Self-organization of regular surface pattern under ion beam erosion was described in detail by Navez in 1962. Several years later in 1986 Bradley and Harper (BH) published the first self-consistent theory on this phenomenon based on the competition of surface roughening described by Sigmund's sputter theory and surface smoothing by Mullins-Herring diffusion. Many papers that followed BH theory introduced other processes responsible for the surface patterning e.g. viscous flow, redeposition, phase separation, preferential sputtering, etc. The present understanding is still not sufficient to specify the dominant driving forces responsible for self-organization. 3D atomistic simulations can improve the understanding by reproducing the pattern formation with the detailed microscopic description of the driving forces. 2D simulations published so far can contribute to this understanding only partially. A novel program package for 3D atomistic simulations called TRIDER (TRansport of Ions in matter with DEfect Relaxation), which unifies full collision cascade simulation with atomistic relaxation processes, has been developed. The collision cascades are provided by simulations based on the Binary Collision Approximation, and the relaxation processes are simulated with the 3D lattice kinetic Monte-Carlo method. This allows, without any phenomenological model, a full 3D atomistic description on experimental spatiotemporal scales. Recently discussed new mechanisms of surface patterning like ballistic mass drift or the dependence of the local morphology on sputtering yield are inherently included in our atomistic approach. The atomistic 3D simulations do not depend so much on experimental assumptions like reported 2D simulations or continuum theories. The 3D computer experiments can even be considered as 'cleanest' possible experiments for checking continuum theories. This work aims mainly at the methodology of a novel atomistic approach, showing that: (i) In general, sputtering is not the dominant driving force responsible for the ripple formation. Processes like bulk and surface defect kinetics dominate the surface morphology evolution. Only at grazing incidence the sputtering has been found to be a direct cause of the ripple formation. Bradley and Harper theory fails in explaining the ripple dynamics because it is based on the second-order-effect 'sputtering'. However, taking into account the new mechanisms, a 'Bradley-Harper equation' with redefined parameters can be derived, which describes pattern formation satisfactorily. (ii) Kinetics of (bulk) defects has been revealed as the dominating driving force of pattern formation. Constantly created defects within the collision cascade, are responsible for local surface topography fluctuation and cause surface mass currents. The mass currents smooth the surface at normal and close to normal ion incidence angles, while ripples appear first at incidence angles larger than 40°. The evolution of bimetallic interfaces under ion irradiation is another application of TRIDER described in this thesis. The collisional mixing is in competition with diffusion and phase separation. The irradiation with He ions is studied for two extreme cases of bimetals: (i) Irradiation of interfaces formed by immiscible elements, here Al and Pb. Ballistic interface mixing is accompanied by phase separation. Al and Pb nanoclusters show a self-ordering (banding) parallel to the interface. (ii) Irradiation of interfaces by intermetallics forming species, here Pt and Co. Well-ordered layers of phases of intermetallics appear in the sequence Pt/Pt3Co/PtCo/PtCo3/Co. The TRIDER program package has been proven to be an appropriate technique providing a complete picture of mixing mechanisms.

Η υπέρταση είναι ένας από τους σημαντικότερους παράγοντες που αυξάνει τα καρδιαγγειακά επεισόδια τα οποία ευθύνονται περίπου για το ήμισυ των θανατηφόρων επεισοδίων στους ενήλικους. To σύστημα ρενίνης-αγγειοτασίνης-αλδοστερόνης (ΣΡΑΑ) διαδραματίζει καθοριστικό ρόλο στην παθοφυσιολογία των καρδιαγγειακών νόσων. Η αναστολή του ΣΡΑΑ σε παθολογικές καταστάσεις μπορεί να πραγματοποιηθεί με αναστολή του ενζύμου της ρενίνης ή παρεμπόδιση της σύνδεσης της ΑΙΙ με τους υποδοχείς ΑΤ1. Έχει διατυπωθεί η υπόθεση ότι τα αμφοτερικά μόρια για να αλληλεπιδράσουν με τον υποδοχέα θα πρέπει πρώτα να εισδύσουν σε κατάλληλη τοπογραφική θέση στις βιολογικές μεμβράνες και μετά με διάχυση να προσεγγίσουν το ενεργό κέντρο όπου όταν προσδεθούν με μία σειρά αντιδράσεων θα εξασκήσουν τη βιολογική τους δράση. Για την κατανόηση του ρόλου των μεμβρανών στο σύστημα ΣΡΑΑ μελετήθηκαν οι αλληλεπιδράσεις της αλισκιρένης (αναστολέας ρενίνης) και ολμεσαρτάνης (ανταγωνιστής αγγειοτασίνης ΙΙ) σε μοντέλα διπλοστιβάδων διπαλμιτικής φωσφατιδυλοχολίνης με ή χωρίς χοληστερόλη. Οι μελέτες διεξήχθησαν κάνοντας χρήση Πυρηνικού Μαγνητικού Συντονισμού (υγρής και στερεής κατάστασης), Διαφορικής Θερμιδομετρίας Σάρωσης, Φασματοσκοπίας Raman και Περίθλασης Ακτίνων-Χ. Σύγκριση των πειραματικών αποτελεσμάτων με άλλες σαρτάνες που μελετήθηκαν κάνοντας χρήση τις ίδιες τεχνικές απόδειξαν ότι όλα τα φάρμακα του ΣΡΑΑ εντοπίζονται στην ενδιάμεση φάση όπου εξασκούν διαφορετικές υδρόφιλες και λιπόφιλες αλληλεπιδράσεις. Επομένως το κάθε φάρμακο αποτυπώνει τη δική του σφραγίδα μέσα στις λιπιδικές διπλοστιβάδες. Αυτή η μοναδικότητα στις αλληλεπιδράσεις κάθε φαρμάκου με τις λιπιδικές διπλοστιβάδες ίσως να σχετίζεται και με τη μοναδικότητα του στο φαρμακευτικό του προφίλ. Ένα άλλο ενδιαφέρον αποτέλεσμα που προέκυψε από τις μελέτες είναι ότι η ολμεσαρτάνη σε μεθανολικό διάλυμα τόσο σε χαμηλή θερμοκρασία όσο και σε θερμοκρασία δωματίου δεν είναι σταθερή και μετατρέπεται στο αιθερικό της παράγωγο το οποίο ταυτοποιήθηκε φασματοσκοπικά. Στις ίδιες συνθήκες δεν παρατηρήθηκε εστεροποίηση. / Hypertension is one of the major risk factors responsible for the increase of half of the cardiovascular episodes in the adults. The system of Renin-Angiotensin-Aldosterone (RAAS) plays a determinative role in the pathophysiology of cardiovascular diseases. In a pathological state the aim is to block the generation of Angiotensin II through inhibition of rennin or angiotensin converting enzymes or its action on AT1 receptor. It has been hypothesized that amphiphilic molecules in order to exert their action on the receptor site, they have first to enter into the lipidic core of the lipid bilayers and then diffuse towards the active site. Thus, if this mechanism is applied, the lipidic part of the membrane bilayers appears to play an important role in the membrane action. To comprehend on the membrane:drug interactions we have studied the effects of olmesartan and aliskiren using dipalmitoylphosphatidylcholine bilayers with or without cholesterol. Various physical chemical methodologies such as liquid and solid state NMR , x-ray diffraction, Raman spectroscopy and Differential Scanning Calorimetry have been applied. The comparative results with other SARTANs showed that all drugs of the RAAS system act on the polar group and upper part of the alkyl chain, but exert different interactions. Thus, each drug is characterized by its own fingerprint in terms of its interactions and this may explain its unique pharmacological profile. Another, intriguing result derived from this thesis dissertation is the observation that olmesartan in methanolic solution is converted to its ether analogue. This isolated product was unambiguously structurally elucidated using a combination of LC-MS and 2D NMR spectroscopy.

No description available.

Self-organization of regular surface pattern under ion beam erosion was described in detail by Navez in 1962. Several years later in 1986 Bradley and Harper (BH) published the first self-consistent theory on this phenomenon based on the competition of surface roughening described by Sigmund's sputter theory and surface smoothing by Mullins-Herring diffusion. Many papers that followed BH theory introduced other processes responsible for the surface patterning e.g. viscous flow, redeposition, phase separation, preferential sputtering, etc. The present understanding is still not sufficient to specify the dominant driving forces responsible for self-organization. 3D atomistic simulations can improve the understanding by reproducing the pattern formation with the detailed microscopic description of the driving forces. 2D simulations published so far can contribute to this understanding only partially. A novel program package for 3D atomistic simulations called TRIDER (TRansport of Ions in matter with DEfect Relaxation), which unifies full collision cascade simulation with atomistic relaxation processes, has been developed. The collision cascades are provided by simulations based on the Binary Collision Approximation, and the relaxation processes are simulated with the 3D lattice kinetic Monte-Carlo method. This allows, without any phenomenological model, a full 3D atomistic description on experimental spatiotemporal scales. Recently discussed new mechanisms of surface patterning like ballistic mass drift or the dependence of the local morphology on sputtering yield are inherently included in our atomistic approach. The atomistic 3D simulations do not depend so much on experimental assumptions like reported 2D simulations or continuum theories. The 3D computer experiments can even be considered as 'cleanest' possible experiments for checking continuum theories. This work aims mainly at the methodology of a novel atomistic approach, showing that: (i) In general, sputtering is not the dominant driving force responsible for the ripple formation. Processes like bulk and surface defect kinetics dominate the surface morphology evolution. Only at grazing incidence the sputtering has been found to be a direct cause of the ripple formation. Bradley and Harper theory fails in explaining the ripple dynamics because it is based on the second-order-effect 'sputtering'. However, taking into account the new mechanisms, a 'Bradley-Harper equation' with redefined parameters can be derived, which describes pattern formation satisfactorily. (ii) Kinetics of (bulk) defects has been revealed as the dominating driving force of pattern formation. Constantly created defects within the collision cascade, are responsible for local surface topography fluctuation and cause surface mass currents. The mass currents smooth the surface at normal and close to normal ion incidence angles, while ripples appear first at incidence angles larger than 40°. The evolution of bimetallic interfaces under ion irradiation is another application of TRIDER described in this thesis. The collisional mixing is in competition with diffusion and phase separation. The irradiation with He ions is studied for two extreme cases of bimetals: (i) Irradiation of interfaces formed by immiscible elements, here Al and Pb. Ballistic interface mixing is accompanied by phase separation. Al and Pb nanoclusters show a self-ordering (banding) parallel to the interface. (ii) Irradiation of interfaces by intermetallics forming species, here Pt and Co. Well-ordered layers of phases of intermetallics appear in the sequence Pt/Pt3Co/PtCo/PtCo3/Co. The TRIDER program package has been proven to be an appropriate technique providing a complete picture of mixing mechanisms.

In the first part of the thesis, the molecular structure and electronic properties of phospholipids at the single molecule level and also for a monolayer structure are investigated via ab initio calculations under different degrees of hydration. The focus of the study is on phosphatidylcholines, in particular dipalmitoylphosphatidylcholine (DPPC), which are the most abundant phospholipids in biological membranes. Upon hydration, the phospholipid shape into a sickle-like structure. The hydration dramatically alters the surface potential, dipole and quadrupole moments of the lipids, and probably guides the interactions of the lipids with other molecules and the communication between cells. The vibrational spectrum of DPPC and DPPC-water complexes are completely assigned and it is shown that water hydrating the lipid head groups enables efficient energy transfer across membrane leaflets on sub-picosecond time scales. Moreover, the vibrational modes and lifetimes of pure and hydrated DPPC lipids, at human body temperature, are estimated by performing ab initio molecular dynamics simulations. The vibrational modes of the water molecules close to the head group of DPPC are active in the frequency range between 0.5 - 55 THz, with a peak at 2.80 THz in the energy spectrum. The computed lifetimes for the high-frequency modes agree well with recent data measured at room temperature, where high-order phonon scattering is not negligible. The structure and auto-ionization of water at the water-phospholipid interface are investigated by ab initio molecular dynamics and ab initio Monte Carlo simulations using local density approximation and generalized gradient approximation for the exchange-correlation energy functional. Depending on the lipid head group, strongly enhanced ionization is observed, leading to dissociation of several water molecules into H+ and OH- per lipid. The results can shed light on the phenomena of the high proton conductivity along membranes that has been reported experimentally. In the second part of the thesis, Monte Carlo simulations of the lipid bilayer, on the basis of a coarse grained model, are performed to gain insight into the mechanical properties of planar lipid bilayers. By using a rescaling method, the Poisson's ratio is calculated for different phases. Additional information on the bending rigidity, determined from height fluctuations on the basis of the Helfrich Hamiltonian, allows for calculation of the Young's modulus for each phase. In addition, the free energy barrier for lipid flip-flop process in the fluid and gel phases are estimated. The main rate-limiting step to complete a flip-flop process is related to a free energy barrier that has to be crossed in order to reach the center of the bilayer. The free energy cost for performing a lipid flip-flop in the gel phase is found to be five times greater than in the fluid phase, demonstrating the rarity of such events in the gel phase. Moreover, an energy barrier is estimated for formation of transient water pores that often precedes lipid translocation events and accounts for the rate-limiting step of these pore-associated lipid translocation processes.