Computer simulations of microstructures related to the olivine spinel transition

Tiefherd-Beben, die im oberen Erdmantel in einer Tiefe von ca. 400 km auftreten, werden gewöhnlich mit dem in gleicher Tiefe auftretenden druckabhängigen, polymorphen Phasenübergang von Olivine (α-Phase) zu Spinel (β-Phase) in Verbindung gebracht. Es ist jedoch nach wie vor unklar, wie der Phasenübergang mit dem mechanischen Versagen des Mantelmaterials zusammenhängt. Zur Zeit werden im Wesentlichen zwei Modelle diskutiert, die entweder Mikrostrukturen, die durch den Phasenübergang entstehen, oder aber die rheologischen Veränderungen des Mantelgesteins durch den Phasenübergang dafür verantwortlich machen. Dabei sind Untersuchungen der Olivin→Spinel Umwandlung durch die Unzugänglichkeit des natürlichen Materials vollständig auf theoretische Überlegungen sowie Hochdruck-Experimente und Numerische Simulationen beschränkt. Das zentrale Thema dieser Dissertation war es, ein funktionierendes Computermodell zur Simulation der Mikrostrukturen zu entwickeln, die durch den Phasenübergang entstehen. Des Weiteren wurde das Computer Modell angewandt um die mikrostrukturelle Entwicklung von Spinelkörnern und die Kontrollparameter zu untersuchen. Die Arbeit ist daher in zwei Teile unterteilt: Der erste Teil (Kap. 2 und 3) behandelt die physikalischen Gesetzmäßigkeiten und die prinzipielle Funktionsweise des Computer Modells, das auf der Kombination von Gleichungen zur Errechnung der kinetischen Reaktionsgeschwindigkeit mit Gesetzen der Nichtgleichgewichtsthermodynamik unter nicht-hydostatischen Bedingungen beruht. Das Computermodell erweitert ein Federnetzwerk der Software latte aus dem Programmpaket elle. Der wichtigste Parameter ist dabei die Normalspannung auf der Kornoberfläche von Spinel. Darüber hinaus berücksichtigt das Programm die Latenzwärme der Reaktion, die Oberflächenenergie und die geringe Viskosität von Mantelmaterial als weitere wesentliche Parameter in der Berechnung der Reaktionskinetic. Das Wachstumsverhalten und die fraktale Dimension von errechneten Spinelkörnern ist dabei in guter Übereinstimmung mit Spinelstrukturen aus Hochdruckexperimenten. Im zweiten Teil der Arbeit wird das Computermodell angewandt, um die Entwicklung der Oberflächenstruktur von Spinelkörnern unter verschiedenen Bedigungen zu eruieren. Die sogenannte ’anticrack theory of faulting’, die den katastrophalen Verlauf der Olivine→Spinel Umwandlung in olivinhaltigem Material unter differentieller Spannung durch Spannungskonzentrationen erklärt, wurde anhand des Computermodells untersucht. Der entsprechende Mechanismus konnte dabei nicht bestätigt werden. Stattdessen können Oberflächenstrukturen, die Ähnlichkeiten zu Anticracks aufweisen, durch Unreinheiten des Materials erklärt werden (Kap. 4). Eine Reihe von Simulationen wurde der Herleitung der wichtigsten Kontrollparameter der Reaktion in monomineralischem Olivin gewidmet (Kap. 5 and Kap. 6). Als wichtigste Einflüsse auf die Kornform von Spinel stellten sich dabei die Hauptnormalspannungen auf dem System sowie Heterogenitäten im Wirtsminerals und die Viskosität heraus. Im weiteren Verlauf wurden die Nukleierung und das Wachstum von Spinel in polymineralischen Mineralparagenesen untersucht (Kap. 7). Die Reaktionsgeschwindigkeit der Olivine→Spinel Umwandlung und die Entwicklung von Spinelnetzwerken und Clustern wird durch die Gegenwart nicht-reaktiver Minerale wie Granat oder Pyroxen erheblich beschleunigt. Die Bildung von Spinelnetzwerken hat das Potential, die mechanischen Eigenschaften von Mantelgestein erheblich zu beeinflussen, sei es durch die Bildung potentieller Scherzonen oder durch Gerüstbildung. Dieser Lokalisierungprozess des Spinelwachstums in Mantelgesteinen kann daher ein neues Erklärungsmuster für Tiefbeben darstellen.

Phytoplankton Response to Environmental Variables and Organic Pollutants. Laboratory Cultures and Numerical Simulations Experiments

Herbicides are becoming emergent contaminants in Italian surface, coastal and ground waters, due to their intensive use in agriculture. In marine environments herbicides have adverse effects on non-target organisms, as primary producers, resulting in oxygen depletion and decreased primary productivity. Alterations of species composition in algal communities can also occur due to the different sensitivity among the species. In the present thesis the effects of herbicides, widely used in the Northern Adriatic Sea, on different algal species were studied. The main goal of this work was to study the influence of temperature on algal growth in the presence of the triazinic herbicide terbuthylazine (TBA), and the cellular responses adopted to counteract the toxic effects of the pollutant (Chapter 1 and 2). The development of simulation models to be applied in environmental management are needed to organize and track information in a way that would not be possible otherwise and simulate an ecological prospective. The data collected from laboratory experiments were used to simulate algal responses to the TBA exposure at increasing temperature conditions (Chapter 3). Part of the thesis was conducted in foreign countries. The work presented in Chapter 4 was focused on the effect of high light on growth, toxicity and mixotrophy of the ichtyotoxic species Prymnesium parvum. In addition, a mesocosm experiment was conducted in order to study the synergic effect of the pollutant emamectin benzoate with other anthropogenic stressors, such as oil pollution and induced phytoplankton blooms (Chapter 5).

Modeling and simulations of some anisotropic soft-matter systems: from biaxial to chiral materials

We have modeled various soft-matter systems with molecular dynamics (MD) simulations. The first topic concerns liquid crystal (LC) biaxial nematic (Nb) phases, that can be possibly used in fast displays. We have investigated the phase organization of biaxial Gay-Berne (GB) mesogens, considering the effects of the orientation, strength and position of a molecular dipole. We have observed that for systems with a central dipole, nematic biaxial phases disappear when increasing dipole strength, while for systems characterized by an offset dipole, the Nb phase is stabilized at very low temperatures. In a second project, in view of their increasing importance as nanomaterials in LC phases, we are developing a DNA coarse-grained (CG) model, in which sugar and phosphate groups are represented with Lennard-Jones spheres, while bases with GB ellipsoids. We have obtained shape, position and orientation parameters for each bead, to best reproduce the atomistic structure of a B-DNA helix. Starting from atomistic simulations results, we have completed a first parametrization of the force field terms, accounting for bonded (bonds, angles and dihedrals) and non-bonded interactions (H-bond and stacking). We are currently validating the model, by investigating stability and melting temperature of various sequences. Finally, in a third project, we aim to explain the mechanism of enantiomeric discrimination due to the presence of a chiral helix of poly(gamma-benzyl L-glutamate) (PBLG), in solution of dimethylformamide (DMF), interacting with chiral or pro-chiral molecules (in our case heptyl butyrate, HEP), after tuning properly an atomistic force field (AMBER). We have observed that DMF and HEP molecules solvate uniformly the PBLG helix, but the pro-chiral solute is on average found closer to the helix with respect to the DMF. The solvent presents a faster isotropic diffusion, twice as HEP, also indicating a stronger interaction of the solute with the helix.

Numerical simulations of microphysical processes in pyro-convective clouds

Hochreichende Konvektion über Waldbränden ist eine der intensivsten Formen von atmosphärischer Konvektion. Die extreme Wolkendynamik mit hohen vertikalen Windgeschwindigkeiten (bis 20 m/s) bereits an der Wolkenbasis, hohen Wasserdampfübersättigungen (bis 1%) und die durch das Feuer hohen Anzahlkonzentration von Aerosolpartikeln (bis 100000 cm^-3) bilden einen besonderen Rahmen für Aerosol-Wolken Wechselwirkungen.Ein entscheidender Schritt in der mikrophysikalischen Entwicklung einer konvektiven Wolke ist die Aktivierung von Aerosolpartikeln zu Wolkentropfen. Dieser Aktivierungsprozess bestimmt die anfängliche Anzahl und Größe der Wolkentropfen und kann daher die Entwicklung einer konvektiven Wolke und deren Niederschlagsbildung beeinflussen. Die wichtigsten Faktoren, welche die anfängliche Anzahl und Größe der Wolkentropfen bestimmen, sind die Größe und Hygroskopizität der an der Wolkenbasis verfügbaren Aerosolpartikel sowie die vertikale Windgeschwindigkeit. Um den Einfluss dieser Faktoren unter pyro-konvektiven Bedingungen zu untersuchen, wurden numerische Simulationen mit Hilfe eines Wolkenpaketmodells mit detaillierter spektraler Beschreibung der Wolkenmikrophysik durchgeführt. Diese Ergebnisse können in drei unterschiedliche Bereiche abhängig vom Verhältnis zwischen vertikaler Windgeschwindigkeit und Aerosolanzahlkonzentration (w/NCN) eingeteilt werden: (1) ein durch die Aerosolkonzentration limitierter Bereich (hohes w/NCN), (2) ein durch die vertikale Windgeschwindigkeit limitierter Bereich (niedriges w/NCN) und (3) ein Übergangsbereich (mittleres w/NCN). Die Ergebnisse zeigen, dass die Variabilität der anfänglichen Anzahlkonzentration der Wolkentropfen in (pyro-) konvektiven Wolken hauptsächlich durch die Variabilität der vertikalen Windgeschwindigkeit und der Aerosolkonzentration bestimmt wird. rnUm die mikrophysikalischen Prozesse innerhalb der rauchigen Aufwindregion einer pyrokonvektiven Wolke mit einer detaillierten spektralen Mikrophysik zu untersuchen, wurde das Paketmodel entlang einer Trajektorie innerhalb der Aufwindregion initialisiert. Diese Trajektore wurde durch dreidimensionale Simulationen eines pyro-konvektiven Ereignisses durch das Model ATHAM berechnet. Es zeigt sich, dass die Anzahlkonzentration der Wolkentropfen mit steigender Aerosolkonzentration ansteigt. Auf der anderen Seite verringert sich die Größe der Wolkentropfen mit steigender Aerosolkonzentration. Die Reduzierung der Verbreiterung des Tropfenspektrums stimmt mit den Ergebnissen aus Messungen überein und unterstützt das Konzept der Unterdrückung von Niederschlag in stark verschmutzen Wolken.Mit Hilfe des Models ATHAM wurden die dynamischen und mikrophysikalischen Prozesse von pyro-konvektiven Wolken, aufbauend auf einer realistischen Parametrisierung der Aktivierung von Aerosolpartikeln durch die Ergebnisse der Aktivierungsstudie, mit zwei- und dreidimensionalen Simulationen untersucht. Ein modernes zweimomenten mikrophysikalisches Schema wurde in ATHAM implementiert, um den Einfluss der Anzahlkonzentration von Aerosolpartikeln auf die Entwicklung von idealisierten pyro-konvektiven Wolken in US Standardamtosphären für die mittleren Breiten und den Tropen zu untersuchen. Die Ergebnisse zeigen, dass die Anzahlkonzentration der Aerosolpartikel die Bildung von Regen beeinflusst. Für geringe Aerosolkonzentrationen findet die rasche Regenbildung hauptsächlich durch warme mikrophysikalische Prozesse statt. Für höhere Aerosolkonzentrationen ist die Eisphase wichtiger für die Bildung von Regen. Dies führt zu einem verspäteten Einsetzen von Niederschlag für verunreinigtere Atmosphären. Außerdem wird gezeigt, dass die Zusammensetzung der Eisnukleationspartikel (IN) einen starken Einfluss auf die dynamische und mikrophysikalische Struktur solcher Wolken hat. Bei sehr effizienten IN bildet sich Regen früher. Die Untersuchung zum Einfluss des atmosphärischen Hintergrundprofils zeigt eine geringe Auswirkung der Meteorologie auf die Sensitivität der pyro-konvektiven Wolken auf diernAerosolkonzentration. Zum Abschluss wird gezeigt, dass die durch das Feuer emittierte Hitze einen deutlichen Einfluss auf die Entwicklung und die Wolkenobergrenze von pyro-konvektive Wolken hat. Zusammenfassend kann gesagt werden, dass in dieser Dissertation die Mikrophysik von pyrokonvektiven Wolken mit Hilfe von idealisierten Simulation eines Wolkenpaketmodell mit detaillierte spektraler Mikrophysik und eines 3D Modells mit einem zweimomenten Schema im Detail untersucht wurde. Es wird gezeigt, dass die extremen Bedingungen im Bezug auf die vertikale Windgeschwindigkeiten und Aerosolkonzentrationen einen deutlichen Einfluss auf die Entwicklung von pyro-konvektiven Wolken haben.

Simulations of charge transport in organic compounds

To aid the design of organic semiconductors, we study the charge transport properties of organic liquid crystals, i.e. hexabenzocoronene and carbazole macrocycle, and single crystals, i.e. rubrene, indolocarbazole and benzothiophene derivatives (BTBT, BBBT). The aim is to find structure-property relationships linking the chemical structure as well as the morphology with the bulk charge carrier mobility of the compounds. To this end, molecular dynamics (MD) simulations are performed yielding realistic equilibrated morphologies. Partial charges and molecular orbitals are calculated based on single molecules in vacuum using quantum chemical methods. The molecular orbitals are then mapped onto the molecular positions and orientations, which allows calculation of the transfer integrals between nearest neighbors using the molecular orbital overlap method. Thus we obtain realistic transfer integral distributions and their autocorrelations. In case of organic crystals the differences between two descriptions of charge transport, namely semi-classical dynamics (SCD) in the small polaron limit and kinetic Monte Carlo (KMC) based on Marcus rates, are studied. The liquid crystals are investigated solely in the hopping limit. To simulate the charge dynamics using KMC, the centers of mass of the molecules are mapped onto lattice sites and the transfer integrals are used to compute the hopping rates. In the small polaron limit, where the electronic wave function is spread over a limited number of neighboring molecules, the Schroedinger equation is solved numerically using a semi-classical approach. The results are compared for the different compounds and methods and, where available, with experimental data. The carbazole macrocycles form columnar structures arranged on a hexagonal lattice with side chains facing inwards, so columns can closely approach each other allowing inter-columnar and thus three-dimensional transport. When taking only intra-columnar transport into account, the mobility is orders of magnitude lower than in the three-dimensional case. BTBT is a promising material for solution-processed organic field-effect transistors. We are able to show that, on the time-scales of charge transport, static disorder due to slow side chain motions is the main factor determining the mobility. The resulting broad transfer integral distributions modify the connectivity of the system but sufficiently many fast percolation paths remain for the charges. Rubrene, indolocarbazole and BBBT are examples of crystals without significant static disorder. The high mobility of rubrene is explained by two main features: first, the shifted cofacial alignment of its molecules, and second, the high center of mass vibrational frequency. In comparsion to SCD, only KMC based on Marcus rates is capable of describing neighbors with low coupling and of taking static disorder into account three-dimensionally. Thus it is the method of choice for crystalline systems dominated by static disorder. However, it is inappropriate for the case of strong coupling and underestimates the mobility of well-ordered crystals. SCD, despite its one-dimensionality, is valuable for crystals with strong coupling and little disorder. It also allows correct treatment of dynamical effects, such as intermolecular vibrations of the molecules. Rate equations are incapable of this, because simulations are performed on static snapshots. We have thus shown strengths and weaknesses of two state of the art models used to study charge transport in organic compounds, partially developed a program to compute and visualize transfer integral distributions and other charge transport properties, and found structure-mobility relations for several promising organic semiconductors.

Parallelization of the algorithm WHAM with NVIDIA CUDA.

The aim of my thesis is to parallelize the Weighting Histogram Analysis Method (WHAM), which is a popular algorithm used to calculate the Free Energy of a molucular system in Molecular Dynamics simulations. WHAM works in post processing in cooperation with another algorithm called Umbrella Sampling. Umbrella Sampling has the purpose to add a biasing in the potential energy of the system in order to force the system to sample a specific region in the configurational space. Several N independent simulations are performed in order to sample all the region of interest. Subsequently, the WHAM algorithm is used to estimate the original system energy starting from the N atomic trajectories. The parallelization of WHAM has been performed through CUDA, a language that allows to work in GPUs of NVIDIA graphic cards, which have a parallel achitecture. The parallel implementation may sensibly speed up the WHAM execution compared to previous serial CPU imlementations. However, the WHAM CPU code presents some temporal criticalities to very high numbers of interactions. The algorithm has been written in C++ and executed in UNIX systems provided with NVIDIA graphic cards. The results were satisfying obtaining an increase of performances when the model was executed on graphics cards with compute capability greater. Nonetheless, the GPUs used to test the algorithm is quite old and not designated for scientific calculations. It is likely that a further performance increase will be obtained if the algorithm would be executed in clusters of GPU at high level of computational efficiency. The thesis is organized in the following way: I will first describe the mathematical formulation of Umbrella Sampling and WHAM algorithm with their apllications in the study of ionic channels and in Molecular Docking (Chapter 1); then, I will present the CUDA architectures used to implement the model (Chapter 2); and finally, the results obtained on model systems will be presented (Chapter 3).

Hydrodynamical simulations of early-type galaxies: effects of galaxy shape and stellar dynamics on hot coronae

Early-Type galaxies (ETGs) are embedded in hot (10^6-10^7 K), X-ray emitting gaseous haloes, produced mainly by stellar winds and heated by Type Ia supernovae explosions, by the thermalization of stellar motions and occasionally by the central super-massive black hole (SMBH). In particular, the thermalization of the stellar motions is due to the interaction between the stellar and the SNIa ejecta and the hot interstellar medium (ISM) already residing in the ETG. A number of different astrophysical phenomena determine the X-ray properties of the hot ISM, such as stellar population formation and evolution, galaxy structure and internal kinematics, Active Galactic Nuclei (AGN) presence, and environmental effects. With the aid of high-resolution hydrodynamical simulations performed on state-of-the-art galaxy models, in this Thesis we focus on the effects of galaxy shape, stellar kinematics and star formation on the evolution of the X-ray coronae of ETGs. Numerical simulations show that the relative importance of flattening and rotation are functions of the galaxy mass: at low galaxy masses, adding flattening and rotation induces a galactic wind, thus lowering the X-ray luminosity; at high galaxy masses the angular momentum conservation keeps the central regions of rotating galaxies at low density, whereas in non-rotating models a denser and brighter atmosphere is formed. The same dependence from the galaxy mass is present in the effects of star formation (SF): in light galaxies SF contributes to increase the spread in Lx, while at high galaxy masses the halo X-ray properties are marginally sensitive to SF effects. In every case, the star formation rate at the present epoch quite agrees with observations, and the massive, cold gaseous discs are partially or completely consumed by SF on a time-scale of few Gyr, excluding the presence of young stellar discs at the present epoch.

Analysis of cone-beam ct dose in image-guided radiation therapy for brain and prostate cancer patients via gpu-based Monte Carlo simulations

La radioterapia guidata da immagini (IGRT), grazie alle ripetute verifiche della posizione del paziente e della localizzazione del volume bersaglio, si è recentemente affermata come nuovo paradigma nella radioterapia, avendo migliorato radicalmente l’accuratezza nella somministrazione di dose a scopo terapeutico. Una promettente tecnica nel campo dell’IGRT è rappresentata dalla tomografia computerizzata a fascio conico (CBCT). La CBCT a kilovoltaggio, consente di fornire un’accurata mappatura tridimensionale dell’anatomia del paziente, in fase di pianificazione del trattamento e a ogni frazione del medisimo. Tuttavia, la dose da imaging attribuibile alle ripetute scansioni è diventata, negli ultimi anni, oggetto di una crescente preoccupazione nel contesto clinico. Lo scopo di questo lavoro è di valutare quantitativamente la dose addizionale somministrata da CBCT a kilovoltaggio, con riferimento a tre tipici protocolli di scansione per Varian OnBoard Imaging Systems (OBI, Palo Alto, California). A questo scopo sono state condotte simulazioni con codici Monte Carlo per il calcolo della dose, utilizzando il pacchetto gCTD, sviluppato sull’architettura della scheda grafica. L’utilizzo della GPU per sistemi server di calcolo ha permesso di raggiungere alte efficienze computazionali, accelerando le simulazioni Monte Carlo fino a raggiungere tempi di calcolo di ~1 min per un caso tipico. Inizialmente sono state condotte misure sperimentali di dose su un fantoccio d’acqua. I parametri necessari per la modellazione della sorgente di raggi X nel codice gCTD sono stati ottenuti attraverso un processo di validazione del codice al fine di accordare i valori di dose simulati in acqua con le misure nel fantoccio. Lo studio si concentra su cinquanta pazienti sottoposti a cicli di radioterapia a intensità modulata (IMRT). Venticinque pazienti con tumore al cervello sono utilizzati per studiare la dose nel protocollo standard-dose head e venticinque pazienti con tumore alla prostata sono selezionati per studiare la dose nei protocolli pelvis e pelvis spotlight. La dose media a ogni organo è calcolata. La dose media al 2% dei voxels con i valori più alti di dose è inoltre computata per ogni organo, al fine di caratterizzare l’omogeneità spaziale della distribuzione.

Molecular dynamics simulations of sheared brush-like systems

Mit Hilfe von Molekulardynamik-Simulationen untersuchen wir bürstenartige Systeme unter guten Lösungsmittelbedingungen. Diese Systeme sind, dank ihren vielfältigen Beschaffenheiten, die von Molekularparametern und äußeren Bedingungen abhängig sind, wichtig für viele industrielle Anwendungen. Man vermutet, dass die Polymerbürsten eine entscheidende Rolle in der Natur wegen ihrer einzigartigen Gleiteigenschaften spielen. Ein vergröbertes Modell wird verwendet, um die strukturellen und dynamischen Eigenschaften zweier hochkomprimierter Polymerbürsten, die eine niedrige Reibung aufweisen, zu untersuchen. Allerdings sind die Lubrikationseigenschaften dieser Systeme, die in vielen biologischen Systemen vorhanden sind, beeinflußt. Wir untersuchen so-genannte "weiche Kolloide", die zwischen den beiden Polymerbürsten eingebettet sind, und wie diese Makroobjekte auf die Polymerbürsten wirken.rnrnNicht-Gleichgewichts-Molekulardynamik-Simulationen werden durchgeführt, in denen die hydrodynamischen Wechselwirkungen durch die Anwendung des DPD-Thermostaten mit expliziten Lösungsmittelmolekülen berücksichtigt werden. Wir zeigen, dass die Kenntnis der Gleichgewichtseigenschaften des Systems erlaubt, dynamische Nichtgleichgewichtsigenschaften der Doppelschicht vorherzusagen.rnrnWir untersuchen, wie die effektive Wechselwirkung zwischen kolloidalen Einschlüßen durch die Anwesenheit der Bürsten (in Abhängigkeit der Weichheit der Kolloide und der Pfropfdichte der Bürsten) beeinflußt wird. Als nächsten Schritt untersuchen wir die rheologische Antwort von solchen komplexen Doppelschichten auf Scherung. Wir entwickeln eine Skalen-Theorie, die die Abhängigkeit der makroskopischen Transporteigenschaften und der lateralen Ausdehnung der verankerten Ketten von der Weissenberg Zahl oberhalb des Bereichs, in dem die lineare Antwort-Theorie gilt, voraussagt. Die Vorhersagen der Theorie stimmen gut mit unseren und früheren numerischen Ergebnissen und neuen Experimenten überein. Unsere Theorie bietet die Möglichkeit, die Relaxationszeit der Doppelschicht zu berechnen. Wenn diese Zeit mit einer charakteristischen Längenskala kombiniert wird, kann auch das ''transiente'' (nicht-stationäre) Verhalten beschrieben werden.rnrnrnWir untersuchen die Antwort des Drucktensors und die Deformation der Bürsten während der Scherinvertierung für grosse Weissenberg Zahlen. Wir entwickeln eine Vorhersage für die charakteristische Zeit, nach der das System wieder den stationären Zustand erreicht.rnrnrnElektrostatik spielt eine bedeutende Rolle in vielen biologischen Prozessen. Die Lubrikationseigenschaften der Polymerbürsten werden durch die Anwesenheit langreichweitiger Wechselwirkungen stark beeinflusst. Für unterschiedliche Stärken der elektrostatischen Wechselwirkungen untersuchen wir rheologische Eigenschaften der Doppelschicht und vergleichen mit neutralen Systemen. Wir studieren den kontinuierlichen Übergang der Systemeigenschaften von neutralen zu stark geladenen Bürsten durch Variation der Bjerrumlänge und der Ladungsdichte.

Computational Methods in Biophysics and Medicinal Chemistry: Applications and Challenges

In this thesis I described the theory and application of several computational methods in solving medicinal chemistry and biophysical tasks. I pointed out to the valuable information which could be achieved by means of computer simulations and to the possibility to predict the outcome of traditional experiments. Nowadays, computer represents an invaluable tool for chemists. In particular, the main topics of my research consisted in the development of an automated docking protocol for the voltage-gated hERG potassium channel blockers, and the investigation of the catalytic mechanism of the human peptidyl-prolyl cis-trans isomerase Pin1.

Computational strategies to include protein flexibility in Ligand Docking and Virtual Screening

The dynamic character of proteins strongly influences biomolecular recognition mechanisms. With the development of the main models of ligand recognition (lock-and-key, induced fit, conformational selection theories), the role of protein plasticity has become increasingly relevant. In particular, major structural changes concerning large deviations of protein backbones, and slight movements such as side chain rotations are now carefully considered in drug discovery and development. It is of great interest to identify multiple protein conformations as preliminary step in a screening campaign. Protein flexibility has been widely investigated, in terms of both local and global motions, in two diverse biological systems. On one side, Replica Exchange Molecular Dynamics has been exploited as enhanced sampling method to collect multiple conformations of Lactate Dehydrogenase A (LDHA), an emerging anticancer target. The aim of this project was the development of an Ensemble-based Virtual Screening protocol, in order to find novel potent inhibitors. On the other side, a preliminary study concerning the local flexibility of Opioid Receptors has been carried out through ALiBERO approach, an iterative method based on Elastic Network-Normal Mode Analysis and Monte Carlo sampling. Comparison of the Virtual Screening performances by using single or multiple conformations confirmed that the inclusion of protein flexibility in screening protocols has a positive effect on the probability to early recognize novel or known active compounds.

Properties of cosmic voids in dark energy simulations

The last decade has witnessed the establishment of a Standard Cosmological Model, which is based on two fundamental assumptions: the first one is the existence of a new non relativistic kind of particles, i. e. the Dark Matter (DM) that provides the potential wells in which structures create, while the second one is presence of the Dark Energy (DE), the simplest form of which is represented by the Cosmological Constant Λ, that sources the acceleration in the expansion of our Universe. These two features are summarized by the acronym ΛCDM, which is an abbreviation used to refer to the present Standard Cosmological Model. Although the Standard Cosmological Model shows a remarkably successful agreement with most of the available observations, it presents some longstanding unsolved problems. A possible way to solve these problems is represented by the introduction of a dynamical Dark Energy, in the form of the scalar field ϕ. In the coupled DE models, the scalar field ϕ features a direct interaction with matter in different regimes. Cosmic voids are large under-dense regions in the Universe devoided of matter. Being nearby empty of matter their dynamics is supposed to be dominated by DE, to the nature of which the properties of cosmic voids should be very sensitive. This thesis work is devoted to the statistical and geometrical analysis of cosmic voids in large N-body simulations of structure formation in the context of alternative competing cosmological models. In particular we used the ZOBOV code (see ref. Neyrinck 2008), a publicly available void finder algorithm, to identify voids in the Halos catalogues extraxted from CoDECS simulations (see ref. Baldi 2012 ). The CoDECS are the largest N-body simulations to date of interacting Dark Energy (DE) models. We identify suitable criteria to produce voids catalogues with the aim of comparing the properties of these objects in interacting DE scenarios to the standard ΛCDM model, at different redshifts. This thesis work is organized as follows: in chapter 1, the Standard Cosmological Model as well as the main properties of cosmic voids are intro- duced. In chapter 2, we will present the scalar field scenario. In chapter 3 the tools, the methods and the criteria by which a voids catalogue is created are described while in chapter 4 we discuss the statistical properties of cosmic voids included in our catalogues. In chapter 5 the geometrical properties of the catalogued cosmic voids are presented by means of their stacked profiles. In chapter 6 we summarized our results and we propose further developments of this work.

Thermodynamic concepts in adaptive resolution simulations

This thesis work is devoted to the conceptual and technical development of the Adaptive Resolution Scheme (AdResS), a molecular dynamics method that allows the simulation of a system with different levels of resolution simultaneously. The simulation domain is divided into high and low resolution zones and a transition region that links them, through which molecules can freely diffuse.rnThe first issue of this work regards the thermodynamic consistency of the method, which is tested and verified in a model liquid of tetrahedral molecules. The results allow the introduction of the concept of the Thermodynamic Force, an external field able to correct spurious density fluctuations present in the transition region in usual AdResS simulations.rnThe AdResS is also applied to a system where two different representations with the same degree of resolution are confronted. This simple test extends the method from an Adaptive Resolution Scheme to an Adaptive Representation Scheme, providing a way of coupling different force fields based on thermodynamic consistency arguments. The Thermodynamic Force is successfully applied to the example described in this work as well.rnAn alternative approach of deducing the Thermodynamic Force from pressure consistency considerations allows the interpretation of AdResS as a first step towards a molecular dynamics simulation in the Grand Canonical ensemble. Additionally, such a definition leads to a practical way of determining the Thermodynamic Force, tested in the well studied tetrahedral liquid. The effects of AdResS and this correction on the atomistic domain are analyzed by inspecting the local distribution of velocities, radial distribution functions, pressure and particle number fluctuation. Their comparison with analogous results coming from purely atomistic simulations shows good agreement, which is greatly improved under the effect of the external field.rnA further step in the development of AdResS, necessary for several applications in biophysics and material science, consists of its application to multicomponent systems. To this aim, the high-resolution representation of a model binary mixture is confronted with its coarse-grained representation systematically parametrized. The Thermodynamic Force, whose development requires a more delicate treatment, also gives satisfactory results.rnFinally, AdResS is tested in systems including two-body bonded forces, through the simulation of a model polymer allowed to adaptively change its representation. It is shown that the distribution functions that characterize the polymer structure are in practice not affected by the change of resolution.rnThe technical details of the implementation of AdResS in the ESPResSo package conclude this thesis work.

Modeling and simulations of nanoparticles in liquid crystalline systems

The aim of this work is to investigate, using extensive Monte Carlo computer simulations, composite materials consisting of liquid crystals doped with nanoparticles. These systems are currently of great interest as they offer the possibility of tuning the properties of liquid crystals used in displays and other devices as well as providing a way of obtaining regularly organized systems of nanoparticles exploiting the molecular organization of the liquid crystal medium. Surprisingly enough, there is however a lack of fundamental knowledge on the properties and phase behavior of these hybrid materials, making the route to their application an essentially empirical one. Here we wish to contribute to the much needed rationalization of these systems studying some basic effects induced by different nanoparticles on a liquid crystal host. We investigate in particular the effects of nanoparticle shape, size and polarity as well as of their affinity to the liquid crystal solvent on the stability of the system, monitoring phase transitions, order and molecular organizations. To do this we have proposed a coarse grained approach where nanoparticles are modelled as a suitably shaped (spherical, rod and disk like) collection of spherical Lennard-Jones beads, while the mesogens are represented with Gay-Berne particles. We find that the addition of apolar nanoparticles of different shape typically lowers the nematic–isotropic transition of a non-polar nematic, with the destabilization being greater for spherical nanoparticles. For polar mesogens we have studied the effect of solvent affinity of the nanoparticles showing that aggregation takes places for low solvation values. Interestingly, if the nanoparticles are polar the aggregates contribute to stabilizing the system, compensating the shape effect. We thus find the overall effects on stability to be a delicate balance of often contrasting contributions pointing to the relevance of simulations studies for understanding these complex systems.