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At least 1,099 records · Page 61

Technical Note: Dose gradients and prescription isodose in orthovoltage stereotactic radiosurgery

Purpose: The purpose of this work is to examine the trade-off between prescription isodose and dose gradients in orthovoltage stereotactic radiosurgery. Methods: Point energy deposition kernels (EDKs) describing photon and electron transport were calculated using Monte Carlo methods. EDKs were generated from 10 to 250 keV, in 10 keV increments. The EDKs were converted to pencil beam kernels and used to calculate dose profiles through isocenter from a 4π isotropic delivery from all angles of circularly collimated beams. Monoenergetic beams and an orthovoltage polyenergetic spectrum were analyzed. The dose gradient index (DGI) is the ratio of the 50% prescription isodose volume to the 100% prescription isodose volume and represents a metric by which dose gradients in stereotactic radiosurgery (SRS) may be evaluated. Results: Using the 4π dose profiles calculated using pencil beam kernels, the relationship between DGI and prescription isodose was examined for circular cones ranging from 4 to 18 mm in diameter and monoenergetic photon beams with energies ranging from 20 to 250 keV. Values were found to exist for prescription isodose that optimize DGI. Conclusions: The relationship between DGI and prescription isodose was found to be dependent on both field size and energy. Examining this trade-off is an important consideration for designing optimal SRS systems.

60 APPLIED LIFE SCIENCES↗

Structural and Preclinical Studies of Computationally Designed Non-Nucleoside Reverse Transcriptase Inhibitors for Treating HIV infection

The clinical benefits of HIV-1 non-nucleoside reverse transcriptase (RT) inhibitors (NNRTIs) are hindered by their unsatisfactory pharmacokinetic (PK) properties along with the rapid development of drug-resistant variants. However, the clinical efficacy of these inhibitors can be improved by developing compounds with enhanced pharmacological profiles and heightened antiviral activity. We used computational and structure-guided design to develop two next-generation NNRTI drug candidates, compounds I and II, which are members of a class of catechol diethers. We evaluated the preclinical potential of these compounds in BALB/c mice because of their high solubility (510 µg/ml for compound I and 82.9 µg/ml for compound II), low cytotoxicity, and enhanced antiviral activity against wild-type (WT) HIV-1 RT and resistant variants. Additionally, crystal structures of compounds I and II with WT RT suggested an optimal binding to the NNRTI binding pocket favoring the high anti-viral potency. A single intraperitoneal dose of compounds I and II exhibited a prolonged serum residence time of 48 hours and concentration maximum (Cmax) of 4000- to 15,000-fold higher than their therapeutic/effective concentrations. These Cmax values were 4- to 15-fold lower than their cytotoxic concentrations observed in MT-2 cells. Compound II showed an enhanced area under the curve (0–last) and decreased plasma clearance over compound I and efavirenz, the standard of care NNRTI. Hence, the overall (PK) profile of compound II was excellent compared with that of compound I and efavirenz. Furthermore, both compounds were very well tolerated in BALB/c mice without any detectable acute toxicity. Taken together, these data suggest that compounds I and II possess improved anti-HIV-1 potency, remarkable in vivo safety, and prolonged in vivo circulation time, suggesting strong potential for further development as new NNRTIs for the potential treatment of HIV infection.

59 BASIC BIOLOGICAL SCIENCES↗

Spectral broadening and compression of picosecond pulses in air using a multi-pass cell

We report the spectral broadening and post-compression of picosecond pulses using a multi-pass cell (MPC) operating in air. A 2 m-long bi-concave cavity with 41 reflections and 96.4% transmission was designed and implemented, optimized for the compression of 5.5 ps, 4.5 mJ pulses from a Yb:YAG laser operating at 1030 nm. A 19.3-fold spectral broadening was obtained, increasing the bandwidth from 0.3 nm to 5.8 nm, which enabled pulse compression down to 547 fs with a symmetric temporal profile close to the transform limit. These results demonstrate the feasibility of using open-air MPCs for high-energy picosecond pulse post-compression, without the need for sealed chambers, while preserving high mode quality and transmission. Scaling to pulse higher energy is discussed.

Zaldivar Escola, F. [Univ. of Buenos Aires (Argent↗

νBDX: a Coherent Elastic Neutrino Nucleus Scattering (CEνNS) experiment at Jefferson Lab

Particle physics is an ever-changing field seeking to explain phenomena that lie at the limits of our current knowledge. Among discovered and hypothesized interactions, Coherent Elastic Neutrino-Nucleus Scattering (CE?NS) stands out as a fascinating and elusive phenomenon, offering a unique window into the nature of neutrinos and their interactions with matter. CE?NS, a process predicted by the Standard Model, represents one of the subtle ways in which neutrinos can interact with atomic nuclei. Unlike other neutrinonucleus interactions, CE?NS occurs coherently, meaning that the entire nucleus collectively responds to the neutrino-mediated weak force, resulting in small energy transfers to the nucleus as a whole. The extremely rare nature of CE?NS events presents a formidable challenge to experimenters seeking to detect and study these interactions. Recent advances in detector technologies and the implementation of large-scale experiments, such as coherent neutrino scattering experiments at research facilities around the world, have opened up new avenues for exploring this elusive phenomenon. These experiments aim not only to observe CE?NS directly but also to extract valuable information on neutrino properties, nuclear structure, and potential deviations from the Standard Model. This thesis aims to study the feasibility of an experiment to study CE?NS at The Thomas Jefferson National Accelerator Facility, Newport News, VA, USA. This would be an experiment that exploits the production of neutrinos by an electron beam dumped on a thick target (the beam dump). The large quantity of neutrinos produced and their energy profile are well suited to the purpose of studying the CE?NS. In my thesis, I will start from previous studies on CE?NS and from theoretical considerations regarding the process, then quantify the expected events for a hypothetical experiment and possible backgrounds through simulations aimed at optimizing the geometry of the future detector. I will also show some tests on selected detector components that will be part of a first prototype.

Grazzi, Stefano↗

OPF-Learn: An Open-Source Framework for Creating Representative AC Optimal Power Flow Datasets: Preprint

Increasing levels of renewable generation motivate a growing interest in data-driven approaches for AC optimal power flow (AC OPF) to manage uncertainty. However, a lack of disciplined dataset creation and benchmarking prohibits useful comparison between approaches in the literature. To instigate confidence, models must be able to reliably predict solutions across a wide range of operating conditions. This paper develops the OPF-Learn package for Julia and Python which uses a computationally efficient approach to create representative datasets that span a wide spectrum of the AC OPF feasible region. Load profiles are uniformly sampled from a convex set that contains the AC OPF feasible set. For each infeasible point found, the convex set is reduced using infeasibility certificates, found by utilizing properties of a relaxed formulation. The framework is shown to generate datasets which are more representative of the entire feasible space versus traditional techniques seen in the literature, improving machine learning model performance.

dataset↗

Coupling of high-resolution mass spectrometer and photosynthesis system for comprehensive leaf volatile metabolite profiling

Background Leaf-level biogenic volatile organic compounds (BVOCs) emissions represent a major source of organic gases in the atmosphere, influencing both climate and air quality. These emissions are strongly driven by environmental perturbations, which affect individual plant- to ecosystem-level processes. Uncovering all the BVOCs and understanding how their emissions respond to altered environmental conditions provide critical insights into vegetation-driven changes in atmospheric chemistry. We developed a tandem instrumentation setup that integrates a proton transfer reaction time-of-flight mass spectrometer (PTR-ToF-MS) with parts-per-trillion detection limits and a photosynthetic infrared gas exchange system for the untargeted survey of all the BVOCs. This novel system enables simultaneous, real-time monitoring of BVOC emissions and photosynthetic parameters at the leaf level, offering new opportunities to disentangle the physiological and environmental drivers of VOC release. Furthermore, we established the VOC Analysis and Processing Optimization Resource (VAPOR), an open-access software tool designed for rapid data post-processing and the analysis of the variability of hundreds of BVOCs. We assessed the performance of the tandem system under varying background conditions, using standard gas mixtures and a range of environmental factors. Results Blank emissions were substantially lower for major BVOCs (e.g., isoprene) compared to those observed in plant emissions. Despite this, the observation of background-level VOCs highlights the importance of routinely acquiring and accounting for blank measurements in analyses using the coupled instrumentation. Introduction of known VOC concentrations to the system demonstrated a linear response across different compounds with varying molecular compositions, indicating minimal gas loss regardless of chemical moieties within the coupled instrumentation. We applied the optimized system to investigate the physiological mechanisms driving BVOC emissions across different genotypes of poplar and pennycress. The high mass resolution capabilities of the PTR-ToF-MS, coupled with comprehensive VAPOR-driven data analysis, enabled the identification of several important BVOCs, including methanol and methanethiol; these BVOCs displayed substantial variation across pennycress genotypes and showed concentrations ~ 100–350% higher than the blank. Moreover, isoprene emissions varied significantly among poplar genotypes grown in different potting media. Conclusions Tandem instrumentation offers a powerful tool for profiling volatile molecular markers and elucidating their genetic and environmental underpinnings. This approach enhances our ability to predict BVOC emissions in response to genotype by environmental interactions and contributes to a deeper understanding of vegetation responses to environmental changes.

Biogenic volatile organic compounds↗

Modeling and Characterization of Surface Discharges in Insulating Material for Spacers: Electrode Shape, Discharge Mode, and Revision of the Creepage Concept

In the design of MV AC and DC spacers, the predominant factors are surface and interface conditions. Design is generally carried out on specifications and standards which are based on long-term experience and lab testing. However, the diffusion of power electronics with a trend to increase electric field, switching frequency, and rise time to achieve higher power density calls for an innovative, global approach to optimized insulation system design. A new methodology, based on field simulation, discharge modeling, and partial discharge inception measurements, called the three-leg approach, can form the basis to optimize insulation design for any type of supply voltage waveform. This paper focuses on the influence of the type of electrode on the inception and phenomenology of surface discharges and, as a consequence, on the interpretation of the results used for application of the three-leg approach. It is demonstrated that a typical electrode system used for insulating material testing can generate both gas and surface discharges at the triple point, when the electrodes have a smooth profile that is used to avoid corona or flashover. Hence, testing partial discharge may not provide a straightforward indication of the surface discharge inception and, thus, be partially misleading for insulation design. Another takeover is that such analysis must benefit from PD testing tools endowed with analytics able to provide automatic identification of the type of defect generating PD, i.e., internal, surface, and corona, since design and remedy actions can be taken, and adequate insulating materials developed, only knowing the type of source generating PD. Hence, testing partial discharge may not provide a straightforward indication of surface discharge inception and, thus, be partially misleading for insulation design. In addition to the importance of the three-leg approach to favor reliable and optimized design of insulation systems, there is a clear need to have a PD testing tool endowed with analytics. It should preferably be able to provide automatic identification of the type of defect generating PD, i.e., internal, surface, and corona.

36 MATERIALS SCIENCE↗

Grid-responsive hydrogen production: Capital utilization and current density vs. efficiency in variable electricity markets

To achieve low-cost hydrogen production from water electrolyzers, grid tied electrolysis may need to operate dynamically to minimize the cost of supplying energy to the electrolyzer stack and produce hydrogen during low-cost hours and turn off/down during high-cost hours. Operating systems in this way can decrease capital utilization (capacity factor) and electricity costs. This strategy would shift the dominant cost drivers away from electricity (and thus efficiency) to the capital costs of the system, due to the underutilized capital when operating at low-capacity factors. Increasing the operational current density of the system could, in effect, reduce the capital cost of the system while producing hydrogen at a lower efficiency on a per unit energy basis. In the variable electricity cost profiles analyzed in this paper, increasing the current density for liquid alkaline from 0.5 A/cm2 to 1.5 Ac/m2 and proton exchange membrane electrolyzers from 2 A/cm2 to 4 A/cm2 resulted in substantial reductions in the levelized cost of hydrogen. Additionally, as capacity factors and electricity costs decrease, the optimal operating current density of the electrolyzer systems analyzed increases. These findings suggest R&D efforts should focus on increasing the operational current densities, reducing the turn down ratios, and understanding the durability implications of those strategies on low-temperature liquid alkaline and proton exchange membrane electrolyzers.

08 HYDROGEN↗

A holistic approach to the optimization of neutron beam transport at the LANSCE facility

An advanced neutron beam collimation system has been developed as part of an effort to optimize neutron beam transport at the Weapons Neutron Research (WNR) Facility, located within the Los Alamos Neutron Science Center (LANSCE). The goal of this work was to develop and demonstrate techniques to tailor neutron delivery in order to provide maximum available flux on sample with a specific beam profile, while simultaneously reducing unwanted background. A holistic approach was taken, upgrading the facility spallation target, facility metrology infrastructure, and flight path shutter insert to support the implementation of this advanced collimation system. Here, modern instruments and software were employed to conduct facility surveys, characterization of as-built geometry of critical components, 3D ray tracing and neutron transport calculations. Beam images and flux measurements were acquired after installation to evaluate the performance of the collimation system and to demonstrate consistent agreement with MCNP simulations which showed an 87% increase of flux on sample while providing suppression of background neutron impingement on the sample frame by 10 3 .

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DIII-D High Field Side Lower Hybrid Current Drive Experiment Overview

In preparation for high field side lower hybrid current drive (HFS LHCD) experiments in DIII-D, the HFS LHCD was to be commissioned and physics experiments commence once the system operated up to 300 kW for 0.5 s. The initial physics experiments sought to characterize coupling, wave propagation, and driven current measurements. In HFS LHCD first campaign, the maximum power was limited to <200 kW due to waveguide pressure leaks limiting the number of available modules and power per module. Here we summarize commissioning progress and initial physics observations. The HFS LHCD coupler was optimized for high qmin, DIII-D discharges where efficient off-axis current at r/a~0.6-0.8 is desired. The coupler n|| spectrum is peaked at 2.7 and is predicted to generate ~0.14 MA/MW coupled for 1.6 MW injected. In preparation, the HFS scrape-off layer density profile was characterized and found to have steeper profiles and lower fluctuation levels than the low field side. Furthermore, the HFS SOL density profile can be accurately predicted using global plasma quantities using machine learning. Thus far, one module has injected ~100 kW for 0.5 s with <5% reflected power. Nonthermal electrons have been observed on lower frequency channels of the electron cyclotron emission radiometer correlated with the LH power indicating core wave absorption. To avoid 30R neutral beam heat flux, a split launcher is proposed to avoid the high heat flux region while maintaining power spectrum and directivity.

Wukitch, Stephen J. [Massachusetts Inst. of Techno↗

Effective work function engineering for a TiN/XO(X = La, Zr, Al)/SiO{sub 2} stack structures

In this study, we demonstrated that work function engineering is possible over a wide range (+200 mV to −430 mV) in a TiN/XO (X = La, Zr, or Al)/SiO{sub 2} stack structures. From ab initio simulations, we selected the optimal material for the work function engineering. The work function engineering mechanism was described by metal diffusion into the TiN film and silicate formation in the TiN/SiO{sub 2} interface. The metal doping and the silicate formation were confirmed by transmission electron microscopy and energy dispersive spectroscopy line profiling, respectively. In addition, the amount of doped metal in the TiN film depended on the thickness of the insertion layer XO. From the work function engineering technique, which can control a variety of threshold voltages (Vth), an improvement in transistors with different V{sub th} values in the TiN/XO/SiO{sub 2} stack structures is expected.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

SU-F-P-34: Commission of Enhanced Dynamic Wedge of Varian Truebeam Linac System with Feature Study

Purpose: To evaluate an Enhanced Dynamic Wedge (EDW) as part of machine commission process with feature study. Methods: The EDW system in this study was from a Truebeam, which is the Linear accelerator manufactured by Varian Medical Systems. The EDW feature vectors includes selected elements. These elements were dosimetric output spots check, field size, wedge angles, dose rate, collimator orientation, and different energy settings. Point dose measurement was done by a PTW farmer chamber, and profiles were measured by Gafchromic EBT2 films positing at different depths of the Solidwater based on the study elements. The output spot measurements were done with PTW farmer chamber with Solidwater setting for all orientation and wedge angles in the EDW system. The profiles comparisons were done by IMRT measurement function in RIT software at version 6.3. And the films were scanned by Vidar scanner. Dosimetry calculation were done by using the same Solidwater scanned by GE LightSpeed CT in Eclipse Treatment Planning System (TPS). Then measurements were compared to simulation results in TPS. Results: The energy average percentage difference between chamber measurement and TPS was 0.16% with standard deviation (SD) at 0.93%. For selected features, the average percentage difference between film measurement and computation was 0.93% with SD at 1.55% in horizontal profiles, and 1.18% with SD at 0.98% at vertical profiles. The average gamma difference for film measurement and TPS computing results was at 0.924 with SD at 0.314. Conclusion: A feature vector was developed to describe the commission of EDW, and developing a complete set of features for sufficiency of commission of a LINAC function could provide optimal commission instance with acceptable confident level of clinical application of the machine. Given the institution specific vector pattern and big data process, it could provide wide range clinical outcome comparison information in application of EDW.

60 APPLIED LIFE SCIENCES↗

Planarization of Isolated Defects on ICF Target Capsule Surfaces by Pulsed Laser Ablation

Demanding surface quality requirements for inertial confinement fusion (ICF) capsules motivated the development of a pulsed laser ablation method to reduce or eliminate undesirable surface defects. The pulsed laser ablation technique takes advantage of a full surface (4π) capsule manipulation system working in combination with an optical profiling (confocal) microscope. Based on the defect topography, the material removal rate, the laser pulse energy and its beam profile, a customized laser raster pattern is derived to remove the defect. The pattern is a table of coordinates and number of pulses that dictate how the defect will be vaporized until its height is level with the capsule surface. This paper explains how the raster patterns are optimized to minimize surface roughness and how surface roughness after laser ablation is simulated. The simulated surfaces are compared with actual ablated surfaces. Large defects are reduced to a size regime where a tumble finishing process produces very high quality surfaces devoid of high mode defects. The combined polishing processes of laser ablation and tumble finishing have become routine fabrication steps for National Ignition Facility capsule production.

36 MATERIALS SCIENCE↗

Sampling Size Optimization for Bioburden Density Estimation in Planetary Protection

Planetary protection (PP) is a discipline that focuses on minimizing the biological contamination of spacecraft to ensure compliance with international policy. Precise estimation of bioburden - the total number of microbes in or on spacecraft hardware – and the bioburden density are of utmost importance for PP. Such estimation is the way concordance with requirements is demonstrated, and it is critical for quantifying the potential risk of inadvertently contaminating other planetary bodies. Although a suite of molecular techniques have been used to thoroughly characterize and profile the microbiome of various cleanroom environments and spacecraft, the gold standard remains the physical enumeration of microbes via culturing of samples directly taken from spacecraft and associated surfaces. However, due to technical, budgetary, and programmatic constraints, only a manageable portion (around 10%) of the entire spacecraft surface is directly sampled with cotton swabs or wipes. To generate the bioburden current best estimate (CBE) for components not directly verifiable, the accepted approach is to apply a NASA-defined bioburden estimate based on the components’ manufacturing or assembly environment. This approach utilizes a prespecified bioburden density estimation that applies a maximum value across the total surface area of the specified component. For hardware components that underwent similar assembly processes, an implied bioburden is adopted for all components, based on a direct verification of a representative component within the same lot. Once all components have a CBE, the bioburden estimates are generated. In previous publication [ 1], we have shown that statistical risks quantifying the accuracy of the estimates for sampled, prespecified, and implied components can be derived and ranked. For mean squared error (MSE) function, the risks are available analytically and hence a cost function can be obtained to optimize the risks with respect to the sampling area and sampling cost. Since the sampling area and sampling cost are two complimentary variables, their sum will have a well-defined minimum. This paper presents the multivariate optimization of the integrated risk of an empirical Bayes estimator to determine the optimal sampling schedule for a given number of components. It is assumed that given a number of components, N, the bioburden density for each component can either be sampled, implied, or prespecified. The multivariate optimization searches through different options to sample, imply or prespecify the bioburden density for a component, and account for the component’s surface area and cost of sampling. The idea of the optimization is based on the observation that the statistical risk of using an estimator is a monotonically decreasing function of the sampled area. The larger the sampled area, the lower the risk of using the estimator as the estimator becomes more and more accurate as the sampling area increases. On the other hand, the cost of sampling is monotonically increasing as the sampled surface grows. This makes the risk and total cost of sampling complimentary variables which can be counterbalanced to achieve an optimal overall value with respect to the sampled surface. In this paper, the integrated risk has been used to quantify the accuracy of the estimator. This risk has been selected because it depends on neither the true value of the parameter nor on the collected data. The cost of each sample was also available to obtain the total cost of sampling of N components. The paper will present the results based on computer-simulated data as well as the data collected during the InSight mission. The computer-simulated data have N components with randomly generated total areas and each component assigned to one of the three categories according to the method of estimating of bioburden density: sampled, implied, or prespecified. The cost of sampling is also available. The cost of sampling is estimated based on a cost model provided by the planetary protection group at JPL. For this paper, the overall cost was assumed to be a linear function of exposure. The optimization process finds the allocation of the components to the three categories that minimizes the tradeoff between integrated risk and total cost. For the InSight data, a set of components is selected representing all three categories, and optimization is performed to determine if the performed allocation was optimal or if a better allocation could have been obtained. To the best of our knowledge, this work is the first attempt not only perform an accurate estimation of bioburden density but also do it in an optimal way.

97 - MATHEMATICS AND COMPUTING↗

Enzymatic and thermodynamic profiles of a heterotetramer lactate dehydrogenase isozyme in swine

Lactate dehydrogenase (LDH) is a glycolytic enzyme that catalyzes the final step of glycolysis and produces NAD{sup +}. In somatic cells, LDH forms homotetramers and heterotetramers that are encoded by two different genes: LDHA (skeletal muscle type, M) and LDHB (heart type, H). Analysis of LDH isozymes is important for understanding the physiological role of homotetramers and heterotetramers and for optimizing inhibition of their enzymatic activity as it may result in distinct effects. Previously, we reported that hydroxychloroquine (HCQ) inhibited LDH activity, but we did not examine isozyme specificity. In the present study, we isolated heterotetrameric LDH (H{sub 2}M{sub 2}) from swine brain, determined its kinetic and thermodynamic properties, and examined the effect of HCQ on its activity compared to homotetrameric LDH isozymes. We show that: (1) the K{sub m} values for H{sub 2}M{sub 2}–mediated catalysis of pyruvate or lactate were intermediate compared to those for the homotetrameric isozymes, M{sub 4} and H{sub 4} whereas the V{sub max} values were similar; (2) the K{sub m} and V{sub max} values for H{sub 2}M{sub 2}–mediated catalysis of NADH were not significantly different among LDH isozymes; (3) the values for activation energy and van't Hoff enthalpy changes for pyruvate reduction of H{sub 2}M{sub 2} were intermediate compared to those for the homotetrameric isozymes; (4) the temperature for half residual activity of H{sub 2}M{sub 2} was closer to that for M{sub 4} than for H{sub 4}. We also show that HCQ had different affinities for various LDH isozymes. - Highlights: • Heterotetrameric (H{sub 2}M{sub 2}) LDH isozyme was isolated from swine brain. • Kinetics of H{sub 2}M{sub 2} were intermediate between the two homotetramers. • Thermodynamics of H{sub 2}M{sub 2} were also intermediate between the two homotetramers. • Hydroxychloroquine inhibited more strongly H{sub 2}M{sub 2} than homotetramers.

60 APPLIED LIFE SCIENCES↗

Understanding GPU Power. A Survey of Profiling, Modeling, and Simulation Methods

Modern graphics processing units (GPUs) have complex architectures that admit exceptional performance and energy efficiency for high throughput applications.Though GPUs consume large amounts of power, their use for high throughput applications facilitate state-of-the-art energy efficiency and performance. Consequently, continued development relies on understanding their power consumption. Our work is a survey of GPU power modeling and profiling methods with increased detail on noteworthy efforts. Moreover, as direct measurement of GPU power is necessary for model evaluation and parameter initiation, internal and external power sensors are discussed. Hardware counters, which are low-level tallies of hardware events, share strong correlation to power use and performance. Statistical correlation between power and performance counters has yielded worthwhile GPU power models, yet the complexity inherent to GPU architectures presents new hurdles for power modeling. Developments and challenges of counter-based GPU power modeling is discussed. Often building on the counter-based models, research efforts for GPU power simulation, which make power predictions from input code and hardware knowledge, provide opportunities for optimization in programming or architectural design. Noteworthy strides in power simulations for GPUs are included along with their performance or functional simulator counterparts when appropriate. Lastly, possible directions for future research are discussed.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

pH-dependent electron transfer reaction and direct bioelectrocatalysis of the quinohemoprotein pyranose dehydrogenase

A pyranose dehydrogenase from Coprinopsis cinerea (CcPDH) is an extracellular quinohemoeprotein, which consists a b-type cytochrome domain, a pyrroloquinoline-quinone (PQQ) domain, and a family 1-type carbohydrate-binding module. The electron transfer reaction of CcPDH was studied using some electron acceptors and a carbon electrode at various pH levels. Phenazine methosulfate (PMS) reacted directly at the PQQ domain, whereas cytochrome c (cyt c) reacted via the cytochrome domain of intact CcPDH. Thus, electrons are transferred from reduced PQQ in the catalytic domain of CcPDH to heme b in the N-terminal cytochrome domain, which acts as a built-in mediator and transfers electron to a heterogenous electron transfer protein. The optimal pH values of the PMS reduction (pH 6.5) and the cyt c reduction (pH 8.5) differ. The catalytic currents for the oxidation of L-fucose were observed within a range of pH 4.5 to 11. Bioelectrocatalysis of CcPDH based on direct electron transfer demonstrated that the pH profile of the biocatalytic current was similar to the reduction activity of cyt c characters. - Highlights: • pH dependencies of activity were different for the reduction of cyt c and DCPIP. • DET-based bioelectrocatalysis of CcPDH was observed. • The similar pH-dependent profile was found with cyt c and electrode. • The present results suggested that IET reaction of CcPDH shows pH dependence.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Multiplexed characterization of rationally designed promoter architectures deconstructs combinatorial logic for IPTG-inducible systems

Abstract A crucial step towards engineering biological systems is the ability to precisely tune the genetic response to environmental stimuli. In the case of Escherichia coli inducible promoters, our incomplete understanding of the relationship between sequence composition and gene expression hinders our ability to predictably control transcriptional responses. Here, we profile the expression dynamics of 8269 rationally designed, IPTG-inducible promoters that collectively explore the individual and combinatorial effects of RNA polymerase and LacI repressor binding site strengths. We then fit a statistical mechanics model to measured expression that accurately models gene expression and reveals properties of theoretically optimal inducible promoters. Furthermore, we characterize three alternative promoter architectures and show that repositioning binding sites within promoters influences the types of combinatorial effects observed between promoter elements. In total, this approach enables us to deconstruct relationships between inducible promoter elements and discover practical insights for engineering inducible promoters with desirable characteristics.

59 BASIC BIOLOGICAL SCIENCES↗