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At least 451 records · Page 25

Substitution Models of Protein Evolution with Selection on Enzymatic Activity

Abstract Substitution models of evolution are necessary for diverse evolutionary analyses including phylogenetic tree and ancestral sequence reconstructions. At the protein level, empirical substitution models are traditionally used due to their simplicity, but they ignore the variability of substitution patterns among protein sites. Next, in order to improve the realism of the modeling of protein evolution, a series of structurally constrained substitution models were presented, but still they usually ignore constraints on the protein activity. Here, we present a substitution model of protein evolution with selection on both protein structure and enzymatic activity, and that can be applied to phylogenetics. In particular, the model considers the binding affinity of the enzyme–substrate complex as well as structural constraints that include the flexibility of structural flaps, hydrogen bonds, amino acids backbone radius of gyration, and solvent-accessible surface area that are quantified through molecular dynamics simulations. We applied the model to the HIV-1 protease and evaluated it by phylogenetic likelihood in comparison with the best-fitting empirical substitution model and a structurally constrained substitution model that ignores the enzymatic activity. We found that accounting for selection on the protein activity improves the fitting of the modeled functional regions with the real observations, especially in data with high molecular identity, which recommends considering constraints on the protein activity in the development of substitution models of evolution.

Ferreiro, David↗

Heralded Multiplexed High-Efficiency Cascaded Source of Dual-Rail Entangled Photon Pairs Using Spontaneous Parametric Down-Conversion

Deterministic sources of high-fidelity entangled qubit pairs encoded in the dual-rail photonic basis, i.e., presence of a single photon in one of two orthogonal modes, are a key enabling technology of many applications of quantum information processing, including high-rate, high-fidelity quantum communications over long distances. The most popular and mature sources of such photonic entanglement, e.g., those that leverage spontaneous parametric down-conversion (SPDC) or spontaneous four-wave mixing, generate an entangled (so-called continuous-variable) quantum state that contains contributions from high-order photon terms that lie outside the span of the dual-rail basis, which is detrimental to most applications. One often uses low pump power to mitigate the effects of those high-order terms. However, that reduces the pair generation rate, and the source becomes inherently probabilistic. We investigate a cascaded source that performs a linear-optical entanglement swap between two SPDC sources, to generate a heralded photonic entangled state that has a higher fidelity (to the ideal Bell state) compared to a free-running SPDC source. Furthermore, with the Bell swap providing a heralding trigger, we show how to build a multiplexed source, which despite reasonable switching losses and detector loss and noise, yields a fidelity versus success probability trade-off of a high-efficiency source of high-fidelity dual-rail photonic entanglement. We find, however, that there is a threshold of 1.5 dB of loss per switch, beyond which multiplexing hurts the fidelity versus success probability trade-off.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Error Estimates for the Optimal Control of a Parabolic Fractional PDE

In this work, we consider the integral definition of the fractional Laplacian and analyze a linear-quadratic optimal control problem for the so-called fractional heat equation; control constraints are also considered. We derive existence and uniqueness results, first order optimality conditions, and regularity estimates for the optimal variables. To discretize the state equation we propose a fully discrete scheme that relies on an implicit finite difference discretization in time combined with a piecewise linear finite element discretization in space. We derive stability results and a novel $L^2(0,T;L^2(\Omega))$ a priori error estimate. On the basis of the aforementioned solution technique, we propose a fully discrete scheme for our optimal control problem that discretizes the control variable with piecewise constant functions, and we derive a priori error estimates for it. We illustrate the theory with one- and two-dimensional numerical experiments.

97 MATHEMATICS AND COMPUTING↗

SDE_quark

This program provides a fixed-grid quadrature algorithm to compute integrals in the self-energy of the quark propagator within the Maris-Tandy model. The quark propagator both on t he spacelike real axis and at complex-valued momenta is determined from its Schwinger-Dyson equation (SDE). We first apply an iterative solver to find the quark propagator on the spacelike real axis. The propagator at complex-valued momenta is then computed from its self-energy based on this solution, where demanding integrals are encountered. In order to compute of these integrals, we apply customized variable transformations for the radial integral after subtracting the asymptotics. We subsequently apply an optional compound of quadrature rules for the angular integral.

Jia, Shaoyang↗

TAS: 89 0227: TAS Recovery Act - Optimization and Control of Electric Power Systems: ARRA

The name SuperOPF is used to refer several projects, problem formulations and soft-ware tools intended to extend, improve and re-define some of the standard methods of optimizing electric power systems. Our work included applying primal-dual interior point methods to standard AC optimal power flow problems of large size, as well as extensions of this problem to include co-optimization of multiple scenarios. The original SuperOPF problem formulation was based on co-optimizing a base scenario along with multiple post-contingency scenarios, where all AC power flow models and constraints are enforced for each, to find optimal energy contracts, endogenously determined locational reserves and appropriate nodal energy prices for a single period optimal power flow problem with uncertainty. This led to example non-linear programming problems on the order of 1 million constraints and half a million variables. The second generation SuperOPF formulation extends this by adding multiple periods and multiple base scenarios per period. It also incorporates additional variables and constraints to model load following reserves, ramping costs, and storage resources. A third generation of the multi-period SuperOPF, adds both integer variables and a receding horizon framework in which the problem type is more challenging (mixed integer), the size is even larger, and it must be solved more frequently, pushing the limits of currently available algorithms and solvers. The consideration of transient stability constraints in optimal power flow (OPF) problems has become increasingly important in modern power systems. Transient stability constrained OPF (TSCOPF) is a nonlinear optimization problem subject to a set of algebraic and differential equations. Solving a TSCOPF problem can be challenging due to (i) the differential-equation constraints in an optimization problem, (ii) the lack of a true analytical expression for transient stability in OPF. To handle the dynamics in TSCOPF, the set of differential equations can be approximated or converted into equivalent algebraic equations before they are included in an OPF formulation. In Chapter 4, a rigorous evaluation of using a predefined and fixed threshold for rotor angles as a mean to determine transient stability of the system is developed. TSCOPF can be modeled as a large-scale nonlinear programming problem including the constraints of differential-algebraic equations (DAE). Solving a TSCOPF problem can be challenging due to (i) the differential-equation constraints in an optimization problem, (ii) the lack of a true analytical expression for transient stability constraint in OPF. Unfortunately, even the current best TSCOPF solvers still suffer from the curse of dimensionality and unacceptable computational time, especially for large-scale power systems with multiple contingencies. In chapter 5, thse issues will be addressed and a new method to incorporate the transient stability constraints will be presented.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Identification of SPR Caverns with Multiple Oil Layers

This analysis shows that when lower density crude oil is injected into the top of an underground salt storage cavern containing more dense crude, separate oil phases can form and coexist indefinitely. This has been observed at the U.S. Strategic Petroleum Reserve in spite of geothermal heating and natural convection, which tend to mix the contents of containers with significant vertical extent subjected to wall and bottom heating. Such persistent layering can create operational challenges for meeting delivery specifications if high-value, low-vapor pressure oil becomes trapped below incoming low-density, high-vapor pressure oil, effectively blocking access to the lower layers until the top layer is removed. Previous conceptual models assumed that the oil injection process mixed incoming oil with resident oil in a storage cavern, forming a single oil phase with relatively homogeneous properties. Here, a review of historical data from the Strategic Petroleum Reserve revealed that several caverns contain multiple oil layers. As a result, oil layering needs to be another variable considered when planning oil movements at SPR in order to optimize low-vapor pressure oil availability to assist in oil delivery blending.

02 PETROLEUM↗

Large Scale MD to Predict Epitope Regions in HIV Env [Slides]

Highly dense carbohydrates located on the surface of the HIV Env protein play a key role in immune evasion. Such evolutionary adaptation hampers any attempt to obtain a full mechanistic understanding of the role played by the glycans in protecting the virus against an effective immune response. Moreover, and due to their chemical variability, an accurate molecular understanding of the so called “glycan shield” is still limited by the lack of effective resolution of state-of-the-art experimental technics. Here, we have used extensive computational modelling in order to fill this gap, addressing the presence of a large glycan variability as observed experimentally. Based on an automated pipeline, we were able to assemble, set-up and simulate via Molecular dynamics hundreds of different glycosylated Env variants at nearly atomic resolution, recapitulating the glycosylation distributions observed experimentally. Results from these simulations were subjected to machine learning and very accurate prediction of simulation derived glycan shielding areas of each glycan as a function of static sequence features. Such predictive models of per-glycan shielding, incorporating both glycan dynamics and heterogeneity, were used to develop a novel sequence-based glycan shield mapping strategy. Parallel to these studies, we also developed an accurate machine learning approach to predict glycan heterogeneity data using sequence features and found good prediction accuracy.

59 BASIC BIOLOGICAL SCIENCES↗

FAIR Data and Interpretable AI Framework for Architectured Metamaterials (Final Report)

This research program established a transformative framework for the discovery and design of mechanical metamaterials, which are architected structures engineered to control physical phenomena like sound and vibration in ways natural materials cannot. To overcome the traditional reliance on trial-and-error, the project developed an interpretable Artificial Intelligence (AI) framework that moves beyond "black box" models to reveal the specific geometric patterns—such as "unit-cell templates"—that govern a material’s performance. A major breakthrough was the development of a hierarchical design method, which allows a single material to block vibrations across multiple frequency ranges simultaneously by layering patterns at different scales without them interfering with one another. This was further expanded to include irregular, graph-based designs that use spanning tree algorithms to ensure structural connectivity while allowing for customized, direction-dependent properties like stiffness and acoustic impedance. Beyond design, the project addressed the practicalities of real-world production by developing uncertainty quantification techniques that account for manufacturing defects and material variability, reducing the need for expensive physical testing by orders of magnitude. To speed up the discovery process, the team implemented Gaussian Process Regression and other surrogate models that provide accurate performance predictions at a fraction of the traditional computational cost. The AI-generated designs were successfully validated through fabrication of physical samples and wave propagation experiments, confirming their ability to accurately guide or reflect waves as predicted. By contributing these tools and high-quality FAIR benchmark datasets to the wider scientific community, this work provides a scalable foundation for advancing technologies in aerospace vibration control, medical imaging, and noise reduction.

36 MATERIALS SCIENCE↗

Using Models to Provide Predicted Ranges for Building-Human Interfaces: Preprint

Most building energy consumption dashboards provide only a snapshot of building performance; whereas some provide more detailed historic data with which to compare current usage. This paper will discuss the Building Agent(tm) platform, which has been developed and deployed in a campus setting at the National Renewable Energy Laboratory as part of an effort to maintain the aggressive energyperformance achieved in newly constructed office buildings and laboratories. The Building Agent(tm) provides aggregated and coherent access to building data, including electric energy, thermal energy, temperatures, humidity, and lighting levels, and occupant feedback, which are displayed in various manners for visitors, building occupants, facility managers, and researchers. This paper focuseson the development of visualizations for facility managers, or an energy performance assurance role, where metered data are used to generate models that provide live predicted ranges of building performance by end use. These predicted ranges provide simple, visual context for displayed performance data without requiring users to also assess historical information or trends. Several energymodelling techniques were explored including static lookup-based performance targets, reduced-order models derived from historical data using main effect variables such as solar radiance for lighting performance, and integrated energy models using a whole-building energy simulation program.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Optimization Algorithm for Criticality Experiment Design Using Whisper

Many criticality experiments performed to aid in nuclear data evaluation are designed to maximize the sensitivity of the system’s effective neutron multiplication factor to a certain nuclide reaction pair over an energy region of interest. This is typically done by evaluating possible designs in a transport code such as MCNP and selecting the one with the highest desired sensitivity. A designer has many tools to try to maximize this sensitivity such as different moderators, reflectors, fuels, and geometries. This balancing act of identifying a critical and maximally sensitive system become very computationally expensive as more variables are added and higher precisions are desired. In order to identify these optimal configurations more efficiently a Particle Swarm Optimization (PSO) algorithm coupled with MCNP has been developed by Los Alamos National Laboratory (LANL). This algorithm has been used to design two upcoming criticality experiments that will be performed at the National Criticality Experiments Research Center (NCERC), located at the Nevada National Security Site, and operated by LANL, the only general-purpose critical experiments laboratory in the United States. PSO uses a population (swarm) of candidate solutions (particles) on a search space of dimensions such as moderator and reflector thicknesses or enrichments and concentrations. These particles move around the search space from generation to generation according to simple rules. Eventually, the swarm converges on the configuration that is both critical and maximally sensitive to a piece of nuclear data. PSO is well suited for criticality experiments as the algorithm is agnostic to the underlying physics, meaning it is effective on many different experimental setups. This algorithm has been modified to maximize the nuclear data similarity coefficient between an application case and an experiment aimed at replicating the application case using WHISPER, a nuclear criticality safety analysis tool. This allows for the efficient design of critical experiments informed by nuclear data sensitives.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Predicting the reliability of an additively-manufactured metal part for the third Sandia fracture challenge by accounting for random material defects

We describe an approach to predict failure in a complex, additively-manufactured stainless steel part as defined by the third Sandia Fracture Challenge. A viscoplastic internal state variable constitutive model was calibrated to fit experimental tension curves in order to capture plasticity, necking, and damage evolution leading to failure. Defects such as gas porosity and lack of fusion voids were represented by overlaying a synthetic porosity distribution onto the finite element mesh and computing the elementwise ratio between pore volume and element volume to initialize the damage internal state variables. These void volume fraction values were then used in a damage formulation accounting for growth of these existing voids, while new voids were allowed to nucleate based on a nucleation rule. Blind predictions of failure are compared to experimental results. The comparisons indicate that crack initiation and propagation were correctly predicted, and that an initial porosity field superimposed as higher initial damage may provide a path forward for capturing material strength uncertainty. Here, the latter conclusion was supported by predicted crack face tortuosity beyond the usual mesh sensitivity and variability in predicted strain to failure; however, it bears further inquiry and a more conclusive result is pending compressive testing of challenge-built coupons to de-convolute materials behavior from the geometric influence of significant porosity.

36 MATERIALS SCIENCE↗

Quark and gluon two-loop beam functions for leading-jet p T and slicing at NNLO

We compute the complete set of two-loop beam functions for the transverse momentum distribution of the leading jet produced in association with an arbitrary colour-singlet system. Our results constitute the last missing ingredient for the calculation of the jet-vetoed cross section at small veto scales at the next-to-next-to-leading order, as well as an important ingredient for its resummation to next-to-next-to-next-to-leading logarithmic order. Our calculation is performed in the soft-collinear effective theory framework with a suitable regularisation of the rapidity divergences occurring in the phase-space integrals. We discuss the occurrence of soft-collinear mixing terms that might violate the factorisation theorem, and demonstrate that they are naturally absorbed into the beam functions at two loops in the exponential rapidity regularisation scheme when performing a multipole expansion of the measurement function. As in our recent computation of the two-loop soft function, we present the results as a Laurent expansion in the jet radius R. We provide analytic expressions for all flavour channels in x space with the exception of a set of R-independent non-logarithmic terms that are given as numerical grids. We also perform a fully numerical calculation with exact R dependence, and find that it agrees with our analytic expansion at the permyriad level or better. Our calculation allows us to define a next-to-next-to-leading order slicing method using the leading-jet p T as a slicing variable. As a check of our results, we carry out a calculation of the Higgs and Z boson total production cross sections at the next-to-next-to-leading order in QCD.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Application of Data Science and Engineering

Metal additive manufacturing (AM) processes exhibit significant variability in the quality and properties of components that are produced. This variability has prevented the widespread adoption of AM in industry. The need for more advanced and descriptive process monitoring, part qualification, and process control has led to an increasing number of sensors on machines and subsequent data to analyze. Increasingly, data science principles are being leveraged in each of these domains in order to process this data and better understand the causes of variability and the corresponding quality inconsistencies that occur in additive manufacturing.

Halsey, William↗

Optimization Using Metamodeling in the Context of Integrated Computational Materials Engineering (ICME)

Predictive Design Technologies, LLC (PDT) proposed to employ Integrated Computational Materials Engineering (ICME) tools to help the manufacturing industry in the United States regain the competitive advantage in the global economy. ICME uses computational materials science tools within a holistic system in order to accelerate materials development, improve design optimization, and unify design and manufacturing. With the advent of accurate modeling and simulation along with significant increases in high performance computing (HPC) power, virtual design and manufacturing using ICME tools provide the means to reduce product development time and cost by alleviating costly trial-and-error physical design iterations while improving overall quality and manufacturing efficiency. To reduce the computational cost necessary for the large-scale HPC simulations and to make the methodology accessible for small and medium-sized manufacturers (SMMs), metamodels are employed. Metamodels are approximate models (functional relationships between input and output variables) that can reduce the simulation times by one to two orders of magnitude. In Phase I, PDT, partnered with Mississippi State University (MSU), demonstrated the feasibility of the proposed methodology by employing MSU?s internal state variable (ISV) plasticity-damage model with the help of metamodels to optimize the microstructure-process-property-cost for tube manufacturing processes used by Plymouth Tube Company (PTC), which involves complicated temperature and mechanical loading histories. PDT quantified the microstructure-property relationships for PTC?s SAE J525 electric resistance-welded cold drawn low carbon hydraulic 1010 steel tube manufacturing processes at seven different material states and calibrated the ISV plasticity material parameters to fit experimental tensile stress-strain curves. PDT successfully performed large scale finite element (FE) simulations in an HPC environment using the ISV plasticity model in Abaqus FE analyses of the tube forming, sizing, drawing, welding, and normalizing processes. The simulation results coupled with the manufacturing cost data were used to develop prototype metamodeling (quick response) codes which could be used to predict and optimize the microstructure-process-property-cost relationships. The developed ICME metamodeling toolkits are flexible enough to be applied to other manufacturing processes (e.g. forging, forming, casting, extrusion, rolling, stamping, and welding/joining) and metamodeling codes can run on laptop computers. Based on the work completed in Phase I, in Phase II, PDT proposes to continue to refine the ISV model by correlating and incorporating the uncertainties in the microstructure, mechanical testing, and modeling. Following the model refinement, FE analyses will be simulated and will provide even more realistic predictions as they include an appropriate window of uncertainty. Using the HPC output (FE analyses) as input, the quick-response metamodel codes will more accurately predict and optimize the microstructure-process-property-cost relationships. Furthermore, PDT propose to employ the ICME metamodeling toolkits to help develop a new tube product using entirely new high strength steel. The modeling of the high strength steel manufacturing process will replace the costly and time consuming trial-and-error methods that were used in the tubing industry previously. This simulation-based process prototyping will greatly benefit our industrial partners by opening up new market spaces due to new products with greater capabilities.

36 MATERIALS SCIENCE↗

Detecting Magnon-phonon coupling in yttrium iron garnet with variable temperature STEM-EELS

Magnons, quanta of spin wave excitations in magnetically ordered materials, have been identified as candidates for several potentially transformative technologies in recent years. Macroscopic techniques, such as neutron scattering or Raman spectroscopy, can be used to identify and analyze magnons, but provide relatively delocalized information about the sample. Understanding how the bonding and local structure of a material interacts with, and influences, the magnon population in a material is a crucial step toward the ability to produce any real-world application utilizing magnons. By leveraging the combined spatial resolution of scanning transmission electron microscopy (STEM) and the energy resolution of monochromated electron energy-loss spectroscopy (EELS) nanoscale analysis of magnons can be performed. While the weak interaction of magnons with the electron beam makes magnon EELS challenging on reasonable timescales, magnon-phonon coupling can be leveraged to understand magnons through their effect on the more easily measured phonons. Here, we examine yttrium iron garnet (YIG) flakes, and demonstrate non-linear, temperature-dependent shifts in the phonon frequencies, consistent with previously described magnon-phonon coupling effects. The ability to measure the temperature-dependence of vibrational frequencies with high precision in individual nanoscale flakes, demonstrates the ability to study magnon-phonon coupling in the STEM with unprecedented spatial resolution.

Reifsnyder, Alexander [ORNL]↗

Tracking Contributions to Human Body Burden of Environmental Chemicals by Correlating Environmental Measurements with Biomarkers

The work addresses current knowledge gaps regarding causes for correlations between environmental and biomarker measurements and explores the underappreciated role of variability in disaggregating exposure attributes that contribute to biomarker levels. Our simulation-based study considers variability in environmental and food measurements, the relative contribution of various exposure sources (indoors and food), and the biological half-life of a compound, on the resulting correlations between biomarker and environmental measurements. For two hypothetical compounds whose half-lives are on the order of days for one and years for the other, we generate synthetic daily environmental concentrations and food exposures with different day-to-day and population variability as well as different amounts of home- and food-based exposure. Assuming that the total intake results only from home-based exposure and food ingestion, we estimate timedependent biomarker concentrations using a one-compartment pharmacokinetic model. Box plots of modeled R 2 values indicate that although the R 2 correlation between wipe and biological (e.g., serum) measurements is within the same range for the two compounds, the relative contribution of the home exposure to the total exposure could differ by up to 20%, thus providing the relative indication of their contribution to body burden. The novel method introduced in this paper provides insights for evaluating scenarios or experiments where sample, exposure, and compound variability must be weighed in order to interpret associations between exposure data.

59 BASIC BIOLOGICAL SCIENCES↗

On the cause of variability of the cosmic ray spectrum in the knee region

Cosmic ray (CR) energy spectra for H, He, Si, and Fe nuclei with energy-to-charge number ratios ℰ/Z in the range from 10 to 5 × 10{sup 7} GeV are studied using observational data obtained at different times in different energy ranges: AMS-02, CREAM, Tibet ASγ, Tibet (hybrid), GRAPES-3, KASCADE, and KASCADE-Grande. Comparison of the H and He CR fluxes according to the KASCADE and KASCADE-Grande data (for different models of deconvolving CR spectra) with the Tibet ASγ and Tibet (hybrid) data obtained at another time in the range of ℰ/Z ∼ 3 × 10{sup 6} GeV demonstrates space weather-caused variability of the CR flux. This feature of CR energy spectra in the Tibet ASγ data is most clearly observed in the spectra of heavier nuclei (Si and Fe) according to the KASCADE-Grande and GRAPES-3 data. The variability in the energy spectra of all CRs in the vicinity of the “knee” is shown in the data of Yakutsk EAS, CASA-BLANCA, and Tibet-III experiments. The variability of the CR flux on a time scale on the order of several years exists only if the source corresponding to the peak in the energy spectrum is situated at a distance of no more than 1 pc from the Sun. Rapid surfatron acceleration of CRs may result from colliding interstellar clouds nearest to the Sun (LIC and G). This acceleration mechanism allows one to explain the variability of the CR spectrum in the range 10{sup 3} GeV < ℰ/Z < 10{sup 8} GeV. Conditions for the trapping of strongly relativistic Fe nuclei by an electromagnetic wave, the dynamics of the components of the particle velocity and momentum, and the dependence of the particle acceleration rate on the initial parameters of the problem are analyzed using numerical calculations. The structure of the phase plane of the accelerated Fe nuclei is examined. Optimal conditions for the implementation of ultrarelativistic surfatron acceleration of Fe nuclei by an electromagnetic wave are formulated.

79 ASTRONOMY AND ASTROPHYSICS↗

PV output smoothing using a battery and natural gas engine-generator.

In some situations involving weak grids or high penetration scenarios, the variability of photovoltaic systems can affect the local electrical grid. In order to mitigate destabilizing effects of power fluctuations, an energy storage device or other controllable generation or load can be used. This paper describes the development of a controller for coordinated operation of a small gas engine-generator set (genset) and a battery for smoothing PV plant output. There are a number of benefits derived from using a traditional generation resource in combination with the battery; the variability of the photovoltaic system can be reduced to a specific level with a smaller battery and Power Conditioning System (PCS) and the lifetime of the battery can be extended. The controller was designed specifically for a PV/energy storage project (Prosperity) and a gas engine-generator (Mesa Del Sol) currently operating on the same feeder in Albuquerque, New Mexico. A number of smoothing simulations of the Prosperity PV were conducted using power data collected from the site. By adjusting the control parameters, tradeoffs between battery use and ramp rates could be tuned. A cost function was created to optimize the control in order to balance, in this example, the need to have low ramp rates with reducing battery size and operation. Simulations were performed for cases with only a genset or battery, and with and without coordinated control between the genset and battery, e.g., without the communication link between sites or during a communication failure. The degree of smoothing without coordinated control did not change significantly because the battery dominated the smoothing response. It is anticipated that this work will be followed by a field demonstration in the near future.

Johnson, Jay Dean↗