Atomistic simulations of liquid crystals in the bulk and at their interfaces

In this thesis, we have dealt with several problems concerning liquid crystals (LC) phases, either in the bulk or at their interfaces, by the use of atomistic molecular dynamics (MD) simulations. We first focused our attention on simulating and characterizing the bulk smectic phase of 4-n-octyl-4'-cyanobiphenyl (8CB), allowing us to investigate the antiparallel molecular arrangement typical of SmAd smectic phases. A second topic of study was the characterization of the 8CB interface with vacuum by simulating freely suspended thin films, which allowed us to determine the influence of the interface on the orientational and positional order. Then we investigated the LC-water and LC-electrolyte water solution interface. This interface has recently found application in the development of sensors for several compounds, including biological molecules, and here we tried to understand the re-orientation mechanism of LC molecules at the interface which is behind the functioning of these sensors. The characterization of this peculiar interface has incidentally led us to develop a polarizable force field for the pentyl-cyanobiphenyl mesogen, whose process of parametrization and validation is reported here in detail. We have shown that this force field is a significant improvement over its previous, static charge non polarizable version in terms of density, orientational order parameter and translational diffusion.

Simulations for Gravitational Lensing of 21 cm Radiation at EoR and Post-EoR Redshifts

21 cm cosmology opens an observational window to previously unexplored cosmological epochs such as the Epoch of Reionization (EoR), the Cosmic Dawn and the Dark Ages using powerful radio interferometers such as the planned Square Kilometer Array (SKA). Among all the other applications which can potentially improve the understanding of standard cosmology, we study the promising opportunity given by measuring the weak gravitational lensing sourced by 21 cm radiation. We performed this study in two different cosmological epochs, at a typical EoR redshift and successively at a post-EoR redshift. We will show how the lensing signal can be reconstructed using a three dimensional optimal quadratic lensing estimator in Fourier space, using single frequency band or combining multiple frequency band measurements. To this purpose, we implemented a simulation pipeline capable of dealing with issues that can not be treated analytically. Considering the current SKA plans, we studied the performance of the quadratic estimator at typical EoR redshifts, for different survey strategies and comparing two thermal noise models for the SKA-Low array. The simulation we performed takes into account the beam of the telescope and the discreteness of visibility measurements. We found that an SKA-Low interferometer should obtain high-fidelity images of the underlying mass distribution in its phase 1 only if several bands are stacked together, covering a redshift range that goes from z=7 to z=11.5. The SKA-Low phase 2, modeled in order to improve the sensitivity of the instrument by almost an order of magnitude, should be capable of providing images with good quality even when the signal is detected within a single frequency band. Considering also the serious effect that foregrounds could have on this detections, we discussed the limits of these results and also the possibility provided by these models of measuring an accurate lensing power spectrum.

Zoomed simulations of Halo segregation in cosmological models with two species of coupled dark matter

La materia ordinaria copre soli pochi punti percentuali della massa-energia totale dell'Universo, che è invece largamente dominata da componenti “oscure”. Il modello standard usato per descriverle è il modello LambdaCDM. Nonostante esso sembri consistente con la maggior parte dei dati attualmente disponibili, presenta alcuni problemi fondamentali che ad oggi restano irrisolti, lasciando spazio per lo studio di modelli cosmologici alternativi. Questa Tesi mira a studiare un modello proposto recentemente, chiamato “Multi-coupled Dark Energy” (McDE), che presenta interazioni modificate rispetto al modello LambdaCDM. In particolare, la Materia Oscura è composta da due diversi tipi di particelle con accoppiamento opposto rispetto ad un campo scalare responsabile dell'Energia Oscura. L'evoluzione del background e delle perturbazioni lineari risultano essere indistinguibili da quelle del modello LambdaCDM. In questa Tesi viene presentata per la prima volta una serie di simulazioni numeriche “zoomed”. Esse presentano diverse regioni con risoluzione differente, centrate su un singolo ammasso di interesse, che permettono di studiare in dettaglio una singola struttura senza aumentare eccessivamente il tempo di calcolo necessario. Un codice chiamato ZInCo, da me appositamente sviluppato per questa Tesi, viene anch'esso presentato per la prima volta. Il codice produce condizioni iniziali adatte a simulazioni cosmologiche, con differenti regioni di risoluzione, indipendenti dal modello cosmologico scelto e che preservano tutte le caratteristiche dello spettro di potenza imposto su di esse. Il codice ZInCo è stato usato per produrre condizioni iniziali per una serie di simulazioni numeriche del modello McDE, le quali per la prima volta mostrano, grazie all'alta risoluzione raggiunta, che l'effetto di segregazione degli ammassi avviene significativamente prima di quanto stimato in precedenza. Inoltre, i profili radiale di densità ottenuti mostrano un appiattimento centrale nelle fasi iniziali della segregazione. Quest'ultimo effetto potrebbe aiutare a risolvere il problema “cusp-core” del modello LambdaCDM e porre limiti ai valori dell'accoppiamento possibili.

Molecular dynamics simulations of silicate and borate glasses and melts : structure, diffusion dynamics and vibrational properties

Molecular dynamics simulations of silicate and borate glasses and melts: Structure, diffusion dynamics and vibrational properties. In this work computer simulations of the model glass formers SiO2 and B2O3 are presented, using the techniques of classical molecular dynamics (MD) simulations and quantum mechanical calculations, based on density functional theory (DFT). The latter limits the system size to about 100−200 atoms. SiO2 and B2O3 are the two most important network formers for industrial applications of oxide glasses. Glass samples are generated by means of a quench from the melt with classical MD simulations and a subsequent structural relaxation with DFT forces. In addition, full ab initio quenches are carried out with a significantly faster cooling rate. In principle, the structural properties are in good agreement with experimental results from neutron and X-ray scattering, in all cases. A special focus is on the study of vibrational properties, as they give access to low-temperature thermodynamic properties. The vibrational spectra are calculated by the so-called ”frozen phonon” method. In all cases, the DFT curves show an acceptable agreement with experimental results of inelastic neutron scattering. In case of the model glass former B2O3, a new classical interaction potential is parametrized, based on the liquid trajectory of an ab initio MD simulation at 2300 K. In this course, a structural fitting routine is used. The inclusion of 3-body angular interactions leads to a significantly improved agreement of the liquid properties of the classical MD and ab initio MD simulations. However, the generated glass structures, in all cases, show a significantly lower fraction of 3-membered planar boroxol rings as predicted by experimental results (f=60%-80%). The largest boroxol ring fraction of f=15±5% is observed in the full ab initio quenches from 2300 K. In case of SiO2, the glass structures after the quantum mechanical relaxation are the basis for calculations of the linear thermal expansion coefficient αL(T), employing the quasi-harmonic approximation. The striking observation is a change change of sign of αL(T) going along with a temperature range of negative αL(T) at low temperatures, which is in good agreement with experimental results.

Monte Carlo simulations of nucleation of colloidal crystals

A crystal nucleus in a finite volume may exhibit phase coexistence with a surrounding fluid. The thermodynamic properties of the coexisting fluid (pressure and chemical potential) are enhanced relative to their coexistence values. This enhancement is uniquely related to the surface excess free energy. rnA model for weakly attractive soft colloidal particles is investigated, the so called Asakura-Oosawa model. In simulations, this model allows for the calculation of the pressure in the liquid using the virial formula directly. The phase coexistence pressure in the thermodynamic limit is obtained from the interface velocity method. We introduce a method by which the chemical potential in dense liquids can be measured. There is neither a need to locate the interface nor to compute the anisotropic interfacial tension to obtain nucleation barriers. Therefore, our analysis is appropriate for nuclei of arbitrary shape. Monte Carlo simulations over a wide range of nucleus volumes yield to nucleation barriers independent from the total system volume. The interfacial tension is determined via the ensemble-switch method, hence a detailed test of classical nucleation theory is possible. The anisotropy of the interfacial tension and the resulting non-spherical shape has only a minor effect on the barrier for the Asakura-Oosawa model.

Data analysis and simulations of VIRTIS venus spectra

VIRTIS, a bordo di Venus Express, è uno spettrometro in grado di operare da 0.25 a 5 µm. Nel periodo 2006-2011 ha ricavato un'enorme mole di dati ma a tutt'oggi le osservazioni al lembo sono poco utilizzate per lo studio delle nubi e delle hazes, specialmente di notte. Gli spettri al lembo a quote mesosferiche sono dominati dalla radianza proveniente dalle nubi e scatterata in direzione dello strumento dalle hazes. L'interpretazione degli spettri al lembo non può quindi prescindere dalla caratterizzazione dell'intera colonna atmosferica. L'obiettivo della tesi è di effettuare un’analisi statistica sulle osservazioni al nadir e proporre una metodologia per ricavare una caratterizzazione delle hazes combinando osservazioni al nadir e al lembo. La caratterizzazione delle nubi è avvenuta su un campione di oltre 3700 osservazioni al nadir. È stato creato un ampio dataset di spettri sintetici modificando, in un modello iniziale, vari parametri di nube quali composizione chimica, numero e dimensione delle particelle. Un processo di fit è stato applicato alle osservazioni per stabilire quale modello potesse descrivere gli spettri osservati. Si è poi effettuata una analisi statistica sui risultati del campione. Si è ricavata una concentrazione di acido solforico molto elevata nelle nubi basse, pari al 96% in massa, che si discosta dal valore generalmente utilizzato del 75%. Si sono poi integrati i risultati al nadir con uno studio mirato su poche osservazioni al lembo, selezionate in modo da intercettare nel punto di tangenza la colonna atmosferica osservata al nadir, per ricavare informazioni sulle hazes. I risultati di un modello Monte Carlo indicano che il numero e le dimensioni delle particelle previste dal modello base devono essere ridotte in maniera significativa. In particolare si osserva un abbassamento della quota massima delle hazes rispetto ad osservazioni diurne.

Galactic fountain flows in high-resolution hydrodynamical simulations of galaxy disks

Feedback from the most massive components of a young stellar cluster deeply affects the surrounding ISM driving an expanding over-pressured hot gas cavity in it. In spiral galaxies these structures may have sufficient energy to break the disk and eject large amount of material into the halo. The cycling of this gas, which eventually will fall back onto the disk, is known as galactic fountains. We aim at better understanding the dynamics of such fountain flow in a Galactic context, frame the problem in a more dynamic environment possibly learning about its connection and regulation to the local driving mechanism and understand its role as a metal diffusion channel. The interaction of the fountain with a hot corona is hereby analyzed, trying to understand the properties and evolution of the extraplanar material. We perform high resolution hydrodynamical simulations with the moving-mesh code AREPO to model the multi-phase ISM of a Milky Way type galaxy. A non-equilibrium chemical network is included to self consistently follow the evolution of the main coolants of the ISM. Spiral arm perturbations in the potential are considered so that large molecular gas structures are able to dynamically form here, self shielded from the interstellar radiation field. We model the effect of SN feedback from a new-born stellar cluster inside such a giant molecular cloud, as the driving force of the fountain. Passive Lagrangian tracer particles are used in conjunction to the SN energy deposition to model and study diffusion of freshly synthesized metals. We find that both interactions with hot coronal gas and local ISM properties and motions are equally important in shaping the fountain. We notice a bimodal morphology where most of the ejected gas is in a cold $10^4$ K clumpy state while the majority of the affected volume is occupied by a hot diffuse medium. While only about 20\% of the produced metals stay local, most of them quickly diffuse through this hot regime to great scales.

Numerical simulations of the effects of residual stresses in adhesively bonded composite specimen

In this work the problem of performing a numerical simulation of quasi-static crack propagation within an adhesive layer of a bonded joint under Mode I loading affected by stress field changes due to thermal-chemical shrinkage induced by cure process is addressed. Secondly, a parametric study on fracture critical energy, cohesive strength and Young's modulus is performed. Finally, a particular case of adhesive layer stiffening is simulated in order to verify qualitatively the major effect.

Investigation of spectral stability of X-ray tubes by simulations and experimental spectrum measurements

L'obiettivo di questo lavoro è quello di analizzare la stabilità di uno spettro raggi X emesso da un tubo usurato per analisi cardiovascolari, in modo da verificare il suo comportamento. Successivamente questo tipo di analisi sarà effettuata su tubi CT. Per raggiungere questo scopo è stato assemblato un particolare set-up con un rivelatore al germanio criogenico in modo da avere la miglior risoluzione energetica possibile ed alcuni particolari collimatori così da ridurre il flusso fotonico per evitare effetti di pile-up. Il set-up è stato costruito in modo da avere il miglior allineamento possibile nel modo più veloce possibile, e con l'obiettivo di rendere l'intero sistema portabile. Il tubo usato è un SRM Philips tube per analisi cardiovascolari; questa scelta è stata fatta in modo da ridurre al minimo i fattori esterni (ottica elettromagnetica, emettitori) e concentrare l'attenzione solo sugli effetti, causati dalle varie esposizioni, sull'anodo (roughness e bending) e sul comportamento di essi durante il surriscaldamento e successivo raffreddamento del tubo. I risultati mostrano come durante un'esposizione alcuni fattori di usura del tubo possono influire in maniera sostanziale sullo spettro ottenuto e quindi alterare il risultato. Successivamente, nell'elaborato, mediante il software Philips di ricostruzione e simulazione dello spettro si è cercato di riprodurre, variando alcuni parametri, la differenza riscontrata sperimentalmente in modo da poter simulare l'instabilità e correggere i fattori che la causano. I risultati sono interessanti non solo per questo esperimento ma anche in ottica futura, per lo sviluppo di applicazioni come la spectral CT. Il passo successivo sarà quello di spostare l'attenzione su un CT tube e verificare se l'instabilità riscontrata in questo lavoro è persiste anche in una analisi più complessa come quella CT.

Dynamic computer simulations of electrophoresis: a versatile research and teaching tool

Software is available, which simulates all basic electrophoretic systems, including moving boundary electrophoresis, zone electrophoresis, ITP, IEF and EKC, and their combinations under almost exactly the same conditions used in the laboratory. These dynamic models are based upon equations derived from the transport concepts such as electromigration, diffusion, electroosmosis and imposed hydrodynamic buffer flow that are applied to user-specified initial distributions of analytes and electrolytes. They are able to predict the evolution of electrolyte systems together with associated properties such as pH and conductivity profiles and are as such the most versatile tool to explore the fundamentals of electrokinetic separations and analyses. In addition to revealing the detailed mechanisms of fundamental phenomena that occur in electrophoretic separations, dynamic simulations are useful for educational purposes. This review includes a list of current high-resolution simulators, information on how a simulation is performed, simulation examples for zone electrophoresis, ITP, IEF and EKC and a comprehensive discussion of the applications and achievements.

Comparison of actual surgical outcomes and 3-dimensional surgical simulations

PURPOSE: The advent of imaging software programs has proved to be useful for diagnosis, treatment planning, and outcome measurement, but precision of 3-dimensional (3D) surgical simulation still needs to be tested. This study was conducted to determine whether the virtual surgery performed on 3D models constructed from cone-beam computed tomography (CBCT) can correctly simulate the actual surgical outcome and to validate the ability of this emerging technology to recreate the orthognathic surgery hard tissue movements in 3 translational and 3 rotational planes of space. MATERIALS AND METHODS: Construction of pre- and postsurgery 3D models from CBCTs of 14 patients who had combined maxillary advancement and mandibular setback surgery and 6 patients who had 1-piece maxillary advancement surgery was performed. The postsurgery and virtually simulated surgery 3D models were registered at the cranial base to quantify differences between simulated and actual surgery models. Hotelling t tests were used to assess the differences between simulated and actual surgical outcomes. RESULTS: For all anatomic regions of interest, there was no statistically significant difference between the simulated and the actual surgical models. The right lateral ramus was the only region that showed a statistically significant, but small difference when comparing 2- and 1-jaw surgeries. CONCLUSIONS: Virtual surgical methods were reliably reproduced. Oral surgery residents could benefit from virtual surgical training. Computer simulation has the potential to increase predictability in the operating room.

Atomistic simulations of 2D bicomponent self-assembly: from molecular recognition to self-healing

Supramolecular two-dimensional engineering epitomizes the design of complex molecular architectures through recognition events in multicomponent self-assembly. Despite being the subject of in-depth experimental studies, such articulated phenomena have not been yet elucidated in time and space with atomic precision. Here we use atomistic molecular dynamics to simulate the recognition of complementary hydrogen-bonding modules forming 2D porous networks on graphite. We describe the transition path from the melt to the crystalline hexagonal phase and show that self-assembly proceeds through a series of intermediate states featuring a plethora of polygonal types. Finally, we design a novel bicomponent system possessing kinetically improved self-healing ability in silico, thus demonstrating that a priori engineering of 2D self-assembly is possible.

Retrieval simulations of the vertical profiles of water vapour and other chemical species in the Martian atmosphere using PACS

Water vapour, despite being a minor constituent in the Martian atmosphere with its precipitable amount of less than 70 pr. μm, attracts considerable attention in the scientific community because of its potential importance for past life on Mars. The partial pressure of water vapour is highly variable because of its seasonal condensation onto the polar caps and exchange with a subsurface reservoir. It is also known to drive photochemical processes: photolysis of water produces H, OH, HO2 and some other odd hydrogen compounds, which in turn destroy ozone. Consequently, the abundance of water vapour is anti-correlated with ozone abundance. The Herschel Space Observatory provides for the first time the possibility to retrieve vertical water profiles in the Martian atmosphere. Herschel will contribute to this topic with its guaranteed-time key project called "Water and related chemistry in the solar system". Observations of Mars by Heterodyne Instrument for the Far Infrared (HIFI) and Photodetector Array Camera and Spectrometer (PACS) onboard Herschel are planned in the frame of the programme. HIFI with its high spectral resolution enables accurate observations of vertically resolved H2O and temperature profiles in the Martian atmosphere. Unlike HIFI, PACS is not capable of resolving the line-shape of molecular lines. However, our present study of PACS observations for the Martian atmosphere shows that the vertical sensitivity of the PACS observations can be improved by using multiple-line observations with different line opacities. We have investigated the possibility of retrieving vertical profiles of temperature and molecular abundances of minor species including H2O in the Martian atmosphere using PACS. In this paper, we report that PACS is able to provide water vapour vertical profiles for the Martian atmosphere and we present the expected spectra for future PACS observations. We also show that the spectral resolution does not allow the retrieval of several studied minor species, such as H2O2, HCl, NO, SO2, etc.