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At least 757 records · Page 42

Optimization of electroporation method and promoter evaluation for type-1 methanotroph, Methylotuvimicrobium alcaliphilum

Methanotrophic bacteria are promising hosts for methane bioconversion to biochemicals or bioproducts. However, due to limitations associated with long genetic manipulation timelines and, lack of choice in genetic tools required for strain engineering, methanotrophs are currently not employed for bioconversion technologies. In this study, a rapid and reproducible electroporation protocol is developed for type 1 methanotroph, Methylotuvimicrobium alcaliphilum using common laboratory solutions, analyzing optimal electroshock voltages and post-shock cell recovery time. Successful reproducibility of the developed method was achieved when different replicative plasmids were assessed on lab adapted vs. wild-type M. alcaliphilum strains (DASS vs. DSM19304). Overall, a ∼ 3-fold decrease in time is reported with use of electroporation protocol developed here, compared to conjugation, which is the traditionally employed approach. Additionally, an inducible (3-methyl benzoate) and a constitutive (sucrose phosphate synthase) promoter is characterized for their strength in driving gene expression.

59 BASIC BIOLOGICAL SCIENCES↗

Method for estimating optimal spectral and energy parameters of laser irradiation in photodynamic therapy of biological tissue

We have solved the problem of layer-by-layer laser-light dosimetry in biological tissues and of selecting an individual therapeutic dose in laser therapy. A method is proposed for real-time monitoring of the radiation density in tissue layers in vivo, concentrations of its endogenous (natural) and exogenous (specially administered) chromophores, as well as in-depth distributions of the spectrum of light action on these chromophores. As the background information use is made of the spectrum of diffuse light reflected from a patient's tissue, measured by a fibre-optic spectrophotometer. The measured spectrum is quantitatively analysed by the method of approximating functions for fluxes of light multiply scattered in tissue and by a semi-analytical method for calculating the in-depth distribution of the light flux in a multi-layered medium. We have shown the possibility of employing the developed method for monitoring photosensitizer and oxyhaemoglobin concentrations in tissue, light power absorbed by chromophores in tissue layers at different depths and laser-induced changes in the tissue morphology (vascular volume content and ratios of various forms of haemoglobin) during photodynamic therapy. (biophotonics)

60 APPLIED LIFE SCIENCES↗

Nitric acid treated multi-walled carbon nanotubes optimized by Taguchi method

Electron transfer rate (ETR) of CNTs can be enhanced by increasing the amounts of COOH groups to their wall and opened tips. With the aim to achieve the highest production amount of COOH, Taguchi robust design has been used for the first time to optimize the surface modification of MWCNTs by nitric acid oxidation. Three main oxidation parameters which are concentration of acid, treatment temperature and treatment time have been selected as the control factors that will be optimized. The amounts of COOH produced are measured by using FTIR spectroscopy through the absorbance intensity. From the analysis, we found that acid concentration and treatment time had the most important influence on the production of COOH. Meanwhile, the treatment temperature will only give intermediate effect. The optimum amount of COOH can be achieved with the treatment by 8.0 M concentration of nitric acid at 120 °C for 2 hour.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Development of an optimized and scalable method for isolation of umbilical cord blood-derived small extracellular vesicles for future clinical use

Abstract Extracellular vesicles (EV) are a promising therapeutic tool in regenerative medicine. These particles were shown to accelerate wound healing, through delivery of regenerative mediators, such as microRNAs. Herein we describe an optimized and upscalable process for the isolation of EV smaller than 200 nm (sEV), secreted by umbilical cord blood mononuclear cells (UCB-MNC) under ischemic conditions and propose quality control thresholds for the isolated vesicles, based on the thorough characterization of their protein, lipid and RNA content. Ultrafiltration and size exclusion chromatography (UF/SEC) optimized methodology proved superior to traditional ultracentrifugation (UC), regarding production time, standardization, scalability, and vesicle yield. Using UF/SEC, we were able to recover approximately 400 times more sEV per mL of media than with UC, and upscaling this process further increases EV yield by about 3-fold. UF/SEC-isolated sEV display many of the sEV/exosomes classical markers and are enriched in molecules with anti-inflammatory and regenerative capacity, such as hemopexin and miR-150. Accordingly, treatment with sEV promotes angiogenesis and extracellular matrix remodeling, in vitro. In vivo, UCB-MNC-sEV significantly accelerate skin regeneration in a mouse model of delayed wound healing. The proposed isolation protocol constitutes a significant improvement compared to UC, the gold-standard in the field. Isolated sEV maintain their regenerative properties, whereas downstream contaminants are minimized. The use of UF/SEC allows for the standardization and upscalability required for mass production of sEV to be used in a clinical setting.

Cardoso, Renato M. S.↗

Analysis of the SiMPL Method for Density-Based Topology Optimization

We present a rigorous convergence analysis of a new method for density-based topology optimization that provides pointwise bound-preserving design updates and faster convergence than other popular first-order topology optimization methods. Due to its strong bound preservation, the method is exceptionally robust, as demonstrated in numerous examples here and in the companion article [D. Kim et al., Struct. Multidiscip. Optim., 68 (2025), 74]. Furthermore, it is easy to implement with clear structure and analytical expressions for the updates. Our analysis covers two versions of the method, characterized by the employed line search strategies. We consider a modified Armijo backtracking line search and a Bregman backtracking line search. For both line search algorithms, our algorithm delivers a strict monotone decrease in the objective function and further intuitive convergence properties, e.g., strong and pointwise convergence of the density variables on the active sets, norm convergence to zero of the increments, convergence of the Lagrange multipliers, and more. In addition, the numerical experiments demonstrate apparent mesh-independent convergence of the algorithm. Here, we refer to the new algorithm as the SiMPL method (pronounced “simple”), which stands for Sigmoidal Mirror descent with a Projected Latent variable.

97 MATHEMATICS AND COMPUTING↗

Fermi-Löwdin-orbital self-interaction correction using the optimized-effective-potential method within the Krieger-Li-Iafrate approximation

Perdew-Zunger self-interaction correction (PZ-SIC) offers a route to remove self interaction errors on an orbital-by-orbital basis. A recent formulation of PZ-SIC by Pederson, Ruzsinszky and Perdew proposes restricting the unitary transformation to localized orbitals called Fermi-Löwdin orbitals. This formulation, called the FLOSIC method, simplifies PZ-SIC calculations and was implemented self-consistently using a Jacobi-like (FLOSIC-Jacobi) iteration scheme. In this work we implement the FLOSIC approach using the Krieger-Li-Iafrate (KLI) approximation to the optimized effective potential (OEP). We compare the results of present FLOSIC-KLI approach with FLOSIC-Jacobi scheme for atomic energies, atomization energies, ionization energies, barrier heights, polarizability of chains of hydrogen molecules etc. to validate the FLOSIC-KLI approach. The FLOSICKLI approach, which is within the realm of Kohn-Sham theory, predicts smaller energy gaps between frontier orbitals due to the lowering of eigenvalues of the lowest unoccupied orbitals. Results show that atomic energies, atomization energies, ionization energy as an absolute of highest occupied orbital eigenvalue, and polarizability of chains of hydrogen molecules between the two methods agree within 2%. Lastly the FLOSIC-KLI approach is used to determine the vertical ionization energies of water clusters.

74 ATOMIC AND MOLECULAR PHYSICS↗

Improving Empirical Magnetic Field Models by Fitting to In Situ Data Using an Optimized Parameter Approach

A method for comparing and optimizing the accuracy of empirical magnetic field models using in situ magnetic field measurements is presented in this paper. The optimization method minimizes a cost function—τ—that explicitly includes both a magnitude and an angular term. A time span of 21 days, including periods of mild and intense geomagnetic activity, was used for this analysis. A comparison between five magnetic field models (T96, T01S, T02, TS04, and TS07) widely used by the community demonstrated that the T02 model was, on average, the most accurate when driven by the standard model input parameters. The optimization procedure, performed in all models except TS07, generally improved the results when compared to unoptimized versions of the models. Additionally, using more satellites in the optimization procedure produces more accurate results. This procedure reduces the number of large errors in the model, that is, it reduces the number of outliers in the error distribution. The TS04 model shows the most accurate results after the optimization in terms of both the magnitude and direction, when using at least six satellites in the fitting. It gave a smaller error than its unoptimized counterpart 57.3% of the time and outperformed the best unoptimized model (T02) 56.2% of the time. Its median percentage error in |B| was reduced from 4.54% to 3.84%. Finally, the difference among the models analyzed, when compared in terms of the median of the error distributions, is not very large. However, the unoptimized models can have very large errors, which are much reduced after the optimization.

58 GEOSCIENCES↗

Optimized anion exchange column isolation of zirconium-89 (89Zr) from yttrium cyclotron target: Method development and implementation on an automated fluidic platform

Zirconium-89 (89Zr), produced by the (p,n) reaction from naturally monoisotopic yttrium (natY), is a promising positron emitting isotope for immunoPET imaging. Its long half-life of 78.4 h is sufficient for evaluating slow physiological processes. A prototype automated fluidic system, coupled to on-line and in-line detectors, has been constructed to facilitate development of new 89Zr purification methodologies. The highly reproducible reagent delivery platform and near-real time monitoring of column effluents allows for efficient method optimization. The separation of Zr from dissolved Y metal targets was evaluated using several anion exchange resins. Each resin was evaluated against its ability to quantitatively capture Zr from a load solution that is high in dissolved Y. The most appropriate anion exchange resin for this application was identified, and the separation method was optimized. The method is capable of a high Y decontamination factor (>105) and has been shown to separate Fe, an abundant contaminant in Y foils, from the 89Zr elution fraction. Finally, the performance of the method was evaluated using cyclotron bombarded Y foil targets. The separation method was shown to achieve >95% recovery of the 89Zr present in the foils. The 89Zr eluent, however, was in a chemical matrix not immediately conducive to labeling onto proteins. The main intent of this study was to develop a tandem column 89Zr purification process, wherein the anion exchange column method described here is the first separation in a dual-column purification process.

Zirconium-89, ImmunoPET, medical isotope, automati↗

A feasibility study: Selection of a personalized radiotherapy fractionation schedule using spatiotemporal optimization

Purpose: To investigate the impact of using spatiotemporal optimization, i.e., intensity-modulated spatial optimization followed by fractionation schedule optimization, to select the patient-specific fractionation schedule that maximizes the tumor biologically equivalent dose (BED) under dose constraints for multiple organs-at-risk (OARs). Methods: Spatiotemporal optimization was applied to a variety of lung tumors in a phantom geometry using a range of tumor sizes and locations. The optimal fractionation schedule for a patient using the linear-quadratic cell survival model depends on the tumor and OAR sensitivity to fraction size (α/β), the effective tumor doubling time (T{sub d}), and the size and location of tumor target relative to one or more OARs (dose distribution). The authors used a spatiotemporal optimization method to identify the optimal number of fractions N that maximizes the 3D tumor BED distribution for 16 lung phantom cases. The selection of the optimal fractionation schedule used equivalent (30-fraction) OAR constraints for the heart (D{sub mean} ≤ 45 Gy), lungs (D{sub mean} ≤ 20 Gy), cord (D{sub max} ≤ 45 Gy), esophagus (D{sub max} ≤ 63 Gy), and unspecified tissues (D{sub 05} ≤ 60 Gy). To assess plan quality, the authors compared the minimum, mean, maximum, and D{sub 95} of tumor BED, as well as the equivalent uniform dose (EUD) for optimized plans to conventional intensity-modulated radiation therapy plans prescribing 60 Gy in 30 fractions. A sensitivity analysis was performed to assess the effects of T{sub d} (3–100 days), tumor lag-time (T{sub k} = 0–10 days), and the size of tumors on optimal fractionation schedule. Results: Using an α/β ratio of 10 Gy, the average values of tumor max, min, mean BED, and D{sub 95} were up to 19%, 21%, 20%, and 19% larger than those from conventional prescription, depending on T{sub d} and T{sub k} used. Tumor EUD was up to 17% larger than the conventional prescription. For fast proliferating tumors with T{sub d} less than 10 days, there was no significant increase in tumor BED but the treatment course could be shortened without a loss in tumor BED. The improvement in the tumor mean BED was more pronounced with smaller tumors (p-value = 0.08). Conclusions: Spatiotemporal optimization of patient plans has the potential to significantly improve local tumor control (larger BED/EUD) of patients with a favorable geometry, such as smaller tumors with larger distances between the tumor target and nearby OAR. In patients with a less favorable geometry and for fast growing tumors, plans optimized using spatiotemporal optimization and conventional (spatial-only) optimization are equivalent (negligible differences in tumor BED/EUD). However, spatiotemporal optimization yields shorter treatment courses than conventional spatial-only optimization. Personalized, spatiotemporal optimization of treatment schedules can increase patient convenience and help with the efficient allocation of clinical resources. Spatiotemporal optimization can also help identify a subset of patients that might benefit from nonconventional (large dose per fraction) treatments that are ineligible for the current practice of stereotactic body radiation therapy.

60 APPLIED LIFE SCIENCES↗

Trip optimization system and method for a train

A system for operating a train having one or more locomotive consists with each locomotive consist comprising one or more locomotives, the system including a locator element to determine a location of the train, a track characterization element to provide information about a track, a sensor for measuring an operating condition of the locomotive consist, a processor operable to receive information from the locator element, the track characterizing element, and the sensor, and an algorithm embodied within the processor having access to the information to create a trip plan that optimizes performance of the locomotive consist in accordance with one or more operational criteria for the train.

42 ENGINEERING↗

A method for determining optimal electric range by considering electric vehicle lightweighting on perceived ownership cost

The limited driving range due to high costs and low energy densities of batteries constraints the battery electric vehicle (BEV) market growth. Lightweighting in theory can reduce energy consumption rate and extend the driving range. The knowledge gap is to quantitatively link the cost-effectiveness of light-weight technologies with range extension and consumer acceptance of BEVs. In this study, a physics-based energy consumption model of BEVs is constructed and associated with a statistics-based model on the basis of travel surveys. A perceived cost of ownership (PCO) is then developed by adding intangible costs to traditional total cost of ownership models. We estimate, at the disaggregate vehicle model and driver level and the aggregate market level, 1) the extended range due to lightweighting for a given battery size; and 2) the optimal electric range based on lightweighting decisions. The cost-effectiveness of lightweighting for BEV range extension is found to vary with income-dependent daily range limitation value, driving patterns and lightweighting technology costs. In general, adopting lightweighting in BEVs is more cost-effective for consumers with higher daily limitation value, as well as for those with higher driving intensity or suitable daily driving patterns. When the lightweighting involves a higher vehicle production cost, less lightweighting could reduce the overall PCO for BEV owners. 4 of the selected top ten BEV models are found to benefit from additional 2.09%–4.45% lightweighting. Finally, the method built in this study can guide automakers in planning R&D investments in battery and lightweighting technologies.

33 ADVANCED PROPULSION SYSTEMS↗

An adaptive sampling augmented Lagrangian method for stochastic optimization with deterministic constraints

The primary goal of this paper is to provide an efficient solution algorithm based on the augmented Lagrangian framework for optimization problems with a stochastic objective function and deterministic constraints. Our main contribution is combining the augmented Lagrangian framework with adaptive sampling, resulting in an efficient optimization methodology validated with practical examples. To achieve the presented efficiency, here we consider inexact solutions for the augmented Lagrangian subproblems, and through an adaptive sampling mechanism, we control the variance in the gradient estimates. Furthermore, we analyze the theoretical performance of the proposed scheme by showing equivalence to a gradient descent algorithm on a Moreau envelope function, and we prove sublinear convergence for convex objectives and linear convergence for strongly convex objectives with affine equality constraints. The worst-case sample complexity of the resulting algorithm, for an arbitrary choice of penalty parameter in the augmented Lagrangian function, is $\mathscr{O}$(ϵ -3-δ ) , where ϵ > 0 is the expected error of the solution and δ > 0 is a user-defined parameter. If the penalty parameter is chosen to be $\mathscr{O}$(ϵ -1 ), we demonstrate that the result can be improved to $\mathscr{O}$(ϵ -2 ) , which is competitive with the other methods employed in the literature. Moreover, if the objective function is strongly convex with affine equality constraints, we obtain $\mathscr{O}$(ϵ -1 log(1/ϵ)) complexity. Finally, we empirically verify the performance of our adaptive sampling augmented Lagrangian framework in machine learning optimization and engineering design problems, including topology optimization of a heat sink with environmental uncertainty.

97 MATHEMATICS AND COMPUTING↗

Using projection operators with maximum overlap methods to simplify challenging self-consistent field optimization

Maximum overlap methods are effective tools for optimizing challenging ground- and excited-state wave functions using self-consistent field models such as Hartree-Fock and Kohn-Sham density functional theory. Nevertheless, such models have shown significant sensitivity to the user-defined initial guess of the target wave function. Here in this work, a projection operator framework is defined and used to provide a metric for non-aufbau orbital selection in maximum-overlap-methods. The resulting algorithms, termed the Projection-based Maximum Overlap Method (PMOM) and Projection-based Initial Maximum Overlap Method (PIMOM), are shown to perform exceptionally well when using simple user-defined target solutions based on occupied/virtual molecular orbital permutations. This work also presents a new metric that provides a simple and conceptually convenient measure of agreement between the desired target and the current or final SCF results during a calculation employing a maximum-overlap method.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Instrument design optimization with computational methods

Using Finite Element Analysis to approximate the solution of differential equations, two different instruments in experimental Hall C at the Thomas Jefferson National Accelerator Facility are analyzed. The time dependence of density uctuations from the liquid hydrogen (LH2) target used in the Q wea k experiment (2011-2012) are studied with Computational Fluid Dynamics (CFD) and the simulation results compared to data from the experiment. The 2.5 kW liquid hydrogen target was the highest power LH2 target in the world and the first to be designed with CFD at Jefferson Lab. The first complete magnetic field simulation of the Super High Momentum Spectrometer (SHMS) is presented with a focus on primary electron beam deflection downstream of the target. The SHMS consists of a superconducting horizontal bending magnet (HB) and three superconducting quadrupole magnets. The HB allows particles scattered at an angle of 5:5 deg to the beam line to be steered into the quadrupole magnets which make up the optics of the spectrometer. Without mitigation, remnant fields from the SHMS may steer the unscattered beam outside of the acceptable envelope on the beam dump and limit beam operations at small scattering angles. A solution is proposed using optimal placement of a minimal amount of shielding iron around the beam line.

43 PARTICLE ACCELERATORS↗

Hierarchy of model Kohn–Sham potentials for orbital-dependent functionals: A practical alternative to the optimized effective potential method

We describe a method for constructing a hierarchy of model potentials approximating the functional derivative of a given orbital-dependent exchange-correlation functional with respect to electron density. Each model is derived by assuming a particular relationship between the self-consistent solutions of Kohn–Sham (KS) and generalized Kohn–Sham (GKS) equations for the same functional. In the KS scheme, the functional is differentiated with respect to density, in the GKS scheme—with respect to orbitals. The lowest-level approximation is the orbital-averaged effective potential (OAEP) built with the GKS orbitals. The second-level approximation, termed the orbital-consistent effective potential (OCEP), is based on the assumption that the KS and GKS orbitals are the same. It has the form of the OAEP plus a correction term. The highest-level approximation is the density-consistent effective potential (DCEP), derived under the assumption that the KS and GKS electron densities are equal. The analytic expression for a DCEP is the OCEP formula augmented with kinetic-energy-density-dependent terms. In the case of exact-exchange functional, the OAEP is the Slater potential, the OCEP is roughly equivalent to the localized Hartree–Fock approximation and related models, and the DCEP is practically indistinguishable from the true optimized effective potential for exact exchange. All three levels of the proposed hierarchy require solutions of the GKS equations as input and have the same affordable computational cost.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

On optimizing Jacobi–Davidson method for calculating eigenvalues in low dimensional structures using eight band k · p model

The paper presents two ways of improving the Jacobi–Davidson method for calculating the eigenvalues and eigenvectors described by eight-band k · p model for quantum dots and other low dimensional structures. First, the method is extended by the application of time reversal symmetry operator. This extension allows efficient calculations of the twofold degeneracy present in the multiband k · p model and other interior eigenvalues. Second, the preconditioner for the indefinite matrix which comes from the discretization of the eight band k · p Hamiltonian is presented. The construction of this preconditioner is based on physical considerations about energy band structure in the k · p model. On the basis of two real examples, it is shown that the preconditioner can significantly shorten the time needed to calculate the interior eigenvalues, despite the fact that the memory usage of the preconditioner and Hamiltionian is comparable. Finally, some technical details for implementing the eight band k · p Hamiltonian and the eigensolver are provided.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

TU-E-213-03: Tools for Ensuring Quality and Safety

Purpose: To develop the first 4D robust optimization (RO) method accounting for respiratory motion and evaluate its potential to improve plan robustness and optimality compared to 3D RO and PTV-based optimization. Methods: A set of 4D CT images are used to track respiratory motion and deformation of tumors and organs. For each of 10 respiration phases, dose distributions for nine different uncertainty scenarios including the nominal one, those incorporating ±5mm setup uncertainties long x, y and z directions and ±3.5% range uncertainties are calculated. All 90 dose distributions are simultaneously optimized to achieve full dose coverage of 10 CTVs and sparing of normal structures. ITV-based 3D RO and PTV-based optimization based on the average CT are also carried for the same patient using same dose volume constrains. After optimization, 4D robustness evaluation was performed for all resulting plans. The CTV coverage and the sparing of normal tissue in 10 phases are evaluated and compared among the three methods. The widths of DVH bands represent the robustness of dose distributions in the structures. Results: For one patient studied so far, the worst case CTV coverage by the prescription dose among all 90 scenarios is: 99% for 4D RO; 88.9% for 3D RO, and 85.2% for PTV based optimization. 4D RO also results in best robustness with the narrowest DVH’ bandwidths for the CTV. 4D and 3D RO have similar organ sparing while PTV based optimization results in worst organ sparing. Conclusion: 4D robust optimization which accounts for anatomy motion and deformation in the optimization process, significantly improves plan robustness and achieves higher quality treatment plans for lung cancer patients. The method is being evaluated for multiple patients with different tumor and motion characteristics.

60 APPLIED LIFE SCIENCES↗

A projection-based method for topology optimization of structures with graded surfaces

Topology optimization (TO) is a generative design approach that is used to create new structures that are optimal for their purpose. Standard parameterizations of the TOproblem allow exploration of an arbitrarily complex design space, but must be constrained to ensure manufacturability; these constraints tend to be computationally expensive and intrusive to the design process. A relatively new parametrization of the TO problem uses geometry projection of known-manufacturable building blocksinto the design domain, but the existing library of building blocks compatible with projection is small. This project sought to expand this library with new shapes, and to determine whether theaddition of these new shapes could be used to design unit cells for micro-architected materials (MAMs) with improved stiffness-to-weight ratio compared with traditional designs,while retaining compatibility with additive manufacturing processes.Due to a reduction in scope, effort was focused on truss lattices with hollow, tapered, and curved struts. Hollowtruss lattices were found that outperform traditional designs like the octet truss in both stiffness and isotropy, as well as providing a decoupling between the stiffness and relative density. These new designs are expected to improve the performance of functionally graded structures in programmatic applications.

42 ENGINEERING↗