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At least 163 records · Page 9

A Principled Framework to Assess the Information-Theoretic Fitness of Brain Functional Sub-Circuits

In systems and network neuroscience, many common practices in brain connectomic analysis are often not properly scrutinized. One such practice is mapping a predetermined set of sub-circuits, like functional networks (FNs), onto subjects’ functional connectomes (FCs) without adequately assessing the information-theoretic appropriateness of the partition. Another practice that goes unchallenged is thresholding weighted FCs to remove spurious connections without justifying the chosen threshold. This paper leverages recent theoretical advances in Stochastic Block Models (SBMs) to formally define and quantify the information-theoretic fitness (e.g., prominence) of a predetermined set of FNs when mapped to individual FCs under different fMRI task conditions. Our framework allows for evaluating any combination of FC granularity, FN partition, and thresholding strategy, thereby optimizing these choices to preserve the important topological features of the human brain connectomes. By applying to the Human Connectome Project with Schaefer parcellations at multiple levels of granularity, the framework showed that the common thresholding value of 0.25 was indeed information-theoretically valid for group-average FCs, despite its previous lack of justification. Our results pave the way for the proper use of FNs and thresholding methods, and provide insights for future research in individualized parcellations.

Duong-Tran, Duy (ORCID:0009000944967575)↗

GDSA Framework Development and Process Model Integration FY2022

The Spent Fuel and Waste Science and Technology (SFWST) Campaign of the U.S. Department of Energy (DOE) Office of Nuclear Energy (NE), Office of Spent Fuel & Waste Disposition (SFWD) is conducting research and development (R&D) on geologic disposal of spent nuclear fuel (SNF) and high-level nuclear waste (HLW). A high priority for SFWST disposal R&D is disposal system modeling (Sassani et al. 2021). The SFWST Geologic Disposal Safety Assessment (GDSA) work package is charged with developing a disposal system modeling and analysis capability for evaluating generic disposal system performance for nuclear waste in geologic media. This report describes fiscal year (FY) 2022 advances of the Geologic Disposal Safety Assessment (GDSA) performance assessment (PA) development groups of the SFWST Campaign. The common mission of these groups is to develop a geologic disposal system modeling capability for nuclear waste that can be used to assess probabilistically the performance of generic disposal options and generic sites. The modeling capability under development is called GDSA Framework (pa.sandia.gov). GDSA Framework is a coordinated set of codes and databases designed for probabilistically simulating the release and transport of disposed radionuclides from a repository to the biosphere for post-closure performance assessment. Primary components of GDSA Framework include PFLOTRAN to simulate the major features, events, and processes (FEPs) over time, Dakota to propagate uncertainty and analyze sensitivities, meshing codes to define the domain, and various other software for rendering properties, processing data, and visualizing results.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Analytic techniques for solving the transport equations in electroweak baryogenesis

We develop an efficient method for solving transport equations, particularly in the context of electroweak baryogenesis. It provides fully-analytical results under mild approximations and can also test semi-analytical results, which are applicable in more general cases. Key elements of our method include the reduction of the second-order differential equations to first order, representing the set of coupled equations as a block matrix of the particle densities and their derivatives, identification of zero modes, and block decomposition of the matrix. We apply our method to calculate the baryon asymmetry of the Universe (BAU) in a Standard Model effective field theory framework of complex Yukawa couplings to determine the sensitivity of the resulting BAU to modifications of various model parameters and rates, and to estimate the effect of the commonly-used thin-wall approximation.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

QES-Plume v1.0: a Lagrangian dispersion model

Low-cost simulations providing accurate predictions of transport of airborne material in urban areas, vegetative canopies, and complex terrain are demanding because of the small-scale heterogeneity of the features influencing the mean flow and turbulence fields. Common models used to predict turbulent transport of passive scalars are based on the Lagrangian stochastic dispersion model. The Quick Environmental Simulation (QES) tool is a low-computational-cost framework developed to provide high-resolution wind and concentration fields in a variety of complex atmospheric-boundary-layer environments. Part of the framework, QES-Plume, is a Lagrangian dispersion code that uses a time-implicit integration scheme to solve the generalized Langevin equations which require mean flow and turbulence fields. Here, QES-Plume is driven by QES-Winds, a 3D fast-response model that computes mass-consistent wind fields around buildings, vegetation, and hills using empirical parameterizations, and QES-Turb, a local-mixing-length turbulence model. In this paper, the particle dispersion model is presented and validated against analytical solutions to examine QES-Plume’s performance under idealized conditions. In particular, QES-Plume is evaluated against a classical Gaussian plume model for an elevated continuous point-source release in uniform flow, the Lagrangian scaling of dispersion in isotropic turbulence, and a non-Gaussian plume model for an elevated continuous point-source release in a power-law boundary-layer flow. In these cases, QES-Plume yields a maximum relative error below 6 % when compared with analytical solutions. In addition, the model is tested against wind-tunnel data for a uniform array of cubical buildings. QES-Plume exhibits good agreement with the experiment with 99 % of matched zeros and 59 % of the predicted concentrations falling within a factor of 2 of the experimental concentrations. Furthermore, results also emphasize the importance of using high-quality turbulence models for particle dispersion in complex environments. Finally, QES-Plume demonstrates excellent computational performance.

58 GEOSCIENCES↗

A layered 2D computational framework: Theory and applications to nuclear fuel behavior

Nuclear fuel performance computer codes have been developed over the last 50 years to analyze fuel behavior under various operating conditions. Traditionally, these codes used quasi-two-dimensional (also commonly known as 1.5D) representations of the fuel rod, which model the rod using a set of one-dimensional axisymmetric models that represent the behavior at specific axial positions on the rod. Modern fuel performance codes have the ability to investigate full three-dimensional (3D) effects and couple to other physics-based codes for true multiphysics simulations. However, with increasing complexity comes increasing computational costs. Many phenomena of interest involve azimuthally-varying behavior that cannot be represented using the aforementioned quasi-two-dimensional approach, but do not require the use of a full 3D model. To efficiently address these problems, there is a need for a computational framework that provides a compromise between the quasi-two-dimensional and full 3D models. In this paper, we present a new quasi-three-dimensional approach that represents the fuel as a set of 2D planar models that represent the behavior of the fuel cross-section at various axial positions. Presented here are the theory behind the methodology, test cases to illustrate proper implementation, and practical applications of its use in the BISON fuel performance code for a variety of cases in nuclear fuel analysis, such as fuel fracture, axial fuel relocation, and cladding distension and oxidation.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

HEPTAPOD: Orchestrating High Energy Physics Workflows Towards Autonomous Agency

Many workflows in high-energy-physics (HEP) stand to benefit from recent advances in transformer-based large language models (LLMs). While early applications of LLMs focused on text generation and code completion, modern LLMs now support orchestrated agency: the coordinated execution of complex, multi-step tasks through tool use, structured context, and iterative reasoning. We introduce the HEP Toolkit for Agentic Planning, Orchestration, and Deployment (HEPTAPOD), an orchestration framework designed to bring this emerging paradigm to HEP pipelines. The framework enables LLMs to interface with domain-specific tools, construct and manage simulation workflows, and assist in common utility and data analysis tasks through schema-validated operations and run-card-driven configuration. To demonstrate these capabilities, we consider a representative Beyond the Standard Model (BSM) Monte Carlo validation pipeline that spans model generation, event simulation, and downstream analysis within a unified, reproducible workflow. HEPTAPOD provides a structured and auditable layer between human researchers, LLMs, and computational infrastructure, establishing a foundation for transparent, human-in-the-loop systems.

Menzo, Tony [Alabama U.; Fermilab] (ORCID:00000002↗

A novel approach for tetrahedral-element-based finite element simulations of anisotropic hyperelastic intervertebral disc behavior

Intervertebral discs are microstructurally complex spinal tissues that add greatly to the flexibility and mechanical strength of the human spine. Attempting to provide an adjustable basis for capturing a wide range of mechanical characteristics and to better address known challenges of numerical modeling of the disc, we present a robust finite-element-based model formulation for spinal segments in a hyperelastic framework using tetrahedral elements. We evaluate the model stability and accuracy using numerical simulations, with particular attention to the degenerated intervertebral discs and their likely skewed and narrowed geometry. To this end, 1) annulus fibrosus is modeled as a fiber-reinforced Mooney-Rivlin type solid for numerical analysis. 2) An adaptive state-variable dependent explicit time step is proposed and utilized here as a computationally efficient alternative to theoretical estimates. 3) Tetrahedral-element-based FE models for spinal segments under various loading conditions are evaluated for their use in robust numerical simulations. For flexion, extension, lateral bending, and axial rotation load cases, numerical simulations reveal that a suitable framework based on tetrahedral elements can provide greater stability and flexibility concerning geometrical meshing over commonly employed hexahedral-element-based ones for representation and study of spinal segments in various stages of degeneration.

59 BASIC BIOLOGICAL SCIENCES↗

Nuclear Reaction Data Evaluations for Nuclear Applications Physics and modeling [Slides]

This presentation provides an evaluation workflow scheme for the project. It also discusses nuclear data libraries, including an overview of worldwide nuclear data libraries and current funding agencies. The presentation also discusses the theoretical framework commonly used in the evaluated work, including the R-matrix theory (≈ up to a few keVs for heavy nuclei) as well as pre-equilibrium (PE) and Hauser-Feshbach (HF) theory (⪆1 MeV for medium/heavy nuclei). Inclusion of experimental effects are also discussed. Examples of evaluated work, including theory, experiments, and applications are discussed, specifically n+ 28,29,30 Si evaluation (direct capture component), n+ 53 Cr evaluation (strong multiple scattering effects), n+ 239 Pu(n,γf) reaction (fluctuations in neutron multiplicities), and α+ 17,18 O evaluations (emerging neutron spectra).

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Extreme Water Uptake of Hygroscopic Hydrogels through Maximized Swelling‐Induced Salt Loading

Abstract Hygroscopic hydrogels are emerging as scalable and low‐cost sorbents for atmospheric water harvesting, dehumidification, passive cooling, and thermal energy storage. However, devices using these materials still exhibit insufficient performance, partly due to the limited water vapor uptake of the hydrogels. Here, the swelling dynamics of hydrogels in aqueous lithiumchloride solutions, the implications on hydrogel salt loading, and the resulting vapor uptake of the synthesized hydrogel–salt composites are characterized. By tuning the salt concentration of the swelling solutions and the cross‐linking properties of the gels, hygroscopic hydrogels with extremely high salt loadings are synthesized, which enable unprecedented water uptakes of 1.79 and 3.86 gg −1 at relative humidity (RH) of 30% and 70%, respectively. At 30% RH, this exceeds previously reported water uptakes of metal–organic frameworks by over 100% and of hydrogels by 15%, bringing the uptake within 93% of the fundamental limit of hygroscopic salts while avoiding leakage problems common in salt solutions. By modeling the salt‐vapor equilibria, the maximum leakage‐free RH is elucidated as a function of hydrogel uptake and swelling ratio. These insights guide the design of hydrogels with exceptional hygroscopicity that enable sorption‐based devices to tackle water scarcity and the global energy crisis.

Graeber, Gustav↗

Evaluation and Optimization of Snow Albedo Scheme in Noah-MP Land Surface Model Using In Situ Spectral Observations in the Colorado Rockies

The Biosphere-Atmosphere Transfer Scheme (BATS) ground snow albedo algorithm is commonly used in land-surface models (LSM), weather forecasting and research applications. This study addresses key uncertainties in BATS simulated ground snow albedo within the Noah-MP LSM framework through evaluation and optimization of the Noah-MP BATS ground snow albedo formulation using 2-band (visible and near-infrared (NIR)) in situ albedo observations at Rocky Mountain field stations. The Noah-MP BATS ground snow albedo scheme is extremely sensitive to its input parameters. Namely, an ensemble generated by varying BATS input parameters within potentially plausible ranges provides an average daily range (maximum ensemble member minus minimum ensemble member) of ground snow albedo exceeding 0.45 in visible and NIR bands. Parameter optimization improves agreement between simulated and in situ observed ground snow albedo in visible, NIR and broadband spectrums. Importantly, optimized parameters result in reduced biases relative to observed fresh-snow albedo and better agreement with observed albedo decay. Our analysis across different sites supports that the optimized BATS ground snow albedo parameters are appropriate to transfer in space and time, at least within the region studied (the central-southern Rocky Mountains). The primary error source remaining after parameter optimization is that observed fresh-snow albedo is highly variable, particularly in the NIR spectrum, whereas BATS fresh-snow albedo is constant, an issue which requires further investigation. This study shows significant correlations between observed fresh-snow albedo and surface meteorological conditions (e.g., downward shortwave radiation and temperature) which can support future model development that attempts to include a time-varying formulation for fresh-snow albedo.

54 ENVIRONMENTAL SCIENCES↗

Seed coat transcriptomic profiling of 5-593, a genotype important for genetic studies of seed coat color and patterning in common bean ( Phaseolus vulgaris L.)

Common bean (Phaseolus vulgaris L.) market classes have distinct seed coat colors, which are directly related to the diverse flavonoids found in the mature seed coat. To understand and elucidate the molecular mechanisms underlying the regulation of seed coat color, RNA-Seq data was collected from the black bean 5-593 and used for a differential gene expression and enrichment analysis from four different seed coat color development stages. 5-593 carries dominant alleles for 10 of the 11 major genes that control seed coat color and expression and has historically been used to develop introgression lines used for seed coat genetic analysis. Pairwise comparison among the four stages identified 6,294 differentially expressed genes (DEGs) varying from 508 to 5,780 DEGs depending on the compared stages. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that phenylpropanoid biosynthesis, flavonoid biosynthesis, and plant hormone signal transduction comprised the principal pathways expressed during bean seed coat pigment development. Transcriptome analysis suggested that most structural genes for flavonoid biosynthesis and some potential regulatory genes were significantly differentially expressed. Further studies detected 29 DEGs as important candidate genes governing the key enzymatic flavonoid biosynthetic pathways for common bean seed coat color development. Additionally, four gene models, Pv5-593.02G016100, 593.02G078700, Pv5-593.02G090900, and Pv5-593.06G121300, encode MYB-like transcription factor family protein were identified as strong candidate regulatory genes in anthocyanin biosynthesis which could regulate the expression levels of some important structural genes in flavonoid biosynthesis pathway. These findings provide a framework to draw new insights into the molecular networks underlying common bean seed coat pigment development.

60 APPLIED LIFE SCIENCES↗

Temporally continuous thermofluidic–thermomechanical modeling framework for metal additive manufacturing

Additive manufacturing (AM) is known to generate large magnitudes of residual stresses (RS) within builds due to steep and localized thermal gradients. In the current state of commercial AM technology, manufacturers generally perform heat treatments in effort to reduce the generated RS and its detrimental effects on part distortion and in-service failure. Computational models that effectively simulate the deposition process can provide valuable insights to improve RS distributions. Accordingly, it is common to employ Computational fluid dynamics (CFD) models or finite element (FE) models. While CFD can predict geometric and thermal-fluid behavior, it cannot predict the structural response (e.g., stress–strain) behavior. On the other hand, an FE model can predict mechanical behavior, but it lacks the ability to predict geometric and fluid behavior. Thus, an effectively integrated thermofluidic–thermomechanical modeling framework that exploits the benefits of both techniques while avoiding their respective limitations can offer valuable predictive capability for AM processes. In contrast to previously published efforts, the work herein describes a one-way coupled CFD-FEA framework that abandons major simplifying assumptions, such as geometric steady-state conditions, the absence of material plasticity, and the lack of detailed RS evolution/accumulation during deposition, as well as insufficient validation of results. Here, the presented framework is demonstrated for a directed energy deposition (DED) process, and experiments are performed to validate the predicted geometry and RS profile. Both single- and double-layer stainless steel 316L builds are considered. Geometric data is acquired via 3D optical surface scans and X-ray micro-computed tomography, and residual stress is measured using neutron diffraction (ND). Comparisons between the simulations and measurements reveal that the described CFD-FEA framework is effective in capturing the coupled thermomechanical and thermofluidic behaviors of the DED process. The methodology presented is extensible to other metal AM processes, including power bed fusion and wire-feed-based AM.

42 ENGINEERING↗

Direct Estimation of Parameters in ODE Models Using WENDy: Weak-Form Estimation of Nonlinear Dynamics

Abstract We introduce the Weak-form Estimation of Nonlinear Dynamics (WENDy) method for estimating model parameters for non-linear systems of ODEs. Without relying on any numerical differential equation solvers, WENDy computes accurate estimates and is robust to large (biologically relevant) levels of measurement noise. For low dimensional systems with modest amounts of data, WENDy is competitive with conventional forward solver-based nonlinear least squares methods in terms of speed and accuracy. For both higher dimensional systems and stiff systems, WENDy is typically both faster (often by orders of magnitude) and more accurate than forward solver-based approaches. The core mathematical idea involves an efficient conversion of the strong form representation of a model to its weak form, and then solving a regression problem to perform parameter inference. The core statistical idea rests on the Errors-In-Variables framework, which necessitates the use of the iteratively reweighted least squares algorithm. Further improvements are obtained by using orthonormal test functions, created from a set of $$C^{\infty }$$ C ∞ bump functions of varying support sizes.We demonstrate the high robustness and computational efficiency by applying WENDy to estimate parameters in some common models from population biology, neuroscience, and biochemistry, including logistic growth, Lotka-Volterra, FitzHugh-Nagumo, Hindmarsh-Rose, and a Protein Transduction Benchmark model. Software and code for reproducing the examples is available at https://github.com/MathBioCU/WENDy .

97 MATHEMATICS AND COMPUTING↗

Adaptive language model training for molecular design

Abstract The vast size of chemical space necessitates computational approaches to automate and accelerate the design of molecular sequences to guide experimental efforts for drug discovery. Genetic algorithms provide a useful framework to incrementally generate molecules by applying mutations to known chemical structures. Recently, masked language models have been applied to automate the mutation process by leveraging large compound libraries to learn commonly occurring chemical sequences (i.e., using tokenization) and predict rearrangements (i.e., using mask prediction). Here, we consider how language models can be adapted to improve molecule generation for different optimization tasks. We use two different generation strategies for comparison, fixed and adaptive. The fixed strategy uses a pre-trained model to generate mutations; the adaptive strategy trains the language model on each new generation of molecules selected for target properties during optimization. Our results show that the adaptive strategy allows the language model to more closely fit the distribution of molecules in the population. Therefore, for enhanced fitness optimization, we suggest the use of the fixed strategy during an initial phase followed by the use of the adaptive strategy. We demonstrate the impact of adaptive training by searching for molecules that optimize both heuristic metrics, drug-likeness and synthesizability, as well as predicted protein binding affinity from a surrogate model. Our results show that the adaptive strategy provides a significant improvement in fitness optimization compared to the fixed pre-trained model, empowering the application of language models to molecular design tasks.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

PyARC Status Report: New Integrations and Upgrades to the Fast Reactor Analysis Workflow Management Tool

PyARC was initially developed as an open source tool to support fast reactor analyses using the Argonne Reactor Computation (ARC) code suite as a part of the Nuclear Energy Advanced Modeling and Simulation (NEAMS) Workbench initiative in FY17. The goal of this initiative is to provide a common user interface for model generation, real-time validation, execution, output processing, and visualization for all integrated codes. This is accomplished through the reliance on tools available in the Workbench framework and runtime environment. While initially developed to support the ARC codes, PyARC was extended in FY22 to wrap other NEAMS and non-ARC codes, including Griffin and OpenMC, in the supported other neutronics workflows, and support users in the adoption of NEAMS-supported high fidelity analysis codes. Most recently, NUBOW-3D, a recently adopted ARC code, was integrated to support reactor bowing calculations as well. Integration of these codes into the NEAMS Workbench directly benefits the advanced reactor modeling community by: • Providing a set of controlled, maintained, documented and validated scripts to generate inputs, which promotes best practices, reduces the learning curve, and facilitates project collaboration. • Improving the user experience: the Workbench interface provides assistance for building an input through auto-completion, real-time validation, document navigation, and geometry and results visualization. • Automating complex calculations and workflows for reactor analysis. • Helping users transition to using high-fidelity NEAMS codes along-side the ARC codes. In FY22, a progress report was published that described the state of each of the tools integrated into PyARC. Since then, there have been many enhancements and upgrades to the existing integrations as well as entirely new code integrations as well. This report details all new integrations and major developments in PyARC since the version 2.0.0 release highlighted in the FY22 report.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Commutative Algebra Modeling in Materials Science – A Case Study on Metal–Organic Frameworks (MOFs)

Metal-organic frameworks (MOFs) are a class of important crystalline and highly porous materials whose hierarchical geometry and chemistry hinder interpretable predictions in materials properties. Commutative algebra is a branch of abstract algebra that has been rarely applied in data and material sciences. We introduce the first ever commutative algebra modeling and prediction in materials science. Specifically, category-specific commutative algebra (CSCA) is proposed as a new framework for MOF representation and learning. It integrates element-based categorization with multiscale algebraic invariants to encode both local coordination motifs and global network organization of MOFs. These algebraically consistent, chemically aware representations enable compact, interpretable, and data efficient modeling of MOF properties such as Henry’s constants and uptake capacities for common gases. Compared to traditional geometric and graph-based approaches, CSCA achieves comparable or superior predictive accuracy while substantially improving interpretability and stability across data sets. By aligning commutative algebra with the chemical hierarchy, the CSCA establishes a rigorous and generalizable paradigm for understanding structure and property relationships in porous materials and provides a nonlinear algebra-based framework for data-driven material discovery.

Khaemba, Caleb S.↗

Method for Coupled Electromagnetic and Circuit Simulations to Evaluate Surge Arrester Performance in Protecting Equipment Against E1 HEMP

Surge arrester behavioral modeling for realistic systems embedded in an E1 high-altitude electromagnetic pulse environment inherently encompasses three interconnected complications: (1) the need to account for signal propagation across two domains, electromagnetics and electrical; (2) the need to include both linear and nonlinear circuit components in the analysis; and (3) the need to understand that the over-current and over-voltage mitigation performance is dependent not only on the properties of the surge arrester and protected load but also on the topology of the overall electrical network. This study presents a framework to address these challenges in a systematic manner to consider the effectiveness of protective measures for a common class of equipment in power generation facilities. Full-wave simulations were carried out to derive circuit-domain (i.e., lumped element–based) equivalent models for the excitation waveform and the physical components of the system. Then, these equivalent models were imported to a circuit solver and combined with a high-frequency surge arrester model to evaluate mitigation performance. The methodology outlined is general enough such that it can be applied for other electromagnetic interference problems that involve E2/E3 HEMP or microwave emissions.

42 ENGINEERING↗

Optimization of the BDX experiment for Light Dark Matter searches at JLab

The Light Dark Matter (LDM) hypothesis postulates the existence of a new class of sub GeV particles, neutral under Standard Model (SM) interactions. In its simplest form, LDM consists of particles ¿ with masses below 1 GeV/c2, interacting with SM particles via a new force mediated by a light, spin-1 boson A0, commonly referred to as “Dark Photon”. This framework envisions a distinct “Dark Sector” with its own particles and interactions, offering a theoretically well motivated explanation for Dark Matter, consistent with astrophysical observations and a thermal production mechanism. The Beam Dump eXperiment (BDX) is an approved experiment at Jefferson Lab designed to search for Light Dark Matter. BDX will utilize an 11 GeV electron beam impinging on a thick target to produce a forward-boosted secondary beam of Light Dark Matter particles, which will then be detected by a dedicated downstream detector. Approved in 2018, BDX is expected to be commissioned in 2026 and run in 2027-2029. My thesis focuses on the preparatory work to deploy the BDX experiment. The detector design has been optimized to balance practicality with enhanced Light Dark Matter detection capabilities. Extensive characterization of detector components has been performed to ensure a precise understanding of detector response. A custom Monte Carlo framework has been developed to simulate Light Dark Matter signal and explore various theoretical models of interest. Additionally, a comprehensive data analysis framework has been developed to maximize the experiment sensitivity to Light Dark Matter, with optimizations based on expected detector performance. The ultimate goal of this thesis is to optimize BDX as a flagship experiment in Light Dark Matter searches, enabling it to probe different Dark Matter models.

Spreafico, M. [Univ. of Genova (Italy)]↗