Network theory approach for data evaluation in the dynamic force spectroscopy of biomolecular interactions

Investigations of molecular bonds between single molecules and molecular complexes by the dynamic force spectroscopy are subject to large fluctuations at nanoscale and possible other aspecific binding, which mask the experimental output. Big efforts are devoted to develop methods for effective selection of the relevant experimental data, before taking the quantitative analysis of bond parameters. Here we present a methodology which is based on the application of graph theory. The force-distance curves corresponding to repeated pulling events are mapped onto their correlation network (mathematical graph). On these graphs the groups of similar curves appear as topological modules, which are identified using the spectral analysis of graphs. We demonstrate the approach by analyzing a large ensemble of the force-distance curves measured on: ssDNA-ssDNA, peptide-RNA (system from HIV1), and peptide-Au surface. Within our data sets the methodology systematically separates subgroups of curves which are related to different intermolecular interactions and to spatial arrangements in which the molecules are brought together and/or pulling speeds. This demonstrates the sensitivity of the method to the spatial degrees of freedom, suggesting potential applications in the case of large molecular complexes and situations with multiple binding sites

EKSTRAKCIJA I ANALIZA KONDENZIRANIH TANINA CASTANEA SATIVA MIIL.

Proanthocyanidins, also known as condensed tannins are widespread in woody plants, but are also found in certain forages. Castanea sativa Mill. are exploited for various purposes, but a little is known about potential of this species and possible application in diet and therapy. The parts of chestnut such as: seed, peeled seed, brown seed shell, red internal seed shell, leaves, catkin, spiny bur, as well as the new and old chestnut bark were extracted with 50% ethanol as an extragents. Contents of total phenolics and total flavonoids were measured by application of the standard colorimetric assay. The total condensed tannins content estimated was highest in red internal seed shell 15.29%CE (vanillin assay) and 3.12%CT (acid butanol assay). Also high content of total phenolic compounds and condensed tannins had extracts of catkin, brown seed shell of chestnut and new chestnut bark. Extracts of C. sativa Mill. can be a potential resource of natural tannins with possible application in diet and therapy.Proantocijanidini, poznati kao kondenzirani tanini su jako rasprostranjeni u drvenastim biljkama, a pronađeni su i u hrani. Castanea sativa Mill. se dosta koristi za različite namjene, međutim malo je poznat njegov potencijal i moguća primjena u dijeti i terapiji. Dijelovi kestena kao što su; cijeli plod, srž ploda, vanjska smeđa kora ploda, crvena unutrašnja kora ploda, list, resa, ježura, kao i nova i stara kora drveta su ekstrahirani primjenom 50% etanola kao ekstragensa. Sadržaj ukupnih fenola i flavonoida je određen primjenom standardnih kolorimetrijskih testova. Sadržaj ukupnih kondenziranih tanina je najviši u crvenoj unutrašnjoj kori 15,29%CE (vanilin test) i 3,12%CT (kiseli butanolni test). Visok sadržaj ukupnih fenolnih tvari i kondenziranih tanina je određen u ekstraktima rese, vanjske smeđe kore i nove kore drveta. Ekstrakti C. sativa Mill. mogu biti potencijalna sirovina koja sadrži prirodne tanine sa mogućom primjenom u dijeti i terapiji

Eriophyoidea) the parasites of plant species from the family Brassicaceae

Rod Aceria obuhvata preko 1000 vrsta, parazita raznih monokotiledonih i dikotiledonih biljaka, i smatra se taksonomski problematičnim, usled nejasnog taksonomsog statusa velikog broja vrsta. Šest vrsta roda Aceria je do sada opisano sa biljnih vrsta iz 16 rodova familije Brassicaceae: Aceria drabae (Nal.), Aceria capsellae (Nal.), Aceria cardaminesbellidifoliae (Liro), Aceria cardaminis (Cotte), Aceria ciansensis (Cotte) i Aceria longior (Nal.). Većina pomenutih vrsta se smatra varijetetima ili sinonimima A. drabae, tako de je nerazjašnjeno da li se radi o jednoj oligofagnoj vrsti ili je u pitanju kompleks kriptičkih monofagnih vrsta. Među navedenim vrstama ističe se A. drabae, usled moguće primene u klasičnoj biološkoj kontroli korova Lepidium draba L. Ciljevi istraživanja su bili ispitivanje interspecijske morfološke i genetičke varijabilnosti populacija Aceria spp. koje su u asocijaciji sa različitim domaćinima iz familije Brassicaceae, ispitivanje intraspecijske varijabilnosti populacija Aceria spp. koje su u asocijaciji sa jednim domaćinom, identifikovanje i opis eventualnih kriptičkih vrsta, revidiranje liste domaćina za A. drabae kao i prikaz anatomsko-morfoloških promena koje na vrstama iz famiije Brassicaceae formiraju vrste roda Aceria. Tokom istraživanja pregledano je 355 uzoraka biljnih vrsta iz familije Brassicaceae, sakupljenih sa 162 lokaliteta. Od 26 identifikovanih, na osam biljnih vrsta registrovane su vrste roda Aceria. Prilikom opisa ili dopune opisa taksona mereno je 65 morfoloških karaktera ženki, mužjaka i juvenilnih jedinki, a za uporedne kvantitativne morfometrijske analize merena su 23 karaktera protoginih ženki. Utvrđivanje vаrijаbilnosti populacija Aceria spp. nа molekulаrnom nivou izvršena je аnаlizom sekvenci COI mtDNK. Morfološka i genetička varijabilnost analizirana je za šest populacija Aceria spp. sa različitih biljaka domaćina (Aurinia petraea (Ard.) Schur, Berteroa incana (L.) DC., Capsella bursa - pastoris (L.) Medik., Cardamine hirsuta L., Lepidium draba i Sisymbrium orientale L.)...The genus Aceria includes over 1000 species of parasites of various monocotyledonous and dicotyledonous plants and it is considered taxonomically problematic due to undefined taxonomic status of these numerous species. Six species of the genus Aceria from 16 plant genera belonging to the Brassicaceae family have been described so far: Aceria drabae (Nal.), Aceria capsellae (Nal.), Aceria cardaminesbellidifoliae (Liro), Aceria cardaminis (Cotte), Aceria ciansensis (Cotte) and Aceria longior (Nal.). Most of the mentioned species are considered to be varieties or synonyms of A. drabae, so it is still not clarified whether this is an oligophagous species or it is a complex of cryptic monophagous species. A. drabae stands out among the listed species because of its potential use in classical biological control of the weed Lepidium draba L. The objectives of the study were to investigate interspecific morphological and genetic variability of populations of Aceria spp. which are in association with different hosts from the family Brassicaceae, to study the intraspecific variability of Aceria spp. which are in association with one host, to identify and describe possible cryptic species and revise the list of hosts for A. drabae, as well as to present anatomical and/or morphological alterations on the species from the family Brassicaceae caused by species of the genus Aceria. During the research, 355 samples of plant species from the family Brassicaceae, collected from 162 localities, were examined. Out of 26 identified plant species, eight were associated with the species from the genus Aceria. Descriptions or additional descriptions of certain taxa were based on 65 morphological characters of females, males and juveniles, while for the comparative quantitative morphometric analysis 23 characters of protogyne females were measured. Population variability of Aceria spp. at the molecular level was performed by analysing the COI mtDNA sequences..

Experimental analysis and FEM modelling of a cutting tool vibrations

Presented in this paper is a comparative analysis of vibrations, measured during machining process and modelled by FEM. Moreover, microscopic structure of chip cross section was analyzed in order to establish the frequency of lamellae generation and its influence on the total level of vibrations of the cutting tool. Based on the results thus obtained, a method was proposed which allows determination of tool wear degree through separation of reliable indicators from the high-frequency spectrum of the measured vibration signals. This investigation showed that the change of chip segmentation frequency significantly influences the output vibration signal within the high-frequency spectrum, and is a function of tool wear degree

Spin excitations in the skymion host Cu2OSeO3

We have used inelastic neutron scattering to measure the magnetic excitation spectrum along the high-symmetry directions of the first Brillouin zone of the magnetic skyrmion hosting compound Cu$_2$OSeO$_3$. The majority of our scattering data are consistent with the expectations of a recently proposed model for the magnetic excitations in Cu$_2$OSeO$_3$, and we report best-fit parameters for the dominant exchange interactions. Important differences exist, however, between our experimental findings and the model expectations. These include the identification of two energy scales that likely arise due to neglected anisotropic interactions. This feature of our work suggests that anisotropy should be considered in future theoretical work aimed at the full microscopic understanding of the emergence of the skyrmion state in this material.Comment: 5 pages, 6 figure

Aromatička svojstva potpunih benzenoidnih ugljikovodika

We consider a family of structurally closely related fully-benzenoid hydrocarbons of increasing number of fused benzene rings. Local and global aromatic properties of such molecules are investigated with a particular interest in investigating the role of the finite size of such molecules in modelling the high-polymer or even graphite. An interesting alternation of local properties for benzene rings in a similar environment was observed.Razmatrana je skupina strukturno vrlo sličnih potpunih benzenoidnih ugljikovodika. Studirana su lokalna i globalna svojstva ovih molekula, a naročita je pažnja posvećena ulozi konačne veličine studiranih molekula u modeliranju benzenoidnih polimera ili čak grafita. Opažena je interesantna pojava da lokalna svojstva benzenskih prstenova alterniraju u sličnom okolišu, iako razlike u veličinama opadaju rastom veličine molekule

Calibrating whole building energy model: a case study using BEMS data

This paper describes a Calibration methodology which is specifically configured to best match actual building performance, based on a case study conducted to calibrate whole building energy model using Building Energy Management System (BEMS) measured data. It details the calibration approach which was designed to meet the specific characteristic of the spaces, systems and energy use in the pilot school building. Two calibration methods were developed; one is for electrical and the other is for thermal energy along with calibrated weather file. The result shows excellent correlation with the measured electricity and room air temperature and demonstrates the effectiveness of the methodology. Mean Bias Error (MBE) and Cumulative Variation of Root Mean Squared Error (CVRMSE) for electricity consumption is 6% and 14% respectively and -5 and 7% for air temperature