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At least 955 records · Page 53

Covalency of M–N Bonds in Isomorphous Lanthanide and Actinide 5-(2-Pyridyl)-1H-tetrazolate Complexes

Experimental and computational analyses of [M(pdtz) 3 (H 2 O) 3 ]·3.5H 2 O (M 3+ = Pu 3+ −Cm 3+ , La 3+ −Nd 3+ , and Sm 3+ −Ho 3+ , pdtz− = 5-(2-pyridyl)-1H-tetrazolate) were conducted to understand potential differences in bonding between lanthanide and actinide complexes with a N-donor ligand. Structural analyses show that the An−N bond distances in the Pu 3+ , Am 3+ , and Cm 3+ complexes are within error of one another. Whereas in the lanthanide series, there is a nearly linear decrease in the Ln−N bond lengths from La 3+ to Ho 3+ (excluding Pm 3+ ). The An−N bond lengths are ∼0.015 Å shorter than their similarly-sized lanthanide analogs, in agreement with computational results that suggest greater covalent character in these bonds versus those with lanthanides. QTAIM analysis indicates that the An−N orbital mixing remains essentially unchanged from Pu 3+ to Cm 3+ , consistent with the nearly identical An−N bond lengths. However, upon deconvolution of the NLMOs into orbital compositions, the metal orbital contributions to An−N bonding decreases slightly overall wherein the 6d involvement remains constant, 7s involvement slightly increases, and 5f participation decreases. The molecular orbital energy diagram indicates that energy degeneracy between the 5f metal and 2p ligand orbitals increases from Pu 3+ to Cm 3+ and counteracts the contraction of the 5f orbtials. Together with prior reports of decreasing energy degeneracy between 5f and 3p orbitals from Np 3+ to Cf 3+ , these observations provide guidance on understanding how chemical bonding evolves in the actinide series.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structures and function of a tailoring oxidase in complex with a nonribosomal peptide synthetase module

Nonribosomal peptide synthetases (NRPSs) are large modular enzymes that synthesize secondary metabolites and natural product therapeutics. Most NRPS biosynthetic pathways include an NRPS and additional proteins that introduce chemical modifications before, during or after assembly-line synthesis. The bacillamide biosynthetic pathway is a common, three-protein system, with a decarboxylase that prepares an NRPS substrate, an NRPS, and an oxidase. Here, the pathway is reconstituted in vitro. The oxidase is shown to perform dehydrogenation of the thiazoline in the peptide intermediate while it is covalently attached to the NRPS, as the penultimate step in bacillamide D synthesis. Structural analysis of the oxidase reveals a dimeric, two-lobed architecture with a remnant RiPP recognition element and a dramatic wrapping loop. The oxidase forms a stable complex with the NRPS and dimerizes it. We visualized co-complexes of the oxidase bound to the elongation module of the NRPS using X-ray crystallography and cryo-EM. The three active sites (for adenylation, condensation/cyclization, and oxidation) form an elegant arc to facilitate substrate delivery. The structures enabled a proof-of-principle bioengineering experiment in which the BmdC oxidase domain is embedded into the NRPS.

59 BASIC BIOLOGICAL SCIENCES↗

Small-world complex network generation on a digital quantum processor

Abstract Quantum cellular automata (QCA) evolve qubits in a quantum circuit depending only on the states of their neighborhoods and model how rich physical complexity can emerge from a simple set of underlying dynamical rules. The inability of classical computers to simulate large quantum systems hinders the elucidation of quantum cellular automata, but quantum computers offer an ideal simulation platform. Here, we experimentally realize QCA on a digital quantum processor, simulating a one-dimensional Goldilocks rule on chains of up to 23 superconducting qubits. We calculate calibrated and error-mitigated population dynamics and complex network measures, which indicate the formation of small-world mutual information networks. These networks decohere at fixed circuit depth independent of system size, the largest of which corresponding to 1,056 two-qubit gates. Such computations may enable the employment of QCA in applications like the simulation of strongly-correlated matter or beyond-classical computational demonstrations.

97 MATHEMATICS AND COMPUTING↗

Binding of the substrate analog methanol in the oxygen-evolving complex of photosystem II in the D1-N87A genetic variant of cyanobacteria

The solar water-splitting protein complex, photosystem II (PSII), catalyzes one of the most energetically demanding reactions in nature by using light energy to drive a catalyst capable of oxidizing water. The water oxidation reaction is catalyzed at the Mn 4 Ca-oxo cluster in the oxygen-evolving complex (OEC), which cycles through five light-driven S-state intermediates (S 0 –S 4 ). A detailed mechanism of the reaction remains elusive as it requires knowledge of the delivery and binding of substrate water in the higher S-state intermediates. In this paper, we use two-dimensional (2D) hyperfine sublevel correlation spectroscopy, in conjunction with quantum mechanics/molecular mechanics (QM/MM) and density functional theory (DFT), to probe the binding of the substrate analog, methanol, in the S 2 state of the D1-N87A variant of PSII from Synechocystis sp. PCC 6803. The results indicate that the size and specificity of the “narrow” channel is altered in D1-N87A PSII, allowing for the binding of deprotonated 13 C-labeled methanol at the Mn4(IV) ion of the catalytic cluster in the S 2 state. This has important implications on the mechanistic models for water oxidation in PSII.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Coupled charge and energy transfer dynamics in light harvesting complexes from a hybrid hierarchical equations of motion approach

Here, we describe a method for simulating exciton dynamics in protein–pigment complexes, including effects from charge transfer as well as fluorescence. The method combines the hierarchical equations of motion, which are used to describe quantum dynamics of excitons, and the Nakajima–Zwanzig quantum master equation, which is used to describe slower charge transfer processes. We study the charge transfer quenching in light harvesting complex II, a protein postulated to control non-photochemical quenching in many plant species. Using our hybrid approach, we find good agreement between our calculation and experimental measurements of the excitation lifetime. Furthermore, our calculations reveal that the exciton energy funnel plays an important role in determining quenching efficiency, a conclusion we expect to extend to other proteins that perform protective excitation quenching. This also highlights the need for simulation methods that properly account for the interplay of exciton dynamics and charge transfer processes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Interacting dust grains in complex plasmas: Ion wake formation and the electric potential

Dust grains have been used as minimally invasive probes to determine plasma parameters including the plasma density, temperature, and electric field in a plasma discharge. However, the dust grains in a plasma generate local potential disturbances due to the collection of charge and the subsequent electrostatic interactions between the dust and charged plasma particles. Dust grains in close proximity to one another exhibit interesting non-reciprocal interactions and self-organize into structures such as one-dimensional filamentary chains, two-dimensional “zigzags,” and three-dimensional helices, among others. The formation of these structures suggests that although the dust grains may be less invasive than traditional plasma probes, the disturbance to the local plasma environment introduced by dust grains is non-trivial. Commonly used analytic forms of the electric potential describing complex plasmas have failed to resolve the near-dust region, and as a result are insufficient to provide insight about the formation of complex dust structures. Here, we use an N-body simulation to compute the electric potential from ion densities near various dust grain configurations. We provide an alternative description to the standard analytic model for the electric potential of dust and ion wakes based on a Gaussian shaped cloud of ions. The electric potential obtained from simulations is used to identify minimum energy configurations for two and three dust grains. It is further demonstrated that the minimum potential region identified for N dust grains and their associated ion wakes does not predict the minimum-energy configuration of N + 1 dust grains.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Functional enzyme–polymer complexes

Significance The use of biological enzyme catalysts could have huge ramifications for chemical industries. However, these enzymes are often inactive in nonbiological conditions, such as high temperatures, present in industrial settings. Here, we show that the enzyme PETase (polyethylene terephthalate [PET]), with potential application in plastic recycling, is stabilized at elevated temperature through complexation with random copolymers. We demonstrate this through simulations and experiments on different types of substrates. Our simulations also provide strategies for designing more enzymatically active complexes by altering polymer composition and enzyme charge distribution.

59 BASIC BIOLOGICAL SCIENCES↗

Driving force and pathway in polyelectrolyte complex coacervation

There is notable discrepancy between experiments and coarse-grained model studies regarding the thermodynamic driving force in polyelectrolyte complex coacervation: experiments find the free energy change to be dominated by entropy, while simulations using coarse-grained models with implicit solvent usually report a large, even dominant energetic contribution in systems with weak to intermediate electrostatic strength. Here, using coarse-grained, implicit-solvent molecular dynamics simulation combined with thermodynamic analysis, we study the potential of mean force (PMF) in the two key stages on the coacervation pathway for symmetric polyelectrolyte mixtures: polycation–polyanion complexation and polyion pair–pair condensation. We show that the temperature dependence in the dielectric constant of water gives rise to a substantial entropic contribution in the electrostatic interaction. By accounting for this electrostatic entropy, which is due to solvent reorganization, we find that under common conditions (monovalent ions, room temperature) for aqueous systems, both stages are strongly entropy-driven with negligible or even unfavorable energetic contributions, consistent with experimental results. Furthermore, for weak to intermediate electrostatic strengths, this electrostatic entropy, rather than the counterion-release entropy, is the primary entropy contribution. From the calculated PMF, we find that the supernatant phase consists predominantly of polyion pairs with vanishingly small concentration of bare polyelectrolytes, and we provide an estimate of the spinodal of the supernatant phase. Finally, we show that prior to contact, two neutral polyion pairs weakly attract each other by mutually induced polarization, providing the initial driving force for the fusion of the pairs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Scattering evidence of positional charge correlations in polyelectrolyte complexes

Polyelectrolyte complexation plays an important role in materials science and biology. The internal structure of the resultant polyelectrolyte complex (PEC) phase dictates properties such as physical state, response to external stimuli, and dynamics. Small-angle scattering experiments with X-rays and neutrons have revealed structural similarities between PECs and semidilute solutions of neutral polymers, where the total scattering function exhibits an Ornstein–Zernike form. In spite of consensus among different theoretical predictions, the existence of positional correlations between polyanion and polycation charges has not been confirmed experimentally. Here, we present small-angle neutron scattering profiles where the polycation scattering length density is matched to that of the solvent to extract positional correlations among anionic monomers. The polyanion scattering functions exhibit a peak at the inverse polymer screening radius of Coulomb interactions, q* ≈ 0.2 Å –1 . This peak, attributed to Coulomb repulsions between the fragments of polyanions and their attractions to polycations, is even more pronounced in the calculated charge scattering function that quantifies positional correlations of all polymer charges within the PEC. Screening of electrostatic interactions by adding salt leads to the gradual disappearance of this correlation peak, and the scattering functions regain an Ornstein–Zernike form. Experimental scattering results are consistent with those calculated from the random phase approximation, a scaling analysis, and molecular simulations.

74 ATOMIC AND MOLECULAR PHYSICS↗

Engineering transformation pathways in an Al 0.3 CoFeNi complex concentrated alloy leads to excellent strength–ductility combination

Guided by thermodynamic modeling, engineering phase transformation pathways via thermo-mechanical processing, in a complex concentrated alloy/high entropy alloy (HEA) of composition Al 0.3 CoFeNi, lead to a novel multi-scale microstructure consisting of fine-scale FCC + L1 2 grains mixed with B2 + BCC grains. The two-step pathway comprises initial decomposition of the parent single-phase FCC to form a fine-grained FCC + B2 microstructure, which further decomposes in the second step into the complex four-phase mixture, exhibiting an excellent combination of tensile yield stress of ~1490 MPa, ultimate tensile strength of ~1663 MPa, with a good ductility of ~12% at room temperature. This paper reports a novel multi-phase microstructure in a HEA/CCA similar to the microstructure observed in dual-phase stainless steel. This report exemplifies the novelty of HEA/CCA compositional space.

36 MATERIALS SCIENCE↗

Layered complex networks as fluctuation amplifiers

Abstract In complex networked systems theory, an important question is how to evaluate the system robustness to external perturbations. With this task in mind, I investigate the propagation of noise in multi-layer networked systems. I find that, for a two layer network, noise originally injected in one layer can be strongly amplified in the other layer, depending on how well-connected are the complex networks in each layer and on how much the eigenmodes of their Laplacian matrices overlap. These results allow to predict potentially harmful conditions for the system and its sub-networks, where the level of fluctuations is important, and how to avoid them. The analytical results are illustrated numerically on various synthetic networks.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Learning a general model of single phase flow in complex 3D porous media

Modeling effective transport properties of 3D porous media, such as permeability, at multiple scales is challenging as a result of the combined complexity of the pore structures and fluid physics—in particular, confinement effects which vary across the nanoscale to the microscale. While numerical simulation is possible, the computational cost is prohibitive for realistic domains, which are large and complex. Although machine learning (ML) models have been proposed to circumvent simulation, none so far has simultaneously accounted for heterogeneous 3D structures, fluid confinement effects, and multiple simulation resolutions. By utilizing numerous computer science techniques to improve the scalability of training, we have for the first time developed a general flow model that accounts for the pore-structure and corresponding physical phenomena at scales from Angstrom to the micrometer. Using synthetic computational domains for training, our ML model exhibits strong performance (R 2 = 0.9) when tested on extremely diverse real domains at multiple scales.

36 MATERIALS SCIENCE↗

Taxogenomic analysis of Pichia senei sp. nov. and new insights into hybridization events in the Pichia cactophila species complex

Three strains of a novel yeast species were isolated from necrotic cactus tissues of Cereus saddianus and Micranthocereus dolichospermaticus and from phytotelmata of Bromelia karatas. DNA sequence analysis of the Internal Transcribed Spacer (ITS) region and D1/D2 domains of the large subunit ribosomal RNA, along with whole genome phylogenomic analysis, showed that this yeast is most closely related to Pichia insulana, Pichia cactophila, and Pichia inconspicua. The new species differs by 10–13 nucleotide substitutions from these species in D1/D2 sequences and exhibits <90% genome-wide average nucleotide identity to them. The name Pichia senei sp. nov. is proposed for the novel species, which is homothallic and produces asci with one to four hat-shaped ascospores. The holotype is CBS 16311 (MycoBank MB 858723). Taxogenomic analyses of the P. cactophila species complex, including P. senei, provide new insights about the hybridizations events that shaped this group. Pichia insulana and P. inconspicua are identified as the parental lineages that originated P. cactophila, and P. senei also appears closely related to one of the progenitors of P. inconspicua. We assess phylogeny, heterozygosity, and ploidy to explore the processes shaping diversity, showing how genomic data support yeast species delimitation and reveal complex hybridization.

59 BASIC BIOLOGICAL SCIENCES↗

Cellulose synthesis complexes are homo-oligomeric and hetero-oligomeric in Physcomitrium patens

The common ancestor of seed plants and mosses contained homo-oligomeric cellulose synthesis complexes (CSCs) composed of identical subunits encoded by a single CELLULOSE SYNTHASE (CESA) gene. Seed plants use different CESA isoforms for primary and secondary cell wall deposition. Both primary and secondary CESAs form hetero-oligomeric CSCs that assemble and function in planta only when all the required isoforms are present. The moss Physcomitrium (Physcomitrella) patens has seven CESA genes that can be grouped into two functionally and phylogenetically distinct classes. Previously, we showed that PpCESA3 and/or PpCESA8 (class A) together with PpCESA6 and/or PpCESA7 (class B) form obligate hetero-oligomeric complexes required for normal secondary cell wall deposition. Here, we show that gametophore morphogenesis requires a member of class A, PpCESA5, and is sustained in the absence of other PpCESA isoforms. Further, PpCESA5 also differs from the other class A PpCESAs as it is able to self-interact and does not co-immunoprecipitate with other PpCESA isoforms. These results are consistent with the hypothesis that homo-oligomeric CSCs containing only PpCESA5 subunits synthesize cellulose required for gametophore morphogenesis. Analysis of mutant phenotypes also revealed that, like secondary cell wall deposition, normal protonemal tip growth requires class B isoforms (PpCESA4 or PpCESA10), along with a class A partner (PpCESA3, PpCESA5, or PpCESA8). Thus, P. patens contains both homo-oligomeric and hetero-oligomeric CSCs.

59 BASIC BIOLOGICAL SCIENCES↗

Li 4 Ru 2 OCl 10 ·10H 2 O: crystal structure, magnetic properties and bonding interactions in ruthenium-oxo complexes

The results of the structural determination, magnetic characterization, and theoretical calculations of a new ruthenium-oxo complex, Li 4 [Ru 2 OCl 10 ]·10H 2 O, are presented. Single crystals were grown using solvent methods and the crystal structure was characterized by single crystal X-ray diffraction. Li 4 [Ru 2 OCl 10 ]·10H 2 O crystallizes into a low-symmetry triclinic structure ($P\bar1$) due to the much smaller Li + cation compared to K + cation in the tetragonal complex K 4 [Ru 2 OCl 10 ]·H 2 O. The X-ray photoelectron spectra confirm only the single valent Ru 4+ in Li 4 [Ru 2 OCl 10 ]·10H 2 O even though two distinct Ru sites exist in the crystal structure. Magnetic measurements reveal the diamagnetic property of Li 4 [Ru 2 OCl 10 ]·10H 2 O with unpaired electrons existing on Ru 4+ . Furthermore, the molecular orbital analysis matches well with the observed UV and magnetic measurements.

36 MATERIALS SCIENCE↗

Embracing fine-root system complexity in terrestrial ecosystem modeling

Projecting the dynamics and functioning of the biosphere requires a holistic consideration of whole-ecosystem processes. However, biases toward leaf, canopy, and soil modeling since the 1970s have constantly left fine-root systems being rudimentarily treated. As accelerated empirical advances in the last two decades establish clearly functional differentiation conferred by the hierarchical structure of fine-root orders and associations with mycorrhizal fungi, a need emerges to embrace this complexity to bridge the data-model gap in still extremely uncertain models. In this work, we propose a three-pool structure comprising transport and absorptive fine roots with mycorrhizal fungi (TAM) to model vertically resolved fine-root systems across organizational and spatial–temporal scales. Emerging from a conceptual shift away from arbitrary homogenization, TAM builds upon theoretical and empirical foundations as an effective and efficient approximation that balances realism and simplicity. A proof-of-concept demonstration of TAM in a big-leaf model both conservatively and radically shows robust impacts of differentiation within fine-root systems on simulating carbon cycling in temperate forests. Theoretical and quantitative support warrants exploiting its rich potentials across ecosystems and models to confront uncertainties and challenges for a predictive understanding of the biosphere. Echoing a broad trend of embracing ecological complexity in integrative ecosystem modeling, TAM may offer a consistent framework where modelers and empiricists can work together toward this grand goal.

59 BASIC BIOLOGICAL SCIENCES↗

Low-Order Preconditioning for the High-Order Finite Element de Rham Complex

Here, we present a unified framework for constructing spectrally equivalent low-order-refined discretizations for the high-order finite element de Rham complex. This theory covers diffusion problems in H 1 , H(curl), and H(div) and is based on combining a low-order discretization posed on a refined mesh with a high-order basis for Nédélec and Raviart–Thomas elements that makes use of the concept of polynomial histopolation (polynomial fitting using prescribed mean values over certain regions). This spectral equivalence, coupled with algebraic multigrid methods constructed using the low-order discretization, results in highly scalable matrix-free preconditioners for high-order finite element problems in the full de Rham complex. Additionally, a new lowest-order (piecewise constant) preconditioner is developed for high-order interior penalty discontinuous Galerkin (DG) discretizations, for which spectral equivalence results and convergence proofs for algebraic multigrid methods are provided. In all cases, the spectral equivalence results are independent of polynomial degree and mesh size; for DG methods, they are also independent of the penalty parameter. These new solvers are flexible and easy to use; any “black-box” preconditioner for low-order problems can be used to create an effective and efficient preconditioner for the corresponding high-order problem. A number of numerical experiments are presented, based on an implementation in the finite element library MFEM. A range of challenging three-dimensional problems are used to corroborate the theoretical properties and demonstrate the flexibility and scalability of the method.

97 MATHEMATICS AND COMPUTING↗

Reducing Operator Complexity of Galerkin Coarse-grid Operators with Machine Learning

Here, we propose a data-driven and machine-learning-based approach to compute non-Galerkin coarse-grid operators in multigrid (MG) methods, addressing the well-known issue of increasing operator complexity. Guided by the MG theory on spectrally equivalent coarse-grid operators, we have developed novel machine learning algorithms that utilize neural networks combined with smooth test vectors from multigrid eigenvalue problems. The proposed method demonstrates promise in reducing the complexity of coarse-grid operators while maintaining overall MG convergence for solving parametric partial differential equation problems. Numerical experiments on anisotropic rotated Laplacian and linear elasticity problems are provided to showcase the performance and comparison with existing methods for computing non-Galerkin coarse-grid operators.

97 MATHEMATICS AND COMPUTING↗