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At least 271 records · Page 15

Exploring the Structural, Dynamic, and Functional Properties of Metal–Organic Frameworks through Molecular Modeling

This review spotlights the role of atomic-level modeling in research on metal-organic frameworks (MOFs), especially the key methodologies of density functional theory (DFT), Monte Carlo (MC) simulations, and molecular dynamics (MD) simulations. The discussion focuses on how periodic and cluster-based DFT calculations can provide novel insights into MOF properties, with a focus on predicting structural transformations, understanding thermodynamic properties and catalysis, and providing information or properties that are fed into classical simulations such as force field parameters or partial charges. Classical simulation methods, highlighting force field selection, databases of MOFs for high-throughput screening, and the synergistic nature of MC and MD simulations, are described. By predicting equilibrium thermodynamic and dynamic properties, these methods offer a wide perspective on MOF behavior and mechanisms. Additionally, the incorporation of machine learning (ML) techniques into quantum and classical simulations is discussed. These methods can enhance accuracy, expedite simulation setup, reduce computational costs, as well as predict key parameters, optimize geometries, and estimate MOF stability. By charting the growth and promise of computational research in the MOF field, the aim is to provide insights and recommendations to facilitate the incorporation of computational modeling more broadly into MOF research.

36 MATERIALS SCIENCE↗

Learning robust parameter inference and density reconstruction in flyer plate impact experiments

Estimating physical parameters or material properties from experimental observations is a common objective in many areas of physics and material science. In many experiments, especially in shock physics, radiography is the primary means of observing the system of interest. However, radiography does not provide direct access to key state variables, such as density, which prevents the application of traditional parameter estimation approaches. Here we focus on flyer plate impact experiments on porous materials, and resolving the underlying parameterized equation of state (EoS) and crush porosity model parameters given radiographic observation(s). We use machine learning as a tool to demonstrate with high confidence that using only high impact velocity data does not provide sufficient information to accurately infer both EoS and crush model parameters, even with fully resolved density fields or a dynamic sequence of images. We thus propose an observable data set consisting of low and high impact velocity experiments/simulations that capture different regimes of compaction and shock propagation, and proceed to introduce a generative machine learning approach which produces a posterior distribution of physical parameters directly from radiographs. We demonstrate the effectiveness of the approach in estimating parameters from simulated flyer plate impact experiments, and show that the obtained estimates of EoS and crush model parameters can then be used in hydrodynamic simulations to obtain accurate and physically admissible density reconstructions. Finally, we examine the robustness of the approach to model mismatches, and find that the learned approach can provide useful parameter estimates in the presence of out-of-distribution radiographic noise and previously unseen physics, thereby promoting a potential breakthrough in estimating material properties from experimental radiographic images.

97 MATHEMATICS AND COMPUTING↗

Vibrational dynamics of zero-field-splitting hamiltonian in gadolinium-based MRI contrast agents from ab initio molecular dynamics

The electronic relaxation of gadolinium complexes used as MRI contrast agents was studied theoretically by following the short time evolution of zero-field-splitting parameters. The statistical analysis of ab initio molecular dynamics trajectories provided a clear separation between static and transient contributions to the zero-field-splitting. For the latter, the correlation time was estimated at approximately 0.1 ps. The influence of the ligand was also probed by replacing one pendant arm of our reference macrocyclic complex by a bulkier phosphonate arm. In contrast to the transient contribution, the static zero-field-splitting was significantly influenced by this substitution.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Soil-related developments of the Biome-BGCMuSo v6.2 terrestrial ecosystem model

Terrestrial biogeochemical models are essential tools to quantify climate–carbon cycle feedback and plant–soil relations from local to global scale. In this study, a theoretical basis is provided for the latest version of the Biome-BGCMuSo biogeochemical model (version 6.2). Biome-BGCMuSo is a branch of the original Biome-BGC model with a large number of developments and structural changes. Earlier model versions performed poorly in terms of soil water content (SWC) dynamics in different environments. Moreover, lack of detailed nitrogen cycle representation was a major limitation of the model. Since problems associated with these internal drivers might influence the final results and parameter estimation, additional structural improvements were necessary. In this paper the improved soil hydrology as well as the soil carbon and nitrogen cycle calculation methods are described in detail. Capabilities of the Biome-BGCMuSo v6.2 model are demonstrated via case studies focusing on soil hydrology, soil nitrogen cycle, and soil organic carbon content estimation. Soil-hydrology-related results are compared to observation data from an experimental lysimeter station. The results indicate improved performance for Biome-BGCMuSo v6.2 compared to v4.0 (explained variance increased from 0.121 to 0.8 for SWC and from 0.084 to 0.46 for soil evaporation; bias changed from -0.047 to -0.007 m 3 m -3 for SWC and from -0.68 to -0.2 mm d -1 for soil evaporation). Simulations related to nitrogen balance and soil CO 2 efflux were evaluated based on observations made in a long-term field experiment under crop rotation. The results indicated that the model is able to provide realistic nitrate content estimation for the topsoil. Soil nitrous oxide (N 2 O) efflux and soil respiration simulations were also realistic, with overall correspondence with the observations (for the N 2 O efflux simulation bias was between -0.13 and -0.1 mgNm -2 d -1 , and normalized root mean squared error (NRMSE) was 32.4 %–37.6 %; for CO 2 efflux simulations bias was 0.04–0.17 gCm -2 d -1 , while NRMSE was 34.1 %–40.1 %). Sensitivity analysis and optimization of the decomposition scheme are presented to support practical application of the model. The improved version of Biome-BGCMuSo has the ability to provide more realistic soil hydrology representation as well as nitrification and denitrification process estimation, which represents a major milestone.

58 GEOSCIENCES↗

Identification and system parameter estimation methods for a Pyrofusion neutron source - 372

Pyrofusion sources are compact, low power systems which are capable of producing short intense pulses of neutrons from D-D fusion reactions. A model structure has been derived from the underlying physics principles and it is shown that the dominant non-linear dynamics pose significant challenges to the system control. This paper presents the methods under development to construct, estimate and analyse nonlinear grey-box models of Pyrofusion systems from measured data. The methods have been trialled on data sets obtained from the publications of previous Pyrofusion research groups. The results indicate the promising potential application of these methods to the system identification of profusion device characteristics to support model verification, pulse characterisation and prediction of operational capabilities. The identified models are shown to exhibit satisfactory analogous cause-and-effect behaviour. (authors)

07 ISOTOPE AND RADIATION SOURCES↗

Assessment and Improvement Proposals for High-Pressure Rinsing Processes during Cleanroom Preparation of Superconducting Radio-Frequency Cavities for Particle Accelerators

The goal of this internship is to develop a fluid dynamics characterization of the high-pressure flow used for cleaning the internal surface of the SRF cavities. Initially, the High Pressure Rinsing (HPR) process is introduced, focusing on the problems of the SRF cavities and how this method can be used to increase their acceleration efficiency and performance. The characterization of the problem is then presented, including an introduction to the multiphase flow modeling and the analysis of the Fermilab facility for the HPR. To accomplish the goal, a preliminary estimation of the variables was performed using MATLAB. Then, multiple 2D simulations were developed with Ansys Fluent, and the influence of the main parameter was investigated. The simulation results are then presented and analysed, with a focus on the possible future developments of the HPR process fluid dynamic characterization.

43 PARTICLE ACCELERATORS↗

Convergence in simulating global soil organic carbon by structurally different models after data assimilation

Abstract Current biogeochemical models produce carbon–climate feedback projections with large uncertainties, often attributed to their structural differences when simulating soil organic carbon (SOC) dynamics worldwide. However, choices of model parameter values that quantify the strength and represent properties of different soil carbon cycle processes could also contribute to model simulation uncertainties. Here, we demonstrate the critical role of using common observational data in reducing model uncertainty in estimates of global SOC storage. Two structurally different models featuring distinctive carbon pools, decomposition kinetics, and carbon transfer pathways simulate opposite global SOC distributions with their customary parameter values yet converge to similar results after being informed by the same global SOC database using a data assimilation approach. The converged spatial SOC simulations result from similar simulations in key model components such as carbon transfer efficiency, baseline decomposition rate, and environmental effects on carbon fluxes by these two models after data assimilation. Moreover, data assimilation results suggest equally effective simulations of SOC using models following either first‐order or Michaelis–Menten kinetics at the global scale. Nevertheless, a wider range of data with high‐quality control and assurance are needed to further constrain SOC dynamics simulations and reduce unconstrained parameters. New sets of data, such as microbial genomics‐function relationships, may also suggest novel structures to account for in future model development. Overall, our results highlight the importance of observational data in informing model development and constraining model predictions.

54 ENVIRONMENTAL SCIENCES↗

DONKEY: A Flexible and Accurate Algorithm for Clustering

We propose an accurate clustering algorithm suitable for the varied and multidimensional data sets that correspond to temporal snapshots from on-the-fly nonadiabatic trajectory-based simulations of photoexcited dynamics. The algorithm approximates the underlying probability density function using variable kernel density estimation, with local maxima corresponding to cluster centers. Each data point is then assigned to one of the maxima by employing a maximization procedure. Finally, clusters artificially separated by minor fluctuations in the probability density are merged. The algorithm does not require parameter tuning, which ensures flexibility and reduces the risk of bias. It is tested on several synthetic data sets, where it consistently outperforms conventional clustering algorithms. As a final example, the algorithm is applied to the excited dynamics of the norbornadiene ⇌ quadricyclane (C 7 H 8 ) molecular photoswitch, demonstrating how distinct reaction pathways can be identified.

algorithms↗

Measurement of elastic precursor decay in pre-heated aluminum films under ultra-fast laser generated shocks

Here, this article presents results from laser-driven shock compression experiments performed on pre-heated pure aluminum films at temperatures ranging from 23 to 400 °C. The samples were vapor deposited on the surface of a 500 μm thick sapphire substrate and mounted onto a custom holder with an integrated ring-heater to enable variable initial temperature conditions. A chirped pulse amplified laser was used to generate a pulse for both shocking the films and for probing the free surface velocity using Ultrafast Dynamic Ellipsometry. The particle velocity traces measured at the free surface clearly show elastic and plastic wave separation, which was used to estimate the decay of the elastic precursor amplitude over propagation distances ranging from 0.278 to 4.595 μm. Elastic precursors (which also correspond to dynamic material strength under uniaxial strain) of increasing amplitudes were observed with increasing initial sample temperatures for all propagation distances, which is consistent with expectations for aluminum in a deformation regime where phonon drag limits the mobility of dislocations. The experimental results show peak elastic amplitudes corresponding to axial stresses of over 7.5 GPa; estimates for plastic strain-rates in the samples are of the order 10 9 /s. The measured elastic amplitudes at the micron length scales are compared with those at the millimeter length-scales using a two-parameter model and used to correlate the rate sensitivity of the dynamic strength at strain-rates ranging from 10 3 to 10 9 /s and elevated temperature conditions. The overall trend, as inferred from the experimental data, indicates that the temperature-strengthening effect decreases with increasing plastic strain-rates.

36 MATERIALS SCIENCE↗

Linear two-pool models are insufficient to infer soil organic matter decomposition temperature sensitivity from incubations

Abstract Terrestrial carbon (C)-climate feedbacks depend strongly on how soil organic matter (SOM) decomposition responds to temperature. This dependency is often represented in land models by the parameter Q 10 , which quantifies the relative increase of microbial soil respiration per 10 °C temperature increase. Many studies have conducted paired laboratory soil incubations and inferred “active” and “slow” pool Q 10 values by fitting linear two-pool models to measured respiration time series. Using a recently published incubation study (Qin et al. in Sci Adv 5(7):eaau1218, 2019) as an example, here we first show that the very high parametric equifinality of the linear two-pool models may render such incubation-based Q 10 estimates unreliable. In particular, we show that, accompanied by the uncertain initial active pool size, the slow pool Q 10 can span a very wide range, including values as high as 100, although all parameter combinations are producing almost equally good model fit with respect to the observations. This result is robust whether or not interactions between the active and slow pools are considered (typically these interactions are not considered when interpreting incubation data, but are part of the predictive soil carbon models). This very large parametric equifinality in the context of interpreting incubation data is consistent with the poor temporal extrapolation capability of linear multi-pool models identified in recent studies. Next, using a microbe-explicit SOM model (RESOM), we show that the inferred two pools and their associated parameters (e.g., Q 10 ) could be artificial constructs and are therefore unreliable concepts for integration into predictive models. We finally discuss uncertainties in applying linear two-pool (or more generally multiple-pool) models to estimate SOM decomposition parameters such as temperature sensitivities from laboratory incubations. We also propose new observations and model structures that could enable better process understanding and more robust predictive capabilities of soil carbon dynamics.

54 ENVIRONMENTAL SCIENCES↗

Automated model generation and parameter estimation of building energy models using an ontology-based framework

This study presents a methodology for automated model generation and parameter estimation of building energy models using semantic modeling and Bayesian estimation. Semantic modeling techniques are used to represent the system components and their interactions, facilitating the automatic generation of a simulation model from dynamic component models. The proposed approach is applied to a case study of a ventilation system where a simulation model is generated, calibrated, and assessed through different performance metrics. These metrics demonstrate the accuracy and reliability of both model point estimates and probabilistic prediction intervals across all model outputs. Overall, the proposed methodology offers a systematic and automated approach to model development and calibration in building energy systems, with potential applications in building performance analysis, monitoring, and optimization.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Identified charged hadron production in Au+Au collisions at $\sqrt{s_{NN}}$ = 54.4 GeV with the STAR detector

Here, we present results on the production of 𝜋±, 𝐾±, 𝑝, and $\bar{𝑝}$ in Au+Au collisions at $\sqrt{𝑠_{N⁢N}}$ = 54.4~GeV using the STAR detector at RHIC, at mid-rapidity (|𝑦|< 0.1). Invariant yields of these particles as a function of transverse momentum are shown. We determine bulk properties such as integrated particle yields (𝑑 ⁢𝑁 /𝑑 ⁢𝑦 ), mean transverse momentum (⟨𝑝 𝑇 ⟩), particle ratios, which provide insight into the particle production mechanisms. Additionally, the kinetic freeze-out parameters (𝑇 kin and ⟨𝛽 𝑇 ⟩), which provide information about the dynamics of the system at the time of freeze-out, are obtained. The Bjorken energy density (𝜖 𝐵⁢𝐽 ), which gives an estimate of the energy density in the central rapidity region of the collision zone at the formation time 𝜏, is calculated and presented as a function of multiplicity for various energies. The results are compared with those from the models such as A Multi-Phase Transport (AMPT) and Heavy Ion Jet INteraction Generator (HIJING) for further insights.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

A Nonlinear Direct Power Controller for a Three-Phase Grid-Connected Inverter with Online Parameter Update for PV Application

This work proposes a nonlinear direct power controller for a three-phase grid-connected inverter for photovoltaic application. Grid-connected converters for solar applications require advanced control architectures to ensure optimal operation and extraction of maximum power from the photovoltaic arrays. Therefore, to ensure this, a nonlinear power controller architecture has been proposed to extract the maximum power from the solar arrays and to achieve the most optimal operation. To further improve the performance, a parameter update scheme has been utilized which is based on model reference adaptive system. The latter helps to accomplish not only good dynamic response but also excellent tracking performance. The overall control come estimation architecture is verified based on computer simulations via MATLAB/Simulink and PLECS domain and various important case study results are presented.

direct power control↗

ENSEMBLE KALMAN FILTERS FOR RELIABILITY ESTIMATION IN PERFUSION INFERENCE

We consider the solution of inverse problems in dynamic contrast–enhanced imaging by means of ensemble Kalman filters. Our quantity of interest is blood perfusion, i.e., blood flow rates in tissue. While existing approaches to compute blood perfusion parameters for given time series of radiological measurements mainly rely on deterministic, deconvolution–based methods, we aim at recovering probabilistic solution information for given noisy measurements. To this end, we model radiological image capturing as a sequential data assimilation process and solve it by an ensemble Kalman filter. Thereby, we recover deterministic results as an ensemble–based mean and are able to compute reliability information such as probabilities for the perfusion to be in a given range. Our target application is the inference of blood perfusion parameters in the human brain. A numerical study shows promising results for artificial measurements generated by a digital perfusion phantom.

Engineering↗

2D OR NOT 2D: THE EFFECT OF DIMENSIONALITY ON THE DYNAMICS OF FINGERING CONVECTION AT LOW PRANDTL NUMBER

Fingering convection (otherwise known as thermohaline convection) is an instability that occurs in stellar radiative interiors in the presence of unstable compositional gradients. Numerical simulations have been used in order to estimate the efficiency of mixing induced by this instability. However, fully three-dimensional (3D) computations in the parameter regime appropriate for stellar astrophysics (i.e., low Prandtl number) are prohibitively expensive. This raises the question of whether two-dimensional (2D) simulations could be used instead to achieve the same goals. In this work, we address this issue by comparing the outcome of 2D and 3D simulations of fingering convection at low Prandtl number. We find that 2D simulations are never appropriate. However, we also find that the required 3D computational domain does not have to be very wide: the third dimension only needs to contain a minimum of two wavelengths of the fastest-growing linearly unstable mode to capture the essentially 3D dynamics of small-scale fingering. Narrow domains, however, should still be used with caution since they could limit the subsequent development of any large-scale dynamics typically associated with fingering convection.

79 ASTRONOMY AND ASTROPHYSICS↗

CONTRIBUTIONS OF THE ELASTICITY TO THE PRECESSION OF A TWO-LAYER EARTH MODEL

We focus on the updating of a specific contribution to the precession of the equator in longitude, usually named as “second order.” It stems from the crossing of certain terms of the lunisolar gravitational potential. The IAU2006 precession theory assigns it the value of −46.8 mas/cy that was derived for a rigid Earth model. Instead of that model, we consider a two-layer Earth composed of an elastic mantle and a liquid core, working out the problem within the Hamiltonian framework developed by Getino and Ferrándiz. The targeted effect is obtained without further simplifying assumptions through Hori’s canonical perturbation method applied up to the second order of perturbation. On account of using a more realistic Earth model, the revised value of the second-order contribution is significantly changed and reaches −55.29 mas/cy. That variation of the second-order contribution is larger than other contributions included in IAU2006. It must be compensated with an increase of −8.51 mas/cy in the value of the lunisolar first-order component p{sub A}{sup ′} of the precession of the equator rate, which is derived from the total rate by subtracting the remaining contributions accounted for in IAU2006 precession. The updating of the second-order contribution implies that the p{sub A}{sup ′} parameter has to be changed, from 5040684.593 to 5040693.104 mas/cy in absence of potential revisions of other contributions. It entails a proportional variation of Earth’s dynamical ellipticity H{sub d}, for which the estimation associated with IAU2006, 0.00327379448, should be updated to 0.00327380001, about 1.7 ppm larger.

79 ASTRONOMY AND ASTROPHYSICS↗

Discrete Control of a Dynamical System with Delay Under Conditions of Uncertainty

In this paper, we present a numerical solution of the discrete control problem for the immune response in an infectious disease under conditions of uncertainty. This problem is described by a nonlinear system of ordinary differential equation with delay. Conditions of uncertainty mean that values of the parameters of the model are unknown and their estimates are corrected by new experimental data. We propose an algorithm that allows one, within the framework of the mathematical model of an infectious disease, to construct the control and to identify parameters. By using the algorithm proposed, we develop treatment programs based on immunotherapy. We show that immunotherapy is an effective treatment for all main forms of disease: acute, chronic, and lethal.

60 APPLIED LIFE SCIENCES↗

Estimation of the HIV-1 infection rate and the basic reproductive ratio

This paper proposes and analyzes an alternative method to estimate important parameters of the HIV-1 infection: the infection rate and the basic reproductive ratio (in the presence and absence of the immune response). These parameters are of great relevance, impacting on the infection chronicity. The method consists in comparing clinical data in the chronic stage with predicted equilibrium points of a mathematical model which describes the dynamics of HIV-1 in the acute infection phase. The fact that the method uses only clinical data relating to the chronic stage is an important aspect since most patients are diagnosed at this stage, and thus only have data available for this stage. A comparison between the proposed method and other estimation methods, as well as between numerical simulations, is presented and the results are quite satisfactory. In addition, by applying the proposed method for data of 31 patients, we estimate the basic reproductive ratio in the presence of the immune response and the HIV-1 infection rate for which we obtained a median of 1.95 (IQR 0.55) and 1.96×10{sup −5} mm{sup 3} virions{sup −1} day{sup −1} (IQR 3.52×10{sup −5}), respectively.

60 APPLIED LIFE SCIENCES↗