Molecular dynamics simulations of displacement cascades in Fe-10%Cr systems

Molecular dynamics simulations of the displacement cascades in Fe-10%Cr systems are used to simulate the primary knocked-on atom events of the irradiation damage at temperatures 300,600,and 750 K with primary knockedon atom energies between 1 and 15 keV.The results indicate that the vacancies produced by the cascade are all in the central region of the displacement cascade.During the cascade,all recoil Fe and Cr atoms combine with each other to form Fe-Cr or Fe-Fe interstitial dumbbells as well as interstitial clusters.The number and the size of interstitial clusters increase with the energy of the primary knocked-on atom and the temperature.A few large clusters consist of a large number of Fe interstitials with a few Cr atoms,the rest are Fe-Cr clusters with small and medium sizes.The interstitial dumbbells of Fe-Fe and Fe-Cr are in the 111 and 110 series directions,respectively.     

Efficient computation of operator‐type response sensitivities for uncertainty quantification and predictive modeling: illustrative application to a spent nuclear fuel dissolver model

This work honors the 75th birthday of Professor Ionel Michael Navon by presenting original results highlighting the computational efficiency of the adjoint sensitivity analysis methodology for function‐valued operator responses by means of an illustrative paradigm dissolver model. The dissolver model analyzed in this work has been selected because of its applicability to material separations and its potential role in diversion activities associated with proliferation and international safeguards. This dissolver model comprises eight active compartments in which the 16 time‐dependent nonlinear differential equations modeling the physical and chemical processes comprise 619 scalar and time‐dependent model parameters, related to the model's equation of state and inflow conditions. The most important response for the dissolver model is the time‐dependent nitric acid in the compartment furthest away from the inlet, where measurements are available at 307 time instances over the transient's duration of 10.5 h. The sensitivities to all model parameters of the acid concentrations at each of these instances in time are computed efficiently by applying the adjoint sensitivity analysis methodology for operator‐valued responses. The uncertainties in the model parameters are propagated using the above‐mentioned sensitivities to compute the uncertainties in the computed responses. A predictive modeling formalism is subsequently used to combine the computational results with the experimental information measured in the compartment furthest from the inlet and then predict optimal values and uncertainties throughout the dissolver. This predictive modeling methodology uses the maximum entropy principle to construct an optimal approximation of the unknown a priori distribution for the a priori known mean values and uncertainties characterizing the model parameters and the computed and experimentally measured model responses. This approximate a priori distribution is subsequently combined using Bayes' theorem with the “likelihood” provided by the multi‐physics computational models. Finally, the posterior distribution is evaluated using the saddle‐point method to obtain analytical expressions for the optimally predicted values for the parameters and responses of both multi‐physics models, along with corresponding reduced uncertainties. This work shows that even though the experimental data pertains solely to the compartment furthest from the inlet (where the data were measured), the predictive modeling procedure used herein actually improves the predictions and reduces the predicted uncertainties for the entire dissolver, including the compartment furthest from the measurements, because this predictive modeling methodology combines and transmits information simultaneously over the entire phase‐space, comprising all time steps and spatial locations. Copyright © 2016 John Wiley & Sons, Ltd.     

An Endoplasmic Reticulum Targeting Type I Photosensitizer for Effective Photodynamic Therapy against Hypoxic Tumor Cells

Organelle-targeted type I photodynamic therapy (PDT) shows great potential to overcome the hypoxic microenvironment in solid tumors. The endoplasmic reticulum (ER) is an indispensable organelle in cells with important biological functions. When the ER is damaged due to the production of reactive oxygen species (ROS), the accumulation of misfolded proteins will interfere with ER homeostasis, resulting in ER stress. Here, an ER-targeted benzophenothiazine-based photosensitizer NBS-ER was presented. ER targeting modification significantly reduced the dark toxicity and improved phototoxicity index (PI). NBS-ER could effectively produce O₂⁻⋅ with near-infrared irradiation, making its phototoxicity under hypoxia close to that under normoxia. Meanwhile, the photoinduced ROS triggered ER stress and induced apoptosis. In addition, NBS-ER possessed excellent photodynamic therapeutic effect in 4T1-tumor-bearing mice.     

One Way Traffic: Base-to-Backbone Hole Transfer in Nucleoside Phosphorodithioate

The directionality of the hole-transfer processes between DNA backbone and base was investigated by using phosphorodithioate [P(S⁻)=S] components. ESR spectroscopy in homogeneous frozen aqueous solutions and pulse radiolysis in aqueous solution at ambient temperature confirmed initial formation of G^.+-P(S⁻)=S. The ionization potential of G-P(S⁻)=S was calculated to be slightly lower than that of guanine in 5′-dGMP. Subsequent thermally activated hole transfer from G^.+ to P(S⁻)=S led to dithiyl radical (P-2S^.) formation on the μs timescale. In parallel, ESR spectroscopy, pulse radiolysis, and density functional theory (DFT) calculations confirmed P-2S^. formation in an abasic phosphorodithioate model compound. ESR investigations at low temperatures and higher G-P(S⁻)=S concentrations showed a bimolecular conversion of P-2S^. to the σ²-σ*¹-bonded dimer anion radical [-P-2S 2S-P-]⁻ [ΔG (150 K, DFT)=−7.2 kcal mol⁻¹]. However, [-P-2S 2S-P-]⁻ formation was not observed by pulse radiolysis [ΔG° (298 K, DFT)=−1.4 kcal mol⁻¹]. Neither P-2S^. nor [-P-2S 2S-P-]⁻ oxidized guanine base; only base-to-backbone hole transfer occurs in phosphorodithioate.     

NMR‐based analysis of the chemical composition of Japanese persimmon aqueous extracts

Japanese persimmon (Diospyros kaki L.) is recognized as an outstanding source of biologically active compounds relating to many health benefits. In the present study, NMR spectroscopy provided a comprehensive metabolic overview of Japanese persimmon juice. Detailed signal assignments of Japanese persimmon juice were carried out using various 2D NMR techniques incorporated with broadband water suppression enhanced through T₁ effects (BB‐WET) or WET sequences, and 26 components, including minor components, were identified. In addition, most components were quantitatively evaluated by the integration of signals using conventional ¹H NMR and BB‐WET NMR. This is the first detailed analysis combined with quantitative characterization of chemical components using NMR for Japanese persimmon. Copyright © 2015 John Wiley & Sons, Ltd.     

Detection challenges in quantitative polymer analysis by liquid chromatography

Accurate quantification of polymer distributions is one of the main challenges in polymer analysis by liquid chromatography. The response of contemporary detectors is typically influenced by compositional features such as molecular weight, chain composition, end groups, and branching. This renders the accurate quantification of complex polymers of which there are no standards available, extremely challenging. Moreover, any (programmed) change in mobile‐phase composition may further limit the applicability of detection techniques. Current methods often rely on refractive index detection, which is not accurate when dealing with complex samples as the refractive‐index increment is often unknown. We review current and emerging detection methods in liquid chromatography with the aim of identifying detectors, which can be applied to the quantitative analysis of complex polymers.     

An interview with Sam C. Saunders

Sam C. Saunders, the son of Elizabeth Cundiff and Winston E. Saunders, was born in Richland, OR, on February 24, 1931. The family moved to La Grande, OR, in 1944, where Sam completed high school and two years at Eastern Oregon College. He then received the BSc degree in Mathematics from the University of Oregon, Eugene, OR, in 1952, and he attended the University of Washington, Seattle, WA, receiving a PhD degree under Z. W. Birnbaum. After graduating, he accepted employment at the Boeing Company in its Mathematical Services Unit and, in 1972, a position as a Full Professor at Washington State University, Pullman, WA, from which he retired in 1996.     

Logging damage and injured tree mortality in tropical forest management

Using insights from the forest ecology literature, we analyze the effect of injured trees on stand composition and carbon stored in above‐ground biomass and the implications for forest management decisions. Results from a Faustmann model with data for a tropical forest on Kalimantan show that up to 50% of the basal area of the stand before harvest can consist of injured trees. Considering injured trees leads to an increase in the amount of carbon in above‐ground biomass of up to 165%. These effects are larger under reduced impact logging than under conventional logging. The effects on land expectation value and cutting cycle are relatively small. The results suggest that considering injured trees in models for tropical forest management is important for the correct assessment of the potential of financial programs to store carbon and conserve forest ecosystem services in managed tropical forests, such as reducing emissions from deforestation and forest degradation and payment for ecosystem services. Recommendations for Resource Managers

• Considering the role of injured trees is important for managing tropical forests
• These trees can cover up to 50% of basal area and contain more than 50% of the carbon stored in above‐ground biomass
• Reduced impact logging leads to a larger basal area of injured trees and more carbon stored in injured trees than conventional logging
• Injured trees play an important role when assessing the potential for carbon storage in the context of payment for forest ecosystem services.

     

Development of a method for quantitative determination of the cytotoxic agent piplartine (piperlongumine) in multiple skin layers

This study reports the development of a simple and reproducible method, with high rates of recovery, to extract the cytotoxic agent piplartine from skin layers, and a sensitive and rapid UV‐HPLC method for its quantification. Considering the potential of piplartine for topical treatment of skin cancer, this method may find application for formulation development and pharmacokinetics studies to assess cutaneous bioavailability. Porcine skin was employed as a model for human tissue. Piplartine was extracted from the stratum corneum (SC) and remaining viable skin layers (VS) using methanol, vortex homogenization and bath sonication, and subsequently assayed by HPLC using a C₁₈ column, and 1:1 (v/v) acetonitrile–water (adjusted to pH 4.0 with acetic acid 0.1%) as mobile phase. The quantification limit of piplartine was 0.2 μg/mL (0.6 μm ), and the assay was linear up to 5 μg/mL (15.8 μm ), with within‐day and between‐days assay coefficients of variation and relative errors <15%. Piplartine recovery from SC and VS varied from 86 to 96%. The method was suitable to assay samples from skin penetration studies, enabling detection of differences in cutaneous delivery in different skin compartments resulting from treatment with various formulations and time periods.     

Can a Six‐Letter Alphabet Increase the Likelihood of Photochemical Assault to the Genetic Code?

In 2014, two unnatural nucleosides, d5SICS and dNaM, were shown to selectively base pair and replicate with high fidelity in a modified strain of E. coli, thus effectively expanding its genetic alphabet from four to six letters. More recently, a significant reduction in cell proliferation was reported in cells cultured with d5SICS, and putatively with dNaM, upon exposure to brief periods of near‐visible radiation. The photosensitizing properties of the lowest‐energy excited triplet state of both d5SICS and dNaM were implicated in their cytotoxicity. Importantly, however, the excited‐state mechanisms by which near‐visible excitation populates the triplet states of d5SICS and dNaM are currently unknown. In this study, steady‐state and time‐resolved spectroscopies are combined with quantum‐chemical calculations in order to reveal the excited‐state relaxation mechanisms leading to efficient population of the triplet states in these unnatural nucleosides in solution. It is shown that excitation of d5SICS or dNaM with near‐visible light leads overwhelmingly to ultrafast population of their triplet states on the femtosecond time scale. The results presented in this work lend strong support to the proposal that photoexcitation of these unnatural nucleosides can accelerate oxidatively generated damage to DNA and other biomolecules within the cellular environment.