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At least 91 records · Page 5

Towards verifiable cancer digital twins: tissue level modeling protocol for precision medicine

Cancer exhibits substantial heterogeneity, manifesting as distinct morphological and molecular variations across tumors, which frequently undermines the efficacy of conventional oncological treatments. Developments in multiomics and sequencing technologies have paved the way for unraveling this heterogeneity. Nevertheless, the complexity of the data gathered from these methods cannot be fully interpreted through multimodal data analysis alone. Mathematical modeling plays a crucial role in delineating the underlying mechanisms to explain sources of heterogeneity using patient-specific data. Intra-tumoral diversity necessitates the development of precision oncology therapies utilizing multiphysics, multiscale mathematical models for cancer. This review discusses recent advancements in computational methodologies for precision oncology, highlighting the potential of cancer digital twins to enhance patient-specific decision-making in clinical settings. We review computational efforts in building patient-informed cellular and tissue-level models for cancer and propose a computational framework that utilizes agent-based modeling as an effective conduit to integrate cancer systems models that encode signaling at the cellular scale with digital twin models that predict tissue-level response in a tumor microenvironment customized to patient information. Furthermore, we discuss machine learning approaches to building surrogates for these complex mathematical models. These surrogates can potentially be used to conduct sensitivity analysis, verification, validation, and uncertainty quantification, which is especially important for tumor studies due to their dynamic nature.

60 APPLIED LIFE SCIENCES↗

Sol-gel derived silicate-phosphate glass SiO 2 –P 2 O 5 –CaO–TiO 2 : The effect of titanium isopropoxide on porosity and thermomechanical stability

Despite of several decades lasting extensive research of bioactive and bioresorbable glasses the systematic parametrization and determination of the key factors affecting porosity and thermomechanical characteristics still remains challenging. Here, we present silica-phosphate glasses, with the composition 70SiO 2 - 20P 2 O 5 - (10-x)CaO-xTiO 2 (mol%; x = 0, 2.5, 5, and 7.5), prepared by sol -gel method and reinforced by titanium dioxide via titanium isopropoxide (TTIP) incorporation which demonstrated tunable variation of porosity from micro-to macro -region and superb mechanical integrity during the calcination process. The presence of 7.5 mol% TiO 2 promotes dimensional stability up to 1000°C as investigated by thermomechanical analysis. The XRD showed the dominant presence of silicon phosphate [Si(P 2 O 7 )], titanium phosphate [Ti(P 2 O 7 )] and calcium phosphates [β-Ca(P 2 O 6 ) and γ- Ca 2 (P 2 O 7 )]. The effect of TiO 2 doping on the multiscale morphology and porosity was investigated by means of SEM, MIP, μCT, N 2 adsorption and USAXS/SAXS. Increasing TiO 2 content leads to the formation of open porosity up to 70vol% and drives the formation of a refined interconnected macroporosity of 2-30 μm. In contrast, mesoporosity with a dominance of 3-6nm pores decreases in all samples with increasing TiO 2 content. USAXS/SAXS revealed an increase in primary particle size with increasing TiO 2 content which is in good agreement with the nitrogen physisorption analysis showing that microporosity decreases with increasing TiO2 content.

36 MATERIALS SCIENCE↗

Tracking ion intercalation into layered Ti 3 C 2 MXene films across length scales

Enhancing the energy stored and power delivered by layered materials relies strongly on improved understanding of the intricate interplay of electrolyte ions, solvents, and electrode interactions as well as the role of confinement. Here we report a highly integrated study with multiscale theory/modelling and experiments to track the intercalation of aqueous Li + , Na + , K + , Cs + , and Mg 2+ ions into Ti 3 C 2 MXene. The integrated analysis of experiments assisted by theory/modelling allows for a deep understanding of energy storage processes highlighting the importance of the dynamics of cations, their positionings between MXene sheets, their effects on mechanical properties and capacitive energy storage. Computational simulations and operando calorimetry measurements prove the processes involving cation dehydration and H+ rehydration, showing a good correlation for heat variations between experiments and theory. Operando liquid AFM mapped energy dissipation of ions appears non-uniformly across the MXene surface, indicating heterogeneities of ions inside the MXene and confirming partially the ion behaviour obtained in theory. We directly demonstrate that the average distance between the cation and MXene surface follows a modified two-sided Helmholtz model when plotted versus the open circuit potential capacitance, revealing a different electrical double layer mechanism in confinement. This new fundamental understanding lays the foundation for improved functional devices utilizing electrodes and membranes made of two-dimensional materials.

36 MATERIALS SCIENCE↗

Super-Fermi acceleration in multiscale MHD reconnection

We investigate the Fermi acceleration of charged particles in 2D MHD anti-parallel plasmoid reconnection, finding a drastic enhancement in energization rate ε ˙ over a standard Fermi model of ε ˙ ~ ε. The shrinking particle orbit width around a magnetic island due to E → × B → drift produces a ε ˙ ∥ ~ ε ∥ 1 + 1 / 2 χ power law with χ ~ 0.75. The increase in the maximum possible energy gain of a particle within a plasmoid due to the enhanced efficiency increases with the plasmoid size and is by multiple factors of 10 in the case of solar flares and much more for larger plasmas. Including the effects of the non-constant E → × B → drift rates leads to further variation in power law indices from ≳ 2 to ≲ 1, decreasing with plasmoid size at the time of injection. The implications for energetic particle spectra are discussed alongside applications to 3D plasmoid reconnection and the effects of a guide field.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Offshore wind energy forecasting sensitivity to sea surface temperature input in the Mid-Atlantic

Abstract. As offshore wind farm development expands, accurate wind resource forecasting over the ocean is needed. One important yet relatively unexplored aspect of offshore wind resource assessment is the role of sea surface temperature (SST). Models are generally forced with reanalysis data sets, which employ daily SST products. Compared with observations, significant variations in SSTs that occur on finer timescales are often not captured. Consequently, shorter-lived events such as sea breezes and low-level jets (among others), which are influenced by SSTs, may not be correctly represented in model results. The use of hourly SST products may improve the forecasting of these events. In this study, we examine the sensitivity of model output from the Weather Research and Forecasting model (WRF) 4.2.1 to different SST products. We first evaluate three different data sets: the Multiscale Ultrahigh Resolution (MUR25) SST analysis, a daily, 0.25∘ × 0.25∘ resolution product; the Operational Sea Surface Temperature and Ice Analysis (OSTIA), a daily, 0.054∘ × 0.054∘ resolution product; and SSTs from the Geostationary Operational Environmental Satellite 16 (GOES-16), an hourly, 0.02∘ × 0.02∘ resolution product. GOES-16 is not processed at the same level as OSTIA and MUR25; therefore, the product requires gap-filling using an interpolation method to create a complete map with no missing data points. OSTIA and GOES-16 SSTs validate markedly better against buoy observations than MUR25, so these two products are selected for use with model simulations, while MUR25 is at this point removed from consideration. We run the model for June and July of 2020 and find that for this time period, in the Mid-Atlantic, although OSTIA SSTs overall validate better against in situ observations taken via a buoy array in the area, the two products result in comparable hub-height (140 m) wind characterization performance on monthly timescales. Additionally, during hours-long flagged events (< 30 h each) that show statistically significant wind speed deviations between the two simulations, both simulations once again demonstrate similar validation performance (differences in bias, earth mover's distance, correlation, and root mean square error on the order of 10−1 or less), with GOES-16 winds validating nominally better than OSTIA winds. With a more refined GOES-16 product, which has been not only gap-filled but also assimilated with in situ SST measurements in the region, it is likely that hub-height winds characterized by GOES-16-informed simulations would definitively validate better than those informed by OSTIA SSTs.

17 WIND ENERGY↗

Emerging multiscale insights on microbial carbon use efficiency in the land carbon cycle

Microbial carbon use efficiency (CUE) affects the fate and storage of carbon in terrestrial ecosystems, but its global importance remains uncertain. Accurately modeling and predicting CUE on a global scale is challenging due to inconsistencies in measurement techniques and the complex interactions of climatic, edaphic, and biological factors across scales. The link between microbial CUE and soil organic carbon relies on the stabilization of microbial necromass within soil aggregates or its association with minerals, necessitating an integration of microbial and stabilization processes in modeling approaches. In this perspective, we propose a comprehensive framework that integrates diverse data sources, ranging from genomic information to traditional soil carbon assessments, to refine carbon cycle models by incorporating variations in CUE, thereby enhancing our understanding of the microbial contribution to carbon cycling.

54 ENVIRONMENTAL SCIENCES↗

Collaborative Research: Vlasov–Maxwell Simulations to resolve electron heating and dissipation, in quasiperpendicular shocks (Final Technical Report)

The project is to study electron heating at quasi-perpendicular shocks. We have analyzed measurements from the Magnetosphere Multiscale (MMS) spacecraft and particle-in-cell simulations to address the question. One key discovery is that waves and are excited in the shock transition region, which further develop into complicated structures and thin current layers, which contribute to accelerate and heat electrons. We further investigated the excitation and evolution of these waves and structures, and their association with ion and electron dynamics. In addition, the analysis technique of Vlasov equation terms is further applied to study electron dynamics at the dayside magnetopause, to understand the effect of density, velocity and temperature variations on electron distributions and kinetics.

58 GEOSCIENCES↗

Interactive multiscale modeling to bridge atomic properties and electrochemical performance in Li-CO 2 battery design

Li-CO 2 batteries are promising energy storage systems due to their high theoretical energy density and CO 2 fixation capability, relying on reversible Li 2 CO 3 /C formation during discharge/charge cycles. Here, we present a multiscale modeling framework integrating Density Functional Theory (DFT), Ab-Initio Molecular Dynamics (AIMD), classical Molecular Dynamics (MD), and Finite Element Analysis (FEA) to investigate atomic and cell-level properties. The considered Li-CO 2 battery consists of a lithium metal anode, an ionic liquid electrolyte, and a carbon cloth cathode with Sb 0.67 Bi 1.33 Te 3 catalyst. DFT and AIMD determined the electrical conductivities of Sb 0.67 Bi 1.33 Te 3 and Li 2 CO 3 using the Kubo–Greenwood formalism and studied the CO 2 reduction mechanism on the cathode catalyst. MD simulations calculated the CO 2 diffusion coefficient, Li + transference number, ionic conductivity, and Li + solvation structure. The FEA model, parameterized with atomistic simulation data, reproduced the available experimental voltage–capacity profile at 1 mA/cm 2 and revealed spatio-temporal variations in Li 2 CO 3 /C deposition, porosity, and CO 2 concentration dependence on discharge rates in the cathode. Accordingly, Li 2 CO 3 can form large and thin film deposits, leading to dispersed and local porosity changes at 0.1 mA/cm 2 and 1 mA/cm 2 , respectively. The capacity decreases exponentially from 81,570 mAh/g at 0.1 mA/cm 2 to 6200 mAh/g at 1 mA/cm 2 , due to pore clogging from excessive discharge product deposition that limits CO 2 transport to the cathode interior. Therefore, the performance of Li-CO 2 batteries can be improved by enhancing CO 2 transport, regulating Li 2 CO 3 deposition, and optimizing cathode architecture.

Battery performance↗

Impact of Momentum Perturbation on Convective Boundary Layer Turbulence

Mesoscale-to-microscale coupling is an important tool for conducting turbulence-resolving multiscale simulations of realistic atmospheric flows, which are crucial for applications ranging from wind energy to wildfire spread studies. Different techniques are used to facilitate the development of realistic turbulence in the large-eddy simulation (LES) domain while minimizing computational cost. Here, we explore the impact of a simple and computationally efficient Stochastic Cell Perturbation method using momentum perturbation (SCPM-M) to accelerate turbulence generation in boundary-coupled LES simulations using the Weather Research and Forecasting model. We simulate a convective boundary layer (CBL) to characterize the production and dissipation of turbulent kinetic energy (TKE) and the variation of TKE budget terms. Furthermore, we evaluate the impact of applying momentum perturbations of three magnitudes below, up to, and above the CBL on the TKE budget terms. Momentum perturbations greatly reduce the fetch associated with turbulence generation. When applied to half the vertical extent of the boundary layer, momentum perturbations produce an adequate amount of turbulence. However, when applied above the CBL, additional structures are generated at the top of the CBL, near the inversion layer. The magnitudes of the TKE budgets produced by SCPM-M when applied at varying heights and with different perturbation amplitudes are always higher near the surface and inversion layer than those produced by No-SCPM, as are their contributions to the TKE. This study provides a better understanding of how SCPM-M reduces computational costs and how different budget terms contribute to TKE in a boundary-coupled LES simulation.

17 WIND ENERGY↗

The persistence of large scale structures. Part I. Primordial non-Gaussianity

Abstract We develop an analysis pipeline for characterizing the topology of large scale structure and extracting cosmological constraints based on persistent homology . Persistent homology is a technique from topological data analysis that quantifies the multiscale topology of a data set, in our context unifying the contributions of clusters, filament loops, and cosmic voids to cosmological constraints. We describe how this method captures the imprint of primordial local non-Gaussianity on the late-time distribution of dark matter halos, using a set of N-body simulations as a proxy for real data analysis. For our best single statistic, running the pipeline on several cubic volumes of size 40 (Gpc/h) 3 , we detect f NL loc =10 at 97.5% confidence on ~ 85% of the volumes. Additionally wetest our ability to resolve degeneracies betweenthe topological signature of f NL loc and variation of σ 8 and argue that correctly identifying nonzero f NL loc in this case is possible via an optimal template method. Our method relies on information living at $\mathcal{O}$(10) Mpc/h, a complementary scale with respect to commonly used methods such as the scale-dependent bias in the halo/galaxy power spectrum. Therefore, while still requiring a large volume, our method does not require sampling long-wavelength modes to constrain primordial non-Gaussianity. Moreover, our statistics are interpretable: we are able to reproduce previous results in certain limits and we make new predictions for unexplored observables, such as filament loops formed by dark matter halos in a simulation box.

Astronomy & Astrophysics↗

Multiphase computational fluid dynamics modeling of reacting flows in absorption columns for carbon capture

First-principles derived computational fluid dynamics (CFD) simulations have been proposed as a fundamental tool for investigating solvent-based CO 2 absorption in packed columns due to their ability to accurately represent the underlying nonlinear, multiscale dynamics. Numerous studies have previously utilized such CFD simulations to investigate hydrodynamics of columns with structured and random packings by assessing the key hydrodynamic metrics such as the interfacial and wetted areas. While mapping such metrics for different conditions is essential to the optimization of absorption columns, it is not sufficient, as the CO 2 capture rate depends also on the coupled, nonlinear dynamics from the underlying chemical reaction kinetics, thermodynamics, and heat-transfer rates. In this work, we present detailed CFD simulation results augmented by incorporating the effects of interfacial physical mass transfer of CO 2 , heat release from chemical reaction kinetics, and thermophysical property variations from resulting temperature gradients. We demonstrate the applicability of the proposed approach in numerically assessing the performance of packed columns by evaluating key hydrodynamic quantities, CO 2 absorption rates, and temperature rise in a reference column with packings that are structurally similar to the Sulzer Mellapak™ 250.Y packing, for different solvent inflow velocities and temperatures. Predictions from simulation results are found to be consistent with the trends in experimental observations from the literature, suggesting that the predictive capabilities of the simulation framework can be leveraged to guide the future development of absorber-column designs and optimized process flowsheets.

Absorption columns↗

Insight into ideal shear strength of Ni-based dilute alloys using first-principles calculations and correlational analysis

Here the present work examines the effect of alloying elements (denoted X) on the ideal shear strength for 26 dilute Ni-based alloys, Ni11X, as determined by first-principles calculations of pure alias shear deformations. The variations in ideal shear strength are quantitatively explored with correlational analysis techniques, showing the importance of atomic properties such as size and electronegativity. The shear moduli of the alloys are affirmed to show a strong linear relationship with their ideal shear strengths, while the shear moduli of the individual alloying elements were not indicative of alloy shear strength. Through combination with available ideal shear strength data on Mg alloys, a potential application of the Ni alloy data is demonstrated in the search for a set of atomic features suitable for machine learning applications to mechanical properties. As another illustration, the calculated Ni ideal shear strengths play a key role in a predictive multiscale framework for deformation behavior of single crystal alloys at large strains, as shown by simulated stress–strain curves.

36 MATERIALS SCIENCE↗

Multiscale Modeling Framework for Lithium Nucleation in 3D Porous Carbon Anodes

Porous carbon scaffolds offer a promising route for mitigating non-uniform lithium (Li) plating to enhance the safety and longevity of Li metal batteries. However, the influence of microstructural morphology on Li nucleation is not well understood. Here, we present a multiscale modeling framework to investigate how the porous microstructure of carbon materials affects Li nucleation behavior. Ab initio molecular dynamics simulations quantify the nucleation energy barriers of Li on graphene as a function of Li content, surface curvature, and applied potential, providing key parameters for a classical nucleation theory (CNT) model. From macroscale half-cell simulations, we obtained Li concentration and electrical potential profiles to define boundary conditions for mesoscopic simulations. At the mesoscale, three distinct synthetic 3D microstructures with different porosities and characteristic feature sizes are generated to resolve local distributions of Li flux, current density, and mechanical stress. These outputs are integrated into the CNT model to map spatial variation in nucleation rates. Our findings reveal trade-offs between suppressing nucleation rates and achieving spatial uniformity, offering design guidelines for optimizing porous carbon anodes to balance nucleation control and mechanical integrity.

Materials science↗

Peridynamic Models for Random Media Found by Coarse Graining

Using coarse graining, the upscaled mechanical properties of a solid with small scale heterogeneities are derived. The method maps internal forces at the small scale onto peridynamic bond forces in the coarse grained mesh. These upscaled bond forces are used to calibrate a peridynamic material model with position-dependent parameters. These parameters incorporate mesoscale variations in the statistics of the small scale system. The upscaled peridynamic model can have a much coarser discretization than the original small scale model, allowing larger scale simulations to be performed efficiently. The convergence properties of the method are investigated for representative random microstructures. In conclusion, a bond breakage criterion for the upscaled peridynamic material model is also demonstrated.

36 MATERIALS SCIENCE↗

Mesoscale structural gradients in human tooth enamel

The outstanding mechanical and chemical properties of dental enamel emerge from its complex hierarchical architecture. An accurate, detailed multiscale model of the structure and composition of enamel is important for understanding lesion formation in tooth decay (dental caries), enamel development (amelogenesis) and associated pathologies (e.g., amelogenesis imperfecta or molar hypomineralization), and minimally invasive dentistry. Although features at length scales smaller than 100 nm (individual crystallites) and greater than 50 µm (multiple rods) are well understood, competing field of view and sampling considerations have hindered exploration of mesoscale features, i.e., at the level of single enamel rods and the interrod enamel (1 to 10 µm). Here, we combine synchrotron X-ray diffraction at submicrometer resolution, analysis of crystallite orientation distribution, and unsupervised machine learning to show that crystallographic parameters differ between rod head and rod tail/interrod enamel. This variation strongly suggests that crystallites in different microarchitectural domains also differ in their composition. Thus, we use a dilute linear model to predict the concentrations of minority ions in hydroxylapatite (Mg 2+ and CO 3 2- /Na + ) that plausibly explain the observed lattice parameter variations. While differences within samples are highly significant and of similar magnitude, absolute values and the sign of the effect for some crystallographic parameters show interindividual variation that warrants further investigation. In conclusion, by revealing additional complexity at the rod/interrod level of human enamel and leaving open the possibility of modulation across larger length scales, these results inform future investigations into mechanisms governing amelogenesis and introduce another feature to consider when modeling the mechanical and chemical performance of enamel.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Quantitative approaches for multiscale structural analysis with atomic resolution electron microscopy

Atomic-resolution imaging with scanning transmission electron microscopy is a powerful tool for characterizing the nanoscale structure of materials, in particular features such as defects, local strains, and symmetry-breaking distortions. In addition to advanced instrumentation, the effectiveness of the technique depends on computational image analysis to extract meaningful features from complex datasets recorded in experiments, which can be complicated by the presence of noise and artifacts, small or overlapping features, and the need to scale analysis over large representative areas. Here, we present image analysis approaches which synergize real and reciprocal space information to efficiently and reliably obtain meaningful structural information with picometer scale precision across hundreds of nanometers of material from atomic-resolution electron microscope images. Damping superstructure peaks in reciprocal space allows symmetry-breaking structural distortions to be disentangled from other sources of inhomogeneity and measured with high precision. Real-space fitting of the wavelike signals resulting from Fourier filtering enables absolute quantification of lattice parameter variations and strain, as well as the uncertainty associated with these measurements. Implementations of these algorithms are made available as an open source python package.

36 MATERIALS SCIENCE↗

Multiscale characterization and comparison of historical and modern nuclear graphite grades

Beginning with Chicago Pile I, graphite has been used as a moderator material in nuclear power stations and is considered a potential material for use in future Generation IV advanced reactors. The microstructure of graphite is responsible for much of its mechanical and thermo-physical properties, and how it responds to irradiation. To understand graphite microstructure, it is necessary to understand its porosity at the macro- and micro-scales; and to understand its porosity, it is necessary to characterize the morphological connectivity of the void content and the two main phases of graphite: filler and binder. Here, using several microscopy and analytical techniques, a detailed examination of the heterogeneity, microstructure and pore structure of different graphite grades and their binder and filler phases is presented. Significant differences were found between coarser and finer nuclear grades. Coarse grades have a more diverse range of filler particles, pores and thermal cracks. Finer grades have a more well-defined pore size distribution, fewer variations of filler particles sizes and do not contain as many large thermal cracks. Fine grades tend to have a well-connected network of pores whereas coarser grades contain a larger content of closed porosity. The framework developed within this work can be applied and used to assess the various graphite grades that would down-select materials for specific use in graphite moderated reactor designs.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Towards a Unified theory of Fractional and Nonlocal Vector Calculus

Nonlocal and fractional-order models capture effects that classical partial differential equations cannot describe; for this reason, they are suitable for a broad class of engineering and scientific applications that feature multiscale or anomalous behavior. This has driven a desire for a vector calculus that includes nonlocal and fractional gradient, divergence and Laplacian type operators, as well as tools such as Green’s identities, to model subsurface transport, turbulence, and conservation laws. In the literature, several independent definitions and theories of nonlocal and fractional vector calculus have been put forward. Some have been studied rigorously and in depth, while others have been introduced ad-hoc for specific applications. The goal of this work is to provide foundations for a unified vector calculus by (1) consolidating fractional vector calculus as a special case of nonlocal vector calculus, (2) relating unweighted and weighted Laplacian operators by introducing an equivalence kernel, and (3) proving a form of Green’s identity to unify the corresponding variational frameworks for the resulting nonlocal volume-constrained problems. Here, the proposed framework goes beyond the analysis of nonlocal equations by supporting new model discovery, establishing theory and interpretation for a broad class of operators, and providing useful analogues of standard tools from the classical vector calculus.

97 MATHEMATICS AND COMPUTING↗