Computational Study of the Structure and Thermodynamic Properties of Ammonium Chloride Clusters Using a Parallel J-Walking Approach

The thermodynamic and structural properties of (NH$_4$Cl)$_n$ clusters, n=3-10 are studied. Using the method of simulated annealing, the geometries of several isomers for each cluster size are examined. Jump-walking Monte Carlo simulations are then used to compute the constant-volume heat capacity for each cluster size over a wide temperature range. To carry out these simulations a new parallel algorithm is developed using the Parallel Virtual Machine (PVM) software package. Features of the cluster potential energy surfaces, such as energy differences among isomers and rotational barriers of the ammonium ions, are found to play important roles in determining the shape of the heat capacity curves.Comment: Journal of Chemical Physics, accepted for publicatio

Ammonia Emissions from U.S. Laying Hen Houses in Iowa and Pennsylvania

Ammonia (NH3) emission rates (ER) of ten commercial layer houses (six high-rise or HR houses and four manure- belt or MB houses) with different manure handling or dietary schemes were monitored for one year in Iowa (IA) and Pennsylvania (PA). Gaseous (NH3 and CO2) concentrations of incoming and exhaust air streams were measured using custom-designed portable monitoring units that shared similar performance to EPA-approved measurement apparatus. Building ventilation rates were determined by calibrated CO2 mass balance using the latest metabolic rate data for modern laying hens. The field monitoring involved a total of 386 and 164 house-day measurements or 18,528 and 7,872 30-min emission data points for the HR houses and the MB houses, respectively. The ER showed considerable diurnal and seasonal variations. The annual mean ERs (g NH3 hen-1 d-1) and standard errors were 0.90 ±0.027 for IA-HR houses with standard diet, 0.81 ±0.02 for IA-HR houses with a nutritionally balanced 1% lower crude protein diet, 0.83 ±0.070 for PA-HR houses with standard diet, 0.054 ±0.0035 for IA-MB houses with daily manure removal, and 0.094 ±0.006 for PA-MB houses with twice a week manure removal. Mass balance of nitrogen (N) intake and output performed for IA-HR houses revealed a total N intake recovery of 94% to 101%, further verifying the certainty of the NH3 ER measurements. Results of the study contribute to the U.S. national inventory on NH3 emissions from animal feeding operations, particularly laying hen facilities as affected by housing type, manure handling scheme, crude protein content of the diet, and geographical location

Reducing variability in the cost of energy of ocean energy arrays

Variability in the predicted cost of energy of an ocean energy converter array is more substantial than for other forms of energy generation, due to the combined stochastic action of weather conditions and failures. If the variability is great enough, then this may influence future financial decisions. This paper provides the unique contribution of quantifying variability in the predicted cost of energy and introduces a framework for investigating reduction of variability through investment in components. Following review of existing methodologies for parametric analysis of ocean energy array design, the development of the DTOcean software tool is presented. DTOcean can quantify variability by simulating the design, deployment and operation of arrays with higher complexity than previous models, designing sub-systems at component level. A case study of a theoretical floating wave energy converter array is used to demonstrate that the variability in levelised cost of energy (LCOE) can be greatest for the smallest arrays and that investment in improved component reliability can reduce both the variability and most likely value of LCOE. A hypothetical study of improved electrical cables and connectors shows reductions in LCOE up to 2.51% and reductions in the variability of LCOE of over 50%; these minima occur for different combinations of components.The research leading to this publication is part of the DTOceanPlus project which has received funding from the EuropeanUnion's Horizon 2020 research and innovation programme under grant agreement No 785921. Funding was also received from the European Community's Seventh Framework Programme for the DTOcean Project (grant agreement No. 608597). The contribution of Sandia National Laboratories was funded by the U.S. Department of Energy's Water Power Technologies Office. Sandia National Laboratories is a multi-mission laboratory managed and operated by National Technology and Engineering Solutions of Sandia, LLC., a wholly owned subsidiary of Honeywell International, Inc., for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-NA0003525. This paper describes objective technical results and analysis. Any subjective views or opinions that might be expressed in the paper do not necessarily represent the views of the U.S. Department of Energy or the United States Government. The image of the RM3 device, in Fig. 7, was reproduced with the permission of Sandia National Laboratorie

Arterial inflammation in mice lacking the interleukin 1 receptor antagonist gene

Branch points and flexures in the high pressure arterial system have long been recognized as sites of unusually high turbulence and consequent stress in humans are foci for atherosclerotic lesions. We show that mice that are homozygous for a null mutation in the gene encoding an endogenous antiinflammatory cytokine, interleukin 1 receptor antagonist (IL-1ra), develop lethal arterial inflammation involving branch points and flexures of the aorta and its primary and secondary branches. We observe massive transmural infiltration of neutrophils, macrophages, and CD4(+) T cells. Animals appear to die from vessel wall collapse, stenosis, and organ infarction or from hemorrhage from ruptured aneurysms. Heterozygotes do not die from arteritis within a year of birth but do develop small lesions, which suggests that a reduced level of IL-1ra is insufficient to fully control inflammation in arteries. Our results demonstrate a surprisingly specific role for IL-1ra in the control of spontaneous inflammation in constitutively stressed artery walls, suggesting that expression of IL-1 is likely to have a significant role in signaling artery wall damage

Dynamic oscillatory signatures of central neuropathic pain in spinal cord injury

Central Neuropathic Pain (CNP) is believed to be accompanied by increased activation of the sensory and motor cortices. Our knowledge on this interaction is based mainly on fMRI studies, but there is little direct evidence on how these changes manifest in terms of dynamic neuronal activity. This study reports on the presence of transient EEG based measures of brain activity during motor imagery in spinal cord injured patients with CNP. We analyse dynamic EEG responses during imaginary movements of arms and legs in 3 groups of 10 volunteers each, comprising able-bodied people, paraplegic patients with CNP (lower abdomen and legs) and paraplegic patients without CNP. Paraplegic patients with CNP had increased event-related desynchronisation in the theta, alpha and beta bands (16-24 Hz) during imagination of movement of both non-painful (arms) and painful limbs (legs). Compared to patients with CNP, paraplegics with no pain showed a much reduced power in relaxed state and reduced event-related desynchronisation during imagination of movement. Understanding these complex dynamic, frequency-specific activations in CNP in the absence of nociceptive stimuli could inform the design of interventional therapies for patients suffering from CNP and possibly further understanding of the mechanisms involved

Recruitment of a SAP18-HDAC1 Complex into HIV-1 Virions and Its Requirement for Viral Replication

HIV-1 integrase (IN) is a virally encoded protein required for integration of viral cDNA into host chromosomes. INI1/hSNF5 is a component of the SWI/SNF complex that interacts with HIV-1 IN, is selectively incorporated into HIV-1 (but not other retroviral) virions, and modulates multiple steps, including particle production and infectivity. To gain further insight into the role of INI1 in HIV-1 replication, we screened for INI1-interacting proteins using the yeast two-hybrid system. We found that SAP18 (Sin3a associated protein 18 kD), a component of the Sin3a-HDAC1 complex, directly binds to INI1 in yeast, in vitro and in vivo. Interestingly, we found that IN also binds to SAP18 in vitro and in vivo. SAP18 and components of a Sin3A-HDAC1 complex were specifically incorporated into HIV-1 (but not SIV and HTLV-1) virions in an HIV-1 IN–dependent manner. Using a fluorescence-based assay, we found that HIV-1 (but not SIV) virion preparations harbour significant deacetylase activity, indicating the specific recruitment of catalytically active HDAC into the virions. To determine the requirement of virion-associated HDAC1 to HIV-1 replication, an inactive, transdominant negative mutant of HDAC1 (HDAC1H141A) was utilized. Incorporation of HDAC1H141A decreased the virion-associated histone deacetylase activity. Furthermore, incorporation of HDAC1H141A decreased the infectivity of HIV-1 (but not SIV) virions. The block in infectivity due to virion-associated HDAC1H141A occurred specifically at the early reverse transcription stage, while entry of the virions was unaffected. RNA-interference mediated knock-down of HDAC1 in producer cells resulted in decreased virion-associated HDAC1 activity and a reduction in infectivity of these virions. These studies indicate that HIV-1 IN and INI1/hSNF5 bind SAP18 and selectively recruit components of Sin3a-HDAC1 complex into HIV-1 virions. Furthermore, HIV-1 virion-associated HDAC1 is required for efficient early post-entry events, indicating a novel role for HDAC1 during HIV-1 replication

HIVToolbox, an Integrated Web Application for Investigating HIV

Many bioinformatic databases and applications focus on a limited domain of knowledge federating links to information in other databases. This segregated data structure likely limits our ability to investigate and understand complex biological systems. To facilitate research, therefore, we have built HIVToolbox, which integrates much of the knowledge about HIV proteins and allows virologists and structural biologists to access sequence, structure, and functional relationships in an intuitive web application. HIV-1 integrase protein was used as a case study to show the utility of this application. We show how data integration facilitates identification of new questions and hypotheses much more rapid and convenient than current approaches using isolated repositories. Several new hypotheses for integrase were created as an example, and we experimentally confirmed a predicted CK2 phosphorylation site. Weblink: [http://hivtoolbox.bio-toolkit.com