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At least 91 records · Page 5

Predicting metal-binding proteins and structures through integration of evolutionary-scale and physics-based modeling

Metals are essential elements in all living organisms, binding to approximately 50% of proteins. They serve to stabilize proteins, catalyze reactions, regulate activities, and fulfill various physiological and pathological functions. While there have been many advancements in determining the structures of protein-metal complexes, numerous metal-binding proteins still need to be identified through computational methods and validated through experiments. Here, to address this need, we have developed the ESMBind workflow, which combines evolutionary scale modeling (ESM) for metal-binding prediction and physics-based protein-metal modeling. Our approach utilizes the ESM-2 and ESM-IF models to predict metal-binding probability at the residue level. In addition, we have designed a metal-placement method and energy minimization technique to generate detailed 3D structures of protein-metal complexes. Our workflow outperforms other models in terms of residue and 3D-level predictions. To demonstrate its effectiveness, we applied the workflow to 142 uncharacterized fungal pathogen proteins and predicted metal-binding proteins involved in fungal infection and virulence.

59 BASIC BIOLOGICAL SCIENCES↗

Fluid learning: Mimicking brain computing with neuromorphic nanofluidic devices

Relentlessly rising energy demands in computing call for rethinking hardware paradigms with energy efficiency in mind. Nature’s example—the brain—raises the question: How can these natural computers achieve remarkable feats with minimal energy compared to supercomputers? Neuromorphic computing mimics the brain’s principles, but current neuromorphic concepts using electronic components face scalability and their own power consumption challenges. A potentially revolutionary approach is emerging: computing with ion transport in water through nanochannels. This field offers energy-efficient possibilities by imitating brain-like information processing with different types of ions as carriers. Finally, the goal is to converge advanced nanoscale architectures with brain-inspired efficiency, heralding a new era of computing.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Density functional thermodynamic description of spin, phonon and displacement degrees of freedom in antiferromagnetic-to-paramagnetic phase transition in YNiO 3

This work herein demonstrates a direct density functional description of the finite-temperature thermodynamic properties of solids exhibiting phase transitions through positional and spin symmetry breaking degrees of freedom. A classic example addressed here is the rare-earth (R) nickelates RNiO 3 where the ground state is characterized by crystallographic and magnetic (e.g., antiferromagnetic) long-range order (LRO), whereas the higher temperature paramagnetic phase manifests a range of local spin and positional symmetry breaking motifs with short-range order (SRO). Unlike time-dependent simulations of spin and positional degrees of freedom, in the present work, phases are described via a superposition of static configurations constructed by populating a periodic base lattice supercell allowing for the formation of energy lowing distribution of positional and spin local motifs. The thermal populations of the configurations in such a superposition phase are obtained from the energy-minimized Density Functional Theory (DFT)-calculated partition functions at different temperatures. This approach offers flexible inclusion of different physical contributions to the free energy, such as elastic, electronic and phonon free energies, all obtained from the same underlying DFT total energy calculations of periodic structures. The thermodynamic and magnetic properties of both LRO and SRO crystallographic and spin phases, including antiferromagnetic (AFM) to paramagnetic (PM) Néel phase transition in YNiO3 are studied. Including spin and phonon contributions, we find a DFT-calculated Néel temperature to be 144 K in satisfactory agreement with the experimental value of 145 K; whereas omitting the phonon contribution, one obtains a Néel temperature of 81 K. We present phonon contributions to the DFT-calculated temperature-dependent SRO, heat capacities, and the polymorphous distribution of nonzero local magnetic moments in the PM phase. This approach thus extends to finite temperatures the symmetry-broken DFT description of both the AFM and PM phases, demonstrating that a thermodynamic superposition approach based on symmetry broken configurations evaluated by a mean-field like DFT is sufficient to obtain a consistent description of the thermal physics of the AFM, PM phases and their interconversion in 3d oxides illustrated by YNiO 3 .

36 MATERIALS SCIENCE↗

On the perturbation effect and LET dependence of beam quality correction factors in carbon ion beams

Background: In a recent study, we reported beam quality correction factors, f Q , in carbon ion beams using Monte Carlo (MC) methods for a cylindrical and a parallel-plate ionization chamber (IC). A non-negligible perturbation effect was observed; however, the magnitude of the perturbation correction due to the specific IC subcomponents was not included. Furthermore, the stopping power data presented in the International Commission on Radiation Units and Measurements (ICRU) report 73 were used, whereas the latest stopping power data have been reported in the ICRU report 90. Purpose: The aim of this study was to extend our previous work by computing f Q correction factors using the ICRU 90 stopping power data and by reporting IC-specific perturbation correction factors. Possible energy or linear energy transfer (LET) dependence of the f Q correction factor was investigated by simulating both pristine beams and spread-out Bragg peaks (SOBPs). Methods: The TOol for PArticle Simulation (TOPAS)/GEANT4 MC code was used in this study. A 30 × 30 × 50 cm 3 water phantom was simulated with a uniform 10 × 10 cm 2 parallel beam incident on the surface. A Farmer-type cylindrical IC (Exradin A12) and two parallel-plate ICs (Exradin P11 and A11) were simulated in TOPAS using the manufacturer-provided geometrical drawings. The f Q correction factor was calculated in pristine carbon ion beams in the 150–450 MeV/u energy range at 2 cm depth and in the middle of the flat region of four SOBPs. The k Q correction factor was calculated by simulating the f Qo correction factor in a 60 Co beam at 5 cm depth. The perturbation correction factors due to the presence of the individual IC subcomponents, such as the displacement effect in the air cavity, collecting electrode, chamber wall, and chamber stem, were calculated at 2 cm depth for monoenergetic beams only. Additionally, the mean dose-averaged and track-averaged LET was calculated at the depths at which the f Q was calculated. Results: The ICRU 90 f Q correction factors were reported. The p dis correction factor was found to be significant for the cylindrical IC with magnitudes up to 1.70%. The individual perturbation corrections for the parallel-plate ICs were <1.0% except for the A11 p cel correction at the lowest energy. The f Q correction for the P11 IC exhibited an energy dependence of >1.00% and displayed differences up to 0.87% between pristine beams and SOBPs. Conversely, the f Q for A11 and A12 displayed a minimal energy dependence of <0.50%. The energy dependence was found to manifest in the LET dependence for the P11 IC. A statistically significant LET dependence was found only for the P11 IC in pristine beams only with a magnitude of <1.10%. Conclusions: The perturbation and k Q correction factor should be calculated for the specific IC to be used in carbon ion beam reference dosimetry as a function of beam quality.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

A multiphase flow model of water droplets dielectrophoretic-induced air dehumidification phenomena

Air humidity in indoor spaces plays a critical role in human comfort and health. Dehumidification systems are used for building humidity controls, but they can take significant energy consumption, especially in geographic locations with high outdoor humidity and warm climates. Consequently, there is a growing demand for innovative dehumidification processes that consume minimal energy. Dielectrophoretic air dehumidification represents one such promising approach. However, it has not garnered significant attention due to the absence of engineering models and simulation tools capable of evaluating its performance and limitations at large-scale airflows. A new numerical multiphase CFD model, which is also experimentally validated, is developed in a customized Reacting Foam solver based on OpenFOAM® version 9. The newly developed model seeks to decrease substantial energy consumption and lower costs by leveraging the dielectrophoretic phenomenon to regulate moisture levels in the air. The solver integrates a hybrid Eulerian-Lagrangian framework to track the droplet's trajectory and growth rate while solving the continuum equations for the moist air. An electrospray produces electrically charged droplets, which grow during their in-flight trajectories as water vapor condenses onto their surfaces. The role of electrostatic forces in promoting vapor condensation within a high-gradient electrical field is investigated, and the dielectrophoretic vapor nucleation process on charged water droplets is discussed. The CFD model was validated against results from the literature and from proof-of-concept experiments conducted by the authors, which showed a 2 % air dehumidification with a single electrospray and airflow rate of 5 cubic feet per minute. The simulation results indicated that augmenting the number of electrically charged spray droplets increased the dehumidification of the air to 25 %. The initial mean droplet diameter, the orientation of the injector and relative humidity significantly influence the assessment of dehumidification. As a result, scaling up this approach to larger airflow volumes is identified as a potential future research direction.

42 ENGINEERING↗

Smart Ventilation Controls Boost Energy Efficiency and Indoor Air Quality

The average American household spends more than $2,200 a year on energy, and heating, ventilating, and air conditioning (HVAC) costs comprise nearly half of the bill. This is one reason why home builders focus on tightening building envelopes to save energy. Yet, limiting the potential for air exchange can negatively impact indoor air quality (IAQ). When outdoor conditions are most extreme during occupied periods, there may be comfort implications from continuing high levels of ventilation during associated weather events. This is true even with heat recovery. To mitigate risks, the Florida Solar Energy Center developed and tested approaches for “smart” ventilation system controls that enable more reliable design, installation, and operation to achieve desired IAQ while also minimizing energy and comfort impacts.

Building America↗

Smart Ventilation Controls Boost Energy Efficiency and Indoor Air Quality

The average American household spends more than $2,200 a year on energy, and heating, ventilating, and air conditioning (HVAC) costs comprise nearly half of the bill. This is one reason why home builders focus on tightening building envelopes to save energy. Yet, limiting the potential for air exchange can negatively impact indoor air quality (IAQ). When outdoor conditions are most extreme during occupied periods, there may be comfort implications from continuing high levels of ventilation during associated weather events. This is true even with heat recovery. To mitigate risks, the Florida Solar Energy Center developed and tested approaches for “smart” ventilation system controls that enable more reliable design, installation, and operation to achieve desired IAQ while also minimizing energy and comfort impacts.

30 DIRECT ENERGY CONVERSION↗

Simultaneous mitigation of density and energy errors in approximate DFT for transition metal chemistry (Final Technical Report)

There were three major goals and objectives of this project: 1) Develop tools to understand density-driven errors in transition metal complexes, 2) Evaluate and minimize energy delocalization error and static correlation error through judicious functional choice, and 3) applying this workflow to machine-learning accelerated screening of redox couples. Over the reporting period, we developed a framework for eliminating flat plane errors. We introduced fully non-empirical coefficients. We demonstrated the approach on both molecules and solids. We investigated and eliminated density driven errors and demonstrated their impact on potential energy surfaces. We trained machine learning models both in a method-dependent fashion and to predict errors in method accuracy. We built large data sets of small molecule energetics and multi-reference character.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Quantum Many-Body Theory from a Solution of the N -Representability Problem

Here, in this study, we present a many-body theory based on a solution of the N-representability problem in which the ground-state two-particle reduced density matrix (2-RDM) is determined directly without the many-particle wave function. We derive an equation that re-expresses physical constraints on higher-order RDMs to generate direct constraints on the 2-RDM, which are required for its derivation from an N-particle density matrix, known as N-representability conditions. The approach produces a complete hierarchy of 2-RDM constraints that do not depend explicitly upon the higher RDMs or the wave function. By using the two-particle part of a unitary decomposition of higher order constraint matrices, we can solve the energy minimization by semidefinite programming in a form where the low-rank structure of these matrices can be potentially exploited. We illustrate by computing the ground-state electronic energy and properties of the H 8 ring.

74 ATOMIC AND MOLECULAR PHYSICS↗

GaAs Thermophotovoltaic Patterned Dielectric Back Contact Devices with Improved Sub-Bandgap Reflectance

We demonstrate GaAs thermophotovoltaic (TPV) devices with a patterned dielectric back contact (PDBC) architecture, featuring a dielectric spacer between the semiconductor and back metal contact over most of the back surface for high reflectance, and metal point contacts over a smaller area for electrical conduction. In the TPV application, high sub-bandgap reflectance is needed to reflect unused sub-bandgap photons to the thermal emitter to minimize energy losses in this portion of the thermal spectrum. We explore different PDBC fabrication processes with SU-8 and SiO2 dielectric spacer layers to maximize sub-bandgap reflectance while minimizing series resistance to increase TPV conversion efficiency. We successfully demonstrate GaAs SU-8 PDBC TPV devices with 2200 degrees C blackbody-weighted sub-bandgap reflectance of 94.9% and 96.5% with and without a front metal grid, respectively. This is 0.7% and 2.3% (absolute) higher than the mean sub-bandgap reflectance of 94.2% for GaAs baseline TPV devices with 100% Au back contact with front metal grid. Lower sub-bandgap reflectance in TPV devices with front grids indicates the front grid induces light scattering leading to additional parasitic absorption in the TPV device. We also show that for higher contact coverage fractions, the PDBC reflectance cannot in general be treated by a linear interpolation using simple 1D transfer matrix method modeling and should be treated instead as a diffraction grating by solving Maxwell's equations in 3D.

energy storage↗

Enhancing Header Shape Through Computational Fluid Dynamics for Improved Performance

Shape optimization in power plant design is crucial for maximizing efficiency and minimizing energy losses It impacts performance, cost effectiveness, and environmental sustainability Our project focuses on optimizing header pipe geometry using a method that considers temperature, flow, and pressure distributions, along with structural analysis This approach ensures structural integrity while minimizing material costs

20 FOSSIL-FUELED POWER PLANTS↗

Minimization of Atomic Displacements as a Guiding Principle of the Martensitic Phase Transformation

I this article, we present a unifying description for the martensitic transformation of steel that accounts for important experimentally observable features of the transformation, namely, the Neumann bands, the interfacial (habit) plane between the transformed and untransformed phases and their orientation relationship. It is obtained through a simple geometric minimization of the total distance traveled by all the atoms from the austenite (fcc or γ) phase to the martensite (bcc or α) phase, without the need for any explicit energy minimization. Our description unites previously proposed mechanisms but it does not rely on assumptions and experimental knowledge regarding the shear planes and directions, or external adjustable parameters. We show how the Kurdjumov-Sach orientation relationship between the two phases and the {225}$_γ$ habit plane, which have both been extensively reported in experiments, naturally emerge from the distance minimization. We also propose an explanation for the occurrence of a different orientation relationship (Pitsch) in thin films.

CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSICS↗

Evaluation of Equivalent Battery Model Representations for Thermostatically Controlled Loads in Commercial Buildings

Models for thermostatically controlled loads in commercial buildings often include many parameters and variables compared to residential buildings. As such, it is beneficial to use reduced-order models to represent these resources. A classic example of such a model is the Virtual Battery or Equivalent Battery Model (EBM). In this paper, the typical EBM is extended to higher-order commercial Heating, Ventilation, and Air-conditioning (HVAC) models and adapted for electric water heaters. Finally, we compare the performance of EBMs with detailed thermal models using three classic optimization problems - energy maximization, energy minimization, and power reference tracking. Our results show that the EBM-constrained and detailed thermal model-constrained problems produce similar outcomes in terms of temperature, power, and total energy consumption.

commercial buildings↗

REopt Lite Overview & Training Exercise

This training exercise provides users with an introduction to and hands-on, interactive exploration of REopt Lite's capabilities. REopt Lite is a free, publicly available techno-economic optimization web tool for distributed energy systems, developed at the National Renewable Energy Laboratory (NREL). REopt Lite helps organizations evaluate the economic viability of grid-connected solar photovoltaics (PV), wind turbines, and battery storage; identify system sizes and battery dispatch strategies to minimize energy costs; and estimate how long a system can sustain critical load during a grid outage. The model is formulated as a mixed-integer linear program based in an underlying application programming interface (API) that is also free and publicly available. This training activity is structured as a group exercise. Participants split into eight groups and each group is assigned a different hypothetical site to model and assess the opportunity for solar PV + battery storage. Groups work together to develop results for their site and then re-convene to compare and discuss results, inputs/drivers of the analysis, and other factors impacting the decision-making process for behind-the-meter solar PV and battery storage.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Operational Limits of Redox Metal Oxides Performing Thermochemical Water Splitting

Solar thermochemical hydrogen production is an attractive technology that stores intermittent solar energy in the form of chemical bonds. Efficient operation requires the identification of a redox-active metal oxide (MO x ) material that can achieve high conversion of water to hydrogen at minimal energy input. Water splitting occurs by consecutive reduction and reoxidation reactions of MO x . MO x is reduced to MO x-δ and, in the second step, is reoxidized by water recovering the initial MO x and generate H 2 . The material must reduce at temperatures achievable in concentrated solar receiver/reactors, while maintaining a thermodynamic driving force to split water. At equilibrium, extent of reduction depends on temperature and oxygen partial pressure, and in this analysis, a set of thermodynamic properties, namely, enthalpy and entropy of oxygen vacancy formation, is sufficient to represent MO x . Herein, a method to easily classify materials based on these thermodynamic properties under any condition of oxygen partial pressure and temperature is presented. This method is based on fundamental thermodynamic principles and is applicable for any redox material with known thermodynamic properties. Despite the simplicity of the method, it is believed that this analysis will support future research in targeting thermodynamic properties of redox-active metal oxides.

water splitting↗

Supercritical Treatment Technology for Water Purification (Annual Final Report)

This project continued the development of the Supercritical Water Extraction – Enhanced Targeted Recovery (SWEETR™) technology, a novel desalination process for treating hypersaline brines. The overall objective is to demonstrate the technical and economic feasibility of an innovative, energy efficient, and robust supercritical desalination technology to treat hypersaline solutions and separating saltwater into a pure water stream and valuable recovered solids, resulting in zero liquid discharge (ZLD). The proposed technology, focuses on innovative methods of applying supercritical water to treat highly concentrated brine solutions without incurring a high energy penalty. Integrating the technology with solar energy reduces the energy cost for the system. The results obtained during the proof-of-concept testing demonstrate that the SWEETR™ concept is technically feasible and that supercritical water treatment is a viable option with strong merit for treating high salinity waters. The strategic design of the system provides the opportunity to localize the supercritical zone, which helps reduce the overall energy cost associated with the desalination process. The process can be tuned to remove only the amount of salts required to make the treated water “fit for purpose”, providing further opportunities to minimize energy costs. The ability to destroy organic compounds associated with the water while simultaneously being able to desalinate makes SWEETR™ uniquely fitted for treating aqueous streams such as produced water from oil and gas extraction which contain small amounts of organics. Such mixed contaminant streams pose an extreme challenge for other treatment options. Future work will further develop the SWEETR™ technology to take it from the bench-scale to the pilot-scale, and ready the technology for commercial application.

04 OIL SHALES AND TAR SANDS↗

Optimization of key energy and performance metrics for drug product manufacturing

During the development of pharmaceutical manufacturing processes, detailed systems-based analysis and optimization are required to control and regulate critical quality attributes within specific ranges, to maintain product performance. As discussions on carbon footprint, sustainability, and energy efficiency are gaining prominence, the development and utilization of these concepts in pharmaceutical manufacturing are seldom reported, which limits the potential of pharmaceutical industry in maximizing key energy and performance metrics. Based on an integrated modeling and techno-economic analysis framework previously developed by the authors, this study presents the development of a combined sensitivity analysis and optimization approach to minimize energy consumption while maintaining product quality and meeting operational constraints in a pharmaceutical process. The optimal input process conditions identified were validated against experiments and good agreement resulted between simulated and experimental data. Here, the results also allowed for a comparison of the capital and operational costs for batch and continuous manufacturing schemes under nominal and optimized conditions. Using the nominal batch operations as a basis, the optimized batch operation results in a 71.7% reduction of energy consumption, whereas the optimized continuous case results in an energy saving of 83.3%.

59 BASIC BIOLOGICAL SCIENCES↗

Building Automation

In this chapter, we focus on both need-based and vision-based control innovation for building automation for HVAC systems. After providing a brief background that describes different HVAC architectures and products, we describe the control challenges and opportunities from a needs-based point of view, at the equipment level, the systems level, and the building level. At the equipment level, increased use of continuously variable actuation such as variable speed compressors and fans, requires application of robust multivariable control that must consider various types of nonlinear behavior across increasingly larger operating envelopes. The objective at this level is to achieve robust and energy efficient operation. At the system level, coupled and interactive dynamics among subsystems are increasingly important to consider, and functional integration of these subsystems, along with set points and operating schedules are designed to minimize energy consumption and improve occupant comfort. At the building level, issues such as integration among other building systems, such as the building envelope and the electric grid, offer opportunities to develop new types of demand response and grid-interactive behaviors and technologies. At the higher levels, system dynamics and robust stability are less of an issue, similar to process control applications, while optimization and integration are more important, although dynamic stability is increasing an issue at the higher levels too. From a vision-driven innovation point of view, we describe three areas that will require sustained research efforts and will eventually impact building automation: Digital Twins, Model Predictive Control, and Grid Interactive Buildings.

Bortoff, Scott↗