Comparison of thermodynamic stabilities and mechanical properties of CO2, SiO2, and GeO2 polymorphs by first-principles calculations

The recent discovery that molecular CO(2) transforms under compression into carbon four-coordinated, 3-dimensional network solid phases has generated considerable interests on possible new phases in the fourth-main-group elemental oxides. Based on density-functional theory calculations, we have investigated the thermodynamic stability, mechanical properties and electronic structure of proposed guest-free clathrates, quartz and cristobalite phases for CO(2), SiO(2), and GeO(2), and the dry ice phase for CO(2). It was predicted that a GeO(2) clathrate, likely a semiconductor, could be synthesized presumably with some suitable guest molecules. The hypothetical CO(2) guest-free clathrate phase was found hardly to be formed due to the large energy difference with respect to the other polymorphs. This phase is unstable at all pressures, which is also implied by its different electronic structure in comparison with SiO(2) and GeO(2). Finally, the SiO(2) clathrate presents a uniquely high bulk modulus, which is higher than that of quartz and three times of the experimental data, might not be a weak point of ab-initio calculations such as pseudopotentials, correlation functional etc., instead it can be readily understood by the constraint as imposed by the high symmetry. Either temperature or an "exhausted" relaxation (without any symmetry constraint) can remedy this problem.     

Mimics of small ribozymes utilizing a supramolecular scaffold

For elucidating the mechanism of the general acid/base catalysis of the hydrolysis of RNA phosphodiester bonds, a number of cleaving agents having two cyclen moieties tethered to a 1,3,5-triazine core have been prepared and their ability to bind and cleave uridylyl-3',5'-uridine (UpU) studied over a wide pH range. Around neutral pH, the cleaving agents form a highly stable ternary complex with UpU and Zn(II) through coordination of the uracil N3 and the cyclen nitrogen atoms to the Zn(II) ions. Under conditions where the triazine core exists in the deprotonated neutral form, hydrolysis of UpU, but not of adenylyl-3',5'-adenosine (ApA), is accelerated by approximately two orders of magnitude in the presence of the cleaving agents, suggesting general base rather than metal ion catalysis. The probable mechanism of the observed catalysis and implications to understanding the general acid/base-catalyzed phosphodiester hydrolysis by ribozymes are discussed.     

N-Naphthyl peptoid foldamers exhibiting atropisomerism

We introduce peptoid oligomers incorporating N-(1)-naphthyl glycine monomers. Axial chirality was established due to restricted rotation about the C-N(aryl) bond. Atropisomerism of both linear and cyclic peptoids was investigated by computational analysis, dynamic HPLC, and X-ray crystallographic studies.     

Informatics methods to enable sharing of quantitative imaging research data

Introduction

The National Cancer Institute Quantitative Research Network (QIN) is a collaborative research network whose goal is to share data, algorithms and research tools to accelerate quantitative imaging research. A challenge is the variability in tools and analysis platforms used in quantitative imaging. Our goal was to understand the extent of this variation and to develop an approach to enable sharing data and to promote reuse of quantitative imaging data in the community.

Methods

We performed a survey of the current tools in use by the QIN member sites for representation and storage of their QIN research data including images, image meta-data and clinical data. We identified existing systems and standards for data sharing and their gaps for the QIN use case. We then proposed a system architecture to enable data sharing and collaborative experimentation within the QIN.

Results

There are a variety of tools currently used by each QIN institution. We developed a general information system architecture to support the QIN goals. We also describe the remaining architecture gaps we are developing to enable members to share research images and image meta-data across the network.

Conclusions

As a research network, the QIN will stimulate quantitative imaging research by pooling data, algorithms and research tools. However, there are gaps in current functional requirements that will need to be met by future informatics development. Special attention must be given to the technical requirements needed to translate these methods into the clinical research workflow to enable validation and qualification of these novel imaging biomarkers.     

Quark dynamics, thermal QCD, and the gravity dual

We perform a holographic renormalization of the supergravity action and compute the stress tensor of the dual gauge theory incorporating the logarithmic running of the gauge coupling. From the stress tensor we obtain the shear viscosity and the entropy of the medium at temperature T, and investigate the ratio η/s.     

Performance measures for targeted energy transfer and resonance capture cascading in nonlinear energy sinks

In vibrating mechanical systems, the targeted energy transfer mechanism (TET) of nonlinear energy sinks (NES) is employed as an alternative to linear tuned mass dampers (TMD) as passive vibrations absorbers for transient vibrations. The major advantages a NES has over a linear TMD are (1) an increased robustness to detuning and (2) the ability to dissipate multiple frequencies with only a single NES through so-called resonance capture cascading (RCC). The performance, especially the speed, of TET and RCC has rarely been a topic of research. In this research, algebraic performance measures for the speed of both TET and RCC are derived, called the pumping time and the cascading time, respectively. It shows that cascading time can be seen as a sum of single-mode pumping times, by introducing a novel modal decomposition. The strength of both measures is that they do not require numerical simulations, allowing easy optimization of the NES. The influence of different nonlinearities on the TET and RCC performance is investigated. Actual numerical simulations presented in the study validate the merit of both the pumping time and cascading time.     

Molecular dynamics simulations,docking and MMGBSA studies of newly designed peptide-conjugated glucosyloxy stilbene derivatives with tumor cell receptors

Molecular Diversity - In this work, for the first time, we designed derivatives of beta-D-glucosyloxy-3-hydroxy-trans-stiblene-2-carboxylic acid (GHS), by conjugating GHS with tumor targeting...     

Analysis of nitromethane from samples exposed in vitro to chloropicrin by stable isotope dilution headspace gas chromatography with mass spectrometry

Chloropicrin (trichloronitromethane) is a widely used soil fumigant and an old chemical warfare agent. The metabolism of chloropicrin is not well known in mammals but nitromethane has been shown to be one of its main metabolites. Here, a fast and simple headspace gas chromatography with mass spectrometry method was applied for the measurement of nitromethane from aqueous samples. The analytical method was validated using stable isotope labeled internal standard and a small sample volume of 260 μL. No conventional sample preparation steps were needed. The method was accurate (relative standard deviations ≤1.5%) and linear (R² = 0.9996) within the concentration range of 0.1?6.0 μg/mL. This method was used to measure nitromethane in in vitro incubations with human and pig liver cell fractions containing enzymes for xenobiotic metabolism, exposed to chloropicrin. The results indicate that the presence of glutathione is necessary for the formation of nitromethane from chloropicrin. Also, nitromethane was formed mostly in liver cytosol fractions, but not in microsomal fractions after the incubation with chloropicrin. Our results suggest that although nitromethane is not the unequivocal biomarker of chloropicrin exposure, this method could be applied for screening the elevated levels in humans after chloropicrin exposure.