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We use small angle X-ray scattering (SAXS) to characterise a class of star diblock polymers with a nanogel core on which the outer block arms are comprised of random copolymers of temperature sensitive PEGMA with pH sensitive basic (PDMAEMA) and acidic (PMAA) monomers. The acquired SAXS data show that many of the nanogel star polymers undergo a sharp structural transition over a narrow range of pH, but with unexpectedly large shifts in the apparent pKa with respect to that of the acidic or basic monomer unit, the linear polymer form or even an alternate star polymer with a tightly cross-linked core chemistry. We have demonstrated a distinct and quantifiable structural response for the nanogel star copolymers by altering the core or by pairing the monomers PDMAEMA–PEGMA and PMAA–PEGMA to achieve structural transitions that have typically been observed in stars through changes in arm length and number.

Changes in rotation have been observed in LHCD experiments. From these observations, reversals in intrinsic torque have been inferred. This paper identifies the mechanism for intrinsic torque reversal linked to magnetic shear (͉). Gyrokinetic simulations demonstrate that as compared to the normal ͉ case, the intrinsic torque reverses, for ͉ < ͉crit. Analysis shows that the reversal occurs due to the dominance of the symmetry breaking mechanism in residual stress due to the synergy of toroidal coupling and the intensity gradient. This mechanism is a consequence of ballooning structure at weak ͉. Gyrokinetic simulation gives ͉crit ≈ 0.3 for trapped electron modes (TEM) and ͉crit ≈ 1.1 for ion temperature gradient (ITG) modes. The value of ͉crit is consistent with results from the Alcator C-Mod LHCD experiments, for which ͉ > 0 in the whole plasma column and ͉crit ≈ 0.2 ∼ 0.3 exp (Rice et al Phys. Rev. Lett. 111 125003).

The links between the microscopic dynamics and macroscopic threshold physics of the L → H transition are elucidated. Emphasis is placed on understanding the physics of power threshold scalings, and especially on understanding the minimum in the power threshold as a function of density Pthr (n). By extending a numerical 1D model to evolve both electron and ion temperatures, including collisional coupling, we find that the decrease in Pthr (n) along the low-density branch is due to the combination of an increase in collisional electron-to-ion energy transfer and an increase in the heating fraction coupled to the ions. Both processes strengthen the edge diamagnetic electric field needed to lock in the mean electric field shear for the L → H transition. The increase in Pthr (n) along the high-density branch is due to the increase with ion collisionality of damping of turbulence-driven shear flows. Turbulence driven shear flows are needed to trigger the transition by extracting energy from the turbulence. Thus, we identify the critical transition physics components of the separatrix ion heat flux and the zonal flow excitation. The model reveals a power threshold minimum in density scans as a crossover between the threshold decrease supported by an increase in heat fraction received by ions (directly or indirectly, from electrons) and a threshold increase, supported by the rise in shear flow damping. The electron/ion heating mix emerges as important to the transition, in that it, together with electron-ion coupling, regulates the edge diamagnetic electric field shear. The importance of possible collisionless electron-ion heat transfer processes is explained.

An overview of the physics of intrinsic torque is presented, with special emphasis on the phenomenology of intrinsic toroidal rotation in tokamaks, its theoretical understanding, and the variety of momentum transport bifurcation dynamics. Ohmic reversals and electron cyclotron heating-driven counter torque are discussed in some detail. Symmetry breaking by lower single null versus upper single null asymmetry is related to the origin of intrinsic torque at the separatrix. © 2013 IAEA, Vienna.

Application of lower hybrid (LH) current drive in tokamak plasmas can induce both co- and countercurrent directed changes in toroidal rotation, depending on the core q profile. For discharges with q(0)

Several seemingly unrelated effects in Alcator C-Mod ohmic L-mode plasmas are shown to be closely connected: non-local heat transport, core toroidal rotation reversals, energy confinement saturation and up/down impurity density asymmetries. These phenomena all abruptly transform at a critical value of the collisionality. At low densities in the linear ohmic confinement regime, with collisionality ν* 0.35 (evaluated inside of the q = 3/2 surface), heat transport exhibits non-local behaviour, core toroidal rotation is directed co-current, edge impurity density profiles are up/down symmetric and a turbulent feature in core density fluctuations with kθ up to 15 cm-1 (kθρs ∼ 1) is present. At high density/collisionality with saturated ohmic confinement, electron thermal transport is diffusive, core rotation is in the counter-current direction, edge impurity density profiles are up/down asymmetric and the high k θ turbulent feature is absent. The rotation reversal stagnation point (just inside of the q = 3/2 surface) coincides with the non-local electron temperature profile inversion radius. All of these observations suggest a possible unification in a model with trapped electron mode prevalence at low collisionality and ion temperature gradient mode domination at high collisionality. © 2013 IAEA, Vienna.

Ohmic energy confinement saturation is found to be closely related to core toroidal rotation reversals in Alcator C-Mod tokamak plasmas. Rotation reversals occur at a critical density, depending on the plasma current and toroidal magnetic field, which coincides with the density separating the linear Ohmic confinement regime from the saturated Ohmic confinement regime. The rotation is directed co-current at low density and abruptly changes direction to counter-current when the energy confinement saturates as the density is increased. Since there is a bifurcation in the direction of the rotation at this critical density, toroidal rotation reversal is a very sensitive indicator in the determination of the regime change. The reversal and confinement saturation results can be unified, since these processes occur in a particular range of the collisionality.

Direction reversals of intrinsic toroidal rotation have been observed in diverted Alcator C-Mod Ohmic L-mode plasmas following electron density ramps. For low density discharges, the core rotation is directed cocurrent, and reverses to countercurrent following an increase in the density above a certain threshold. Such reversals occur together with a decrease in density fluctuations with 2 cm(-1)≤k(θ)≤11 cm(-1) and frequencies above 70 kHz. There is a strong correlation between the reversal density and the density at which the Ohmic L-mode energy confinement changes from the linear to the saturated regime.

Abstract Background Based on positive findings from a randomized controlled trial, Kaiser Permanente's national executive leadership group set an expectation that all Kaiser Permanente and partner hospitals would implement a consultative model of interdisciplinary, inpatient-based palliative care (IPC). Within one year, the number of IPC consultations program-wide increased almost tenfold from baseline, and the number of teams nearly doubled. We report here results from a qualitative evaluation of the IPC initiative after a year of implementation; our purpose was to understand factors supporting or impeding the rapid and consistent spread of a complex program. Methods Quality improvement study using a case study design and qualitative analysis of in-depth semi-structured interviews with 36 national, regional, and local leaders. Results Compelling evidence of impacts on patient satisfaction and quality of care generated 'pull' among adopters, expressed as a remarkably high degree of conviction about the value of the model. Broad leadership agreement gave rise to sponsorship and support that permeated the organization. A robust social network promoted knowledge exchange and built on an existing network with a strong interest in palliative care. Resource constraints, pre-existing programs of a different model, and ambiguous accountability for implementation impeded spread. Conclusions A complex, hospital-based, interdisciplinary intervention in a large health care organization spread rapidly due to a synergy between organizational 'push' strategies and grassroots-level pull. The combination of push and pull may be especially important when the organizational context or the practice to be spread is complex.

The simulation of chemical reactions is an anticipated application of quantum computers. Using a Diels-Alder reaction as a test case, in this study we explore the potential applications of quantum algorithms and hardware in investigating chemical reactions. Our specific goal is to calculate the activation barrier of a reaction between ethylene and cyclopentadiene forming a transition state. To achieve this goal, we use quantum algorithms for near-term quantum hardware (entanglement forging and quantum subspace expansion) and classical post-processing (many-body perturbation theory) in concert. We conduct simulations on IBM quantum hardware using up to 8 qubits, and compute accurate activation barrier in the reaction between cyclopentadiene and ethylene by accounting for both static and dynamic electronic correlation. This work illustrates a hybrid quantum-classical computational workflow to study chemical reactions on near-term quantum devices, showcasing the potential for performing quantum chemistry simulations on quantum hardware to predict activation barriers in agreement with those predicted by CASCI.

The SPARC tokamak is a high-field, Bt0 ∼12 T, medium-sized, R0 = 1.85 m, tokamak that is presently under construction in Devens, MA, led by Commonwealth Fusion Systems. It will be used to de-risk the high-field tokamak path to a fusion power plant and demonstrate the commercial viability of fusion energy. SPARC's first campaign plan is to achieve Qfus > 1 using an ICRF-heated, <10 MW, high current, Ip ∼ 8.5 MA, L-mode fueled by D-T gas injection, and its second campaign will investigate H-mode operations in D-D. To facilitate plasma control and scientific learning, a targeted set of ∼50 plasma diagnostics are being designed and built for operation during these campaigns. While nearly all diagnostics are based on established techniques, the pace of deployment, relative to the first plasma, and the harshness of the thermal, electromagnetic, and radiation environment are unprecedented for medium-sized tokamaks. An overview of the SPARC diagnostic set is given, providing context to further details communicated by the SPARC team in companion publications that are system-specific. The system engineering philosophy for SPARC diagnostics is outlined, and the design and engineering verification process for components inside and outside the primary vacuum boundary are described. Diagnostics are mounted directly to the vacuum vessel as well as housed within a series of eight midplane and 24 off-midplane replaceable port plugs. With limited exceptions, signal conditioning, digitization electronics and cameras as well as lasers and microwave sources are localized to a series of five Diagnostic Lab spaces, totaling ∼350 m2, located >15 m from the center of the tokamak, on the other side of a 2.4 m concrete shielding wall. A series of 31 large-scale penetrations have been included in the SPARC Tokamak Hall to facilitate integration of early campaign diagnostics and to provide upgradability., (© 2024 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC) license (https://creativecommons.org/licenses/by-nc/4.0/).)

The in-vessel silicon diode arrays that are used for soft x-ray detection in many tokamaks are sensitive to neutron damage, making them unsuitable for burning plasma devices such as SPARC. In such a device, the silicon diodes would need to be placed far from the plasma-limiting their field of view-or an alternative detector could be used. Here, we present the design of a camera containing an array of chemical vapor deposition single-crystal diamonds, which will be placed in the upper and lower port plugs of the SPARC tokamak with a large enough view of the poloidal cross section to enable tomographic inversion. The camera design presented here is optimized to provide a wide field of view of the poloidal cross section. Simulated plasma conditions are used to estimate the x-ray signal that this detector array will receive and to fine-tune the camera placement within the tokamak., (© 2024 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC) license (https://creativecommons.org/licenses/by-nc/4.0/).)

SPARC will be outfitted with three systems of x-ray crystal spectrometer arrays. Two of these are designed using cylindrically bent crystals to achieve high spectral-resolution for ion temperature and toroidal velocity measurements via imaging He-like Kr and Ne-like Xe. The last acts as a spectral survey system to monitor Ne-like W and nearby H- and He-like emission from Cr, Fe, Co, Ni, and Cu. Line radiation intensities are calculated using the Flexible Atomic Code for atomic data and ColRadPy for collisional-radiative modeling, then convoluted with a Voigt line shape. Free-free, free-bound, and two-photon continuum radiation is also included. The ToFu code is used to perform volume-of-sight integration to produce synthetic detector images. In addition, presented is cross-validation performed using the XICSRT Monte Carlo ray-tracing code. Ion temperature and toroidal velocity profiles are reconstructed using ToFu via tomographic inversion., (© 2024 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).)

Modeling chemical reactions with quantum chemical methods is challenging when the electronic structure varies significantly throughout the reaction and when electronic excited states are involved. Multireference methods, such as complete active space self-consistent field (CASSCF), can handle these multiconfigurational situations. However, even if the size of the needed active space is affordable, in many cases, the active space does not change consistently from reactant to product, causing discontinuities in the potential energy surface. The localized active space SCF (LASSCF) is a cheaper alternative to CASSCF for strongly correlated systems with weakly correlated fragments. The method is used for the first time to study a chemical reaction, namely the bond dissociation of a mono-, di-, and triphenylsulfonium cation. LASSCF calculations generate smooth potential energy scans more easily than the corresponding, more computationally expensive CASSCF calculations while predicting similar bond dissociation energies. Our calculations suggest a homolytic bond cleavage for di- and triphenylsulfonium and a heterolytic pathway for monophenylsulfonium., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

FastFish-ID via Closed-Tube barcoding is a portable platform for rapid and accurate identification of fish species that was conceived at Brandeis University, commercialized at Thermagenix, Inc., and further improved at Ecologenix, LLC (see Chap. 17 in this volume). This chapter focuses on the use of FastFish-ID for (1) identification of intraspecies variants, (2) quantitative use of FastFish-ID to measure the decay of fresh fish, and (3) use of FastFish-ID for the identification of dried and processed shark fins., (© 2024. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

FastFish-ID for rapid and accurate identification of fish species was conceived at Brandeis University based on pioneering work on Closed-Tube Barcoding (Rice et al., Mitochondrial DNA Part A 27(2):1358-1363, 2016; Sirianni et al., Genome 59:1049-1061, 2016). FastFish-ID was subsequently validated and commercialized at Thermagenix, Inc. using a portable device and high-precision PCR (Naaum et al., Food Res Int 141:110035, 2021). The motivation for these efforts was the pressing need for a technology that could be widely used throughout the seafood supply chain to combat IUU Fishing (Helyar et al., PLOS ONE 9, 2014) and overfishing (FAO, State of the World Fisheries and Aquaculture 2018. http://www.fao.org/documents/card/en/c/I9540EN/ , 2018), along with seafood fraud and mislabeling (Watson et al., Fish Fish 17:585-595, 2015). These destructive practices are wasting fish stocks, frustrating attempts to achieve seafood sustainability, endangering oceanic ecosystems, and causing consumers billions of dollars each year (Porterfield et al., Oceana: February, 2022). During the past three Covid19 pandemic years, EcologeniX, LLC has taken over further development and optimization of FastFish-ID. The present chapter provides an overview of the improvements introduced throughout the FastFish-ID process., (© 2024. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

Advances in quantum computation for electronic structure, and particularly heuristic quantum algorithms, create an ongoing need to characterize the performance and limitations of these methods. Here we discuss some potential pitfalls connected with the use of hardware-efficient Ansätze in variational quantum simulations of electronic structure. We illustrate that hardware-efficient Ansätze may break Hamiltonian symmetries and yield nondifferentiable potential energy curves, in addition to the well-known difficulty of optimizing variational parameters. We discuss the interplay between these limitations by carrying out a comparative analysis of hardware-efficient Ansätze versus unitary coupled cluster and full configuration interaction, and of second- and first-quantization strategies to encode Fermionic degrees of freedom to qubits. Our analysis should be useful in understanding potential limitations and in identifying possible areas of improvement in hardware-efficient Ansätze.

The computational description of correlated electronic structure, and particularly of excited states of many-electron systems, is an anticipated application for quantum devices. An important ramification is to determine the dominant molecular fragmentation pathways in photo-dissociation experiments of light-sensitive compounds, like sulfonium-based photo-acid generators used in photolithography. Here we simulate the static and dynamical electronic structure of the H 3 S + molecule, taken as a minimal model of a triply-bonded sulfur cation, on a superconducting quantum processor of the IBM Falcon architecture. To this end, we generalize a qubit reduction technique termed entanglement forging or EF [A. Eddins et al. , Phys. Rev. X Quantum , 2022, 3 , 010309], currently restricted to the evaluation of ground-state energies, to the treatment of molecular properties. While in a conventional quantum simulation a qubit represents a spin-orbital, within EF a qubit represents a spatial orbital, reducing the number of required qubits by half. We combine the generalized EF with quantum subspace expansion [W. Colless et al. , Phys. Rev. X , 2018, 8 , 011021], a technique used to project the time-independent Schrodinger equation for ground- and excited-states in a subspace. To enable experimental demonstration of this algorithmic workflow, we deploy a sequence of error-mitigation techniques. We compute dipole structure factors and partial atomic charges along ground- and excited-state potential energy curves, revealing the occurrence of homo- and heterolytic fragmentation. This study is an important step towards the computational description of photo-dissociation on near-term quantum devices, as it can be generalized to other photodissociation processes and naturally extended in different ways to achieve more realistic simulations., Competing Interests: There are no conflicts to declare., (This journal is © The Royal Society of Chemistry.)

Quantum simulations of the hydroxide anion and hydroxyl radical are reported, employing variational quantum algorithms for near-term quantum devices. The energy of each species is calculated along the dissociation curve, to obtain information about the stability of the molecular species being investigated. It is shown that simulations restricted to valence spaces incorrectly predict the hydroxyl radical to be more stable than the hydroxide anion. Inclusion of dynamical electron correlation from nonvalence orbitals is demonstrated, through the integration of the variational quantum eigensolver and quantum subspace expansion methods in the workflow of N -electron valence perturbation theory, and shown to correctly predict the hydroxide anion to be more stable than the hydroxyl radical, provided that basis sets with diffuse orbitals are also employed. Finally, we calculate the electron affinity of the hydroxyl radical using an aug-cc-pVQZ basis on IBM's quantum devices.

Optimized operation of fusion devices demands detailed understanding of plasma transport, a problem that must be addressed with advances in both measurement and data analysis techniques. In this work, we adopt Bayesian inference methods to determine experimental particle transport, leveraging opportunities from high-resolution He-like ion spectra in a tokamak plasma. The Bayesian spectral fitting code is used to analyze resonance (w), forbidden (z), intercombination (x, y), and satellite (k, j) lines of He-like Ca following laser blow-off injections on Alcator C-Mod. This offers powerful transport constraints since these lines depend differently on electron temperature and density, but also differ in their relation to Li-like, He-like, and H-like ion densities, often the dominant Ca charge states over most of the C-Mod plasma radius. Using synthetic diagnostics based on the AURORA package, we demonstrate improved effectiveness of impurity transport inferences when spectroscopic data from a progressively larger number of lines are included.

Quantum chemistry simulations of some industrially relevant molecules are reported, employing variational quantum algorithms for near-term quantum devices. The energies and dipole moments are calculated along the dissociation curves for lithium hydride (LiH), hydrogen sulfide, lithium hydrogen sulfide, and lithium sulfide. In all cases, we focus on the breaking of a single bond to obtain information about the stability of the molecular species being investigated. We calculate energies and a variety of electrostatic properties of these molecules using classical simulators of quantum devices, with up to 21 qubits for lithium sulfide. Moreover, we calculate the ground-state energy and dipole moment along the dissociation pathway of LiH using IBM quantum devices. This is the first example, to the best of our knowledge, of dipole moment calculations being performed on quantum hardware.

Quantum chemistry studies of biradical systems are challenging due to the required multiconfigurational nature of the wavefunction. In this work, Variational Quantum Eigensolver (VQE) is used to compute the energy profile for the lithium superoxide dimer rearrangement, involving biradical species, on quantum simulators and devices. Considering that current quantum devices can only handle limited number of qubits, we present guidelines for selecting an appropriate active space to perform computations on chemical systems that require many qubits. We show that with VQE performed with a quantum simulator reproduces results obtained with full-configuration interaction (Full CI) for the chosen active space. However, results deviate from exact values by about 39 mHa for calculations on a quantum device. This deviation can be improved to about 4 mHa using the readout mitigation approach and can be further improved to 2 mHa, approaching chemical accuracy, using the state tomography technique to purify the calculated quantum state.

Seafood represents up to 20% of animal protein consumption in global food consumption and is a critical dietary and income resource for the world's population. Currently, over 30% of marine fish stocks are harvested at unsustainable levels, and the industry faces challenges related to Illegal, Unregulated and Unreported (IUU) fishing. Accurate species identification is one critical component of successful stock management and helps combat fraud. Existing DNA-based technologies permit identification of seafood even when morphological features are removed, but are either too time-consuming, too expensive, or too specific for widespread use throughout the seafood supply chain. FASTFISH-ID is an innovative commercial platform for fish species authentication, employing closed-tube barcoding in a portable device. This method begins with asymmetric PCR amplification of the full length DNA barcode sequence and subsequently interrogates the resulting single-stranded DNA with a universal set of Positive/Negative probes labeled in two fluorescent colors. Each closed-tube reaction generates two species-specific fluorescent signatures that are then compared to a cloud-based library of previously validated fluorescent signatures. This novel approach results in rapid, automated species authentication without the need for complex, time consuming, identification by DNA sequencing, or repeated analysis with a panel of species-specific tests. Performance of the FASTFISH-ID platform was assessed in a blinded study carried out in three laboratories located in the UK and North America. The method exhibited a 98% success rate among the participating laboratories when compared to species identification via conventional DNA barcoding by sequencing. Thus, FASTFISH-ID is a promising new platform for combating seafood fraud across the global seafood supply chain., (Copyright © 2021 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Quantum simulations of electronic structure with a transformed Hamiltonian that includes some electron correlation effects are demonstrated. The transcorrelated Hamiltonian used in this work is efficiently constructed classically, at polynomial cost, by an approximate similarity transformation with an explicitly correlated two-body unitary operator. This Hamiltonian is Hermitian, includes no more than two-particle interactions, and is free of electron-electron singularities. We investigate the effect of such a transformed Hamiltonian on the accuracy and computational cost of quantum simulations by focusing on a widely used solver for the Schrödinger equation, namely the variational quantum eigensolver method, based on the unitary coupled cluster with singles and doubles (q-UCCSD) Ansatz. Nevertheless, the formalism presented here translates straightforwardly to other quantum algorithms for chemistry. Our results demonstrate that a transcorrelated Hamiltonian, paired with extremely compact bases, produces explicitly correlated energies comparable to those from much larger bases. For the chemical species studied here, explicitly correlated energies based on an underlying 6-31G basis had cc-pVTZ quality. The use of the very compact transcorrelated Hamiltonian reduces the number of CNOT gates required to achieve cc-pVTZ quality by up to two orders of magnitude, and the number of qubits by a factor of three.

Simulating molecules is believed to be one of the early stage applications for quantum computers. Current state-of-the-art quantum computers are limited in size and coherence; therefore, optimizing resources to execute quantum algorithms is crucial. In this work, we develop the second quantization representation of spatial symmetries, which are then transformed to their qubit operator representation. These qubit operator representations are used to reduce the number of qubits required for simulating molecules. We present our results for various molecules and elucidate a formal connection of this work with a previous technique that analyzed generic Z 2 Pauli symmetries.

The most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) is an expanded G 4 C 2 repeat [(G 4 C 2 ) exp ] in C9ORF72. ALS/FTD-associated toxicity has been traced to the RNA transcribed from the repeat expansion [r(G 4 C 2 ) exp ], which sequesters RNA-binding proteins (RBPs) and undergoes repeat-associated non-ATG (RAN) translation to generate toxic dipeptide repeats. Using in vitro and cell-based assays, we identified a small molecule (4) that selectively bound r(G 4 C 2 ) exp , prevented sequestration of an RBP, and inhibited RAN translation. Indeed, biophysical characterization showed that 4 selectively bound the hairpin form of r(G 4 C 2 ) exp , and nuclear magnetic resonance spectroscopy studies and molecular dynamics simulations defined this molecular recognition event. Cellular imaging revealed that 4 localized to r(G 4 C 2 ) exp cytoplasmic foci, the putative sites of RAN translation. Collectively, these studies highlight that the hairpin structure of r(G 4 C 2 ) exp is a therapeutically relevant target and small molecules that bind it can ameliorate c9ALS/FTD-associated toxicity., (Copyright © 2018 Elsevier Ltd. All rights reserved.)

Determination of aromaticity in hydrocarbons may be as simple as determining the average bond length for the molecule of interest. This would greatly assist in classifying the nature of hydrocarbon chemistry, especially for large molecules such as polycyclic aromatic hydrocarbons (PAHs) where today's aromatic classification methods are prohibitively expensive. The average C-C bond lengths for a test set of known aromatic, antiaromatic, and aliphatic cyclic hydrocarbons are computed here, and they show strong delineating patterns for the structural discernment of these aromaticity classifications. Aromatic molecules have average C-C bond lengths of 1.41 Å or less with the largest molecules, PAHs, having the longest average C-C bond lengths; aliphatic species have such lengths of 1.50 Å or more; and antiaromatic species fall between the two. Consequently, a first-order guess as to the aromaticity of a system may simply arise from its geometry. Although this prediction will likely have exceptions, such simple screening can easily classify most cases, and more advanced techniques can be brought to bear on the cases that lie in the boundaries. Benchmarks for hydrocarbons are provided here, but other classes of molecular structural aromaticity likely will have to be defined on an ad hoc basis., Competing Interests: The authors declare no competing financial interest.

Most cases of multidrug-resistant (MDR) tuberculosis (TB) are never diagnosed (328,300 of the ∼490,000 cases in 2016 were missed). The Xpert MTB/RIF assay detects resistance only to rifampin, despite ∼20% of rifampin-resistant cases being susceptible to isoniazid (a critical first-line drug). Consequently, many countries require further testing with the GenoType MTBDR plus assay. However, MTBDR plus is not recommended for use on smear-negative specimens, and thus, many specimens require culture-based drug susceptibility testing. Furthermore, MTBDR plus requires specialized expertise, lengthy hands-on time, and significant laboratory infrastructure and interpretation is not automated. To address these gaps, we evaluated the accuracy of the FluoroType MTBDR (FluoroType) assay. Sputa from 244 smear-positive and 204 smear-negative patients with presumptive TB (Xpert MTB positive, n = 343) were tested. Culture and MTBDR plus on isolates served as reference standards (for active TB and MDR-TB, respectively). Sanger sequencing and MTBDR plus , both of which were performed on sputa, were used to resolve discrepancies. The sensitivity of FluoroType for the detection of M. tuberculosis complex was 98% (95% confidence interval [CI], 95 to 99%) and 92% (95% CI, 84 to 96%) for smear-positive and smear-negative specimens, respectively (232/237 versus 90/98 specimens; P < 0.009). The sensitivity and specificity for smear-negative specimens were 100% and 97%, respectively, for rifampin resistance; 100% and 98%, respectively, for isoniazid resistance; and 100% and 100%, respectively, for MDR-TB. FluoroType identified 98%, 97%, and 97% of the rpoB , katG , and inhA promoter mutations, respectively. FluoroType has excellent sensitivity with sputa equivalent to that of MTBDR plus with the isolates and can provide rapid drug susceptibility testing for rifampin and isoniazid. In addition, the capacity of FluoroType to simultaneously identify virtually all mutations in the rpoB , katG , and inhA promoter may be useful for individualized treatment regimens., (Copyright © 2018 American Society for Microbiology.)

We present an all-atom molecular dynamics study of the effect of a range of organic solvents (dichloromethane, diethyl ether, toluene, methanol, dimethyl sulfoxide, and tetrahydrofuran) on the conformations of a nanogel star polymeric nanoparticle with solvophobic and solvophilic structural elements. These nanoparticles are of particular interest for drug delivery applications. As drug loading generally takes place in an organic solvent, this work serves to provide insight into the factors controlling the early steps of that process. Our work suggests that nanoparticle conformational structure is highly sensitive to the choice of solvent, providing avenues for further study as well as predictions for both computational and experimental explorations of the drug-loading process. Our findings suggest that when used in the drug-loading process, dichloromethane, tetrahydrofuran, and toluene allow for a more extensive and increased drug-loading into the interior of nanogel star polymers of the composition studied here. In contrast, methanol is more likely to support shallow or surface loading and, consequently, faster drug release rates. Finally, diethyl ether should not work in a formulation process since none of the regions of the nanogel star polymer appear to be sufficiently solvated by it.

A long-standing enigma in plasma transport has been resolved by modeling of cold-pulse experiments conducted on the Alcator C-Mod tokamak. Controlled edge cooling of fusion plasmas triggers core electron heating on time scales faster than an energy confinement time, which has long been interpreted as strong evidence of nonlocal transport. This Letter shows that the steady-state profiles, the cold-pulse rise time, and disappearance at higher density as measured in these experiments are successfully captured by a recent local quasilinear turbulent transport model, demonstrating that the existence of nonlocal transport phenomena is not necessary for explaining the behavior and time scales of cold-pulse experiments in tokamak plasmas.

Recent attempts to measure impurity transport in Alcator C-Mod using an x-ray imaging crystal spectrometer and laser blow-off impurity injector have failed to yield unique reconstructions of the transport coefficient profiles. This paper presents a fast, linearized model which was constructed to estimate diagnostic requirements for impurity transport experiments. The analysis shows that the spectroscopic diagnostics on Alcator C-Mod should be capable of inferring simple profiles of impurity diffusion D Z and convection V Z accurate to better than ±10% uncertainty, suggesting that the failure to infer unique D Z and V Z from experimental data is attributable to an inadequate analysis procedure rather than the result of insufficient diagnostics. Furthermore, the analysis reveals that even a modest spatial resolution can overcome a low time resolution. This approach can be adapted to design and verify diagnostics for transport experiments on any magnetic confinement device.

The increasing availability of high-quality experimental data and first-principles calculations creates opportunities for developing more accurate empirical force fields for simulation of proteins. We developed the AMBER-FB15 protein force field by building a high-quality quantum chemical data set consisting of comprehensive potential energy scans and employing the ForceBalance software package for parameter optimization. The optimized potential surface allows for more significant thermodynamic fluctuations away from local minima. In validation studies where simulation results are compared to experimental measurements, AMBER-FB15 in combination with the updated TIP3P-FB water model predicts equilibrium properties with equivalent accuracy, and temperature dependent properties with significantly improved accuracy, in comparison with published models. We also discuss the effect of changing the protein force field and water model on the simulation results.

We present a molecular dynamics study of the effect of core chemistry on star polymer structural and kinetic properties. This work serves to validate the choice of a model adamantane core used in previous simulations to represent larger star polymeric systems in an aqueous environment, as well as to explore how the choice of size and core chemistry using a dendrimer or nanogel core may affect these polymeric nanoparticle systems, particularly with respect to thermosensitivity and solvation properties that are relevant for applications in drug loading and delivery.

A compact multi-energy soft x-ray camera has been developed for time, energy and space-resolved measurements of the soft-x-ray emissivity in magnetically confined fusion plasmas. Multi-energy soft x-ray imaging provides a unique opportunity for measuring, simultaneously, a variety of important plasma properties (T e , n Z , ΔZ eff , and n e,fast ). The electron temperature can be obtained by modeling the slope of the continuum radiation from ratios of the available brightness and inverted radial emissivity profiles over multiple energy ranges. Impurity density measurements are also possible using the line-emission from medium- to high-Z impurities to separate the background as well as transient levels of metal contributions. This technique should be explored also as a burning plasma diagnostic in-view of its simplicity and robustness.

Calibration is a crucial procedure in electron temperature (T e ) inference from a typical electron cyclotron emission (ECE) diagnostic on tokamaks. Although the calibration provides an important multiplying factor for an individual ECE channel, the parameter ΔT e /T e is independent of any calibration. Since an ECE channel measures the cyclotron emission for a particular flux surface, a non-perturbing change in toroidal magnetic field changes the view of that channel. Hence the calibration-free parameter is a measure of T e gradient. B T -jog technique is presented here which employs the parameter and the raw ECE signals for direct measurement of electron temperature gradient scale length.

Here, we present a new approach for increasing the rate and lowering the cost of identifying, cataloging, and monitoring global biodiversity. These advances, which we call Closed-Tube Barcoding, are one application of a suite of proven PCR-based technologies invented in our laboratory. Closed-Tube Barcoding builds on and aims to enhance the profoundly important efforts of the International Barcode of Life initiative. Closed-Tube Barcoding promises to be particularly useful when large numbers of small or rare specimens need to be screened and characterized at an affordable price. This approach is also well suited for automation and for use in portable devices.