El coneixement de la superfície d'energia potencial (PES) ha estat essencial en el món de la química teòrica per tal de discutir tant la reactivitat química com l'estructura i l'espectroscòpia molecular. En el camp de la reactivitat química es hem proposat continuar amb el desenvolupament de nova metodologia dins el marc de la teoria del funcional de la densitat conceptual. En particular aquesta tesis es centrarà en els següents punts:a) El nombre i la naturalesa dels seus punts estacionaris del PES poden sofrir canvis radicals modificant el nivell de càlcul utilitzats, de tal manera que per estar segurs de la seva naturalesa cal anar a nivells de càlcul molt elevats. La duresa és una mesura de la resistència d'un sistema químic a canviar la seva configuració electrònica, i segons el principi de màxima duresa on hi hagi un mínim o un màxim d'energia trobarem un màxim o un mínim de duresa, respectivament. A l'escollir tot un conjunt de reaccions problemàtiques des del punt de vista de presència de punts estacionaris erronis, hem observat que els perfils de duresa són més independents de la base i del mètode utilitzats, a més a més sempre presenten el perfil correcte. b) Hem desenvolupat noves expressions basades en les integracions dels kernels de duresa per tal de determinar la duresa global d'una molècula de manera més precisa que la utilitzada habitualment que està basada en el càlcul numèric de la derivada segona de l'energia respecte al número d'electrons.c) Hem estudiat la validesa del principis de màxima duresa i de mínima polaritzabiliat en les vibracions asimètriques en sistemes aromàtics. Hem trobat que per aquests sistemes alguns modes vibracionals incompleixen aquests principis i hem analitzat la relació d'aquest l'incompliment amb l'efecte de l'acoblament pseudo-Jahn-Teller. A més a més, hem postulat tot un conjunt de regles molt senzilles que ens permetien deduir si una molècula compliria o no aquests principis sense la realització de cap càlcul previ. Tota aquesta informació ha estat essencial per poder determinar exactament quines són les causes del compliment o l'incompliment del MHP i MPP.d) Finalment, hem realitzat una expansió de l'energia funcional en termes del nombre d'electrons i de les coordenades normals dintre del conjunt canònic. En la comparació d'aquesta expansió amb l'expansió de l'energia del nombre d'electrons i del potencial extern hem pogut recuperar d'una altra forma diferent tot un conjunt de relacions ja conegudes entre alguns coneguts descriptors de reactivitat del funcional de la densitat i en poden establir tot un conjunt de noves relacions i de nous descriptors.Dins del marc de les propietats moleculars es proposa generalitzar i millorar la metodologia pel càlcul de la contribució vibracional (Pvib) a les propietats òptiques no lineals (NLO). Tot i que la Pvib no s'ha tingut en compte en la majoria dels estudis teòrics publicats de les propietats NLO, recentment s'ha comprovat que la Pvib de diversos polímers orgànics amb altes propietats òptiques no lineals és fins i tot més gran que la contribució electrònica. Per tant, tenir en compte la Pvib és essencial en el disseny dels nous materials òptics no lineals utilitzats en el camp de la informàtica, les telecomunicacions i la tecnologia làser. Les principals línies d'aquesta tesis sobre aquest tema són:a) Hem calculat per primera vegada els termes d'alt ordre de Pvib de diversos polímers orgànics amb l'objectiu d'avaluar la seva importància i la convergència de les sèries de Taylor que defineixen aquestes contribucions vibracionals.b) Hem avaluat les contribucions electròniques i vibracionals per una sèrie de molècules orgàniques representatives utilitzant diferents metodologies, per tal de poder de determinar quina és la manera més senzilla per poder calcular les propietats NLO amb una precisió semiquantitativa. / The knowledge of the potential energy surface (PES) has been essential in the world of the theoretical chemistry to discuss such as the chemistry reactivity as the molecular spectroscopy. In the reactivity chemistry we are interested to develop new methodology in the field of the conceptual functional density theory. This thesis will be center in the following points:a) The number and character of the different stationary points of the PES can have radical changes modifying the calculation level used. This fact produces that to be sure of the character of a stationary point is necessary to arrive a very precise calculation level. The hardness is a measure of the resistance of a chemistry system to change his electronic configuration, and taking into account the maximum hardness principle, where there is a minimum or a maximum of energy, there also is a minimum or a maximum of hardness, respectively. Choosing a set of problematic reactions in the number of stationary points, we noted that the hardness is more independent of the base and the method used and it always shows the correct shape.b) We made new expressions based in the integrations of the hardness kernel to predict the global hardness of a molecule in a more precise way that the numerical second derivative of the energy respect to the number of electrons.c) We studied the validity of the maximum hardness and the minimum polarizability principles in the asymmetric vibrations in aromatic systems. We found that for theses systems some vibrational modes break these principles and we studied the relationship of this non-fulfillment with the pseudo-Jahn-Teller effect. Moreover, we postulated a set of simple rules, that allows deducing if a molecule will follow or not these rules without a previous calculation. All this information has been essential to exactly determine the reasons of the fulfillment or non-fulfillment of the MHP and MPP.d) Finally, we made an expansion of the functional energy respect to the number of electrons and the normal coordinates into the canonic ensemble. The comparison of this expansion with the expansion of the energy respect to the number of electrons and the external potential give the recuperation of some know relations between traditional reactivity descriptors of DFT, but a different way, and establish a set of new relations and descriptors.In the field of molecular properties we propose to generalize and improve the methodology to calculate the vibrational contribution (Pvib) to the non-linear optical properties (NLO). Despite of that the Pvib is not taking account into the majority of the theoretical studies published of the properties NLO, it has recently been checked that the Pvib of different organic molecules with high NLO properties is bigger that the electronic contribution. Thus, the Pvib is essential to pattern new NLO materials used in informatics, telecommunications, and laser technology. The main lines of the research about this subject are:a) We have calculated for the first time the high terms of the Pvib for different organic polymer with the goal to evaluate the importance and the convergence of the Taylor series that define the vibrational contributions.b) We have evaluated the electronic and vibrational contributions for different representative organic molecules using different methodologies to predict the cheaper way to calculate the NLO properties with semi quantitative precision.

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Living cells accumulate compensatory solutes for protection against the harmful effects of extreme environmental conditions such as high salinity, temperature and desiccation. Even at high concentrations these solutes do not disrupt the normal cellular functions and at times counteract by stabilizing the cellular components. These properties of compensatory solutes have been exploited for stabilizing proteins and cells in vitro. Betaines are widespread natural compensatory solutes that have also been used in other applications such as therapeutic agents and polymerase chain reaction (PCR) enhancers. Some biomedical applications of novel synthetic analogues of natural betaines were investigated. Natural compensatory solutes are either dipolar zwitterionic compounds or polyhydroxyl compounds, and the physical basis of compensation may differ between these, so one focus was on synthetic betaines with hydroxyl substituents. The majority of the synthetic solutes stabilized different model proteins against stress factors such as high and low temperatures. The presence of hydroxyl groups improved protection against desiccation. The observed stabilization effect is not just on the catalytic activity of the enzyme, but also on its structural conformation. Synthetic compensatory solutes have a potential application as protein stabilizers. Dimethylthetin was evaluated as a therapeutic agent and found to be harmful in a sheep model. However, from the study we were able to generate a large-animal continuous ambulatory peritoneal dialysis (CAPD) model and showed that glycine betaine could be added to the dialysis fluid in chronic renal failure. Some synthetic compensatory solutes reduce the melting temperatures of DNA better than most natural solutes. Synthetic solutes were identified that have potential to enhance PCR and could replace some reagents marketed by commercial suppliers. Density, viscosity and molecular model data on the solutes showed correlations with the biochemical effects of the solutes, but no physical measurements were found that reliably predicted their potential for biotechnological applications.

Cette thèse traite du contrôle et de la caractérisation de l'alignement et de l'orientation du point de vue théorique et expérimental. L'alignement d'une molécule linéaire consiste à obtenir une probabilité élevée de localisation de l'axe internucléaire symétrique autour de l'axe de polarisation du champ tandis que l'orientation privilégie un sens particulier le long du champ. L'orientation à l'aide d'impulsions bi couleur (2+1) non résonnantes est étudiée en détail et les conditions permettant d'obtenir une orientation efficace sont examinées. Un schéma bi couleur où la deuxième harmonique est en quasi-résonance avec un niveau vibrationnel de la molécule est également étudié. Cette technique présente l'avantage d'offrir un paramètre supplémentaire à savoir l'écart à la résonance qui peut être ajusté de manière à optimiser l'orientation moléculaire. Finalement une nouvelle technique expérimentale de détection de l'alignement moléculaire est présentée. Celle-ci permet une détection monocoup de l'alignement moléculaire sur une étendue temporelle jusqu'alors inégalée. / This thesis is about the control and characterisation of the alignment and orientation of molecules by ultra short laser pulses on a theoretical and experimental approach. Alignment corresponds to a symmetric angular distribution of the molecular axis peaked along the laser field axis, whereas orientation provides an asymmetric distribution favouring one spatial direction. Orientation by sudden two-colour (2+1) pulses is studied extensively for the non resonant case and conditions required for achieving significant orientation are explored. A second two-colour scheme, where the second harmonic is in quasi resonance with a vibrational level of the molecule, is also presented and discussed. The last technique has the advantage to offer the detuning of the laser frequency as an additional free parameter, which can be adjusted to enhance molecular orientation. A new experimental polarization imaging 2D technique for the detection alignment is also developed. Experimental results on single shot detection of molecular alignment achieved over an unprecedented temporal span are presented.

This thesis deals with several aspects of the structure and dynamics of water molecules confined in nanoscopic pores. Water molecules confined in hydrophobic nanocavities exhibit unusual structural and dynamic properties. Confining walls of single-wall carbon nanotubes (SWCNTs) promote strong inter-water hydrogen bonding which in turn leads to several novel structural, dynamic and thermodynamic features not found in bulk water. Confined water molecules form ordered hydrogen-bonded networks, exhibit exceptionally high flow rates as compared to conventional flow in pipes, allow fast proton conduction and exhibit various other anomalous properties. Proteins are known to exploit some of the properties of confined water to perform certain physiological functions. Various properties of confined water can also be exploited in the design of nanofludic devices such as those for desalination and flow sensors. In addition, water molecules confined in SWCNTs and near graphene sheets serve as model systems to study various effects of confinement on the properties of liquids. In this thesis, we present the results of detailed molecular dynamics simulation studies of confined water molecules. In chapter 1, we summarize the findings of existing simulations and experimental studies of bulk and confined water molecules. We also highlight the significance of studying the structure and dynamics of confined water molecules in biological and biotechnological applications. Chapter 2 provides a brief ac-count of the methods and techniques used to perform the simulations described in subsequent chapters of the thesis. We also present a brief overview of the methods used to extract physical properties of water molecules from simulation data, with emphasis on the Two Phase Thermodynamics (2PT) method which we have used to compute the entropy of confined and bulk water molecules. In chapter 3, we discuss the thermodynamics of water entry in SWCNTs of various diameters. Experiments and computer simulations demonstrate that water spontaneously fills the interior of a carbon nanotube. Given the hydrophobic nature of the interior of carbon nanotubes and the strong confinement produced by narrow nanotubes, the spontaneous entry of water molecules in the pores of such nanotubes is surprising. To gain a quantitative thermodynamic understanding of this phenomenon, we use the recently developed Two Phase Thermodynamics (2PT) method to compute translational and rotational entropies of water molecules confined in SWCNTs and show that the increase in energy of a water molecule inside the nanotube is compensated by the gain in its rotational entropy. The confined water is in equilibrium with the bulk water and the Helmholtz free energy per water molecule of confined water is the same as that in the bulk within the accuracy of the simulation results. A comparison of translational and rotational spectra of water molecules confined in carbon nanotubes with those of bulk water shows significant shifts in the positions of spectral peaks that are directly related to the tube radius. These peaks are experimentally accessible and can be used to characterize water dynamics from spectroscopy experiments. We have also computed the free-energy transfer when a bulk water molecule enters a SWCNT for various temperatures and carbon-water interactions. We show that for reduced carbon-oxygen interaction, the free energy transfer is unfavourable and the SWCNT remains unoccupied for significant periods of time. As the temperature is increased, the free energy of confined water becomes unfavourable and reduced occupancy of water is observed. Bulk water exhibits many anomalous properties. No single water model is able to reproduce all properties of bulk water. Different empirical water models have been developed to reproduce different properties of water. In chapter 4, a comparative study of the structure, dynamics and thermodynamic proper-ties of water molecules confined in narrow SWCNTs, obtained from simulations using several water models including polarizable ones, is presented. We show that the inclusion of polarizability quantitatively affects the nature of hydro-gen bonding which governs different properties of water molecules. The SPC/E water model is shown to reproduce results in close agreement with those from polarizable water models with much less computational cost. In chapter 5, we report results obtained from simulations of the properties of water confined in the space between two planar surfaces. We consider three cases: two graphene surfaces, two Boron Nitride (BN) surfaces and one graphene and one BN surface. This is the first detailed study of the behaviour of water near extended BN surfaces. We show that the hydrophilic nature of the BN surface leads to several interesting effects on the dynamics of water molecules near it. We have observed a change in the activation energy, extracted from the temperature dependence of the translational and rotational dynamics, near 280K. This change in activation energy coincides with a change in the structure of the confined sheet of water, indicated by a sudden change in energy. We have also found signatures of glassy dynamics at low temperatures for all three cases, the glassy effects being the strongest for water molecules confined between two BN sheets. These results are similar to those of earlier studies in which novel phases of water have been found for water molecules confined between other surfaces at high pressure. In chapter 6, we have described our observation of a novel phenomenon exhibited by water molecules flowing through a SWCNT under a pressure gradient. We have shown that the flow induces changes in the orientation of the water molecules flowing through the nanotube. In particular, the dipole moments of the water molecules inside the nanotube get aligned along the axis of the nanotube under the effect of the flow. With increasing flow velocities, the net dipole moment first increases and eventually saturates to a constant value. This behaviour is similar to the Langevin theory of paramagnetism with the flow velocity acting as an effective aligning field. Preferential entry of water molecules with dipole moments pointing inward is shown to be the main cause of this effect. This observation provides a way to control the dipolar alignment of water molecules inside nano-channels, with possible applications in nanofluidic devices. Chapter 7 contains a summary of our main results and a few concluding re-marks.

Humanitarian clearance of minefields is most often carried out by hand, conventionally using a a metal detector and a probe. Detection is a very slow process, as every piece of detected metal must treated as if it were a landmine and carefully probed and excavated, while many of them are not. The process can be safely sped up by use of Ground-Penetrating Radar (GPR) to image the subsurface, to verify metal detection results and safely ignore any objects which could not possibly be a landmine. In this thesis, we explore the possibility of using Full Wave Inversion (FWI) to improve GPR imaging for landmine detection. Posing the imaging task as FWI means solving the large-scale, non-linear and ill-posed optimisation problem of determining the physical parameters of the subsurface (such as electrical permittivity) which would best reproduce the data. This thesis begins by giving an overview of all the mathematical and implementational aspects of FWI, so as to provide an informative text for both mathematicians (perhaps already familiar with other inverse problems) wanting to contribute to the mine detection problem, as well as a wider engineering audience (perhaps already working on GPR or mine detection) interested in the mathematical study of inverse problems and FWI.We present the first numerical 3D FWI results for GPR, and consider only surface measurements from small-scale arrays as these are suitable for our application. The FWI problem requires an accurate forward model to simulate GPR data, for which we use a hybrid finite-element boundary-integral solver utilising first order curl-conforming N\'d\'{e}lec (edge) elements. We present a novel `line search' type algorithm which prioritises inversion of some target parameters in a region of interest (ROI), with the update outside of the area defined implicitly as a function of the target parameters. This is particularly applicable to the mine detection problem, in which we wish to know more about some detected metallic objects, but are not interested in the surrounding medium. We may need to resolve the surrounding area though, in order to account for the target being obscured and multiple scattering in a highly cluttered subsurface. We focus particularly on spatial sensitivity of the inverse problem, using both a singular value decomposition to analyse the Jacobian matrix, as well as an asymptotic expansion involving polarization tensors describing the perturbation of electric field due to small objects. The latter allows us to extend the current theory of sensitivity in for acoustic FWI, based on the Born approximation, to better understand how polarization plays a role in the 3D electromagnetic inverse problem. Based on this asymptotic approximation, we derive a novel approximation to the diagonals of the Hessian matrix which can be used to pre-condition the GPR FWI problem.

No description available.