Kirchhoff's Loop Law and the maximum entropy production principle

In contrast to the standard derivation of Kirchhoff's loop law, which invokes electric potential, we show, for the linear planar electric network in a stationary state at the fixed temperature,that loop law can be derived from the maximum entropy production principle. This means that the currents in network branches are distributed in such a way as to achieve the state of maximum entropy production.Comment: revtex4, 5 pages, 2 figure

Mcmbrane Potential as a Coupling Agent for Photophosphorylation by Bacteriorhodopsin and ATP-ase Containing Artificial Membrane

The steady state kinetic and thermodynamic properties of a »minimal« photosynthetic system containing two different proton pumps in the planar artificial membrane have been considered. The light activated proton pump, modelled after bacteriorhodopsin (bR), and\u27 the ATP-using proton pump, modelled after Neurospora ATP-ase, were interacting only through the common photopotential developed by bR. In the stationary state of the illuminated coupled system the following properties were calculated by Hill\u27s diagram method: proton flux for each macromolecule, photopotential, total effective force, efficiency of free energy storage, efficiency of light free energy utilization, entropy production, and adenylate energy charge in the internal compartment

Mehanizam toksičnosti i detoksikacije organofosfornih spojeva s naglaskom na istraživanja u Hrvatskoj

This review comprises studies on the mechanisms of toxicity and detoxication of organophosphorus (OP) compounds done in Croatia in different research areas. One area is the synthesis of antidotes against OP poisoning and their in vivo testing in experimental animals. In vitro studies included in this review focus on the mechanisms of reversible inhibition of acetylcholinesterase (AChE) and butyrylcholinesterase (BChE), protection of cholinesterases from inhibition by OPs, and reactivation of phosphylated cholinesterases. The third area comprises distribution profiles of BChE and paraoxonase (PON) phenotypes in selected population groups and the detection of OPs and metabolites in humans. Finally, methods are described for the detection of OP compounds in human blood and other media by means of cholinesterase inhibitionPrikazana su istraživanja vođena u Hrvatskoj na različitim područjima mehanizma toksičnosti i detoksikacije organofosfornih (OP) spojeva. Jedno je područje sinteza antidota protiv otrovanja OP spojevima i testiranje in vivo antidota na eksperimentalnim životinjama. Istraživanja in vitro odnose se na mehanizam reverzibilne inhibicije acetilkolinesteraze (AChE) i buturilkolinesteraze (BChE), zaštitu kolinesteraza od inhibicije OP spojevima te reaktivaciju fosfiliranih kolinesteraza. Treće je područje distribucija fenotipova BChE i paraoksonaze (PON) u odabranim populacijama te detekcija OP spojeva i njihovih metabolita u ljudima. Na kraju su opisane metode detekcije OP spojeva u ljudskoj krvi i drugim medijima koje se osnivaju na inhibiciji kolinesteraza

The impact of ship traffic and harbor activities on the atmospheric pollution in two northern adriatic ports: Venice and Rijeka

The aim of the POSEIDON project is to quantify the relative contribution of maritime traffic and harbor activities to atmospheric pollutants concentration in four port-cities of the Adriatic Sea. This study focuses on the harbors of Venice and Rijeka. In order to investigate the main pollution sources, emission inventories were used as input for receptor models: PMF (positive matrix factorization) and PCA (principal components analysis); moreover source identification was also conducted using PAHs diagnostic ratios. The ship traffic impact was quantified: i) on gaseous and particulate PAHs, collected using a new method which consisted in a double simultaneous sampling, in different wind sectors; ii) applying PMF to data of metals, PAHs and ions in PM10; iii) using the vanadium concentration according to the Agrawal methodology

An FPGA Implementation to Detect Selective Cationic Antibacterial Peptides

Exhaustive prediction of physicochemical properties of peptide sequences is used in different areas of biological research. One example is the identification of selective cationic antibacterial peptides (SCAPs), which may be used in the treatment of different diseases. Due to the discrete nature of peptide sequences, the physicochemical properties calculation is considered a high-performance computing problem. A competitive solution for this class of problems is to embed algorithms into dedicated hardware. In the present work we present the adaptation, design and implementation of an algorithm for SCAPs prediction into a Field Programmable Gate Array (FPGA) platform. Four physicochemical properties codes useful in the identification of peptide sequences with potential selective antibacterial activity were implemented into an FPGA board. The speed-up gained in a single-copy implementation was up to 108 times compared with a single Intel processor cycle for cycle. The inherent scalability of our design allows for replication of this code into multiple FPGA cards and consequently improvements in speed are possible. Our results show the first embedded SCAPs prediction solution described and constitutes the grounds to efficiently perform the exhaustive analysis of the sequence-physicochemical properties relationship of peptides

Impact of maritime transport on particulate matter concentrations and chemical compositions in four port-cities of the Adriatic/Ionian area: an overview of the results of POSEIDON project

Pollutant emissions from ships and harbour activities constitute an important source of pollution of coastal areas with potential influences on the climate and the health of their inhabitants. A recent review (Viana et al., 2014) shows that these emissions could have an important impact on the Mediterranean and that there is a lack of data for the Eastern and South-Eastern part of this area. This work presents an analysis of the impact of ship emissions to atmospheric particle concentrations (PM) in four important port-cities (Patras Greece, Brindisi and Venice Italy, and Rijeka Croatia) of the Adriatic/Ionian area. The study was performed within the POSEIDON project (Pollution monitoring of ship emissions: an integrated approach for harbours of the Adriatic basin, funded within the MED Programme 2007-2013). The study uses an integrated approach using emission inventories, dispersion modelling and measurements taken at high temporal resolution (1 min) and low temporal resolution for chemical characterization of PM. The emission inventories of the four port-cities show that ships contribute between 11.7% and 31.0% of the total PM emissions being a source locally comparable with road traffic (ranging between 11.8% and 26.6%). The source apportionment using the receptor model PMF showed and oil combustion source (that includes ship emissions), characterized by V and Ni, in Brindisi, Venice and Rijeka with V/Ni ratio ranging between 1.4 and 4.2 indicating local differences in chemical profiles of the emissions. The V concentrations were used to evaluate the contributions of primary ship emissions to PM (Agrawal et al., 2009) that resulted between 1.3% and 2.8%. The contribution to secondary sulphate was 11% of PM2.5 in Brindisi (Cesari et al., 2014). The analysis of high-temporal resolution measurements taken near the harbour areas of Venice, Patras and Brindisi showed a contribution of ship emissions to PM2.5 varying between 3.5% and 7.4%. The relative contribution to particle number concentrations (PNC) was larger at all sites (between 6% and 26%). This demonstrates that ship particulate missions include mainly small and ultrafine particles. The trend of the impact of passenger ships primary emissions to PM2.5 concentrations in Venice between 2007 and 2012 showed a decrease from 7% (+-1%) to 3.5% (+-1%) even if the gross tonnage of ship traffic increased in the same period by 47% (Contini et al., 2015). This was a consequence of the use of low-sulphur content fuels due to the application of local mitigation strategies and of the European Directive 2005/33/EC. The WRF-CAMx modeling system was applied over the Central and Eastern Mediterranean so as to identify the air quality impact of ship emissions. The zero-out modelling method was implemented involving model simulations performed while including and omitting the ship emissions. The results for both gaseous and particulate pollutant concentrations generally show a fairly good agreement with observations at the areas under study. Agrawal et al., 2009. Environmental Science and Technology 43, 5398-5402. Cesari et al., 2014. Science of the Total Environment 497-498, 392-400. Contini et al., 2015. Atmospheric Environment 102, 183-190. Viana et al., 2014. Atmospheric Environment 90, 96-105

Surface Energy Budgets of Arctic Tundra During Growing Season

This study analyzed summer observations of diurnal and seasonal surface energy budgets across several monitoring sites within the Arctic tundra underlain by permafrost. In these areas, latent and sensible heat fluxes have comparable magnitudes, and ground heat flux enters the subsurface during short summer intervals of the growing period, leading to seasonal thaw. The maximum entropy production (MEP) model was tested as an input and parameter parsimonious model of surface heat fluxes for the simulation of energy budgets of these permafrost‐underlain environments. Using net radiation, surface temperature, and a single parameter characterizing the thermal inertia of the heat exchanging surface, the MEP model estimates latent, sensible, and ground heat fluxes that agree closely with observations at five sites for which detailed flux data are available. The MEP potential evapotranspiration model reproduces estimates of the Penman‐Monteith potential evapotranspiration model that requires at least five input meteorological variables (net radiation, ground heat flux, air temperature, air humidity, and wind speed) and empirical parameters of surface resistance. The potential and challenges of MEP model application in sparsely monitored areas of the Arctic are discussed, highlighting the need for accurate measurements and constraints of ground heat flux.Plain Language SummaryGrowing season latent and sensible heat fluxes are nearly equal over the Arctic permafrost tundra regions. Persistent ground heat flux into the subsurface layer leads to seasonal thaw of the top permafrost layer. The maximum energy production model accurately estimates the latent, sensible, and ground heat flux of the surface energy budget of the Arctic permafrost regions.Key PointThe MEP model is parsimonious and well suited to modeling surface energy budget in data‐sparse permafrost environmentsPeer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/150560/1/jgrd55584.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/150560/2/jgrd55584_am.pd

Multi-genome identification and characterization of chlamydiae-specific type III secretion substrates: the Inc proteins

<p>Abstract</p> <p>Background</p> <p><it>Chlamydiae </it>are obligate intracellular bacteria that multiply in a vacuolar compartment, the inclusion. Several chlamydial proteins containing a bilobal hydrophobic domain are translocated by a type III secretion (TTS) mechanism into the inclusion membrane. They form the family of Inc proteins, which is specific to this phylum. Based on their localization, Inc proteins likely play important roles in the interactions between the microbe and the host. In this paper we sought to identify and analyze, using bioinformatics tools, all putative Inc proteins in published chlamydial genomes, including an environmental species.</p> <p>Results</p> <p>Inc proteins contain at least one bilobal hydrophobic domain made of two transmembrane helices separated by a loop of less than 30 amino acids. Using bioinformatics tools we identified 537 putative Inc proteins across seven chlamydial proteomes. The amino-terminal segment of the putative Inc proteins was recognized as a functional TTS signal in 90% of the <it>C. trachomatis </it>and <it>C. pneumoniae </it>sequences tested, validating the data obtained <it>in silico</it>. We identified a <it>macro </it>domain in several putative Inc proteins, and observed that Inc proteins are enriched in segments predicted to form coiled coils. A surprisingly large proportion of the putative Inc proteins are not constitutively translocated to the inclusion membrane in culture conditions.</p> <p>Conclusions</p> <p>The Inc proteins represent 7 to 10% of each proteome and show a great degree of sequence diversity between species. The abundance of segments with a high probability for coiled coil conformation in Inc proteins support the hypothesis that they interact with host proteins. While the large majority of Inc proteins possess a functional TTS signal, less than half may be constitutively translocated to the inclusion surface in some species. This suggests the novel finding that translocation of Inc proteins may be regulated by as-yet undetermined mechanisms.</p