Life cycle and ecology of the loggerhead turtle (Caretta caretta, Linnaeus, 1758): development and application of the Dynamic Energy Budget model

Short layman summary: Question driving my research was "What are the effects of plastic ingestion on loggerhead turtle's biology and ecology?". The overall aim was to provide new insights into processes important for the life cycle and ecology (growth, maturation, and reproduction) of this protected migratory species. Using the collected experimental and literature data, I developed a model based on the Dynamic Energy Budget theory that spans the full life cycle of the turtle. The model was then used to compare North Atlantic and Mediterranean populations, and to study the environmental (food density and temperature) and anthropogenic (plastic pollution) pressures on loggerhead turtles. Some of the results were surprising. I could explain from the differences in parameter values between both populations, why North Atlantic individuals that visit the Mediterranean See cannot reproduce there. The local population manages to do so by adaptation to the low level of food availability in this sea: they mature at a smaller size. This shows that this species lives at the edge of its capabilities, which also became visible in another more shocking way: the consumption of plastic lowers food intake. If plastic occupies only 3% of the storage-gut capacity, this has already major effects on the ultimate size they can obtain and dramatically reduces reproductive output. Such volumes are already encountered in practice, highlighting the importance of responsible management of waste

Neurochemical, molecular and behavioral response to pharmacological activation of serotonin system in rats with altered serotonin homeostasis

Serotoninski prijenosnik (5HT prijenosnik, 5HTT) predstavlja ciljnu molekulu djelovanja antidepresivnih lijekova iz skupine selektivnih inhibitora povratnog unosa serotonina (SSRI). Iako često korišteni, ovi lijekovi ostvaruju terapijski učinak samo kod manjeg broja (do 50 %) bolesnika, a razlozi za to nisu poznati. Nalaz povezanosti terapijskog odgovora s polimorfizmom gena za 5HTT uputio je na moguću ulogu konstitucijske serotoninske homeostaze u kliničkom odgovoru na SSRI. Primjenom originalnog životinjskog modela, Wistar-Zagreb 5HT štakor, čije sublinije imaju konstitucijski pojačanu (5HT-visoki) ili smanjenu (5HT-niski) aktivnost trombocitnog 5HTT, u ovom radu je istražen odnos između konstitucijske 5HT homeostaze i odgovora na tretman SSRI-om. Farmakološka aktivacija 5HT sustava izazvana je jednokratnom ili kroničnom primjenom SSRI-a fluoksetina, a cilj je bio usporediti sublinije s obzirom na učinke fluoksetina na (i) aktivnost 5HTT i razinu 5HT u mozgu i na periferiji, (ii) razinu mRNA za 5HTT i receptor 5HT1A u mozgu te (iii) odabrana ponašanja modulirana serotoninom. Jednokratni tretman fluoksetinom doveo je do inhibicije aktivnosti trombocitnog 5HTT, koja je bila jače izražena kod životinja iz 5HT-visoke sublinije, te do porasta razine plazmatskog 5HT, koji je bio veći kod životinja iz 5HT-niske sublinije. Kronična primjena lijeka dovela je do značajnog pada razine trombocitnog serotonina, koji je bio veći kod životinja iz 5HT-niske sublinije, te do pada plazmatskog serotonina, koji je bio veći kod životinja iz 5HT-visoke sublinije. Smanjenje ponašanja nalik na anksioznost, kao i porast istraživačke i lokomotorne aktivnosti nakon kroničnog tretmana fluoksetinom bilo je prisutno samo kod životinja iz 5HT-visoke sublinije, a praćeno je promjenama u mozgu koje su bile vidljive kao tendencija povećanja ekspresije gena za 5HT1A receptor u hipokampusu te ekspresije gena za 5HTT u regiji jezgara rafe. S druge strane, kod životinja iz 5HT- niske sublinije, kronična primjena fluoksetina dovela je do pada kortikalne ekspresije mRNA za 5HTT i receptor 5HT1A, te tendencije pada razine 5HT u moždanoj kori, dok učinci na ponašanje nisu bili značajni. Rezultati istraživanja pokazuju da je konstitucijska serotoninska homeostaza važan čimbenik odgovora na tretman fluoksetinom. Sublinije Wistar- Zagreb 5HT štakora mogu biti koristan model u istraživanju neurobiološke osnove različitog odgovora pojedinaca na terapiju antidepresivima, kao i za vrednovanje trombocita kao perifernog modela za predviđanje terapijskog odgovora

Hibridni spoj strukturiranoga silicija i organskoga poluvodiča za detekciju infracrvene svjetlosti

Otkrićem osjetljivosti hibridnih silicij/organskih fotodioda u bliskom infracrvenom području dodan je još jedan pretendent u utrci za nasljednika tehnologije InGaAs detektora u bliskom infracrvenom području. No, unatoč potencijalnim prednostima hibridne silicijske tehnologije, slabi odziv ovih fotodioda nije dozvolio potencijalne primjene, ali je izazvao akademski interes i potaknuo nastavak istraživanja. Tema ovoga rada je istraživanje mogućnosti poboljšanja odziva takvih fotodioda strukturiranjem silicijske podloge na nano i mikro skali prije nanošenja sloja organskog poluvodiča. Pretpostavka o mogućem poboljšanju svojstava strukturiranjem došla je iz tehnologije fotonaponskih ćelija, u kojima se strukturiranje površine koristi u svrhu zatočenja svjetlosti višestrukim refleksijama i povećanjem efektivne površine koja apsorbira svjetlost. U tu svrhu pripremljene su kemijskim metodama strukturirane površine silicija na nano i mikro skali, te hijerarhijski organizirane strukture. Na takvim podlogama deponirani su tanki slojevi organskog poluvodiča tirskog purpura metodom epitaksijalnog rasta u reaktoru s vrućim stjenkama. Na silicij i organski sloj nanešeni su ohmski aluminijski kontakti, čime je formirana fotodioda. Odziv fotodiode testiran je laserskom svjetlošću u bliskom infracrvenom području. Za sve metode strukturiranja ostvareno je višestruko pojačanje fotostruje u odnosu na hibridne fotodiode pripremljene na ravnim podlogama u jednakim uvjetima kao i strukturirane fotodiode. Najveće pojačanje, od do dva reda veličine, opaženo je na podlogama čija je površina strukturiranima u silicijske mikropiramide anizotropnim jetkanjem (100) orijentirane pločice silicija. Mjerenjem spektralnog odziva izmjeren je odziv od 4-5 mA/W u uvjetima reverzne polarizacije od -1V na telekomunikacijskoj valnoj duljini od 1550 nm. Mjerenjima apsorptancije u vidljivom i infracrvenom spektralnom području isključeno je zatočenje svjetlosti kao uzrok pojačanja fotostruje, a mjerenjem efektivne površine isključeno je povećanje efektivne površine. Predložen je model djelovanja hetero-fotodiode koji pretpostavlja zapinjanje Fermijeve i LUMO razine organskog poluvodiča unutar procjepa silicija. Kao razlog pojačanja fotostruje predložen je model pojačanja električnog polja na oštrim vrhovima strukturiranih podloga.Discovery of the sensitivity of the hybrid silicon/organic photodiodes in the near-infrared spectral range in 2009 by G. Matt in Linz has sparked not only purely academic interest, since the photo-sensitivity came from the sub-bandgap region of the both members that formed the hybrid heterojunction, but also has provoked interest with particular applications in mind. The telecom industry, using the spectral range of 1,3-1,6 μm for the long-range fiber telecommunications, is one of the possible users of such photodiodes if they could surpass the incumbent InGaAs photodetector technology ideally in both price and performance. However, the first photodiodes even after the optimization of the organic layer have remained far outside of the responsivity range necessary for the use in telecommunications. The topic of this thesis is the research of the possible improvement in responsivity of such photodiodes by structuring the silicon substrate on nano- and micro-scales prior to deposition of the thin organic layer. The assumption of improvement in photocurrent by the surface structuring came from research in the photovoltaics, where micro-structuring has been for a long time used for anti-reflection purposes, and as of recently nano and hierarchical structuring has successfully been used for light trapping and increase in cell effective surface area. To test the hypothesis differently structured silicon substrates were prepared by simple and affordable chemical etching methods. Surfaces with nano, micro or hierarchical micro-nano surface structuring were prepared, on top of which thin layers of organic semiconductor tyrian purple was deposited by hot-wall epitaxy, a vacuum deposition method known for producing high-quality films or small-molecule organic semiconductors. Ohmic contacts based on thin vacuum-evaporated aluminum films were placed on both silicon and organic semiconductor, forming a back-illuminated photodiode. Photoresponse of the diode was measured by J-V measurments under the excitation of nearinrfared laser light source. For all differently structured photodiodes large improvements in short-circut photocurrent in comparison to photodiodes prepared in the same conditions on planar substrates were observed. The highest improvement, up to two orders of magnitude, was measured for silicon micropyramid structured substrates, prepared by anisotropic etching of (100) oriented crystalline silicon substrates. Measurements of the spectral responsivity showed that the best performing photodiodes had the responsivity in the range of 4-5 mA/W under the reverse polarization of -1 V, at the telecom-relevant wavelenth of 1550 nm. Light trapping as a possible method for improvement of the increase in photocurrent was ruled out by a series of measurements of transmittance and reflectance of the structured heterojunctions in the visible and near-infrared spectral range. By comparison of the increase in effective surface area of the junction between planar and best performing micropyramid structured samples, increase in junction area was also ruled out as a possible mechanism of the increase in photocurrent. Previously published models of the band-diagrams and mechanism of NIR sensitivity of the photodiodes of a type-II heterojunction with the Anderson rule-like band alignment have predicted the dependence of the onset of the photocurrent on the LUMO level of the organic semiconductor. However, the complete lack of such behavior has brought forward an improved model containing the assumption of both the Fermi level and the organic HOMO level pinning to the near-midgap levels in silicon, which would explain the lack of variation of the barrier width measured as the energy of the photons causing the onset of the photocurrent. Electric-field assisted enhancement mechanism is proposed as a mechanism for increase of the photocurrent in the structured samples. It is demonstrated by numeric model that the increase in the electric field at the tip of the pyramid can be up to ten-fold in comparison to the electric field of an equipotential plane. Field-enhanced transport mechanisms such as the Fowler-Nordheim tunneling are strongly non-linearly dependent on the intensity of the electric field. If a mechanism of that type is responsible for the transport at the sharp points of the structured substrates, it would explain large improvements in the photocurrent

Distribution, speciation and fate of trace metals in the stratified Krka river estuary

The distribution, speciation, behaviour, and fate of selected trace metals (TM) (Zn Cd, Pb, Cu, Ni, and Co) were studied in the water column of the highly stratified Krka River estuary, from 2009 to 2013, covering two contrasting seasons (summer/winter). In addition, the study involved measurements of dissolved/particulate organic carbon (DOC/POC) and major physico–chemical parameters (salinity, pH, dissolved oxygen, temperature). Water samples were taken from the three characteristic layers (brackish, the freshwater–seawater interface (FSI), and seawater). Stripping voltammetry (anodic, and adsorptive cathodic) was the primary analytical technique, while the diffusion gradient in thin films (DGT) technique was used as a complementary technique for speciation measurements. The concentrations of all TM were lower in the Krka River than in the open Adriatic which allowed the identification of pathways and processes governing the horizontal and vertical redistribution of TM across the whole estuary, whether they were added into the system by human activity or by ‘‘in-situ’’ processes (e.g. scavenging). Non-conservative behaviour for most of the studied TM observed in the surface layer of the estuary was primarily caused by their input in the Šibenik Bay area. Detailed "mapping" of the bay showed that the harbour and nautical marina are the regions with the highest concentrations of TM. A significant increase of Cu and Zn in the entire estuary transect during the summer period appeared to be directly linked to intensive nautical activity i.e. caused by the release of TM from antifouling paints. The scavenging of metals into the deeper layers, along with the longer residence time of seawater, caused an upstream increase in TM concentrations in the seawater layer. A very good agreement between the vertical profiles of DGT-labile, and dissolved TM concentrations suggests that the DGT technique can be successfully used to determine potentially bioavailable TM concentrations in estuarine conditions. The fraction of DGT-labile TM, which reflects their chemical speciation (primarily, their binding to natural organic ligands), ranged from > 90% for Cd, to < 20% for Cu, but also depends on the concentration ratios of metals and organic ligands. Voltammetric speciation of Cu showed the presence of two types of organic ligands that form strong (L1, 9.6 < logK1 < 11.9) and weak (L2, 7.8 < logK2 < 9.9) Cu complexes. The concentration of weak organic ligands (L2) is correlated with the DOC concentration, and is higher in summer, most probably due to the increased biological activity. The concentration of free Cu ions (the most bioavailable form), at ambient conditions, is regulated primarily by the complexation with strong ligands (L1). For most of the samples, the calculated free Cu slightly exceeds the toxic threshold of 10 pM. However, these values are the result of applied methodology of calculation, and does not necessarily reflect real ambient conditions.Raspodjela i specijacija odabranih metala u tragovima (TM) (Zn Cd, Pb, Cu, Ni i Co), te njihovo ponašanje i sudbina istraživani su u vodenom stupcu vertikalno uslojenog estuarija rijeke Krke tijekom dva kontrastna godišnja doba (ljeto/zima) u periodu od 2009 do 2013. Istraživanja su obuhvaćala i mjerenja otopljenog/partikulatnog organskog ugljika (DOC/POC), te osnovnih fizičko–kemijskih pokazatelja (salinitet, pH, otopljeni kisik, temperatura), a uzorkovanja su provođena u tri karakteristična sloja (boćati sloj, haloklina i morski sloj). Voltammetrija s akumulacijom (anodna i adsorptivna katodna) bila je primarna analitička tehnika, dok je za specijaciju korištena i komplementarna tehnika pasivnog uzorkovanja temeljena na principu difuzijskog gradijenta u tankom filmu (DGT). Koncentracije TM niže su u rijeci Krki nego u vodi otvorenog dijela Jadrana, što je omogućilo identifikaciju puteva i procesa koji reguliraju horizontalnu i vertikalnu preraspodjelu TM u cijelom estuariju, neovisno da li su oni u sustav uneseni ljudskom aktivnošću ili „in-situ“ procesima (npr. tonjenje -„scavenging“). Nekonzervativno ponašanje u površinskom sloju estuarija uočeno za većinu TM uzrokovano je primarno unosom metala u području Šibenskog zaljeva. Detaljno „mapiranje“ zaljeva pokazalo je da su luka i nautička marina područja s najvišom koncentracijom TM. Pokazalo se da je značajan porast Cu i Zn u cijelom estuariju tijekom ljetnih mjeseci u izravnoj vezi s pojačanom nautičkom aktivnošću, odnosno vezani su za otpuštanje metala iz protuobraštajnih boja s plovila. Vertikalni transport TM u dublje slojeve („scavenging“), te dulje vrijeme zadržavanja morske vode uzrokovali su uzvodni porast koncentracije TM u morskom sloju. Vrlo dobro slaganje vertikalnih profila DGT-labilnih i otopljenih koncentracija TM ukazuju da se DGT tehnika može uspješno koristiti za određivanje potencijalno bioraspoloživih koncentracija TM u estuarijskim uvjetima. Udio DGT-labilnih TM odraz je njihove kemijske specijacije (primarno vezanja s prirodnim organskim ligandima), te varira od > 90% za Cd, do < 20% za Cu, ali ovisan je također i o omjeru koncentracije metala i organskih liganada. Voltammetrijska specijacija Cu pokazala je prisutnost dva tipa organskih liganada koji stvaraju jake (L1, 9.6 < logK1< 11.9) odnosno slabe (L2, 7.8 < logK2< 9.9) Cu komplekse. Koncentracija slabijih organskih liganada (L2) u korelaciji je s koncentracijom DOC-a, te je veća ljeti najvjerojatnije zbog povećane biološke aktivnosti. Koncentracija slobodnih iona Cu (vrsta koja je najviše bioraspoloživa) pri okolišnim uvjetima regulirana je u većoj mjeri kompleksiranjem s jakim ligandima (L1). Za većinu uzoraka izračunate vrijednosti slobodnog Cu blago prelaze graničnu toksičnu vrijednost od 10 pM. Međutim, te vrijednosti su rezultat upotrijebljenog načina izračuna i ne odražavaju nužno stvarno stanje

In-depth analysis of the Adriatic Sea bacterial diversity

Bakterije u morskim ekosustavima predstavljaju morfološki, genetički te funkcionalno vrlo raznovrsnu skupinu mikroorganizama. Primjenom 454 pirosekvenciranja gena za 16S rRNA i fluorescencijske in situ hibridizacije kataliziranim taloženjem reportera određena je sezonska dinamika bakterijskih zajednica u otvorenom moru južnog i sjevernog Jadrana, te estuarija rijeke Krke. Brojnost bakterijskih operativnih taksonomskih jedinica i struktura zajednice u svim istraživanim područjima bile su pod utjecajem hidrografskih uvjeta. U južnom Jadranu snažan utjecaj imale su zimsko duboko miješanje vodenog stupca i ingresija Levantinske intermedijarne vode, u sjevernom Jadranu sezonski uvjeti okoliša te protok rijeke Po, a u estuariju rijeke Krke protok rijeke i snažan gradijent saliniteta. Prokariotskim pikoplanktonskim zajednicama Jadranskoga mora dominira klad SAR11 čiji je udio u zajednici bio najveći u oligotrofnom području južnog Jadrana. Razred Betaproteobacteria pojavljivao se u područjima pod utjecajem riječne vode. Predstavnici koljena Actinobacteria pojavljivali su se u svim istraživanim područjima, međutim jedino im je u riječnoj vodi estuarija rijeke Krke brojnost bila povećana sa snažno izraženom sezonalnošću. Morske skupine NS4 i NS5 koljena Bacteroidetes uz klad SAR86 razreda Gammaproteobacteria identificirane su kao podskupine koje su se pojavljivale tijekom fitoplanktonskih cvatova u svim istraživanim područjima. Cijanobakterijske zajednice Jadranskog mora činili su tipični morski rodovi Synechococcus i Prochlorococcus. Povećana prisutnost roda Prochlorococcus detektirana je jedino u južnom Jadranu dok je u sjevernom Jadranu dominirao rod Synechococcus. Tipične dubokooceanske skupine SAR324, SAR202 i SAR406 uz povećanu brojnost arheja karakterizirale su duboke vode Jadrana.Bacteria in marine ecosystems are a morphologically, genetically and functionally diverse group. The seasonal dynamic of bacterial communities in the South and North Adriatic offshore waters and in the Krka river estuary was determined by using a combination of 454 pyrosequencing of the 16S rRNA gene and catalyzed reporter deposition-fluorescence in situ hybridization. Bacterial richness and community structure were strongly influenced by hydrological conditions in all the studied areas. A strong, deep winter mixing of the water column and Levantine intermediate water ingression in the South Adriatic, seasonal environmental conditions and the Po river flow in the North Adriatic and the river flow coupled with a strong salinity gradient in the Krka river estuary had a pronounced impact on bacterial communities. Members of the SAR11 clade were dominating the prokaryotic picoplankton communities in the Adriatic Sea with maximal abundances in the oligotrophic area of the South Adriatic. Betaproteobacteria were mainly appearing in ecosystems under the influence of riverine waters. Members of the phylum Actinobacteria were present in all the studied areas but high abundances with a pronounced seasonality were detected only in the riverine waters of the Krka estuary. Marine groups NS4 and NS5 belonging to the phylum Bacteroidetes together with the gammaproteobacterial SAR86 clade were identified to co- occur with phytoplankton blooms in all the studies areas. Typical marine cyanobacteria, Synechococcus and Prochlorococcus, were dominating the cyanobacterial communities in the Adriatic. Synechococcus was dominating the cyanobacterial communities in the North Adriatic while Prochlorococcus was mainly constrained to the South Adriatic. The Deep Adriatic Sea was characterized by typical bacterial deep ocean clades: SAR324, SAR202 and SAR406. In addition, a higher abundance of Archaea was found in this deep part of the Adriatic Sea

Non-radiative relaxation mechanisms of electronically excited phenylalanine in model peptides

A systematic study of the non-radiative deactivation mechanisms of the three photoexcited N-acetylphenylalanylamide conformers was conducted in order to disclose the experimentally observed conformational dependent lifetime of phenyl vibrationless 1ππ* excited state. The all-atom trajectory surface hopping non-adiabatic molecular dynamics simulations, based on linear response time dependent density functional theory, were utilized for blind screening of relaxation pathways and revealed a number of excitation transfer mechanisms from 1ππ* to the 1nπ* excited states localized on each of the two amide groups. Possible pathways were further refined by obtaining conical intersection barrier energies from corresponding reaction paths constructed at the coupled cluster (CC2) level of theory. Finally, from semiclassical consideration of conical intersection accessibility with only the nuclear zero point vibrational energy and from the increased rigidity of the second amide group towards distorsion upon its methylation, it was concluded that the classically accessible part of conical intersection seam for population transfer to the 1nπ* state of the second amide group is the largest for the conformer with the shortest 1ππ* state lifetime

Solving Large Dense Symmetric Eigenproblem on Hybrid Architectures

Dense symmetric eigenproblem is one of the most significant problems in the numerical linear algebra that arises in numerous research fields such as bioinformatics, computational chemistry, and meteorology. In the past years, the problems arising in these fields become bigger than ever resulting in growing demands in both computational power as well as the storage capacities. In such problems, the eigenproblem becomes the main computational bottleneck for which solution is required an extremely high computational power. Modern computing architectures that can meet these growing demands are those that combine the power of the traditional multi-core processors and the general-purpose GPUs and are called hybrid systems. These systems exhibit very high performance when the data fits into the GPU memory ; however, if the volume of the data exceeds the total GPU memory, i.e. the data is out-of-core from the GPU perspective, the performance rapidly decreases. This dissertation is focused on the development of the algorithms that solve dense symmetric eigenproblems on the hybrid GPU-based architectures. In particular, it aims at developing the eigensolvers that exhibit very high performance even if a problem is out- of-core for the GPU. The developed out-of-core eigensolvers are evaluated and compared on real problems that arise in the simulation of molecular motions. In such problems the data, usually too large to fit into the GPU memory, are stored in the main memory and copied to the GPU memory in pieces. That approach results in the performance drop due to a slow interconnection and a high memory latency. To overcome this problem an approach that applies blocking strategy and re- designs the existing eigensolvers, in order to decrease the volume of data transferred and the number of memory transfers, is presented. This approach designs and implements a set of the block- oriented, communication-avoiding BLAS routines that overlap the data transfers with the number of computations performed. Next, these routines are applied to speed-up the following eigensolvers: the solver based on the multi-stage reduction to a tridiagonal form, the Krylov subspace-based method, and the spectral divide-and-conquer method. Although the out-of-core BLAS routines significantly improve the performance of these three eigensolvers, a careful re-design is required in order to tackle the solution of the large eigenproblems on the hybrid CPU-GPU systems. In the out-of-core multi-stage reduction approach, the factor that mostly influences the performance is the band size of the obtained band matrix. On the other hand, the Krylov subspace- based method, although it is based on the memory- bound BLAS-2 operations, is the fastest method if only a small subset of the eigenpairs is required. Finally, the spectral divide-and- conquer algorithm, which exhibits significantly higher arithmetic cost than the other two eigensolvers, achieves extremely high performance since it can be performed completely in terms of the compute-bound BLAS-3 operations. Furthermore, its high arithmetic cost is further reduced by exploiting the special structure of a matrix. Finally, the results presented in the dissertation show that the three out-of-core eigen- solvers, for a set of the specific macromolecular problems, significantly overcome the multi-core variants and attain high flops rate even if data do not fit into the GPU memory. This proves that it is possible to solve large eigenproblems on modest computing systems equipped with a single GPU

Nucleic acid - small molecule interactions, experimentally based molecular modeling approach

U okviru ove doktorske disertacije metodama molekulskog modeliranja proučavane su interakcije nukleinskih kiselina s nekoliko skupina organskih spojeva: derivatima bisfenantridina, guanidiniokarbonil-pirol- arilnim konjugatima, cijaninskim spojevima, te translacijskim (benzimidazolnim i diaminopiperidinskim) inhibitorima hepatitis C virusa. Istraženi su procesi njihovog kompleksiranja, interkaliranja, vezanja u utor te elektrostatskog međudjelovanja s polinukleotidima. Prve tri skupine spojeva imaju svojstvo molekulskog prepoznavanja nukleobaza, pa mogu poslužiti za razvoj novih specifičnih obilježivača pri istraživanju nukleinskih kiselina, te kao predložak za razvoj antitumorskih i antivirusnih lijekova sa svojstvom selektivnog blokiranja određenih sljedova DNA ili RNA. Kao polazišne točke za modeliranje korišteni su rezultati spektroskopskih mjerenja (UV-Vis i CD spektri, fluorimetrijske titracije) te difrakcijske i NMR analize. Istraživanja su provedena metodama molekulskog modeliranja različitih stupnjeva složenosti. U svrhu određivanja novih parametara korišteni su kvantno mehanički računi. Proučavanje strukture i fleksibilnosti nukleinskih kiselina i njihovih kompleksa s organskim molekulama provedeno je metodama polja sila (molekulska mehanika i molekulska dinamika). Kombinirane kvantno mehaničke – molekulsko mehaničke metode primijenjene su u svrhu ispitivanja utjecaja okoline, preciznije polinukleotidnog lanca i metalnih iona, na raspodjelu naboja na ligandima. Dobiveni rezultati u skladu su s eksperimentalnim saznanjima

Motility of Dictyostelium discoideum cells studied within the framework of a generalized Langevin model

Analizirana je migracija stanica dvaju sojeva D. discoideum, divljeg tipa AX2 i stanica deficijentnih za korteksiline, u različitim fazama životnog ciklusa – vegetativnoj i agregacijski kompetentnoj fazi. Nenadziranom klasifikacijom svih promatranih stanica identificirane su tri skupine koje se razlikuju prvenstveno po srednjoj brzini kretanja i niskofrekventnom području u periodogramu vektora brzine. Za svaku podskupinu stanica identificiranu unutar pojedine biološke populacije određeni su parametri Langevinovog modela proširenog memorijskim članom

Transport properties of semiconductor nanostructures

Poluvodičke nanostrukture su u znanstvenoj zajednici vrlo aktivno područje istraživanja jer omogućuju dizajn materijala s točno određenim električnim svojstvima i kao takve imaju veliku mogućnost primjene kao novi poluvodički elementi, senzori, fotovoltaici i sl. Unatoč višegodišnjim istraživanjima i velikom broju objavljenih znanstvenih radova i dalje je veliki izazov kako napouzdan i ekonomičan način proizvesti nanostrukture točno određenih dimenzija i s malim brojem defekata. U ovom doktoratu proučavana je upotreba tehnike magnetronskog rasprašenja kao jednog od mogućih načina proizvodnje poluvodičkih nanostruktura Si i Ge u različitim okolinama SiO_2(oksida), Si_3N_4 (nitrida) i SiC (karbida). Pronađeno je da temperaturni tretman na 700°C za Gei temperaturni tretman na 1050°C za Si u trajanju od 1h u atmosferi N_2 predstavlja idealni uvjet za stvaranje nanokristaliničnog materijala u oksidnoj matrici. Tehnikom rendgenske difrakcije pokazana je kristaliničnost proizvedenog nano materijala, a fotoluminiscencijom pokazan je uhvat fotona u nanočestici pojavom luminiscencije u vidljivom dijelu spektra. Proučavanje električnih transportnih svojstava napravljeno je korištenjem MOS strukture u kojoj se sloj s poluvodičkim nanomaterijalom nalazio u oksidnoj, nitridnoj i karbidnoj matrici. MOS struktura u smislu defekata na površini između podloge i matrica pokazala je dobru kvalitetu napravljenih uzoraka sa srednjom gustoćom stanja defekata D_it ~ 10^12cm^-2eV^-1 ili manje. Kapacitivno naponskim mjerenjima nađeno je da nanostrukture djeluju kao mjesta uhvata nosioca naboja i uhvat naboja najizraženiji je za uzorak s nanočesticama Ge promjera 2.5 nm u višeslojnoj oksidnoj matrici. Najdominatniji način vođenja struje kroz matricu s nanočesticama u propusno polariziranoj MOS strukturi je pri većim naponima prostornim nabojem ograničena struja (SCLC), a primanjim naponima je ohmski tip vodljivosti. U nepropusnoj polarizaciji MOS strukture za deblje uzorke dominantni način vodljivosti je ohmskog tipa, a za tanje uzorke dominantan način vodljivosti je SCLC tipa bez obzira za naponsko područje. U prisutnosti svjetlosne pobude očekivano konačna struja kroz MOS strukturu raste i u smislu karaktera vodljivosti nema promjene u odnosnu na mjerenja u tami, osim što se za neke uzorke promijenila raspodjela gustoće stanja defekata. U smislu upotrebe poluvodičkih nanostruktura kao fotovoltaika uzorak u kojem su bile nanočestice Si u SiO_2 pokazao je postojanje napona otvorenog kruga pri pobudi svjetlom.In the scientific community semiconductor nano structures are very active field of research because of the possibility to design materials with specifc electrical properties. Such structures have a great potential for the use as new semiconductor devices, sensors, photovoltaics etc. Despite many years of active research and many published papers it is still a big challenge to produce nano structures in a reliable and economical manner with exact size and small number of defects. In this doctoral thesis we applied magnetron sputtering technique to produce semiconductor nano structures of Si and Ge in different environments of SiO2, Si3N4 and SiC. It was found that the temperature annealing process at 1050°C for Si and 700°C for Ge during 1h in the atmosphere of N2 is ideal for creating the nano crystalline Si and Ge. X-ray diffraction reveals the crystallinity of produced nano material and with the luminescence in the visible range the capture of photons in nano crystals is demostrated. The electrical transport properties are studied using MOS structures in which the oxide layer is made with the semiconductor nano material of Si and Ge. The interface defect density of MOS structures shows, a quality of samples with D_it ~ 10^12cm^-2eV^-1. The charge capture in nano crystals is shown with capacitive techniques and is most pronounced for a samples with nano crystals of Ge size of 2.5 nm embedded in multilayer oxide structure. The most dominant way of current transfer through matrix with nano crystals when MOS structure is forward polarised is the space charge limited current (SCLC) for high voltages and the ohmic current for low voltages. For thicker samples the ohmic current is dominant way of charge transfer and for thinner samples the SCLC current is the dominant way of charge transfer in any voltage regime. Measurement under light excitation showed us that the current is getting bigger and the type of conductivity didn't change except for some samples in which the change of density of defect states was noticed. The samples with nano-structure of Si in SiO2 showed the photovoltaic effect after excitation by light source which is interesting for using nano-structures for photovoltaic applications