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Development and validation of a humidified CAPS-PM SSA with an improved methodology to calculate the truncation correction factor
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Truncating the distribution of modulus properties in natural populations of wood
This disclosure is directed to methods of separating wood veneer material by property measurements, and thereafter improving the properties of veneer material with property values lower than a target threshold value, until those materials meet or exceed that threshold values. In some aspects of the disclosure, veneer materials are prepared, non-destructively measured, and separated into passing and failing material collections. The failing material collection may then be treated to improve the density and flexural modulus of the material therein. Also disclosed herein are products and materials incorporating the treated veneer materials according to the disclosed methods.
Human Coronavirus 229E Infection Alters Histone Proteoforms
Viruses rely on host machinery to replicate, and growing evidence demonstrates that they utilize host epigenetic regulation, including histone modification, to modulate host gene expression for their benefit. Herein, we employed top-down proteomics to quantify histone proteoforms in a model human lung cell line following human coronavirus 229E (HCoV-229E) infection and compared them to mock-infected controls. A total of 572 proteoforms from mock-infected and HCoV-229E infected human lung fibroblast (MRC5) cells (N = 5 per condition) were identified; this included 461 histone proteoforms that were assigned to H2A, H2B, H3, or H4. 200 histone proteoforms were quantifiable, and differential abundance analysis revealed several statistically significant changes in both reversible post-translational modifications (e.g. phosphorylation, acetylation) and the truncation states of core histones. Notably, we found decreased abundance of C-terminally truncated histone H2A and N-terminally truncated histone H3 in HCoV-229E-infected samples. These findings underscore the power of top-down proteomics to resolve unique truncation states of proteoforms and support the hypothesis that viruses alter histone length (removing regulatory sites) to influence host gene expression.
Robust Implicit Adaptive Low Rank Time-Stepping Methods for Matrix Differential Equations
In this work, we develop implicit rank-adaptive schemes for time-dependent matrix differential equations. The dynamic low rank approximation (DLRA) is a well-known technique to capture the dynamic low rank structure based on Dirac–Frenkel time-dependent variational principle. In recent years, it has attracted a lot of attention due to its wide applicability. Our schemes are inspired by the three-step procedure used in the rank adaptive version of the unconventional robust integrator (the so called BUG integrator) (Ceruti et al. in BIT Numer Math 62(4):1149–1174, 2022) for DLRA. First, a prediction (basis update) step is made computing the approximate column and row spaces at the next time level. Second, a Galerkin evolution step is invoked using an implicit solves for the small core matrix. Finally, a truncation is made according to a prescribed error threshold. Since the DLRA is evolving the differential equation projected on to the tangent space of the low rank manifold, the error estimate of the BUG integrator contains the tangent projection (modeling) error which cannot be easily controlled by mesh refinement. This can cause convergence issue for equations with cross terms. To address this issue, we propose a simple modification, consisting of merging the row and column spaces from the explicit step truncation method together with the BUG spaces in the prediction step. In addition, we propose an adaptive strategy where the BUG spaces are only computed if the residual for the solution obtained from the prediction space by explicit step truncation method, is too large. Here, we prove stability and estimate the local truncation error of the schemes under assumptions. We benchmark the schemes in several tests, such as anisotropic diffusion, solid body rotation and the combination of the two, to show robust convergence properties.
Classical and quantum computing of shear viscosity for ( 2 + 1 ) D SU(2) gauge theory
We perform a nonperturbative calculation of the shear viscosity for ( 2 + 1 )-dimensional SU(2) gauge theory by using the lattice Hamiltonian formulation. The retarded Green’s function of the stress-energy tensor is calculated from real time evolution via exact diagonalization of the lattice Hamiltonian with a local Hilbert space truncation, and the shear viscosity is obtained via the Kubo formula. When taking the continuum limit, we account for the renormalization group flow of the coupling but no additional operator renormalization. We find the ratio of the shear viscosity and the entropy density η s is consistent with a well-known holographic result 1 4 π at several temperatures on a 4 × 4 honeycomb lattice with the local electric representation truncated at j max = 1 2 . We also find the ratio of the spectral function and frequency ρ x y ( ω ) ω exhibits a peak structure when the frequency is small. Both the exact diagonalization method and simple matrix product state classical simulation method beyond j max = 1 2 on bigger lattices require exponentially growing resources. So we develop a quantum computing method to calculate the retarded Green’s function and analyze various systematics of the calculation including j max truncation and finite size effects, Trotter errors and the thermal state preparation efficiency. Our thermal state preparation method still requires resources that grow exponentially with the lattice size, but with a very small prefactor at high temperature. We test our quantum circuit on both the Quantinuum emulator and the IBM simulator for a small lattice and obtain results consistent with the classical computing ones. Published by the American Physical Society 2024
Trends in spatial correlations, two-phase coexistence, and criticality in a class of type-2 Schloegl models for autocatalysis
A class of type-2 Schloegl models is considered for particles on a square lattice with variable-range cooperativity. These models involve: (i) spontaneous particle annihilation at rate p; (ii) autocatalytic particle creation at unoccupied sites (i, j) with n ⩾ 2 particles within a specified neighborhood, Ω 𝑁 (i, j), of sites at rate $k_n$ = $\frac{^{(^n_2)}}{_{(^N_2)}}$ = $\frac{n{(n-1)}}{_{N(N-1)}}$; and (iii) possible spontaneous particle creation at unoccupied sites at “small” rate ɛ ⩾ 0. In some cases, Ω 𝑁 just includes all symmetry-equivalent sites at a single specific distance 𝑑 (in units of lattice constants) from the unoccupied site, e.g., 𝑑 = 1 (nearest-neighbor sites) where 𝑁 = 4, or 𝑑 = √5 (or √13 or…) where 𝑁 = 8. In other cases, Ω 𝑁 includes sites multiple distances from the unoccupied site, e.g., 𝑑 = {1,√2}, where 𝑁 = 8. Kinetic Monte Carlo (KMC) simulation reveals that these models exhibit a nonequilibrium discontinuous phase transition between high- and low-density states below a critical point, ɛ < ɛ c , with generic two-phase coexistence (2PC) at least for smaller 𝑁. With some exceptions, there is an approach toward mean-field behavior with increasing 𝑁 (so the regime of generic 2PC shrinks, and ɛ c approaches the mean-field value of 1/27). Additional insight into trends is provided by analysis of the exact master equations for the models via hierarchical truncation. These truncations utilize suitably tailored pair approximations which reflect the dominant nonequilibrium spatial correlations. These correlations in turn are shown to reflect the details of the autocatalytic particle creation process. For spatially heterogeneous states, the truncations produce coupled sets of lattice differential equations (LDE) which can describe orientation-dependent propagation of an interface between high- and low-density steady states for ɛ < ɛ c . Pair approximation values of 𝑝 = 𝑝 eq where the interface is stationary, and its orientation-dependence, are in semiquantitative agreement with KMC results. In conclusion, this comparison accounts for propagation failure in the LDE which complicates interpretation.
10-th order of accuracy for numerical solution of 3-D elasticity equations for heterogeneous materials on unfitted Cartesian meshes
We have developed the Optimal Local Truncation Error Method (OLTEM) with 10-th order of accuracy on unfitted Cartesian meshes for a system of 3-D elasticity equations with smooth irregular interfaces. 5 x 5 x 5 = 125-point stencils (similar to those for quadratic finite elements) for elastic heterogeneous materials are used for OLTEM. There are no unknowns at the interface points between different materials; the structure of the global discrete equations is the same for homogeneous and heterogeneous materials. The calculation of unknown stencil coefficients is based on the minimization of the local truncation error of the stencil equations and yields the optimal 10-th order of accuracy for OLTEM on unfitted Cartesian meshes, i.e., the increase by 7 orders in accuracy compared to quadratic finite elements on conformal meshes. A new post-processing procedure provides the 9-th order of accuracy for stresses in the 3-D case. Similar to basic computations it uses OLTEM with the 125-point stencils, the interface conditions and the elasticity equations. It was shown that the use of the elasticity equations for post-processing improves the accuracy of 0.1% stresses by 6 orders compared to post-processing without the use of PDEs. At an accuracy of for stresses, OLTEM with the new post-processing procedure reduces the number of degrees of freedom by 360 - 8000 times compared to quadratic finite elements with similar stencils. OLTEM with the 125-point stencils yields even more accurate results than high-order finite elements with much wider stencils. OLTEM provides accurate numerical results for compressible and nearly incompressible materials.
The Yang-Mills duals of small AdS black holes
Abstract We study the largeNmatrix model for the index of 4d$$ \mathcal{N} $$ N = 4 Yang-Mills theory and its truncations to understand the dual AdS 5 black holes. Numerical studies of the truncated models provide insights on the black hole physics, some of which we investigate analytically with the full Yang-Mills matrix model. In particular, we find many branches of saddle points which describe the known black hole solutions. We analytically construct the saddle points dual to the small black holes whose sizes are much smaller than the AdS radius. They include the asymptotically flat BMPV black holes embedded in large AdS with novel thermodynamic instabilities.
Characterization of the biofilm landscape of Bacillus subtilis by spatial microproteomics
Bulk proteomics has been demonstrated to differentiate subpopulations within bacterial colonies, yet advanced analyses by mass spectrometry imaging (MSI) hold even greater promise for the future. This technology can enable high-throughput spatial phenotyping that can reshape biological discovery by providing visualization of components of various biomolecular mechanisms. With high mass resolving power and high spatial resolution analyses being routine, we can confidently enable intact protein imaging directly from samples with minimal preparation. Pairing those analyses with bulk experimental libraries can provide high confidence in annotations of post-translational modifications (PTMs) and truncations. Revealing PTM localization within the samples unlocks a direct window into unknown biology at the microscale. However, top-down proteomics (TDP) is not commonplace for microbial species, largely due to challenges in identifying detected peptides and proteins; considering the theoretical proteome of even the well-studied model bacterium Bacillus subtilis was only partially mapped recently. With little still known about the form and function of many of these proteins – let alone proteoforms, where PTMs and truncations of the same protein may possess unique physiological roles – there is a wealth of work to be done. Here we jointly apply TDP and MSI to describe the microscale spatial proteomic landscape within B. subtilis and further demonstrate the feasibility of detecting differentiated subpopulations through proteoforms across the biofilm landscape.
Bayesian prior construction for uncertainty quantification in first-principles statistical mechanics
First-principles statistical mechanics enables the prediction of thermodynamic and kinetic properties of materials, but is computationally expensive. Many approaches require surrogate models to calculate energies within Monte Carlo or molecular dynamics simulations. Inexpensive surrogates such as cluster expansions enable otherwise intractable calculations by interpolating data from higher accuracy methods, such as Density Functional Theory (DFT). Surrogate models introduce uncertainty into downstream calculations, in addition to any uncertainty inherent to DFT calculations. Bayesian frameworks address this by quantifying uncertainty and incorporating expert knowledge through priors. However, constructing effective priors remains challenging. This work introduces and describes practical strategies for building Bayesian cluster expansions, focusing on basis truncation, hyperparameter selection, and ground state replication. We analyze multiple basis truncation schemes, compare cross-validation to the evidence-approximation for hyperparameter optimization, and provide methods to find and enforce ground-state-preserving models through priors. Additionally, we compare the uncertainties between different approximations to DFT (LDA, PBE, SCAN) against the uncertainty introduced with the use of cluster expansion surrogate models. These approaches are demonstrated on the BCC Li x Mg 1-x and Li x Al 1-x alloys, which are both of interest for solid-state Li batteries. Our results provide guidelines for constructing and utilizing Bayesian cluster expansions, thereby improving the transparency of materials modeling. Furthermore, the approaches and insights developed in this work can be transferred to a wide range of cluster expansion surrogate models, including the atomic cluster expansion and related machine-learned interatomic potential architectures.
Accelerating multigrid with streaming chiral SVD for Wilson fermions in lattice QCD
A modification to the setup algorithm for the multigrid preconditioner of Wilson fermions in lattice QCD is presented. A larger basis of test vectors than that used in regular multigrid is calculated by the smoother and truncated by singular value decomposition on the chiral components of the test vectors. The truncated basis is used to form the prolongation and restriction matrices of the multigrid hierarchy. This modification of the setup method is demonstrated to increase the convergence of linear solvers on an anisotropic lattice with m π ≈ 239 MeV from the Hadron Spectrum Collaboration and an isotropic lattice with m π ≈ 220 MeV from the MILC Collaboration. The lattice volume dependence of the method is also examined. Increasing the number of test vectors improves speedup up to a point, but storing these vectors becomes impossible in limited memory resources such as GPUs. To address storage cost, we implement a streaming singular value decomposition of the basis of test vectors on the chiral components and demonstrate a decrease in the number of fine level iterations by a factor of 1.7 for m q ≈ m crit
Discovery of Proteoforms Associated With Alzheimer's Disease Through Quantitative Top-Down Proteomics
The complex nature of Alzheimer's disease (AD) and its heterogenous clinical presentation has prompted numerous large-scale - omic analyses aimed at providing a global understanding of the pathophysiological processes involved. AD involves isoforms, proteolytic products, and posttranslationally modified proteins such as amyloid beta (Aβ) and microtubule-associated protein tau. Top-down proteomics directly measures these species and thus, offers a comprehensive view of pathologically relevant proteoforms that are difficult to analyze using traditional proteomic techniques. Here, we broadly explored associations between proteoforms and clinicopathological traits of AD by deploying a quantitative top-down proteomics approach across frontal cortex of 103 subjects selected from the ROS and MAP cohorts. The approach identified 1213 proteins and 11,782 proteoforms, of which 154 proteoforms had at least one significant association with a clinicopathological phenotype. One important finding included identifying Aβ C-terminal truncation state as the key property for differential association between amyloid plaques and cerebral amyloid angiopathy. Furthermore, various N-terminally truncated forms of Aβ had noticeably stronger association with amyloid plaques and global cognitive function. Additionally, we discovered six VGF neuropeptides that were positively associated with cognitive function independent of pathological burden. The database of brain cortex proteoforms provides a valuable context for functional characterization of the proteins involved in AD and other late-onset brain pathologies.
ab initio Sub-Mechanism Development for Cyclopentene Oxidation
To accurately predict low-temperature oxidation behavior, chemical kinetics mechanisms must contain complete reaction networks that include detailed consumption reactions of intermediates produced directly from hydroperoxyalkyl radicals, Q̇OOH, which undergo competing unimolecular reactions and bimolecular reactions with O2. Rates of chain-branching are governed by the flux between the two competing pathways, and inherently depend on temperature, pressure, and oxygen concentration. Neglect of consumption pathways for major oxidation intermediates leads to mechanism truncation error that is ameliorated by expanding the level of detail included in sub-mechanisms and employing ab initio methods for computing rates of elementary reactions and thermochemical properties of species involved. In the present work, an ab initio-derived sub-mechanism is developed using AutoMech to model the chemical kinetics of cyclopentene, a major product of cyclopentane oxidation. The ab initio sub-mechanism builds on a detailed mechanism developed using Reaction Mechanism Generator (RMG) for the specific purpose of determining the extent to which replacing cyclopentene-specific reactions and species with quantum chemical computations reduces model inaccuracies resulting from mechanism truncation error. In an effort to minimize interference from other reactions present during the formation of cyclopentene from cyclopentyl + O2, providing a narrower experimental scope, the model is compared against speciation measurements from jet-stirred reactor (JSR) experiments on cyclopentene oxidation. The experiments utilize vacuum ultraviolet-absorption spectroscopy and mass spectrometry for isomer-resolved speciation of intermediates at 835 Torr from 700 – 950 K. [O2]-dependent experiments were also conducted from 0.057 – 2.01 · 1018 molecules cm–3 at 825 K to examine the influence of oxygen on species profiles. Model predictions using the ab initio-revised mechanism yielded significant improvements in species profiles for both the temperature- and [O2]-dependent measurements, owing in part to increased rates of HOȮ and H2O2 production, which underscores the influence of theoretical calculations of reaction rates involving species produced from Ṙ + O2 such as cyclopentene.
QM Investigation of Rare Earth Ion Interactions with First Hydration Shell Waters and Protein-Based Coordination Models
Here, conventional methods for extracting rare earth metals (REMs) from mined mineral ores are inefficient, expensive, and environmentally damaging. Recent discovery of lanmodulin (LanM), a protein that coordinates REMs with high-affinity and selectivity over competing ions, provides inspiration for new REM refinement methods. Here, we used quantum mechanical (QM) methods to investigate trivalent lanthanide cation (Ln 3+ ) interactions with coordination systems representing bulk solvent water and protein binding sites. Energy decomposition analysis (EDA) showed differences in the energetic components of Ln 3+ interaction with representatives of solvent (water, H 2 O) and protein binding sites (acetate, CH 3 COO – ), highlighting the importance of accurate description of electrostatics and polarization in computational modeling of REM interactions with biological and bioinspired molecules. Relative binding free energies were obtained for Ln 3+ with coordination complexes originating from binding sites in PDB structures of a lanthanum binding peptide (PDB entry 7CCO) and LanM, with explicit consideration of the first hydration shell waters, according to quasi-chemical theory (QCT). Beyond the first shell, the bulk solvent environment was represented with an implicit continuum model. Ln 3+ interactions with (H 2 O) 9 and both binding site models became more favorable, moving down the periodic series. This trend was more pronounced with the protein binding site models than with water, resulting in affinity increasing with periodic number, except for the last REM, Lu 3+ , which bound less favorably than the preceding element, Yb 3+ . Using the truncated 7CCO binding site model, the magnitude and trend of the experimental Ln 3+ relative binding free energies for the whole 7CCO peptide were reproduced. Conversely, the previously reported experimental data for LanM show a preference for the earlier lanthanides; this is likely due to longer-range interactions and cooperative effects, which are not represented by the reduced models. Using the truncated 7CCO binding site model, the magnitude and trend of the experimental Ln 3+ relative binding free energies for the whole 7CCO peptide were reproduced. In contrast to the previously reported experimental data for LanM, the peptide preferentially binds the earlier lanthanides. This difference likely arises due to longer-range interactions and cooperative effects not represented by the peptide. Further investigation of Ln 3+ interactions with whole proteins using polarizable molecular mechanics models with explicit solvent is warranted to understand the influence of longer-ranged interactions, cooperativity, and bulk solvent. Nevertheless, the present work provides new insights into Ln 3+ interactions with biomolecules and presents an effective computational platform for designing specific single-site REM binding peptides more efficiently.
Efficient Modeling of Structural, Electronic, and Optical Properties of Silver and Gold Metal Nanoclusters and Alloys Using Optimized SCC-DFTB Parameters
Computation of optical properties using conventional time-dependent density functional theory (TD-DFT) is time-consuming and memory-intensive. In this study, we investigate the accuracy and efficiency of the density functional tight binding (DFTB) framework with newly optimized Slater–Koster (SK) parameters for modeling the structural, electronic properties, and absorption spectra of silver and gold nanoclusters and their alloys. Our investigation of the ground state (GS) properties demonstrates that the newly developed GS-SK parameters enable DFTB to closely approximate DFT-calculated bond lengths for octahedron, tetrahedron, icosahedra, and truncated octahedron with sizes Ag n /Au n (n = 19, 20, 38, 55), nanoclusters and Ag 20 /Au 20 nanoalloys, with a maximum deviation of approximately 0.15 Å. Formation energy results indicate that the GS-SK parameters can closely estimate changes in formation energies with alloy composition, and the comparison of electronic structures for Ag 20 , Au 20 , and AgAu alloy nanoclusters using the DFTB approximation reveals good agreement in the projected density of states (DOS) profiles and energy levels. A second set of SK parameters, ES-SK, has been developed to describe excited state (ES) properties, including the absorption spectra of silver octahedron Ag 19 , tetrahedral Ag n (n = 20, 56, 84), truncated octahedron Ag 38 , and icosahedra Ag 55 closed-shell clusters and their gold and alloy counterparts over a broad range of alloy compositions. This parametrization uses TD-DFTB calculations and fine-tunes the d and p eigenvalues by comparing them to reference absorption spectra from first-principles TD-DFT. This enables the generation of absorption spectra that closely match the reference spectra when plasmon excitation is dominant, as demonstrated by studying the plasmonic properties of icosahedral Ag n and Au n (n = 309 and 561) nanoparticles. This includes the rapid loss in plasmon quality when Au partially replaces Ag in alloy clusters. Furthermore, these results provide a foundation for addressing computational bottlenecks in plasmonics and with new prospects for applications in the quantum plasmonics for bimetallic alloys.
The impact of environment on size: Galaxies are 50% smaller in the Fornax Cluster compared to the field
Size is a fundamental parameter for measuring the growth of galaxies and the role of the environment on their evolution. However, the conventional size definitions used for this purpose are often biased and miss the diffuse, outermost signatures of galaxy growth, including star formation and gas accretion. We address this issue by examining low surface brightness truncations or galaxy ‘edges’ as a physically motivated tracer of size based on star formation thresholds. Our total sample consists of ∼900 galaxies with stellar masses ranging from 10 5 M ⊙ < M ⋆ < 10 11 M ⊙ . This sample of nearby cluster, group satellite, and nearly isolated field galaxies was compiled using multi-band imaging from the Fornax Deep Survey, deep IAC Stripe 82, and Dark Energy Camera Legacy Surveys. We find that the edge radii scale as R edge ∝ M ⋆ 0.42 , with a very small intrinsic scatter (∼0.07 dex). The scatter is driven by the morphology and environment of galaxies. In both the cluster and field, early-type dwarfs are systematically smaller by approximately 20% compared to late-type dwarfs. However, galaxies in the Fornax cluster are the most impacted. At a fixed stellar mass, edges in the cluster can be found at about 50% smaller radii, and the average stellar surface density at the edges is a factor of two higher, ∼1 M ⊙ /pc 2 . Our findings support the rapid removal of loosely bound neutral hydrogen (H I ) in hot, crowded environments, which truncates galaxies outside-in earlier, preventing the formation of more extended sizes and lower density edges. Our results highlight the importance of deep imaging surveys to the study of low surface brightness imprints of the large-scale structure and environment on galaxy evolution.
Extended dynamic mode decomposition for model reduction in fluid dynamics simulations
High computational cost and storage/memory requirements of fluid dynamics simulations constrain their usefulness as a predictive tool. Reduced-order models (ROMs) provide a viable solution to this challenge by extracting the key underlying dynamics of a complex system directly from data. We investigate the efficacy and robustness of an extended dynamic mode decomposition (xDMD) algorithm in constructing ROMs of three-dimensional cardiovascular computations. Focusing on the ROMs' accuracy in representation and interpolation, we relate these metrics to the truncation rank of singular value decomposition, which underpins xDMD and other approaches to ROM construction. Our key innovation is to relate the truncation rank to the singular values of the original flow problem. This result establishes a priori guidelines for the xDMD deployment and its likely success as a means of data compression and reconstruction of the system's dynamics from dominant spatiotemporal structures present in the data.