PARAMETRIC STUDY OF REAXFF SIMULATION PARAMETERS FOR MOLECULAR DYNAMICS MODELING OF REACTIVE CARBON GASES

Abstract The development of innovative carbon-based materials can be greatly facilitated by molecular modeling techniques. Although the Reax Force Field (ReaxFF) can be used to simulate the chemical behavior of carbon-based systems, the simulation settings required for accurate predictions have not been fully explored. Using the ReaxFF, molecular dynamics (MD) simulations are used to simulate the chemical behavior of pure carbon and hydrocarbon reactive gases that are involved in the formation of carbon structures such as graphite, buckyballs, amorphous carbon, and carbon nanotubes. It is determined that the maximum simulation time step that can be used in MD simulations with the ReaxFF is dependent on the simulated temperature and selected parameter set, as are the predicted reaction rates. It is also determined that different carbon-based reactive gases react at different rates, and that the predicted equilibrium structures are generally the same for the different ReaxFF parameter sets, except in the case of the predicted formation of large graphitic structures with the Chenoweth parameter set under specific conditions.

Effet de la douleur expérimentale tonique sur l’acquisition et la rétention d’une adaptation locomotrice

Introduction : Une proportion importante des individus ayant recours à des services de réadaptation physique vit avec de la douleur et des incapacités locomotrices. Plusieurs interventions proposées par les professionnels de la réadaptation afin de cibler leurs difficultés locomotrices nécessitent des apprentissages moteurs. Toutefois, très peu d’études ont évalué l’influence de la douleur sur l’apprentissage moteur et aucune n’a ciblé l’apprentissage d’une nouvelle tâche locomotrice. L’objectif de la thèse était d’évaluer l’influence de stimulations nociceptives cutanée et musculaire sur l’acquisition et la rétention d’une adaptation locomotrice. Méthodologie : Des individus en santé ont participé à des séances de laboratoire lors de deux journées consécutives. Lors de chaque séance, les participants devaient apprendre à marcher le plus normalement possible en présence d’un champ de force perturbant les mouvements de leur cheville, produit par une orthèse robotisée. La première journée permettait d’évaluer le comportement des participants lors de la phase d’acquisition de l’apprentissage. La seconde journée permettait d’évaluer leur rétention. Selon le groupe expérimental, l’apprentissage se faisait en présence d’une stimulation nociceptive cutanée, musculaire ou d’aucune stimulation (groupe contrôle). Initialement, l’application du champ de force provoquait d’importantes déviations des mouvements de la cheville (i.e. erreurs de mouvement), que les participants apprenaient graduellement à réduire en compensant activement la perturbation. L’erreur de mouvement moyenne durant la phase d’oscillation (en valeur absolue) a été quantifiée comme indicateur de performance. Une analyse plus approfondie des erreurs de mouvement et de l’activité musculaire a permis d’évaluer les stratégies motrices employées par les participants. Résultats : Les stimulations nociceptives n’ont pas affecté la performance lors de la phase d’acquisition de l’apprentissage moteur. Cependant, en présence de douleur, les erreurs de mouvement résiduelles se trouvaient plus tard dans la phase d’oscillation, suggérant l’utilisation d’une stratégie motrice moins anticipatoire que pour le groupe contrôle. Pour le groupe douleur musculaire, cette stratégie était associée à une activation précoce du muscle tibial antérieur réduite. La présence de douleur cutanée au Jour 1 interférait avec la performance des participants au Jour 2, lorsque le test de rétention était effectué en absence de douleur. Cet effet n’était pas observé lorsque la stimulation nociceptive cutanée était appliquée les deux jours, ou lorsque la douleur au Jour 1 était d’origine musculaire. Conclusion : Les résultats de cette thèse démontrent que dans certaines circonstances la douleur peut influencer de façon importante la performance lors d’un test de rétention d’une adaptation locomotrice, malgré une performance normale lors de la phase d’acquisition. Cet effet, observé uniquement avec la douleur cutanée, semble cependant plus lié au changement de contexte entre l’acquisition des habiletés motrices et le test de rétention (avec vs. sans douleur) qu’à une interférence directe avec la consolidation des habiletés motrices. Par ailleurs, malgré l’absence d’influence de la douleur sur la performance des participants lors de la phase d’acquisition de l’apprentissage, les stratégies motrices utilisées par ceux-ci étaient différentes de celles employées par le groupe contrôle.

Rotational and ro-vibrational spectroscopy of small nitrogen-containing species and their astrophysical applications

This thesis presents the study of small nitrogen-bearing molecules, from diatomic radicals to complex organic molecules, by means of rotational and ro-vibrational spectroscopy. Besides their theoretical relevance, which spans from anharmonic force field analyses to energetic and structural properties, I have chosen this family of species because of their astrochemical importance. After some basic knowledge of molecular spectroscopy and astrochemistry is introduced, the instrumentation used during the course of my PhD school is described. Then, the most relevant studies I conducted during the last three years are presented. Generally speaking, a number of molecules of astrophysical relevance have been characterized by means of rotational and ro-vibrational spectroscopy. The sample of studied species is constituted by small radicals (imidogen, amidogen, and titanium nitride), cyanopolyynes (cyanoacetylene) and pre-biotic molecules (aminoacetonitrile): these studies are presented in great detail. Among the results, the first astronomical detection of two deuterated radicals (NHD and ND2) is presented in this thesis.Thanks to our studies, it was possible to clearly identify molecular absorptions of these species towards the pre-stellar core IRAS16293-2422, as recorded by the Herschel Space Observatory mission. These observations confirm the strong deuterium enhancement generally observed in this cloud but they reveal that models underestimate the abundances of NHD and ND2. I also report the detection of vibrationally excited aminoacetonitrile (NH2CH2CN) in Sagittarius B2, as observed in the ReMoCa survey. This is the second detection of aminoacetonitrile in the interstellar medium and the first astronomical observation of its vibrationally hot lines. This represents a small step toward the comprehension on how complex organic molecules are formed and which processes can lead to the formation of glycine. Finally, few general remarks are discussed and the importance of future laboratory studies is pointed out, along with possible perspectives.

Molecular modelling of organic functional materials

The investigation of the mechanisms lying behind the (photo-)chemical processes is fundamental to address and improve the design of new organic functional materials. In many cases, dynamics simulations represent the only tool to capture the system properties emerging from complex interactions between many molecules. Despite the outstanding progresses in calculation power, the only way to carry out such computational studies is to introduce several approximations with respect to a fully quantum mechanical (QM) description. This thesis presents an approach that combines QM calculations with a classical Molecular Dynamics (MD) approach by means of accurate QM-derived force fields. It is based on a careful selection of the most relevant molecular degrees of freedom, whose potential energy surface is calculated at QM level and reproduced by the analytic functions of the force field, as well as by an accurate tuning of the approximations introduced in the model of the process to be simulated. This is made possible by some tools developed purposely, that allow to obtain and test the FF parameters through comparison with the QM frequencies and normal modes. These tools were applied in the modelling of three processes: the npi* photoisomerisation of azobenzene, where the FF description was extended to the excited state too and the non-adiabatic events were treated stochastically with Tully fewest switching algorithm; the charge separation in donors-acceptors bulk heterojunction organic solar cells, where a tight-binding Hamiltonian was carefully parametrised and solved by means of a code, also written specifically; the effect of the protonation state on the photoisomerisation quantum yield of the aryl-azoimidazolium unit of the axle molecule of a rotaxane molecular shuttle. In each case, the QM-based MD models that were specifically developed gave noteworthy information about the investigated phenomena, proving to be a fundamental key for a deeper comprehension of several experimental evidences.

Multiscale modeling of light-harvesting systems based on rhodamine B aggregates

Rhodamine B (RB) has been successfully exploited in the synthesis of light harvesting systems, but since RB is prone to form dimers acting as quenchers for the fluorescence, high energy transfer efficiencies can be reached only when using bulky and hydrophobic counterions acting as spacers between RBs. In this PhD thesis, a multiscale theoretical study aimed at providing insights into the structural, photophysical and optical properties of RB and its aggregates is presented. At the macroscopic level (no atomistic details) a phenomenological model describing the fluorescence decay of RB networks in presence of both quenching from dimers and exciton-exciton annihiliation is presented and analysed, showing that the quenching from dimers affects the decay only at long times, a feature that can be exploited in global fitting analysis to determine relevant chemical and photophysical information. At the mesoscopic level (atomistic details but no electronic structure) the RB aggregation in water in presence of different counterions is studied with molecular dynamics (MD) simulations. A new force field has been parametrized for describing the RB flexibility and the RB-RB interaction driving the dimerization. Simulations correctly predict the RB/counterion aggregation only in presence of bulky and hydrophobic counterion and its ability to prevent the dimerization. Finally, at the microscopic level, DFT calculations are performed to demonstrate the spacing action of bulky counterions, but standard TDDFT calculations are showed to fail in correctly describing the excited states of RB and its dimers. Moreover, also standard procedures proposed in literature for obtaining ad hoc functionals are showed to not work properly. A detailed analysis on the effect of the exact exchange shows that its short-range contribution is the crucial quantity for ameliorating results, and a new functional containing a proper amount of such an exchange is proposed and successfully tested.

Dynamics of galaxies in the cluster environment: a resonant origin for the ISP?

The internal dynamics of elliptical galaxies in clusters depends on many factors, including the environment in which the galaxy is located. In addition to the strong encounters with the other galaxies, we can also consider the gravitational interaction with the ubiquitous Cluster Tidal Field (CTF). As recognized in many studies, one possible way in which CTF affects the dynamics of galaxies inside the cluster is related to the fact that they may start oscillating as “rigid bodies” around their equilibrium positions in the field, with the periods of these oscillations curiously similar to those of stellar orbits in the outer parts of galaxies. Resonances between the two motions are hence expected and this phenomenon could significantly contribute to the formation of the Intracluster Stellar Population (ISP), whose presence is abundantly confirmed by observations. In this thesis work, we propose to study the motion of an elliptical galaxy, modelled as a rigid body, in the CTF, especially when its center of mass traces a quasi-circular orbit in the cluster gravitational potential. This case extends and generalizes the previous models and findings, proceeding towards a much more realistic description of galaxy motion. In addition to this, the presence of a further oscillation, namely that of the entire galaxy along its orbit, will possibly increase the probability of having resonances and, consequently, the rate of ISP production nearly to observed values. Thus, after reviewing the dynamics of a rigid body in a generic force field, we will assess some physically relevant studies and report their main results, discussing their implications with respect to our problem. We will conclude our discussion focusing on the more realistic scenario of an elliptical galaxy whose center of mass moves on a quasi-circular orbit in a spherically symmetric potential. The derivation of the fundamental equations of motion will serve as the basis for future modelling and discussions.

Parametrizzazione e validazione di campi di forza polarizzabili per l'acetonitrile

Il perfezionamento dei campi di forza in meccanica molecolare, necessario per migliorare l’accuratezza della modellazione classica di materiali, è un procedimento dispendioso. L’accuratezza dei campi di forza è tuttavia la chiave per la predizione affidabile di proprietà chimico-fisiche dalle simulazioni MD. A questo scopo, risulta importante l’inclusione esplicita della polarizzazione, trascurata nei campi di forze tradizionali. Il modello dell’oscillatore di Drude rappresenta una soluzione computazionalmente conveniente ed è implementato in diversi software di simulazione. In questo modello, la polarizzazione atomica è resa dall’introduzione di una particella carica e di massa ridotta, ancorata all’atomo polarizzabile. In questo lavoro di tesi abbiamo sviluppato una procedura per ottenere un campo di forza polarizzabile per molecole organiche in fase liquida, prendendo in esame un solvente polare molto comune: l’acetonitrile. Il nostro approccio si serve di calcoli quantomeccanici preliminari per la determinazione dei valori di riferimento di alcune proprietà molecolari: le cariche parziali atomiche, il momento di dipolo e la polarizzabilità. A questi calcoli seguono due fasi di parametrizzazione basate su algoritmi di minimizzazione. La prima fase riguarda la parametrizzazione delle polarizzabilità atomiche descritte con il modello di Drude e ha come scopo la riproduzione della polarizzabilità molecolare quantomeccanica. Nella seconda fase, si sono ottimizzati i parametri del potenziale Lennard-Jones in modo da riprodurre la densità sperimentale a temperatura e pressione ambiente, ottenendo diverse parametrizzazioni del campo di forza polarizzabile. Infine, queste parametrizzazioni sono state confrontate sulla base della loro capacità di riprodurre alcune proprietà di bulk, quali entalpia di vaporizzazione, costante dielettrica, coefficiente di diffusione e specifiche funzioni di distribuzione radiale.

The stochastic design of force-minimized compact magnets for high-field magnetic resonance imaging applications

New designs for force-minimized compact high-field clinical MRI magnets are described. The design method is a modified simulated annealing (SA) procedure which includes Maxwell forces in the error function to be minimized. This permits an automated force reduction in the magnet designs while controlling the overall dimensions of the system. As SA optimization requires many iterations to achieve a final design, it is important that each iteration in the procedure is rapid. We have therefore developed a rapid force calculation algorithm. Novel designs for short 3- and 4-T clinical MRI systems are presented in which force reduction has been invoked. The final designs provide large homogeneous regions and reduced stray fields in remarkable short magnets. A shielded 4-T design that is approximately 30% shorter than current designs is presented. This novel magnet generates a full 50-cm diameter homogeneous region.

Novel system for bite-force sensing and monitoring based on magnetic eear field communication

Intraoral devices for bite-force sensing have several applications in odontology and maxillofacial surgery, as bite-force measurements provide additional information to help understand the characteristics of bruxism disorders and can also be of help for the evaluation of post-surgical evolution and for comparison of alternative treatments. A new system for measuring human bite forces is proposed in this work. This system has future applications for the monitoring of bruxism events and as a complement for its conventional diagnosis. Bruxism is a pathology consisting of grinding or tight clenching of the upper and lower teeth, which leads to several problems such as lesions to the teeth, headaches, orofacial pain and important disorders of the temporomandibular joint. The prototype uses a magnetic field communication scheme similar to low-frequency radio frequency identification (RFID) technology (NFC). The reader generates a low-frequency magnetic field that is used as the information carrier and powers the sensor. The system is notable because it uses an intra-mouth passive sensor and an external interrogator, which remotely records and processes information regarding a patient?s dental activity. This permits a quantitative assessment of bite-force, without requiring intra-mouth batteries, and can provide supplementary information to polysomnographic recordings, current most adequate early diagnostic method, so as to initiate corrective actions before irreversible dental wear appears. In addition to describing the system?s operational principles and the manufacture of personalized prototypes, this report will also demonstrate the feasibility of the system and results from the first in vitro and in vivo trials.

Working together : the final report and recommendations of the Basic Studies National Field Task Force on the Improvement and Reform of American Education.

Includes bibliographical references.

With the Zhob field force, 1890,

Printed in Great Britain.