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New method to process Circular Dichroism experimental data on heat and cold denaturation of polypeptides in water
Artem V. Badasyan, Matjaž Valant, 2018, objavljeni povzetek znanstvenega prispevka na konferenci

Opis: During the past decade the experimental studies of biopolymer conformations have reached an unprecedented level of detailization and allow to study single molecules in vivo [1]. Processing of experimental data essentially relies on theoretical approaches to conformational transitions in biopolymers [2]. However, the models that are currently used, originate from the early 1960's and contain several unjustified assumptions, widely accepted at that time. Thus, the view on the conformational transitions in the polypeptides as a two-state process has very limited applicability because the all-or-none transition mechanism takes place only in short polypeptides with sizes comparable to the spatial correlation length; the original formulation of Zimm-Bragg model is phenomenological and does not allow for a microscopic model for water; the implicit consideration of the water-polypeptide interactions through the ansatz about the quadratic dependence of free energy difference on temperature can only be justified through the assumption of an ideal gas with a constant heat capacity. To get rid of these deficiencies, we augment the Hamiltonian formulation [3] of the Zimm-Bragg model [4] with the term describing the water-polypeptide interactions [5]. The analytical solution of the model results in a formula, ready to be fit to Circular Dichroism (CD) data for both heat and cold denaturation. On the example of several sets of experimental data we show, that our formula results in a significantly better fit, as compared to the existing approaches. Moreover, the application of our procedure allows to compare the strengths of inter- and intra-molecular H-bonds, an information, inaccessible before. References [1] I. König, A. Zarrine-Afsar, M. Aznauryan, A. Soranno, B. Wunderlich, F. Dingfelder, J. C. Stüber, A. Plückthun, D. Nettels, B. Schuler, (2015), Single-molecule spectroscopy of protein conformational dynamics in live eukaryotic cells/Nature Methods, 12, 773-779. [2] J. Seelig, H.-J. Schönfeld, (2016), Thermal protein unfolding by differential scanning calorimetry and circular dichroism spectroscopy. Two-state model versus sequential unfolding/Quarterly Reviews of Biophysics, 49, e9, 1-24. [3] A.V. Badasyan, A. Giacometti, Y. Sh. Mamasakhlisov, V. F. Morozov, A. S. Benight, (2010), Microscopic formulation of the Zimm-Bragg model for the helix-coil transition/Physical Review E, 81, 021921. [4] B. H. Zimm, J. K. Bragg, (1959), Theory of the Phase Transition between Helix and Random Coil in Polypeptide Chains/Journal of Chemical Physics, 31, 526. [5] A. Badasyan, Sh.A. Tonoyan, A. Giacometti, R. Podgornik, V.A. Parsegian, Y.Sh. Mamasakhlisov, V.F. Morozov, (2014), Unified description of solvent effects in the helix-coil transition/Physical Review E, 89, 022723. Corresponding author: Artem Badasyan (
Najdeno v: ključnih besedah
Povzetek najdenega: conformational transitions in biopolymers [2]. However, the models that are currently used, originate from the...
Ključne besede: Biopolymers, Circular Dichroism, Zimm-Bragg model, helix-coil transition.
Objavljeno: 22.10.2018; Ogledov: 1054; Prenosov: 0
.pdf Polno besedilo (83,24 KB)

A map-matching algorithm dealing with sparse cellular fingerprint observations
Andrea Viel, Federico Pittino, Angelo Montanari, Chris Marshall, Donatella Gubiani, Paolo Gallo, Andrea Dalla Torre, 2019, izvirni znanstveni članek

Opis: The widespread availability of mobile communication makes mobile devices a resource for the collection of data about mobile infrastructures and user mobility. In these contexts, the problem of reconstructing the most likely trajectory of a device on the road network on the basis of the sequence of observed locations (map-matching problem) turns out to be particularly relevant. Different contributions have demonstrated that the reconstruction of the trajectory of a device with good accuracy is technically feasible even when only a sparse set of GNSS positions is available. In this paper, we face the problem of coping with sparse sequences of cellular fingerprints. Compared to GNSS positions, cellular fingerprints provide coarser spatial information, but they work even when a device is missing GNSS positions or is operating in an energy saving mode. We devise a new map-matching algorithm, that exploits the well-known Hidden Markov Model and Random Forests to successfully deal with noisy and sparse cellular observations. The performance of the proposed solution has been tested over a medium-sized Italian city urban environment by varying both the sampling of the observations and the density of the fingerprint map as well as by including some GPS positions into the sequence of fingerprint observations.
Najdeno v: ključnih besedah
Povzetek najdenega: ...algorithm, that exploits the well-known Hidden Markov Model and Random Forests to successfully deal with...
Ključne besede: Map-matching algorithm, trajectory, cellular fingerprint, Hidden Markov Model
Objavljeno: 11.06.2019; Ogledov: 999; Prenosov: 38
.pdf Polno besedilo (3,93 MB)

Modelling of Macrosegregation of a Low-Frequency Electromagnetic Direct Chill Casting by a Meshless Method
Vanja Hatić, 2019, doktorska disertacija

Opis: The main aim of the dissertation is to develop a meshless model that describes the solidification and macrosegregation phenomena during the direct chill casting (DCC) of aluminium alloys under the influence of a low-frequency electromagnetic field. Macrosegregation is an undesired consequence of alloy solidification. It represents one of the major casting defects and substantially reduces the quality of the finished product. On the other hand, low-frequency electromagnetic casting (LFEC) is a process that promises to increase greatly the product quality, including the reduction of macrosegregation. The modelling of both processes is of tremendous importance to the metallurgical industry, due to the high costs of experiments during production. The volume-averaging formulation is used for the modelling of the solid-liquid interaction. The conservation equations for mass, energy, momentum, and species are used to model the solidification of aluminium-alloy billets in axysimmetry. The electromagnetic-induction equation is coupled with the melt flow. It is used to calculate the magnetic vector potential and the Lorentz force. The Lorentz force is time-averaged and included in the momentum-conservation equation, which intensifies the melt flow. The effect of Joule heating is neglected in the energy conservation due to its insignificant contribution. The semi-continuous casting process is modelled with the Eulerian approach. This implies that the global computational domain is fixed in space. The inflow of the liquid melt is assumed at the top boundary and the outflow of the solid metal is assumed at the bottom. It is assumed that the whole mushy area is a rigid porous media, which is modelled with the Darcy law. The Kozeny-Carman relation is used for the permeability definition. The incompressible mass conservation is ensured by the pressure correction, which is performed with the fractional step method. The conservation equations and the induction equation are posed in the cylindrical coordinate system. A linearised eutectic binary phase diagram is used to predict the solute redistribution in the solid and liquid phases. The micro model uses the lever rule to determine the temperature and the liquid fraction field from the transport equations. The partial differential equations are solved with the meshless-diffuse-approximate method (DAM). The DAM uses weighted least squares to determine a locally smooth approximation from a discrete set of data. The second-order polynomials are used as the trial functions, while the Gaussian function is used as the weight function. The method is localised by defining a smooth approximation for each computational node separately. This is performed by associating each node with a unique local neighbourhood, which is used for the minimisation. There are 14 nodes included in the local subdomains for the DCC and LFEC simulations. The stability of the advective term is achieved with a shift of the Gaussian weight in the upwind direction. This approach is called the adaptive upwind weight function and is used in the DAM for the first time. The Explicit-Euler scheme is used for temporal discretisation. The use of a meshless method and the automatic node-arrangement generation makes it possible to investigate the complicated flow structures, which are formed in geometrically complex inflow conditions in a straightforward way. A realistic inflow geometry and mould can therefore be included in the model. The number of computational nodes is increased in the mushy zone and decreased in the solid phase, due to the optimisation of the computational time and memory. The computational node arrangement is automatically adapted with time, as the position of the mushy zone is changed in shape and position.
Najdeno v: ključnih besedah
Povzetek najdenega: ...the dissertation is to develop a meshless model that describes the solidification and macrosegregation phenomena...
Ključne besede: low-frequency electromagnetic casting, direct chill casting, macrosegregation, electromagnetic stirring, aluminium alloys, meshless methods, diffuse-approximate method, multiphysics model, solidification
Objavljeno: 25.04.2019; Ogledov: 1001; Prenosov: 61
.pdf Polno besedilo (28,80 MB)

What effect does VOC sampling time have on derived OH reactivity?
Hannah Sonderfeld, Iain R White, Iain C A Goodall, James R Hopkins, Alistair C Lewis, Ralf Koppmann, Paul S Monks, 2016, izvirni znanstveni članek

Opis: State-of-the-art techniques allow for rapid measurements of total OH reactivity. Unknown sinks of OH and oxidation processes in the atmosphere have been attributed to what has been termed ĝ€missingĝ€ OH reactivity. Often overlooked are the differences in timescales over which the diverse measurement techniques operate. Volatile organic compounds (VOCs) acting as sinks of OH are often measured by gas chromatography (GC) methods which provide low-frequency measurements on a timescale of hours, while sampling times are generally only a few minutes. Here, the effect of the sampling time and thus the contribution of unmeasured VOC variability on OH reactivity is investigated. Measurements of VOC mixing ratios by proton transfer reaction time-of-flight mass spectrometry (PTR-ToF-MS) conducted during two field campaigns (ClearfLo and PARADE) in an urban and a semi-rural environment were used to calculate OH reactivity. VOCs were selected to represent variability for different compound classes. Data were averaged over different time intervals to simulate lower time resolutions and were then compared to the mean hourly OH reactivity. The results show deviations in the range of 1 to 25%. The observed impact of VOC variability is found to be greater for the semi-rural site.The selected compounds were scaled by the contribution of their compound class to the total OH reactivity from VOCs based on concurrent gas chromatography measurements conducted during the ClearfLo campaign. Prior to being scaled, the variable signal of aromatic compounds results in larger deviations in OH reactivity for short sampling intervals compared to oxygenated VOCs (OVOCs). However, once scaled with their lower share during the ClearfLo campaign, this effect was reduced. No seasonal effect on the OH reactivity distribution across different VOCs was observed at the urban site.
Najdeno v: ključnih besedah
Ključne besede: Hydroxyl radical, Atmospheric chemistry, Box model
Objavljeno: 18.07.2019; Ogledov: 649; Prenosov: 0

rof. dr. Peter Purg: Novi izobraževalni modeli med umetnostjo, znanostjo in tehnologijami za družbene inovacije.
peter Purg, prispevek na konferenci brez natisa

Najdeno v: ključnih besedah
Povzetek najdenega: ...leonardo da vinci, MAST, KONS, DIVA, izobraževanje, model, inoviranje...
Ključne besede: interdisiplinarnost, inovativnost, leonardo da vinci, MAST, KONS, DIVA, izobraževanje, model, inoviranje
Objavljeno: 18.10.2019; Ogledov: 748; Prenosov: 0
.pdf Polno besedilo (517,92 KB)

DNA-CNT Physisorption
Artem V. Badasyan, predavanje na tuji univerzi

Najdeno v: ključnih besedah
Povzetek najdenega: ...DNA, CNT, zipper model, physisorption...
Ključne besede: DNA, CNT, zipper model, physisorption
Objavljeno: 28.01.2020; Ogledov: 464; Prenosov: 0
.pdf Polno besedilo (416,43 KB)

Statistical mechanics of DNA-nanotube adsorption
Sh. A. Tonoyan, Davit Khechoyan, Yevgeni S. Mamasakhlisov, Artem V. Badasyan, 2019, drugi članki ali sestavki

Opis: Attraction between the polycyclic aromatic surface elements of carbon nanotubes (CNT) and the aromatic nucleotides of deoxyribonucleic acid (DNA) leads to reversible adsorption (physisorption) between the two, a phenomenon related to hybridization. We propose a Hamiltonian formulation for the zipper model that accounts for the DNA-CNT interactions and allows for the processing of experimental data, which has awaited an available theory for a decade.
Najdeno v: ključnih besedah
Povzetek najdenega: ...We propose a Hamiltonian formulation for the zipper model that accounts for the DNA-CNT interactions and...
Ključne besede: DNA-CNT physisorption, zipper model
Objavljeno: 28.01.2020; Ogledov: 488; Prenosov: 0
.pdf Polno besedilo (515,48 KB)

Vojko Hvala, 2020, magistrsko delo

Opis: Ker so se v zadnjih letih investicije v sončne elektrarne skorajda ustavile, nas je zanimalo, ali se investicija v fotovoltaiko v sedanjih razmerah, kot jo nekateri promovirajo in objubljajo, dejansko izide in ali bo kot taka v prihodnosti lahko nadomestila izpad proizvodnje električne energije pri opuščanju fosilnih goriv za zniževanje emisij s toplogrednimi plini. Glavni namen magistskega dela je bil ugotoviti, ali je naložba v fotovoltaiko v trenutnih razmerah smiselna in ekonomsko upravičena s ciljem poiskati najbolj optimalen model financiranja. Metoda dela zajema analizo praktičnega primera naložbe podjetja v fotovoltaični projekt z medsebojno primerjavo drugih modelov in načinov financiranja na osnovi izračunanih ekonomskih kazalnikov. Model izračunov je mogoče uporabiti za presojanje upravičljivosti tudi za druge solarne projekte, ki se nameravajo graditi v prihodnje. Iz ekonomske primerjave modelov financiranja smo ugotovili, da je najprimernješi model ekonomsko upravičljiv le ob upoštevanju določenih meril. Ekonomska upravičljivost investicije omogoča večjo vlogo fotovoltaike v scenariju dolgoročne politike uvajanja obnovljive in čiste energije za cilj zmanjševanja emisij s toplogrednimi plini.
Najdeno v: ključnih besedah
Povzetek najdenega: ...ekonomsko upravičena s ciljem poiskati najbolj optimalen model financiranja. Metoda dela zajema analizo praktičnega primera...
Ključne besede: model financiranja, fotovoltaika, sončna elektrarna, naložba v fotovoltaiko
Objavljeno: 20.07.2020; Ogledov: 412; Prenosov: 28
.pdf Polno besedilo (2,37 MB)

Prenova informacijske podpore za sistemsko ureditev področja skladiščenja in interne logistike v izbranem podjetju
Janoš Morenčič, 2020, magistrsko delo

Opis: V magistrskem delu je predstavljena sistemska ureditev področja skladiščenja in interne logistike s poudarkom na prenovi poslovno informacijske rešitve za podjetje Plastik SI d.o.o. Družba, katere osnovna dejavnost je proizvodnja plastične embalaže, se je v preteklih letih soočila s težavami obravnavanega področja. Ugotovili so, da je bilo neurejeno stanje posledica številnih dejavnikov kot so: slaba prostorska organiziranost skladišč, omejena funkcionalnost informacijske rešitve, nezadostno izvajanje operativnih nalog skladiščenja in interne logistike ter v zadnjem obdobju porast aktivnosti zaradi povečanega obsega proizvodnje. Vodstvo družbe je za rešitev nastalega problema rezerviralo potrebne vire in sredstva ter postavilo jasne in končne cilje v obliki učinkovite podpore procesni funkciji skladiščenja in interne logistike. Pri tem je določilo časovni okvir za izvedbo naloge. Ker so ocenili, da je obravnavano področje kompleksno in obsežno, so nalogo opredelili kot razvojni projekt in na ta način izboljšali možnosti uspeha in doseganja pričakovanih učinkov. Namen projekta, opisanega v magistrskem delu, je bil razviti in implementirati sistemsko rešitev, ki bo temeljila na prenovljeni in nadgrajeni informacijski platformi. Poudarek je bil na upoštevanju dolgoročne vzdržnosti, da bo načrtovana rešitev omogočala kasnejšo razširljivost in morebitne nadgradnje. Rezultat projekta je učinkovita informacijska podpora za skladiščenje in interno logistiko.
Najdeno v: ključnih besedah
Povzetek najdenega: ...Skladišče, interna logistika, projekt, informacijski sistem, model, metodologija, agilnost....
Ključne besede: Skladišče, interna logistika, projekt, informacijski sistem, model, metodologija, agilnost.
Objavljeno: 20.07.2020; Ogledov: 410; Prenosov: 19
.pdf Polno besedilo (4,96 MB)

Večparametrski model za izbiro najugodnejše banke ali hranilnice na Goriškem
Kristina Lancner Zorzut, 2020, magistrsko delo

Opis: V magistrskem delu smo se ukvarjali z vrednotenjem in izbiro najugodnejše banke ali hranilnice na Goriškem. Banke ali hranilnice nas spremljajo na vsakem koraku. Med seboj so si precej podobne, vse namreč ponujajo finančne storitve uporabniku. Vse si želijo privabiti čim več uporabnikov, zato strokovnjaki znotraj vsake posamezne finančne ustanove kreirajo in iščejo posamezne rešitve, kje in kako bi se čimbolj približali čim večji populaciji. Nekatere banke/hranilnice imajo zato nižje stroške na eni strani, druge na drugi. Prav zato smo se hoteli prepričati in sploh ugotoviti, ali obstaja najugodnejša banka/hranilnica na Goriškem ter katera je to. Vrednotenje in izbor je potekal s pomočjo večparametrske metode DEX. Po izbiri kriterijev, ki kar najboljše opišejo delovanje bank/hranilnic, smo po korakih večparametrskega modeliranja izdelali celoten model ter z njim ovrednotili in analizirali naše izbrane banke/hranilnice. Izdelali smo tudi analizo “Kaj-če?”, analizo plus/minus 1 ter analizo selektivne razlage. Končni rezultat je predlog najprimernejše banke/hranilnice. V našem primeru sta to dve: Primorska hranilnica Vipava (PHV) ter Delavska hranilnica (DH), ki sta bili ocenjeni kot ugodni hranilnici, vendar vseeno ne kot najugodnejši. Ugodni sta zato, ker sta po skoraj vseh kriterijih opredeljeni kot ugodni ali srednji. PHV je neugodna samo glede dostopnosti bančnega okenca. Za razliko od PHV je imela DH poleg tega kot neugodno ocenjeno še pridobitev kartice.
Najdeno v: ključnih besedah
Ključne besede: banka, hranilnica, odločitveni model, večparametrsko odločanje, metoda DEX, program DEXi
Objavljeno: 09.12.2020; Ogledov: 96; Prenosov: 7
.pdf Polno besedilo (1,31 MB)

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