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At least 199 records · Page 11

Preserving Lagrangian Structure in Nonlinear Model Reduction with Application to Structural Dynamics

Our work proposes a model-reduction methodology that preserves Lagrangian structure and achieves computational efficiency in the presence of high-order nonlinearities and arbitrary parameter dependence. As such, the resulting reduced-order model retains key properties such as energy conservation and symplectic time-evolution maps. We focus on parameterized simple mechanical systems subjected to Rayleigh damping and external forces, and consider an application to nonlinear structural dynamics. To preserve structure, the method first approximates the system's “Lagrangian ingredients''---the Riemannian metric, the potential-energy function, the dissipation function, and the external force---and subsequently derives reduced-order equations of motion by applying the (forced) Euler--Lagrange equation with these quantities. Moreover, from the algebraic perspective, key contributions include two efficient techniques for approximating parameterized reduced matrices while preserving symmetry and positive definiteness: matrix gappy proper orthogonal decomposition and reduced-basis sparsification. Our results for a parameterized truss-structure problem demonstrate the practical importance of preserving Lagrangian structure and illustrate the proposed method's merits: it reduces computation time while maintaining high accuracy and stability, in contrast to existing nonlinear model-reduction techniques that do not preserve structure.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Effect of water models on structure and dynamics of lignin in solution

Lignin, a major biomass component, can be an excellent source for different monomers in the polymer industry. However, the complex and heterogeneous structure of lignin poses a significant challenge for designing energy-efficient processes for depolymerization. As many proposed depolymerization processes are solvothermal, it is essential to understand the structure and dynamics of lignin in solution, in particular aqueous solution. Here, we utilize molecular dynamics simulations to understand the effect of water models on the structure and dynamics of different model lignin oligomers (softwood and hardwood) as a function of temperature. We have examined three different water models: TIP3P, TIP4P/Ew, and flexible SPC/Fw. We find that the diffusion constant of lignin oligomers in an aqueous solution differs significantly depending on the water model used. The diffusion constant of lignin in the TIP3P water model is almost twice as large as that in SPC/Fw and TIP4P/Ew. The softwood and hardwood oligomers adopt an extended structure in TIP3P water compared to SPC/Fw and TIP4P/Ew. Given the different levels of sensitivity of transport and structural properties of aqueous lignin on water models, it is important to take these into account when discussing results from a specific water model.

09 BIOMASS FUELS↗

A Structure Function Model Recovers the Many Formulations for Air-Water Gas Transfer Velocity: Air-Water Gas Transfer

Two ideas regarding the structure of turbulence near a clear air-water interface are used to derive a waterside gas transfer velocity kL for sparingly and slightly soluble gases. The first is that k L is proportional to the turnover velocity described by the vertical velocity structure function D ww (r), where r is separation distance between two points. The second is that the scalar exchange between the air-water interface and the waterside turbulence can be suitably described by a length scale proportional to the Batchelor scale lB=ηSc -1/2 , where Sc is the molecular Schmidt number and η is the Kolmogorov microscale defining the smallest scale of turbulent eddies impacted by fluid viscosity. Using an approximate solution to the von Kármán-Howarth equation predicting D ww (r) in the inertial and viscous regimes, prior formulations for k L are recovered including (i) k L =$\sqrt{2/15}$Sc -1/2 $v$, v K is the Kolmogorov velocity defined by the Reynolds number v K η/ν = 1 and ν is the kinematic viscosity of water; (ii) surface divergence formulations; (iii) k L ∝ SC -1/2 u * , where u * is the waterside friction velocity; (iv) k L ∝ Sc -1/2 $\sqrt{gv/u_*}$ for Keulegan numbers exceeding a threshold needed for long-wave generation, where the proportionality constant varies with wave age, g is the gravitational acceleration; and (v) k L = $\sqrt{2/15}$Sc -1/2 (vgβ o q o ) 1/4 in free convection, where qo is the surface heat flux and β o is the thermal expansion of water. The work demonstrates that the aforementioned k L formulations can be recovered from a single structure function model derived for locally homogeneous and isotropic turbulence.

54 ENVIRONMENTAL SCIENCES↗

Atomistic modeling of crystal structure of Ca{sub 1.67}SiH{sub x}

The atomic structure of calcium-silicate-hydrate (C{sub 1.67}-S-H{sub x}) has been investigated by theoretical methods in order to establish a better insight into its structure. Three models for C-S-H all derived from tobermorite are proposed and a large number of structures were created within each model by making a random distribution of silica oligomers of different size within each structure. These structures were subjected to structural relaxation by geometry optimization and molecular dynamics steps. That resulted in a set of energies within each model. Despite an energy distribution between individual structures within each model, significant energy differences are observed between the three models. The C-S-H model related to the lowest energy is considered as the most probable. It turns out to be characterized by the distribution of dimeric and pentameric silicates and the absence of monomers. This model has mass density which is closest to the experimental one.

36 MATERIALS SCIENCE↗

Citrate synthase proteins in extremophilic organisms: Studies within a structure-based model

We study four citrate synthase homodimeric proteins within a structure-based coarse-grained model. Two of these proteins come from thermophilic bacteria, one from a cryophilic bacterium and one from a mesophilic organism; three are in the closed and two in the open conformations. Even though the proteins belong to the same fold, the model distinguishes the properties of these proteins in a way which is consistent with experiments. For instance, the thermophilic proteins are more stable thermodynamically than their mesophilic and cryophilic homologues, which we observe both in the magnitude of thermal fluctuations near the native state and in the kinetics of thermal unfolding. The level of stability correlates with the average coordination number for amino acid contacts and with the degree of structural compactness. The pattern of positional fluctuations along the sequence in the closed conformation is different than in the open conformation, including within the active site. The modes of correlated and anticorrelated movements of pairs of amino acids forming the active site are very different in the open and closed conformations. Taken together, our results show that the precise location of amino acid contacts in the native structure appears to be a critical element in explaining the similarities and differences in the thermodynamic properties, local flexibility, and collective motions of the different forms of the enzyme.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Dosage optimization for reducing tumor burden using a phenotype-structured population model with a drug-resistance continuum

Abstract Drug resistance is a significant obstacle to effective cancer treatment. To gain insights into how drug resistance develops, we adopted a concept called fitness landscape and employed a phenotype-structured population model by fitting to a set of experimental data on a drug used for ovarian cancer, olaparib. Our modeling approach allowed us to understand how a drug affects the fitness landscape and track the evolution of a population of cancer cells structured with a spectrum of drug resistance. We also incorporated pharmacokinetic (PK) modeling to identify the optimal dosages of the drug that could lead to long-term tumor reduction. We derived a formula that indicates that maximizing variation in plasma drug concentration over a dosing interval could be important in reducing drug resistance. Our findings suggest that it may be possible to achieve better treatment outcomes with a drug dose lower than the levels recommended by the drug label. Acknowledging the current limitations of our work, we believe that our approach, which combines modeling of both PK and drug resistance evolution, could contribute to a new direction for better designing drug treatment regimens to improve cancer treatment.

Life Sciences & Biomedicine - Other Topics↗

Structure-topology-property correlations of sodium phosphosilicate glasses

In this work, we investigate the correlations among structure, topology, and properties in a series of sodium phosphosilicate glasses with [SiO{sub 2}]/[SiO{sub 2} + P{sub 2}O{sub 5}] ranging from 0 to 1. The network structure is characterized by {sup 29}Si and {sup 31}P magic-angle spinning nuclear magnetic resonance and Raman spectroscopy. The results show the formation of six-fold coordinated silicon species in phosphorous-rich glasses. Based on the structural data, we propose a formation mechanism of the six-fold coordinated silicon, which is used to develop a quantitative structural model for predicting the speciation of the network forming units as a function of chemical composition. The structural model is then used to establish a temperature-dependent constraint description of phosphosilicate glass topology that enables prediction of glass transition temperature, liquid fragility, and indentation hardness. The topological constraint model provides insight into structural origin of the mixed network former effect in phosphosilicate glasses.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

High-Burnup-Structure (HBS): Model Development in MARMOT for HBS Formation and Stability Under Radiation and High Temperature

A detailed phase field model for the formation of High Burnup Structure (HBS) was developed and implemented in MARMOT. The model treats the HBS formation as an irradiation-induced recrystallization. The model takes into consideration the stored energy associated with dislocations formed under irradiation. The accumulation of radiation damage, hence, increases the system free energy and triggers recrystallization. The increase in the free energy due to the formation of new grain boundaries is offset by the reduction in the free energy by creating dislocation-free grains at the expense of the deformed grains. The model was first used to study the growth of recrystallized flat and circular grains. The model reults were shown to agree well with theorrtical predictions. The case of HBS formation in UO2 was then investigated. It was found that a threshold dislocation density of (or equivalently a threshold burn-up of 33-40 GWd/t) is required for HBS formation at 1200K, which is in good agrrement with theory and experiments. In future studies, the presence of gas bubbles and their effect on the formation and evolution of HBS will be considered.

36 MATERIALS SCIENCE↗

A Level Set Model for Structured Mesh Representation of Fibrous Preforms used in Composites Manufacturing

Here, a model for implicit representation of fibrous and woven preforms used for composites manufacturing is described. The method is based on a level set function defined on a structured mesh to implicitly capture the complex fiber and weave geometries. Since most software packages used to model woven preforms are based on unstructured mesh, a numerical model for transforming a discretized surface to a structured mesh representation and vice-a-versa is presented. Specific emphasis is on scalable computation of a level set function for large and complex 3D woven structures from a triangulated surface of the smallest unit (yarn). The model is applied to capture a periodic 3D layered 5-harness satin (5HS) weave geometry on a structured mesh. Geometric transformations needed to efficiently compute the level set function for the 3D structure on a high resolution mesh are described. Effects of mesh resolution on the geometric features such as number of resolved fibers, effective fiber size, and the surface area to volume ratio of the iso-surface are analyzed. Using the distance property of the level set function, an approach to evaluate the structure function resulting from transient evolving topology representing densification due to matrix phase depositions is also presented. The approach captures transition of the geometric characteristic from fiber governed at early stages of densification to yarn governed at the terminal stage.

36 MATERIALS SCIENCE↗

Compositional bowing of band energies and their deformation potentials in strained InGaAs ternary alloys: A first-principles study

Using first-principles calculations, we show that the conduction and valence band energies and their deformation potentials exhibit a non-negligible compositional bowing in strained ternary semiconductor alloys such as InGaAs. The electronic structure of these compounds has been calculated within the framework of local density approximation and hybrid functional approach for large cubic supercells and special quasi-random structures, which represent two kinds of model structures for random alloys. We find that the predicted bowing effect for the band energy deformation potentials is rather insensitive to the choice of the functional and alloy structural model. The direction of bowing is determined by In cations that give a stronger contribution to the formation of the In{sub x}Ga{sub 1−x}As valence band states with x ≳ 0.5, compared to Ga cations.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Novel Coupled Thermochronometric and Geochemical Investigation of Blind Geothermal Resources in Fault-Controlled Dilational Corners

Geothermal plays in extensional and transtensional tectonic environments have long been a major target in the exploration of geothermal resources and the Dixie Valley area has served as a classic natural laboratory for this type of geothermal plays. In recent years, the interactions between normal faults and strike-slip faults, acting either as strain relay zones have attracted significant interest in geothermal exploration as they commonly result in fault-controlled dilational corners with enhanced fracture permeability and thus have the potential to host blind geothermal prospects. Structural ambiguity, complications in fault linkage, etc. often make the selection for geothermal exploration drilling targets complicated and risky. Though simplistic, the three main ingredients of a viable utility-grade geothermal resource are heat, fluids, and permeability. Our new geological mapping and fault kinematic analysis derived a structural model suggest a two-stage structural evolution with (a) middle Miocene N -S trending normal faults (faults cutting across the modern range), - and tiling Olio-Miocene volcanic and sedimentary sequences (similar in style to East Range and S Stillwater Range). NE-trending range-front normal faulting initiated during the Pliocene and are both truncating N-S trending normal faults and reactivating some former normal faults in a right-lateral fashion. Thus the two main fundamental differences to previous structural models are (1) N-S trending faults are pre-existing middle Miocene normal faults and (2) these faults are reactivated in a right-later fashion (NOT left-lateral) and kinematically linked to the younger NE-trending range-bounding normal faults (Pliocene in age). More importantly, this study provides the first constraints on transient fluid flow through the novel application of apatite (U-Th)/He (AHe) and 4 He/ 3 He thermochronometry in the geothermally active Dixie Valley area in Nevada.

(U-Th)/He↗

A structural equation modeling approach to leveraging the power of extant sentiment analysis tools

Machine-derived sentiment analysis has become a pervasive and useful tool to address a wide array of issues in natural language processing. Leading technology companies such as Google now provide sentiment analysis tools (SATs) as readily accessible online products. Academic researchers develop and make available SATs to support the research enterprise. One of the major challenges with SATs is the inconsistencies in results among the various SATs. Consequently, the selection of a SAT for a specific purpose may significantly impact the application. This study addresses the foregoing problem by utilizing structural equation modeling to merge the outputs of SATs to develop a combined sentiment metric without the need for a labeled training dataset. This method is applicable to a wide range of text-based problems, is data-driven, and replicable. It was tested using three publicly available datasets and compared against seven different SATs. The results indicate that as a continous measure, the proposed method outperformed other SATs in the movie reviews and SemEval datasets, and achieved a tie for first place with IBM Watson on the Sentiment 140 dataset. Also, compared to the published major alternatives, the arithmetic mean solution, this approach performed better across these three datasets.

97 MATHEMATICS AND COMPUTING↗

Improving AlphaFold2-based protein tertiary structure prediction with MULTICOM in CASP15

Since the 14th Critical Assessment of Techniques for Protein Structure Prediction (CASP14), AlphaFold2 has become the standard method for protein tertiary structure prediction. One remaining challenge is to further improve its prediction. We developed a new version of the MULTICOM system to sample diverse multiple sequence alignments (MSAs) and structural templates to improve the input for AlphaFold2 to generate structural models. The models are then ranked by both the pairwise model similarity and AlphaFold2 self-reported model quality score. The top ranked models are refined by a novel structure alignment-based refinement method powered by Foldseek. Moreover, for a monomer target that is a subunit of a protein assembly (complex), MULTICOM integrates tertiary and quaternary structure predictions to account for tertiary structural changes induced by protein-protein interaction. The system participated in the tertiary structure prediction in 2022 CASP15 experiment. Our server predictor MULTICOM_refine ranked 3rd among 47 CASP15 server predictors and our human predictor MULTICOM ranked 7th among all 132 human and server predictors. The average GDT-TS score and TM-score of the first structural models that MULTICOM_refine predicted for 94 CASP15 domains are ~0.80 and ~0.92, 9.6% and 8.2% higher than ~0.73 and 0.85 of the standard AlphaFold2 predictor respectively.

59 BASIC BIOLOGICAL SCIENCES↗

Structural coherence model for predicting molten salt thermal conductivity informed by the pair distribution function

To enable thermal behavior prediction and design optimization of molten salt reactors, thermal conductivity of molten salts must be characterized in terms of salt composition and temperature. Current theoretical models fail to provide consistent approximations for all halide mixtures, particularly actinide-bearing melts. This study aims to link the short-range order structure of molten salts to the mean free path of energy carriers through a simple structural coherence model informed by the partial pair distribution function. The proposed method is used to predict the thermal conductivity of 33 alkali and alkaline earth halide salts. Predictions approximate experimental measurements with a mean absolute error of 15.7% for dissociating, complexing, and actinide salts, including unary LiCl, NaCl, and MgCl 2 as well as mixtures LiF–NaF–KF (FLiNaK), LiF–BeF 2 (FLiBe), and NaCl–UCl 3 . The work provides evidence for the validity of energy carrier descriptions of molecular-level heat transfer in molten salts, with implications for improved theories of liquid energy transport in general.

Actinide mixtures↗

Electron density distribution and disordered crystal structure of 8H-SiAlON, Si{sub 3−x}Al{sub 1+x}O{sub x}N{sub 5−x} (x∼2.2)

The 8H-SiAlON crystal with general formula Si{sub 3−x}Al{sub 1+x}O{sub x}N{sub 5−x} was characterized using laboratory X-ray powder diffraction (CuKα{sub 1}), transmission electron microscopy and energy dispersive X-ray spectroscopy. The [Si: Al] molar ratios were determined to be [0.21(1): 0.79(1)], corresponding to x=2.2(1). The Si{sub 0.8(1)}Al{sub 3.2(1)}O{sub 2.2(1)}N{sub 2.8(1)} compound is hexagonal with space group P6{sub 3}/mmc (Z=2). The unit-cell dimensions are a=0.298877(8) nm, c=2.30872(5) nm and V=0.178602(8) nm{sup 3}. The initial structural model was successfully derived by the charge-flipping method and further refined by the Rietveld method. The final structural model showed the positional disordering of two of the three (Si,Al) sites. The maximum-entropy method-based pattern fitting (MPF) method was used to confirm the validity of the split-atom model, in which conventional structure bias caused by assuming intensity partitioning was minimized. The reliability indices calculated from the MPF were R{sub wp}=4.74%, S (=R{sub wp}/R{sub e})=1.30, R{sub p}=3.40%, R{sub B}=1.04% and R{sub F}=0.74%. The disordered crystal structure was successfully described by overlapping four types of domains with ordered atom arrangements. The distribution of atomic positions in each of the domains can be achieved in the space group P6{sub 3}mc. Two of the four types of domains are related by a pseudo-symmetry inversion, and the two remaining domains also have each other the inversion pseudo-symmetry. - Graphical abstract: Bird's eye view of electron densities up to 49.3% (0.071 nm{sup −3}) of the maximum on the plane parallel to (110) with the corresponding atomic arrangements of Si{sub 0.8}Al{sub 3.2}O{sub 2.2}N{sub 2.8}. - Highlights: • Crystal structure of Si{sub 0.8}Al{sub 3.2}O{sub 2.2}N{sub 2.8} is determined by laboratory X-ray powder diffraction. • The atom arrangements are represented by the split-atom model. • The maximum-entropy method-based pattern fitting method is used to confirm the validity of the model. • The disordered structure is described by overlapping four types of domains with ordered atom arrangements.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Uncertainty analysis of terrestrial net primary productivity and net biome productivity in China during 1901-2005

Here, despite the importance of net primary productivity (NPP) and net biome productivity (NBP), estimates of NPP and NBP for China are highly uncertain. To investigate the main sources of uncertainty, we synthesized model estimates of NPP and NBP for China from published literature and the Multi-scale Synthesis and Terrestrial Model Intercomparison Project (MsTMIP). The literature-based results showed that total NPP and NBP in China were 3.35 ± 1.25 and 0.14 ± 0.094 Pg C yr –1 , respectively. Classification and regression tree analysis based on literature data showed that model type was the primary source of the uncertainty, explaining 36% and 64% of the variance in NPP and NBP, respectively. Spatiotemporal scales, land cover conditions, inclusion of the N cycle, and effects of N addition also contributed to the overall uncertainty. Results based on the MsTMIP data suggested that model structures were overwhelmingly important (>90%) for the overall uncertainty compared to simulations with different combinations of time-varying global change factors. The interannual pattern of NPP was similar among diverse studies and increased by 0.012 Pg C yr –1 during 1981–2000. In addition, high uncertainty in China's NPP occurred in areas with high productivity, whereas NBP showed the opposite pattern. Our results suggest that to significantly reduce uncertainty in estimated NPP and NBP, model structures should be substantially tested on the basis of empirical results. To this end, coordinated distributed experiments with multiple global change factors might be a practical approach that can validate specific structures of different models.

54 ENVIRONMENTAL SCIENCES↗