The aptamer LC-18t had stronger binding to cancerous cells in lung tumor tissues and shared the binding site with the original larger aptamer. The suggested approach reveals 3D shapes of aptamers and helps in designing better affinity probes.

59 BASIC BIOLOGICAL SCIENCES↗

Off-Lattice Markov Chain Monte Carlo Simulations of Mechanically Driven Polymers

Here, we develop off-lattice simulations of semiflexible polymer chains subjected to applied mechanical forces by using Markov Chain Monte Carlo. Our approach models the polymer as a chain of fixed length bonds, with configurations updated through adaptive nonlocal Monte Carlo moves. This proposed method enables precise calculation of a polymer’s response to a wide range of mechanical forces, which traditional on-lattice models cannot achieve. Our approach has shown excellent agreement with theoretical predictions of persistence length and end-to-end distance in quiescent states as well as stretching distances under tension. Moreover, our model eliminates the orientational bias present in on-lattice models, which significantly impacts calculations such as the scattering function, a crucial technique for revealing the polymer conformation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Directing Polymorphism of Colloid Crystals Using Conformational Entropy of Polymer Chains

Controlling the polytypes of close-packed structures of spherical colloids is still a challenging problem despite their wide occurrence. Here, in this work, we show that systematic engineering of the polytype structures of close-packed colloids is possible by using the conformational entropy of polymer chains confined in the interstitial space of colloid crystals. Our interstitial space analysis shows that the hexagonal close-packed (HCP) structures offer larger local interstitial space domains, and the structure director chains in favor of HCP counteract the entropic advantages of the face-centered cubic (FCC) lattices. Using model block copolymer colloids and the known lattice entropy of FCC, a proportionality parameter, β CP = 1.91 × 10 –3 ± 3.67 × 10 –4 , for quantifying the conformational entropy contribution toward HCP structures is extracted. This work demonstrates that the interstitial space of colloid crystals serves as a new structure engineering tool for the self-assembly of colloids.

36 MATERIALS SCIENCE↗

Anti-Ebola virus mAb 3A6 protects highly viremic animals from fatal outcome via binding GP(1,2) in a position elevated from the virion membrane

Abstract Monoclonal antibodies (mAbs) against Ebola virus (EBOV) glycoprotein (GP 1,2 ) are the standard of care for Ebola virus disease (EVD). Anti-GP 1,2 mAbs targeting the stalk and membrane proximal external region (MPER) potently neutralize EBOV in vitro and are protective in a mouse model of EVD. However, their neutralization mechanism is poorly understood because they target a GP 1,2 epitope that has evaded structural characterization. Using X-ray crystallography and cryo-electron tomography of mAb 3A6 complexed with its stalk–MPER epitope, we reveal a previously undescribed mechanism in which 3A6 binds to a conformation of GP 1,2 that is lifted from the virion membrane. We further show that in both domestic guinea pig and rhesus monkey EVD models, 3A6 provides therapeutic benefit at high-viremia advanced disease stages and at the lowest dose yet demonstrated for any anti-EBOV mAb-based monotherapy. The findings reported here can guide design of next-generation highly potent anti-EBOV therapeutics and vaccines.

Science & Technology - Other Topics↗

Scaling functions for eigenstate entanglement crossovers in harmonic lattices

For quantum matter, eigenstate entanglement entropies obey an area law or log-area law at low energies and small subsystem sizes and cross over to volume laws for high energies and large subsystems. This transition is captured by crossover functions, which assume a universal scaling form in quantum critical regimes. We demonstrate this for the harmonic lattice model, which describes quantized lattice vibrations and is a regularization for free scalar field theories, modeling, e.g., spin-0 bosonic particles. In one dimension, the ground-state entanglement obeys a log-area law. For dimensions d ≥ 2, it displays area laws, even at criticality. The distribution of excited-state entanglement entropies is found to be sharply peaked around subsystem entropies of corresponding thermodynamic ensembles in accordance with the eigenstate thermalization hypothesis. Numerically, we determine crossover scaling functions for the quantum critical regime of the model and do a large-deviation analysis. We show how infrared singularities of the system can be handled and how to access the thermodynamic limit using a perturbative trick for the covariance matrix. Eigenstates for quasi-free bosonic systems are not Gaussian. Here, we resolve this problem by considering appropriate squeezed states instead. For these, entanglement entropies can be evaluated efficiently.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Cryo-EM structures provide insight into how E. coli F 1 F o ATP synthase accommodates symmetry mismatch

F 1 F o ATP synthase functions as a biological rotary generator that makes a major contribution to cellular energy production. It comprises two molecular motors coupled together by a central and a peripheral stalk. Proton flow through the F o motor generates rotation of the central stalk, inducing conformational changes in the F 1 motor that catalyzes ATP production. Here we present nine cryo-EM structures of E. coli ATP synthase to 3.1–3.4 Å resolution, in four discrete rotational sub-states, which provide a comprehensive structural model for this widely studied bacterial molecular machine. We observe torsional flexing of the entire complex and a rotational sub-step of F o associated with long-range conformational changes that indicates how this flexibility accommodates the mismatch between the 3- and 10-fold symmetries of the F 1 and F o motors. We also identify density likely corresponding to lipid molecules that may contribute to the rotor/stator interaction within the F o motor.

59 BASIC BIOLOGICAL SCIENCES↗

Evaluating Implementations of the Immersed Boundary Method in the Weather Research and Forecasting Model

The terrain-following coordinate system used by many atmospheric models can cause numerical instabilities due to discretization errors as resolved terrain slopes increase and the grid becomes highly skewed. The immersed boundary (IB) method, which does not require the grid to conform to the terrain, has been shown to alleviate these errors, and has been used successfully for high-resolution atmospheric simulations over steep terrain, including vertical building surfaces. Since many previous applications of IB methods to atmospheric models have used very fine grid resolution (5 m or less), the present study seeks to evaluate IB method performance over a range of grid resolutions and aspect ratios. Two classes of IB algorithms, velocity reconstruction and shear stress reconstruction, are tested within the common framework of the Weather Research and Forecasting (WRF) Model. Performance is evaluated in two test cases, one with flat terrain and the other with the topography of Askervein Hill, both under neutrally stratified conditions. WRF-IB results are compared to similarity theory, observations, and native WRF results. Despite sensitivity to the location at which the IB intersects the model grid, the velocity reconstruction IB method shows consistent performance when used with a hybrid RANS/LES surface scheme. The shear stress reconstruction IB method is not sensitive to the grid intersection, but is less consistent and near-surface velocity errors can occur at coarse resolutions. This study represents an initial investigation of IB method variability across grid resolutions in WRF. Future work will focus on improving IB method performance at intermediate to coarse resolutions.

54 ENVIRONMENTAL SCIENCES↗

First-order formalism for β functions in bosonic sigma models from supersymmetry breaking

We consider the renormalization group flow equation for the two-dimensional sigma models with the Kähler target space. The first-order formulation allows us to treat perturbations in these models as current-current deformations. We demonstrate, however, that the conventional first-order formalism misses certain anomalies in the measure, and should be amended. We reconcile beta functions obtained within the conformal perturbation theory for the current-current deformations with traditional “geometric” results obtained in the background field methods, in this way resolving the peculiarities pointed out in O. Gamayun et al. [Peculiarities of beta functions in sigma models, J. High Energy Phys. 10 (2023) 097]. The result is achieved by the supersymmetric completion of the first-order sigma model.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Synthesis, aphicidal activity and conformation of novel insect kinin analogues as potential eco‐friendly insecticides

Abstract BACKGROUND The discovery of ecofriendly insecticides through a new strategy for aphid control is important because of the substantial resistance and unexpected eco‐toxicity to honeybees caused by traditional insecticides. The insect kinins, a class of multifunctional insect neuropeptides, are considered for potential application in pest control. In our previous work we developed several series of insect kinin analogues and found a promising lead II‐1 with good aphicidal activity. To seek further eco‐friendly aphicides, the optimization of II‐1 is carried out in this study. RESULTS Fifteen novel Yaa 3 modified analogues based on the lead II‐1 were synthesized. The aphicidal tests indicated that IV‐3 , IV‐5 and IV‐10 exhibited significant activity against the soybean aphid Aphis glycines with LC 50 values of 0.0029, 0.0072 and 0.0086 mmol L –1 , respectively, higher than that of lead II‐1 and the commercial Pymetrozine. The molecular modeling results showed that analogues II‐1 , IV‐3 , IV‐5 , IV‐7 and IV‐10 formed a β‐turn‐like conformation, while the conformation of analogues IV‐1 , IV‐2 and IV‐9 seemed to be linear. Some structural elements favorable for the activity were proposed based on the conformation‐activity relationship of the analogues. CONCLUSION Insect kinin analogues derived from lead II‐1 by modifying the hydrolysis site Yaa 3 with natural, sterically hindered α‐ and β‐amino acids showed great potential as eco‐friendly insecticides. Inspiringly, the most active analogue IV‐3 can be a candidate for further development. The β‐turn‐like conformation and the orientation of the aromatic rings of the side chain of Phe 2 and Trp 4 may be critical factors beneficial to activity. © 2019 Society of Chemical Industry

Zhang, Chuanliang↗

2025 Status Report - Fiberboard Properties and Degradation Rates for Storage of 9975 Shipping Package in KAC

Fiberboard assemblies in the 9975 package were identified as susceptible to aging and degradation under long-term storage conditions. Thermal, mechanical, and physical properties have been measured on fiberboard samples aging for up to 20 years at accelerated conditions. The aging environments include elevated temperature up to 250 ºF (the maximum allowed service temperature for fiberboard in 9975 packages) and elevated humidity. Accelerated aging results have been analyzed and used to build aging models. Correlations relating several properties (thermal conductivity, energy absorption, weight, dimensions, and density) to their rate of change in potential storage environments have been developed. Combined with an estimate of the actual conditions the fiberboard experiences in K-Area Complex (KAC), these models allow development of service life predictions. KAC completed calculations that supported extending the service life of 9975 packages with 3013 containers in storage from 20 years to 40 years. These calculations addressed the potential for degraded fiberboard properties following 40 years in storage using degradation models. The 40 year storage evaluations assumed the degradation rates from initial values for density, dimensional, and thermal properties were 0.5% per year (i.e., after 40 years, the density, dimensional, and thermal properties of fiberboard were 80% of its initial values). The updated degradation models developed in this report were compared to the assumptions in those calculations, and the current results for fiberboard dimensions, density, axial and radial thermal conductivities, and energy absorption remain consistent with those calculations. Additional data will continue to be collected to permit future refinements to the models and assumptions. Some of the predicted degradation rates presented in this report are purposely high to accelerate aging. These rates relate to environments that do not exist within KAC or are postulated to only occur as upset conditions that are unlikely to persist for an extended period. For a typical package stored in KAC with approximately 10-12 watts internal heat load or less, and ambient temperatures below 90 ºF, the fiberboard assemblies experience storage conditions less severe than any of the aging environments (i.e., under 125 °F) used in this study. Fiberboard in conforming packages with lower internal heat loads should experience little or no degradation and is expected to provide a service life beyond the currently approved 40 year storage period. Packages with higher internal heat loads may not continue to perform their required safety functions beyond 40 years. Ultimately, service life will be determined by the cumulative effect of degradation from all the conditions these packages might encounter. The results and model predictions presented in this report are applicable to 9975 packages with cane or softwood fiberboard overpack assemblies. These degradation models do not address the effects of nonconforming conditions such as the presence of excess moisture and mold or beetle infestations.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Quantum phase transition dynamics in the two-dimensional transverse-field Ising model

The quantum Kibble-Zurek mechanism (QKZM) predicts universal dynamical behavior near the quantum phase transitions (QPTs). It is now well understood for the one-dimensional quantum matter. Higher-dimensional systems, however, remain a challenge, complicated by the fundamentally different character of the associated QPTs and their underlying conformal field theories. In this work, we take the first steps toward theoretical exploration of the QKZM in two dimensions for interacting quantum matter. We study the dynamical crossing of the QPT in the paradigmatic Ising model by a joint effort of modern state-of-the-art numerical methods, including artificial neural networks and tensor networks. As a central result, we quantify universal QKZM behavior close to the QPT. We also note that, upon traversing further into the ferromagnetic regime, deviations from the QKZM prediction appear. We explain the observed behavior by proposing an extended QKZM taking into account spectral information as well as phase ordering. Our work provides a testing platform for higher-dimensional quantum simulators.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗