Development of an Optimization-Based Atomistic-to-Continuum Coupling Method

Atomistic-to-Continuum (AtC) coupling methods are a novel means of computing the properties of a discrete crystal structure, such as those containing defects, that combine the accuracy of an atomistic (fully discrete) model with the efficiency of a continuum model. In this note we extend the optimization-based AtC, formulated in arXiv:1304.4976 for linear, one-dimensional problems to multi-dimensional settings and arbitrary interatomic potentials. We conjecture optimal error estimates for the multidimensional AtC, outline an implementation procedure, and provide numerical results to corroborate the conjecture for a 1D Lennard-Jones system with next-nearest neighbor interactions.Comment: 12 pages, 3 figure

From residue coevolution to protein conformational ensembles and functional dynamics

The analysis of evolutionary amino acid correlations has recently attracted a surge of renewed interest, also due to their successful use in de novo protein native structure prediction. However, many aspects of protein function, such as substrate binding and product release in enzymatic activity, can be fully understood only in terms of an equilibrium ensemble of alternative structures, rather than a single static structure. In this paper we combine coevolutionary data and molecular dynamics simulations to study protein conformational heterogeneity. To that end, we adapt the Boltzmann-learning algorithm to the analysis of homologous protein sequences and develop a coarse-grained protein model specifically tailored to convert the resulting contact predictions to a protein structural ensemble. By means of exhaustive sampling simulations, we analyze the set of conformations that are consistent with the observed residue correlations for a set of representative protein domains, showing that (i) the most representative structure is consistent with the experimental fold and (ii) the various regions of the sequence display different stability, related to multiple biologically relevant conformations and to the cooperativity of the coevolving pairs. Moreover, we show that the proposed protocol is able to reproduce the essential features of a protein folding mechanism as well as to account for regions involved in conformational transitions through the correct sampling of the involved conformers

Quantum transport through a DNA wire in a dissipative environment

Electronic transport through DNA wires in the presence of a strong dissipative environment is investigated. We show that new bath-induced electronic states are formed within the bandgap. These states show up in the linear conductance spectrum as a temperature dependent background and lead to a crossover from tunneling to thermal activated behavior with increasing temperature. Depending on the strength of the electron-bath coupling, the conductance at the Fermi level can show a weak exponential or even an algebraic length dependence. Our results suggest a new environmental-induced transport mechanism. This might be relevant for the understanding of molecular conduction experiments in liquid solution, like those recently performed on poly(GC) oligomers in a water buffer (B. Xu et al., Nano Lett 4, 1105 (2004)).Comment: 5 pages, 3 figure

Complex microwave conductivity of Na-DNA powders

We report the complex microwave conductivity, $\sigma=\sigma_1-i\sigma_2$, of Na-DNA powders, which was measured from 80 K to 300 K by using a microwave cavity perturbation technique. We found that the magnitude of $\sigma_1$ near room temperature was much larger than the contribution of the surrounding water molecules, and that the decrease of $\sigma_1$ with decreasing temperature was sufficiently stronger than that of the conduction of counterions. These results clearly suggest that the electrical conduction of Na-DNA is intrinsically semiconductive.Comment: 16 pages, 7 figure

Separation of Oligosaccharides from Lotus Seeds via Medium-pressure Liquid Chromatography Coupled with ELSD and DAD

peer-reviewedLotus seeds were identified by the Ministry of Public Health of China as both food and medicine. One general function of lotus seeds is to improve intestinal health. However, to date, studies evaluating the relationship between bioactive compounds in lotus seeds and the physiological activity of the intestine are limited. In the present study, by using medium pressure liquid chromatography coupled with evaporative light-scattering detector and diode-array detector, five oligosaccharides were isolated and their structures were further characterized by electrospray ionization-mass spectrometry and gas chromatography-mass spectrometry. In vitro testing determined that LOS3-1 and LOS4 elicited relatively good proliferative effects on Lactobacillus delbrueckii subsp. bulgaricus. These results indicated a structure-function relationship between the physiological activity of oligosaccharides in lotus seeds and the number of probiotics applied, thus providing room for improvement of this particular feature. Intestinal probiotics may potentially become a new effective drug target for the regulation of immunity

High sensitivity GEM experiment on double beta decay of 76-Ge

The GEM project is designed for the next generation 2 beta decay experiments with 76-Ge. One ton of ''naked'' HP Ge detectors (natural at the first GEM-I phase and enriched in 76-Ge to 86% at the second GEM-II stage) are operating in super-high purity liquid nitrogen contained in the Cu vacuum cryostat (sphere with diameter 5 m). The latest is placed in the water shield. Monte Carlo simulation evidently shows that sensitivity of the experiment (in terms of the T1/2 limit for neutrinoless 2 beta decay) is 10^27 yr with natural HP Ge crystals and 10^28 yr with enriched ones. These bounds corresponds to the restrictions on the neutrino mass less than 0.05 eV and 0.015 eV with natural and enriched detectors, respectively. Besides, the GEM-I set up could advance the current best limits on the existence of neutralinos - as dark matter candidates - by three order of magnitudes, and at the same time would be able to identify unambiguously the dark matter signal by detection of its seasonal modulation.Comment: LaTeX, 20 pages, 4 figure

A.S.P.E.N. Parenteral Nutrition Safety Consensus Recommendations

Parenteral nutrition (PN) serves as an important therapeutic modality that is used in adults, children, and infants for a variety of indications. The appropriate use of this complex therapy aims to maximize clinical benefit while minimizing the potential risks for adverse events. Complications can occur as a result of the therapy and as the result of the PN process. These consensus recommendations are based on practices that are generally accepted to minimize errors with PN therapy, categorized in the areas of PN prescribing, order review and verification, compounding, and administration. These recommendations should be used in conjunction with other A.S.P.E.N. publications, and researchers should consider studying the questions brought forth in this document

An experimental and numerical investigation on the process efficiency of the focused TIG welding of Inconel 718 thick plates

A combined experimental and numerical approach was adopted to investigate the focused tungsten inert gas (TIG) welding process by producing bead-on-plate welds in Inconel 718 plates. Experimental investigations were carried out by means of thermocouple measurements and optical macrographs of the weld cross-section. Three dimensional finite element (FE) simulations were conducted using the commercial specialized FE software Sysweld in order to predict the thermal field induced by the process in the plates. The work presents an approach to investigate the process efficiency and calibrate the heat source model in order to produce a full thermal characterization the plasmatron welding apparatus

Multi-performance optimisation framework for the selection of structural alternatives based on sustainable qualities

In recent years, the increasing demand for innovative sustainable policies in building engineering has shifted the decision rationale from traditional performance-based systems towards systems augmented by life-cycle sustainability notions. This paper investigates a novel optimisation framework, which supports the selection of buildings’ structural alternatives at concept stage by applying multiple performance, sustainable requirements. The established model explores ways to effectively compute and process expert knowledge across different stakeholders groups into a consolidated decision-making platform supported by Lean Theory. A systematic procedure based on the Quality Function Deployment is utilised to successfully translate 16 sustainability requirements into 27 corresponding engineering design requirements. The theoretical and mathematical principles of Analytic Network Process are applied on a pilot study to build general decision clusters, identify feedback links amongst the various engineering criteria and determine their inner dependences