Computational Tools Research Articles

Mango wiggler as a novel insertion device providing a large and symmetrical imaging field of view.

A novel insertion device is introduced, designated as the Mango wiggler, designed for synchrotron radiation (SR) imaging that provides a large field of view. This innovative device is constructed from two orthogonal planar wigglers with a small difference in their period lengths, eliciting the phase difference of the magnetic fields to incrementally transitions from 0 to π/2. Such a configuration enlarges the vertical divergence of the light source, as with the horizontal divergence. The appellation `Mango wiggler' derives from the distinctive mango-shaped contour of its radiation field. A comprehensive suite of theoretical analyses and simulations has been executed to elucidate the radiation properties of the Mango wiggler, employing SPECTRA and Mathematica as calculation tools. In conjunction with the ongoing construction of the High Energy Photon Source in Beijing a practical Mango wiggler device has been fabricated for utilization in SR imaging applications. Theoretical analyses were applied to this particular Mango wiggler to yield several theoretical conclusions, and several simulations were performed according to the measured magnetic field results.

Worldline approach for spinor fields in manifolds with boundaries

The worldline formalism is a useful scheme in Quantum Field Theory which has also become a powerful tool for numerical computations. It is based on the first quantisation of a point-particle whose transition amplitudes correspond to the heat-kernel of the operator of quantum fluctuations of the field theory. However, to study a quantum field theory in a bounded manifold one needs to restrict the path integration domain of the point-particle to a specific subset of worldlines enclosed by those boundaries. In the present article it is shown how to implement this restriction for the case of a spinor field in a two-dimensional curved half-plane under MIT bag boundary conditions, and compute the first few heat-kernel coefficients as a verification of the proposed construction. This construction admits several generalisations.

Development and validation of a prediction model for falls among older people using community-based data.

The aim of this study was to develop a calculation tool to predict the risk of falls 1year in the future and to find the cutoff value for detecting a high risk based on a database of individuals who participated in a community-based group exercise. We retrospectively reviewed a total of 7726 physical test and Kihon Checklist data from 2381 participants who participated in community-based physical exercise groups. We performed multilevel logistic regression analysis to estimate the odds ratio of falls for each risk factor and used the variance inflation factor to assess collinearity. We determined a cutoff value that effectively distinguishes individuals who are likely to fall within a year based on both sensitivity and specificity. The final model included variables such as age, sex, weight, balance, standing up from a chair without any aid, history of a fall in the previous year, choking, cognitive status, subjective health, and long-term participation. The sensitivity, specificity, and best cutoff value of our tool were 68.4%, 53.8%, and 22%, respectively. Using our tool, an individual's risk of falls over the course of a year could be predicted with acceptable sensitivity and specificity. We recommend a cutoff value of 22% for use in identifying high-risk populations. The tool may benefit healthcare workers in screening community-dwelling older adults with various levels of risk for falls and support physicians in planning preventative and follow-up care.

Diffusion Analysis of Intracranial Epidermoid, Head and Neck Epidermal Inclusion Cyst, and Temporal Bone Cholesteatoma.

Intracranial epidermoid tumors, temporal bone cholesteatomas, and head and neck epidermoid inclusion cysts are typically slow-growing, benign conditions arising from ectodermal tissue. They exhibit increased signal on DWI. While much of the imaging literature describes these lesions as showing diffusion restriction, we aimed to investigate these qualitative signal intensities and interpretations of restricted diffusion with respect to normal brain structures. This study aimed to quantitatively evaluate the ADC values and histogram features of these lesions. This retrospective study included children with histologically confirmed diagnoses of intracranial epidermoid tumors, temporal bone cholesteatomas, or head and neck epidermoid inclusion cysts. Lesions were segmented, and voxelwise calculation of ADC values was performed along with histogram analysis. ADC calculations were validated with a second analysis software to ensure accuracy. Normal brain ROIs-including the cerebellum, white matter, and thalamus-served as normal comparators. Correlational analysis and Bland-Altman plots assessed agreement among software tools for ADC calculations. Differences in the distribution of values between the lesions and normal brain tissues were assessed using the Wilcoxon rank sum and Kruskal-Wallis tests. Forty-eight pathology-proved cases were included in this study. Among them, 13 (27.1%) patients had intracranial epidermoid tumors, 14 (29.2%) had head and neck epidermoid inclusion cysts, and 21 (43.7%) had temporal bone cholesteatomas. The mean age was 8.67 (SD, 5.30) years, and 27 (52.9%) were female. The intraclass correlation for absolute agreement for lesional ADC between the 2 software tools was 0.997 (95% CI, 0.995-0.998). The intracranial epidermoid tumor, head and neck epidermoid inclusion cyst, and temporal bone cholesteatoma median ADC values were not significantly different (973.7 versus 875.7 versus 933.2 ×10-6 mm2/s, P = .265). However, the ADCs of the 3 types of lesions were higher than those of 3 normal brain tissue types (933 versus 766, × 10-6 mm2/s, P < .0001). The ADC values of intracranial epidermoid tumors, temporal bone cholesteatomas, and head and neck epidermoid inclusion cysts are higher than those of normal brain regions. It is not accurate to simply classify these lesions as exhibiting restricted diffusion or reduced diffusivity without considering the tissue used for comparison. The observed hyperintensity on DWI compared with the brain is likely attributable to a relatively higher contribution of the T2 shinethrough effect.

Pulsed electric field performance calculator tool based on an in vitro human cardiac model.

Pulsed Field Ablation (PFA) is a novel non-thermal method for cardiac ablation, relying on irreversible electroporation induced by high-energy pulsed electric fields (PEFs) to create localized lesions in the heart atria. A significant challenge in optimizing PFA treatments is determining the lethal electric field threshold (EFT), which governs ablation volume and varies with PEF waveform parameters. However, the proprietary nature of device developer's waveform characteristics and the lack of standardized nonclinical testing methods have left optimal EFTs for cardiac ablation uncertain. To address this gap, we introduced a laboratory protocol employing human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) in monolayer format to evaluate the impact of a range of clinically relevant biphasic pulse parameters on lethal EFT and adiabatic heating (AH). Cell death areas were assessed using fluorescent dyes and confocal microscopy, while lethal EFTs were quantified through comparison with electric field numerical simulations. Our study confirmed a strong correlation between cell death in hiPSC-CMs and the number and duration of pulses in each train, with pulse repetition frequency exerting a comparatively weaker influence. Fitting of these results through machine learning algorithms were used to develop an open-source online calculator. By estimating lethal EFT and associated temperature increases for diverse pulse parameter combinations, this tool, once validated, has the potential to significantly reduce reliance on animal models during early-stage device de-risking and performance assessment. This tool also offers a promising avenue for advancing PFA technology for cardiac ablation medical devices to enhance patient outcomes.

Life cycle assessment in net zero energy building scenarios in a tropical country

The recent IPCC 2023 report reiterates that humans are responsible for global warming over the past 200 years, causing a rise in temperature of 1.1 °C above pre-industrial levels, urging the implementation of mitigation options, especially in the building energy sector. One strong mitigation strategy is designing and building net zero energy buildings (NZEB), although their implementation faces challenges such as opposition to change, especially in tropical countries with traditional and conservative design and construction practices. This paper uses data from a pilot NZEB Laboratory building at UCA, El Salvador, and details its results by comparing different construction system scenarios. The present work presents the results of the Life-cycle assessment (LCA) in three popular construction systems in El Salvador, comparing them with the baseline of its current operation, through 3 iterative calculation tools: structural, thermal and carbon footprint estimation, managing to visualize important findings on how vernacular systems could meet the NZEB performance with added insulation in the structural walls. In addition, a triple-axis sustainability analysis (environmental, economic and social) is conducted using the weighted criteria matrix, which provides nuanced results, such as the proportional share of embodied carbon between the proposals, there is not much difference between the results of the proposed systems, but compared to the baseline, the proposals represent a significant increase of more than 50%. Our results show that in this context, the scalability of NZEB buildings is feasible for different construction systems, paving the way for a progressive and incremental.

A new analytical tool for the elastic/plastic buckling design of pressure vessels subjected to external pressure

This paper deals with the elastic/plastic buckling design of pressure vessels under external pressure loading. The objective is to build a simple analytical tool devoted to the elastic and elastoplastic buckling analysis of pressure equipments. This tool is aimed to provide the critical external pressure of cylindrical pressure vessels with ellipsoidal (or possibly hemispherical) heads. Depending on the geometry of the equipment and material parameters, the first buckling pressure may involve either the cylindrical shell or the closure ends, in the elastic or plastic range. The calculation tool will be thus based on a series of exact or approximate analytical solutions of the critical pressure of each part of the considered equipment. In this paper, the elementary shell structures involved in such pressure equipments are first individually examined. The fundamental critical pressures for each of them are recalled or introduced, both in elasticity and plasticity. The new solutions are validated against reference numerical results obtained through finite element computations. Then, approximate solutions of the critical pressure are derived for the same shells, taking account of specific boundary conditions (and not idealized ones, as before) due to the presence of the remaining part of the equipment. In the end, a VBA Excel software is developed. It is able to provide the mappings of the buckling mode type and the corresponding critical pressures for large ranges of geometric and material parameters in a very efficient way. These analytical solutions are finally confronted to numerical calculations performed on complete pressure equipments and they are shown to give quite reliable results. A discussion is also initiated on the use of such a program to update the current design rules in this scope of application.

Loop corrections in the separate universe picture

In inflationary models that produce a spike of power on short scales, back-reaction of small-scale substructure onto large-scale modes is enhanced. Loop corrections that quantify this back-reaction have been evaluated by a number of authors. We argue that the separate universe framework provides a highly convenient tool for such computations. Each loop of interest is characterized by large hierarchies in wavenumber and horizon exit time. The separate universe framework highlights important factorizations involving these hierarchies. We interpret each loop correction in terms of a simple, classical, back-reaction model, and clarify the meaning of the different volume scalings that have been reported in the literature. We argue that significant back-reaction requires both short-scale nonlinearities and long-short couplings that modulate the short-scale power spectrum. In the absence of long-short couplings, only incoherent “shot noise”-like effects are present, which are volume-suppressed. Dropping the shot noise, back-reaction from a particular scale is controlled by a product of f NL-like parameters: an equilateral configuration measuring the nonlinearity of the short-scale modes, and a squeezed configuration measuring the long-short coupling. These may carry important scale dependence controlling the behaviour of the loop in the decoupling limit where the hierarchy of scales becomes large. In single-field models the long-short coupling may be controlled by this hierarchy, in which case the net back-reaction would be safely suppressed. We illustrate our framework using explicit computations in a 3-phase ultra-slow-roll scenario. Our analysis differs from earlier treatments of this model, which did not consistently include the effect of small-scale modes. Finally, we discuss different choices for the smoothing scale used in the separate universe framework and argue the effect can be absorbed into a renormalization of local operators. This complicates interpretation of the loop, because the analytic part of each loop integral is degenerate with unknown, ultraviolet-sensitive contributions.

Orbital-Resolved DFT+U for Molecules and Solids.

We present an orbital-resolved extension of the Hubbard U correction to density-functional theory (DFT). Compared to the conventional shell-averaged approach, the prediction of energetic, electronic and structural properties is strongly improved, particularly for compounds characterized by both localized and hybridized states in the Hubbard manifold. The numerical values of all Hubbard parameters are readily obtained from linear-response calculations. The relevance of this more refined approach is showcased by its application to bulk solids pyrite (FeS2) and pyrolusite (β-MnO2), as well as to six Fe(II) molecular complexes. Our findings indicate that a careful definition of Hubbard manifolds is indispensable for extending the applicability of DFT+U beyond its current boundaries. The present orbital-resolved scheme aims to provide a computationally undemanding yet accurate tool for electronic structure calculations of charge-transfer insulators, transition-metal (TM) complexes and other compounds displaying significant orbital hybridization.

Short- and long-term performance of risk calculation tools for mortality in patients with acute coronary syndrome.

The mortality rate of acute coronary syndrome (ACS) remains high. Therefore, patients with ACS should undergo early risk stratification, for which various risk calculation tools are available. However, it remains uncertain whether the predictive performance varies over time between risk calculation tools for different target periods. This study aimed to compare the predictive performance of risk calculation tools in estimating short- and long-term mortality risks in patients with ACS, while considering different observation periods using time-dependent receiver operating characteristic (ROC) analysis. This study included 404 consecutive patients with ACS who underwent coronary angiography at our hospital from March 2017 to January 2021. The ACTION and GRACE scores for short-term risk stratification purposes and CRUSADE scores for long-term risk stratification purposes were calculated for all participants. The participants were followed up for 36 months to assess mortality. Using time-dependent ROC analysis, we evaluated the area under the curve (AUC) of the ACTION, CRUSADE, and GRACE scores at 1, 6, 12, 24, and 36 months. Sixty-six patients died during the observation periods. The AUCs at 1, 6, 12, 24, and 36 months of the ACTION score were 0.942, 0.925, 0.889, 0.856, and 0.832; those of the CRUSADE score were 0.881, 0.883, 0.862, 0.876, and 0.862; and those of the GRACE score 0.949, 0.928, 0.888, 0.875, and 0.860, respectively. The ACTION and GRACE scores were excellent risk stratification tools for mortality in the short term. The prognostic performance of each risk score was almost similar in the long term, but the CRUSADE score might be a superior risk stratification tool in the longer term than 3 years.

Enhancing OpenEP: atrial conduction velocity and conduction velocity heterogeneity quantification through EP Workbench

Abstract Background Alterations in atrial conduction velocity have been implicated in the pathogenesis of atrial arrhythmias, with conduction velocity thought to be slower and more heterogeneous in areas promoting atrial fibrillation. However, clinical studies of conduction velocity are challenging since there are no available platforms that provide researchers and clinicians with the ability to quantify conduction velocity and analyse conduction heterogeneity from electroanatomic mapping data. Purpose In this paper we sought to address these limitations by enhancing the OpenEP Python library by (1) automating calculations using previously-published conduction velocity estimation algorithms; (2) providing an interactive graphical representing of conduction velocity and conduction heterogeneity and (3) implementing a histogram analysis tool to quantify conduction velocity and enable the identification of slow conduction regions. Method Two well-known and previously published methods for calculating cardiac conduction velocity, Triangulation and polynomial surface fitting, were implemented. Conduction velocity estimation was improved further by excluding regions with wave collisions and focal discharges. These regions were identified using the divergence of conduction velocity vector fields, with positive divergence representing focal sources and negative divergence representing areas of collision. Finally, calculated conduction velocities using electrogram data were interpolated over the surface mesh via Radial Basis Function (RBF) interpolation method. All algorithms were implemented in the OpenEP Python library (openep-py), with visualisation tools provided in the complementary graphical interface, EP Workbench. Results An extensible "Analysis" feature was created in openep-py, to provide conduction velocity and divergence calculations which are fully customisable through the graphical interface based on user preferences. The EP Workbench desktop application displays resulting cardiac surface maps to depict calculated conduction velocity and divergence fields, together with conventional activation and voltage maps (Figure 1). The histogram analysis tool can be used to identify regions of slow conduction velocity from electroanatomic mapping data. Using a threshold of &amp;lt;0.3m/s, two slow conducting channels are visualised on the posterior wall of a test case (Figure 2). The tool is not specific to conduction velocity and may also be used to quantify other data types in EP Workbench. Finally, computed conduction velocity and divergence values and surface maps are stored in the standard OpenEP data structure, allowing further analysis following data export. Conclusion We have extended OpenEP to provide a comprehensive set of tools for conduction velocity calculation and analysis which will facilitate investigation of the structural and functional basis of conduction velocity alterations in disease states.

Digital phantom versus patient-specific radiation dosimetry in adult routine thorax CT examinations.

The aim of this study was to compare the organ doses assessed through a digital phantom-based and a patient specific-based dosimetric tool in adult routine thorax computed tomography (CT) examinations with reference to physical dose measurements performed in anthropomorphic phantoms. Two Monte Carlo based dose calculation tools were used to assess organ doses in routine adult thorax CT examinations. These were a digital phantom-based dosimetry tool (NCICT, National Cancer Institute, USA) and a patient-specific individualized dosimetry tool (ImpactMC, CT Imaging GmbH, Germany). Digital phantoms and patients were classified in four groups according to their water equivalent diameter (Dw). Normalized to volume computed tomography dose index (CTDIvol), organ dose was assessed for lungs, esophagus, heart, breast, active bone marrow, and skin. Organ doses were compared to measurements performed using thermoluminescent detectors (TLDs) in two physical anthropomorphic phantoms that simulate the average adult individual as a male (Alderson Research Labs, USA) and as a female (ATOM Phantoms, USA). The average percent difference of NCICT to TLD and ImpactMC to TLD dose measurements across all organs in both sexes was 13% and 6%, respectively. The average±1 standard deviation in dose values across all organs with NCICT, ImpactMC, and TLDs was±0.06 (mGy/mGy),±0.19 (mGy/mGy), and±0.13 (mGy/mGy), respectively. Organ doses decreased with increasing Dw in both NCICT and ImpactMC. Organ doses estimated with ImpactMC were in closer agreement to TLDs compared to NCICT. This may be attributed to the inherent property of ImpactMC methodology to generate phantoms that resemble the realistic anatomy of the examined patient as opposed to NCICT methodology that incorporates an anatomical discrepancy between phantoms and patients.

Theoretical screening of N-[5'-methyl-3'-isoxasolyl]-N-[(E)-1-(-2-thiophene)] methylidene]amine and its isoxazole based derivatives as donor materials for bulk heterojunction organic solar cells: DFT and TD-DFT investigation.

In the present work, the influence of aromatic ring substitution on a series of small-donor organic molecules (A, B, C, D, and E) with isoxazole cores was investigated for photovoltaic applications in organic solar cells. Frontier molecular orbital analysis, chemical reactivity descriptors, dipole moment, and population analysis showed that all the organic materials have intramolecular charge transfer abilities capable of donating electrons to the acceptor material (PCBM). The required photovoltaic parameters such as Voc, FF, Jsc, LHE, and other associated optoelectronic parameters are reported. The results demonstrate that aromatic ring substitution influences charge transfer and power conversion efficiencies of solar cells. That is, an increase in the aromatic character of a material increases its charge transfer, and as a result, its photovoltaic properties are increased. Additionally, all the investigated derivatives are good charge transporters with suitable electron reorganization energies, which are beneficial for minimizing energy loss. Hence, these organic derivatives with isoxazole backbones are promising materials and may provide fresh insights into the design of new materials for organic solar cell applications. All calculations were performed using DFT and the ORCA 4.1.0 program package as the main tool for geometry optimization and frequency calculations. The Avogadro 1.2.1 visualization tool was used to prepare all input files executed by ORCA 4.1.0. The BP86, B3LYP, and wB97M series of functionals coupled with the def2/TZVP basis set were employed for geometry optimization. All energy-related calculations were carried out using the M06-2x functional. Multiwfn version 3.7 was used for aromaticity and population analysis. Excited state and UV-visible spectra were simulated using the TD-DFT method at the CAM-B3LYP-D3, wB97X-D3, and PBE0-D3 coupled with the ma-def2-TZVP basis set. Moreover, solvent effects were incorporated using the SMD scheme as incorporated in the ORCA software. Lastly, the RIJCOSX approximations were used to speed up calculations while maintaining accuracy.

Evaluation of output factors of different radiotherapy planning systems using Exradin W2 plastic scintillator detector.

This study aims to evaluate the output factors (OPF) of different radiation therapy planning systems (TPSs) using a plastic scintillator detector (PSD). The validation results for determining a practical field size for clinical use were verified. The implemented validation system was an Exradin W2 PSD. The focus was to validate the OPFs of the small irradiation fields of two modeled radiation TPSs using RayStation version 10.0.1 and Monaco version 5.51.10. The linear accelerator used for irradiation was a TrueBeam with three energies: 4, 6, and 10MV. RayStation calculations showed that when the irradiation field size was reduced from 10 × 10 to 0.5 × 0.5cm2, the results were within 2.0% of the measured values for all energies. Similarly, the values calculated using Monaco were within approximately 2.0% of the measured values for irradiation field sizes between 10 × 10 and 1.5 × 1.5cm2 for all beam energies of interest. Thus, PSDs are effective validation tools for OPF calculations in TPS. A TPS modeled with the same source data has different minimum irradiation field sizes that can be calculated. These findings could aid in verification of equipment accuracy for treatment planning requiring highly accurate dose calculations and for third-party evaluation of OPF calculations for TPS.

Multilevel Intervention Stepped Wedge Designs (MLI-SWDs)

Multilevel interventions (MLIs) hold promise for reducing health inequities by intervening at multiple types of social determinants of health consistent with the socioecological model of health. In spite of their potential, methodological challenges related to study design compounded by a lack of tools for sample size calculation inhibit their development. We help address this gap by proposing the Multilevel Intervention Stepped Wedge Design (MLI-SWD), a hybrid experimental design which combines cluster-level (CL) randomization using a Stepped Wedge design (SWD) with independent individual-level (IL) randomization. The MLI-SWD is suitable for MLIs where the IL intervention has a low risk of interference between individuals in the same cluster, and it enables estimation of the component IL and CL treatment effects, their interaction, and the combined intervention effect. The MLI-SWD accommodates cross-sectional and cohort designs as well as both incomplete (clusters are not observed in every study period) and complete observation patterns. We adapt recent work using generalized estimating equations for SWD sample size calculation to the multilevel setting and provide an R package for power and sample size calculation. Furthermore, motivated by our experiences with the ongoing NC Works 4 Health study, we consider how to apply the MLI-SWD when individuals join clusters over the course of the study. This situation arises when unemployment MLIs include IL interventions that are delivered while the individual is unemployed. This extension requires carefully considering whether the study interventions will satisfy additional causal assumptions but could permit randomization in new settings.

Short-flow-time expansion of quark bilinears through next-to-next-to-leading order QCD

The gradient-flow formalism proves to be a useful tool in lattice calculations of quantum chromodynamics. For example, it can be used as a scheme to renormalize composite operators by inverting the short-flow-time expansion of the corresponding flowed operators. In this paper, we consider the short-flow-time expansion of five quark bilinear operators, the scalar, pseudoscalar, vector, axialvector, and tensor currents, and compute the matching coefficients through next-to-next-to-leading order QCD. Among other applications, our results constitute one ingredient for calculating bag parameters of mesons within the gradient-flow formalism on the lattice.

Horizontal Gaze Assessment: An Extensive Narrative Review

Bipedalism was a significant milestone in the evolutionary development of Homo sapiens sapiens, influencing neocortical evolution and subsequent behavioral changes. Coordinated visual and sensory inputs are crucial for posture, environmental interaction, and surgical planning, with horizontal gaze being a pivotal parameter. This narrative review aims to explore various geometric measures used to assess horizontal gaze in patients, highlighting their applications in surgical planning. A literature review was conducted in indexed databases using Mesh terms like "Cervical Vertebrae" and "Visual Fields" along with keywords such as "horizontal gaze" and "sagittal spine parameters." Among 477 initially identified articles, 41 were selected for inclusion after rigorous filtering. The most recognized method for assessing horizontal gaze is the Chin Brow Vertical Angle (CBVA), initially described in patients with ankylosing spondylitis. Clinical photography is employed as a tool for CBVA calculation, while other measures like McGregor slope and Slope of the Line of Sight have been considered as alternatives to CBVA. Each method presents its unique advantages and limitations. This review highlights the need for further research into horizontal gaze measurement methods. Developing novel approaches to determine horizontal gaze can significantly enhance surgical planning and, consequently, improve patient outcomes. The ongoing exploration of these geometric measures offers promising prospects for advancing the field and optimizing patient care.

Performance gap analysis for Korean building energy efficiency certification

Performance gap between predicted and measured building energy use can be caused by simplifications and assumptions introduced in the building energy modeling process, uncertainties in building operation such as heating and cooling setpoint temperature, operational hours, occupant behavior, heat generated from lights and equipment, etc. In South Korea, the building energy efficiency certification system (BEEC) evaluates annual energy use intensity (EUI, kWh/m2/yr) and assigns ten certificate levels using ECO2, a EUI calculation tool developed by the Korean government that is based on ISO 52016 and DIN V 18599. Firstly, we collected information on 158 non-residential BEEC-certified buildings and their actual energy usage data. Subsequently, we analyzed the performance gap between predicted and measured EUI for 158 non-residential buildings in terms of building types, heating and cooling degree days, chiller types, gross floor area, window-wall ratio, and envelope U-value. The study reveals that the performance gap is significant, showing mean absolute error ranging from 21.3 to 417.4 kWh/m2/yr, mean biased error from −3.2 to 73.4 %, and the coefficient of variance of the root mean squared error from 57.0 to 304.9 %, respectively. It is also noteworthy that even individual building’s annual consumption during eight years (2014–2021) is annually fluctuating, indicating that even the performance gap is a moving target. This study reassures that building energy certification in the design stage should be understood as a rating, not for a prediction because of many unpredictable and stochastic behavior of building energy systems and occupants.

Stratified homotopy theory of topological ∞-stacks: A toolbox

We exploit the theory of ∞-stacks to provide some basic definitions and calculational tools regarding stratified homotopy theory of stratified topological stacks.

ARIP: A Tool for Precise Interatomic Contact Area and Volume Calculation in Proteins.

The interplay patterns of amino acid residues are pivotal in determining the tertiary structure and flexibility of proteins, which in turn are intricately linked to their functionality and interactions with other molecules. Here, we introduce ARIP, a novel tool designed to identify contact residues within proteins. ARIP employs a modified version of the dr_sasa algorithm and an atomic overlap weighted algorithm to directly calculate the contact area and volume between atoms based on their van der Waals radius. It also allows for the selection of solvent radii, recognizing that not every atom in proteins can interact with water molecules. The solvent parameters were derived from the analysis of approximately 5000 protein and nucleic acid structures with water molecules determined using X-ray crystallography. One advantage of the modified algorithm is its capability to analyze multiple models within a single PDB file, making it suitable for molecular dynamic capture. The contact volume is symmetrically distributed between the interacting atoms, providing more informative results than contact area for the analysis of intra- and intermolecular interactions and the development of scoring functions. Furthermore, ARIP has been applied to four distinct cases: capturing key residue-residue contacts in NMR structures of P4HB, protein-drug binding of CYP17A1, protein-DNA binding of SPI1, and molecular dynamic simulations of BRD4.