Nonlinear refraction in optical lattices induced by the wave-soliton interference

In the framework of 1D Nonlinear Shrödinger Equation (NSE) we demonstrate how one can control the refractive angle of a fundamental soliton beam passing through an optical lattice, by adjusting either the shape of an individual waveguide or the relative positions of waveguides. Even for a single scatterer its shape has a nontrivial effect on the refraction direction. In the case of shallow modulation we provide an analytical description based of the effect on the soliton perturbation theory. When one considers a lattice of scatterers, there emanates an additional form factor in the radiation density (RD) of emitted waves referring to the wave-soliton beating and interference inside the lattice. We concentrate on the results for two cases: periodic lattice and disordered lattice of scattering shapes. © 2011 IEEE.

Measurement of carotenoid levels in human serum and a catalog of the lutein conformation populations from semi-empirical calculations

Lutein is a principal constituent of the human macular pigment. This study is composed of two projects. The first studies the conformational geometries of lutein and its potential adaptability in biological systems. The second is a study of the response of human subjects to lutein supplements. Using semi-empirical parametric method 3 (PM3) and density functional theory with the B3LYP/6-31G* basis set, the relative energies of s- cis conformers of lutein were determined. All 512 s-cis conformers were calculated with PM3. A smaller, representative group was also studied using density functional theory. PM3 results were correlated systematically to B3LYP values and this enables the results to be calibrated. The relative energies of the conformers range from 1-30 kcal/mole, and many are dynamically accessible at normal temperatures. Four commercial formulations containing lutein were studied. The serum and macular pigment (MP) responses of human subjects to these lutein supplements with doses of 9 or 20 mg/day were measured, relative to a placebo, over a six month period. In each instance, lutein levels in serum increased and correlated with MP increases. The results demonstrate that responses are significantly dependent upon formulation and that components other than lutein have an important influence serum response.

Nonlinear quantum transport in low-dimensional electronic devices

The study of transport processes in low-dimensional semiconductors requires a rigorous quantum mechanical treatment. However, a full-fledged quantum transport theory of electrons (or holes) in semiconductors of small scale, applicable in the presence of external fields of arbitrary strength, is still not available. In the literature, different approaches have been proposed, including: (a) the semiclassical Boltzmann equation, (b) perturbation theory based on Keldysh's Green functions, and (c) the Quantum Boltzmann Equation (QBE), previously derived by Van Vliet and coworkers, applicable in the realm of Kubo's Linear Response Theory (LRT). ^ In the present work, we follow the method originally proposed by Van Wet in LRT. The Hamiltonian in this approach is of the form: H = H 0(E, B) + λV, where H0 contains the externally applied fields, and λV includes many-body interactions. This Hamiltonian differs from the LRT Hamiltonian, H = H0 - AF(t) + λV, which contains the external field in the field-response part, -AF(t). For the nonlinear problem, the eigenfunctions of the system Hamiltonian, H0(E, B), include the external fields without any limitation on strength. ^ In Part A of this dissertation, both the diagonal and nondiagonal Master equations are obtained after applying projection operators to the von Neumann equation for the density operator in the interaction picture, and taking the Van Hove limit, (λ → 0, t → ∞, so that (λ2 t)n remains finite). Similarly, the many-body current operator J is obtained from the Heisenberg equation of motion. ^ In Part B, the Quantum Boltzmann Equation is obtained in the occupation-number representation for an electron gas, interacting with phonons or impurities. On the one-body level, the current operator obtained in Part A leads to the Generalized Calecki current for electric and magnetic fields of arbitrary strength. Furthermore, in this part, the LRT results for the current and conductance are recovered in the limit of small electric fields. ^ In Part C, we apply the above results to the study of both linear and nonlinear longitudinal magneto-conductance in quasi one-dimensional quantum wires (1D QW). We have thus been able to quantitatively explain the experimental results, recently published by C. Brick, et al., on these novel frontier-type devices. ^

Nonlinear quantum transport in low-dimensional electronic devices

The study of transport processes in low-dimensional semiconductors requires a rigorous quantum mechanical treatment. However, a full-fledged quantum transport theory of electrons (or holes) in semiconductors of small scale, applicable in the presence of external fields of arbitrary strength, is still not available. In the literature, different approaches have been proposed, including: (a) the semiclassical Boltzmann equation, (b) perturbation theory based on Keldysh's Green functions, and (c) the Quantum Boltzmann Equation (QBE), previously derived by Van Vliet and coworkers, applicable in the realm of Kubo's Linear Response Theory (LRT). In the present work, we follow the method originally proposed by Van Vliet in LRT. The Hamiltonian in this approach is of the form: H = H°(E, B) + λV, where H0 contains the externally applied fields, and λV includes many-body interactions. This Hamiltonian differs from the LRT Hamiltonian, H = H° - AF(t) + λV, which contains the external field in the field-response part, -AF(t). For the nonlinear problem, the eigenfunctions of the system Hamiltonian, H°(E, B) , include the external fields without any limitation on strength. In Part A of this dissertation, both the diagonal and nondiagonal Master equations are obtained after applying projection operators to the von Neumann equation for the density operator in the interaction picture, and taking the Van Hove limit, (λ → 0 , t → ∞ , so that (λ2 t)n remains finite). Similarly, the many-body current operator J is obtained from the Heisenberg equation of motion. In Part B, the Quantum Boltzmann Equation is obtained in the occupation-number representation for an electron gas, interacting with phonons or impurities. On the one-body level, the current operator obtained in Part A leads to the Generalized Calecki current for electric and magnetic fields of arbitrary strength. Furthermore, in this part, the LRT results for the current and conductance are recovered in the limit of small electric fields. In Part C, we apply the above results to the study of both linear and nonlinear longitudinal magneto-conductance in quasi one-dimensional quantum wires (1D QW). We have thus been able to quantitatively explain the experimental results, recently published by C. Brick, et al., on these novel frontier-type devices.

Estudo in silico das interações da protease NS3-NS2B de DENV-2 com o inibidor peptídico Bz-nKRR-H com finalidades terapêuticas

Dengue virus is an important patogen that causes Dengue desease in all world, and belongs to Flavivirus gender. The virus consists of enveloped RNA with a single strand positive sense, 11Kb genome. The RNA is translated into a polyprotein precursor, wich is cleaved into 3 structural proteins (C, prM e E) and 7 non-structural proteins (NS1, NS2A, NS2B, NS3, NS4A, NS4B e NS5). The NS3 is a multifunctional protein, that besides to promote the polyprotein precursor cleavage, also have NTPase, helicase and RTPase activity. The NS3 needs a hydrophilic segment of 40 residues from the transmembrane NS2B protein (who acts like cofator) to realize this functions. Actually, there's no vacines available on the market, and the treatment are just symptomatic. The tetrapeptide inhibitor Bz-Nle-Lys-Arg-Arg-H (Ki de 5,8-7,0 M) was showed as a potent inhibitor μ for NS3prot in Dengue virus. That is a inteligent alternative to treat the dengue desease. The present work aimed analyse the interactions of the ligand bounded to the activity site to provid a clear and depth vision of that interaction. For this purpouse, it was conducted an in silico study, by using quantum mechanical calculations based on Density Functional Theory (DFT), with Generalized Gradient approximation (GGA) to describe the effects of exchange and correlation. The interaction energy of each amino acid belonging to the binding site to the ligand was calculated the using the method of molecular fragmentation with conjugated caps (MFCC). Besides energy, we calculated the distances, types of molecular interactions and atomic groups involved. The theoretical models used were satisfactory and show a more accurate description when the dielectric constant = 20 ε and 80 was used. The results demonstrate that the interaction energy of the system reached convergence at 13.5 A. Within a radius of 13,5A the most important residues were identified. Met49, Met84 and Asp81 perform interactions of hydrogen with the ligant. The Asp79 and Asp75 residues present high energy of attraction. Arg54, Arg85 and Lys 131 perform hydrogen interactions with the ligand, however, appear in BIRD graph having high repulsion energy with the inhibitor. The data also emphasizes the importance of residue Tyr161 and the involvement of the catalytic triad composed by Asp75, His51 and Ser135

Estudo teórico de intermediários tetraédricos acidez / basicidade e estereosseletividade enzimáticos

The present work aimed first, the theoretical study of tetrahedral intermediate stability formed from carbonyl addition reactions using the second (MP2) and third (MP3) order Møller–Plesset perturbation theory. Linear correlations between electronic energy difference of reactions with Wiberg Indexes and C-O bond lengths were obtained, and was observed that the stability of adducts formed depends directly of electronic density involved between these atoms. The knowing of electronic parameters of these structures has an important hole due to the large use on reactions that in his course forms this tetrahedral intermediate. Employing the ONIOM (B3LYP:AMBER) methodology, was evaluated the stereoselectivity of a enzymatic reaction between CAL B enzyme and a long chain ester. In this study, were obtained the electronic energies of ground state and intermediate state of transesterification rate-determing step from two possible proquirals faces Re and Si. The objective was study the enantioselectivity of CAL B and rationalizes it using quantum theory of atoms in molecules (QTAIM). A theoretical study employing inorganic compounds was performed using ab initio CBS-QB3 method aiming to find a link between thermodynamic and equilibrium involving acids and bases. The results observed showed an excellent relationship between difference in Gibbs free energy, ΔG of acid dissociation reaction and ΔG of hydrolysis reaction of the corresponding conjugate base. It was also observed, a relationship between ΔG of hydrolysis reaction of conjugate acids and their corresponding atomic radius showing that stability plays an important role in hydrolysis reactions. The importance of solvation in acid/base behavior when compared to theoretical and experimental ΔG´s also was evaluated.

Bioquímica quântica na diferenciação dos níveis de ativação de receptores AMPA por agonistas parciais Wilardina

In the central nervous system (CNS) of mammalian, fast synaptic transmission between nerve cells is performed primarily by α-amino-3-hydroxy-5-methyl-4- isoxazolepropionic acid (AMPA) receptors, an ionotropic glutamate receptor that is related with learning, memory and homeostasis of the nervous system. Impairments in their functions are correlated with development of many brain desorders, such as epilepsy, schizophrenia, autism, Parkinson and Alzheimer. The use of willardiine analogs has been shown a powerful tool to understanding of activation and desensitization mechanisms of this receptors, because the modification of a single ligand atom allows the observation of varying levels of efficacy. In this work, taking advantage of Fluorine Willardiine (1.35Å), Hydrogen Willardiine (1.65Å), Bromine Willardiine (1.8Å) and Iodine Willardiine (2.15Å) structures co-crystalized with GluA2 with codes 1MQI, 1MQJ, 1MQH and 1MQG, we attempted to energetically differentiate the four ligands efficacy. The complexes were submitted to energetic calculations based on density functional theory (DFT), under the optics of molecular fractionation with conjugate caps (MFCC) method. Obtained results show a relationship between the energetic values and willardiines efficacy order (FW> HW > BrW > IW), also show the importance of E705, R485, Y450, S654, T655, T480 e P478 as the amino acids that contribute most strongly with the interaction of four partial agonists. Furthermore, we outlined the M708 behaviour, attracted by FW and HW ligands, and repels by BrW and IW. With the datas reported on this work, it is possible for a better understanding of the AMPA receptor, which can serve as an aid in the development of new drugs for this system.

Estudo teórico das propriedades eletrônicas e termodinâmicas de nanofitas quasiperiódicas BCN

Nanoscale materials composed of boron, nitrogen, and carbon have unique properties and may be useful in new technologies. In this thesis, we investigate some properties of BCN nanoribbons constructed according to the Fibonacci quasiperiodic sequence. We analyze properties such as structural stability, electronic density of states, electronic specific heat, band structure, and energy band gap. We have performed first-principles calculations based on density functional theory implemented in the SIESTA code. The results showed that nanoribbons present a fixed value of the formation energy. The electronic density of states was used to calculate the specific heat. We found an oscillatory behavior of the electronic specific heat, in the low temperature regime. We analyze the electronic band structure to determine the energy band gap. The energy band gap oscillates as a function of the Fibonacci generation index n. Our work suggest that appropriate choice of the building block materials of the quasiperiodic sequence, may lead to a tuneable band gap of the quasiperiodic nanoribbons.

Il polimorfismo del paracetamolo: indagine mediante spettroscopia Raman e metodi computazionali

Lo studio del polimorfismo gioca un ruolo fondamentale in diversi ambiti di ricerca, con applicazioni importanti nel campo dei semi conduttori organici e dei farmaci, dovuto al fatto che i diversi polimorfi di una sostanza presentano proprietà chimico-fisiche distinte. Questo lavoro di tesi si è focalizzato sullo studio del polimorfismo del paracetamolo, principio attivo (API) di diversi farmaci molto utilizzati, attraverso l’utilizzo della microscopia Raman. La microscopia Raman è una tecnica efficace per l’indagine del polimorfismo di materiali organici ed inorganici, in quanto permette di monitorare la presenza di diverse fasi solide e le loro trasformazioni su scala micrometrica. Le differenze di struttura cristallina che caratterizzano i polimorfi vengono analizzate attraverso gli spettri Raman nella regione dei modi reticolari (10-150 cm^{-1}), le cui frequenze sondano le interazioni inter-molecolari, molto sensibili anche a lievi differenze di impaccamento molecolare. Con questa tecnica abbiamo caratterizzato le forme I, II, III (quella elusiva) e diverse miscele di fase di paracetamolo su campioni ottenuti con numerose tecniche di crescita dei cristalli. Per questa tesi è stato svolto anche uno studio computazionale, attraverso metodi Density Functional Theory (DFT) per la molecola isolata e metodi di minimizzazione dell’energia e di dinamica reticolare per i sistemi cristallini. Abbiamo inoltre verificato se il modello di potenziale di letteratura scelto (Dreiding [Mayo1990]) fosse adatto per descrivere la molecola di paracetamolo, le strutture dei suoi polimorfi e i relativi spettri vibrazionali.

Charge compensation and Ce3+ formation in trivalent doping of the CeO2(110) surface: The key role of dopant ionic radius

In this paper, we use density functional theory corrected for on-site Coulomb interactions (DFT + U) and hybrid DFT (HSE06 functional) to study the defects formed when the ceria (110) surface is doped with a series of trivalent dopants, namely, Al3+, Sc3+, Y3+, and In 3+. Using the hybrid DFT HSE06 exchange-correlation functional as a benchmark, we show that doping the (110) surface with a single trivalent ion leads to formation of a localized MCe / + O O • (M = the 3+ dopant), O- hole state, confirming the description found with DFT + U. We use DFT + U to investigate the energetics of dopant compensation through formation of the 2MCe ′ +VO ̈ defect, that is, compensation of two dopants with an oxygen vacancy. In conjunction with earlier work on La-doped CeO2, we find that the stability of the compensating anion vacancy depends on the dopant ionic radius. For Al3+, which has the smallest ionic radius, and Sc3+ and In3+, with intermediate ionic radii, formation of a compensating oxygen vacancy is stable. On the other hand, the Y3+ dopant, with an ionic radius close to that of Ce4+, shows a positive anion vacancy formation energy, as does La3+, which is larger than Ce4+ (J. Phys.: Condens. Matter 2010, 20, 135004). When considering the resulting electronic structure, in Al3+ doping, oxygen hole compensation is found. However, Sc 3+, In3+, and Y3+ show the formation of a reduced Ce3+ cation and an uncompensated oxygen hole, similar to La3+. These results suggest that the ionic radius of trivalent dopants strongly influences the final defect formed when doping ceria with 3+ cations. In light of these findings, experimental investigations of these systems will be welcome.

Lead oxide-modified TiO2 photocatalyst: tuning light absorption and charge carrier separation by lead oxidation state

Modification of TiO2 with metal oxide nanoclusters such as FeOx, NiOx has been shown to be a promising approach to the design of new photocatalysts with visible light absorption and improved electron–hole separation. To study further the factors that determine the photocatalytic properties of structures of this type, we present in this paper a first principles density functional theory (DFT) investigation of TiO2 rutile(110) and anatase(001) modified with PbO and PbO2 nanoclusters, with Pb2+ and Pb4+ oxidation states. This allows us to unravel the effect of the Pb oxidation state on the photocatalytic properties of PbOx-modified TiO2. The nanoclusters adsorb strongly at all TiO2 surfaces, creating new Pb–O and Ti–O interfacial bonds. Modification with PbO and PbO2 nanoclusters introduces new states in the original band gap of rutile and anatase. However the oxidation state of Pb has a dramatic impact on the nature of the modifications of the band edges of TiO2 and on the electron–hole separation mechanism. PbO nanocluster modification leads to an upwards shift of the valence band which reduces the band gap and upon photoexcitation results in hole localisation on the PbO nanocluster and electron localisation on the surface. By contrast, for PbO2 nanocluster modification the hole will be localised on the TiO2 surface and the electron on the nanocluster, thus giving rise to two different band gap reduction and electron–hole separation mechanisms. We find no crystal structure sensitivity, with both rutile and anatase surfaces showing similar properties upon modification with PbOx. In summary the photocatalytic properties of heterostructures of TiO2 with oxide nanoclusters can be tuned by oxidation state of the modifying metal oxide, with the possibility of a reduced band gap causing visible light activation and a reduction in charge carrier recombination.

Loading effect in copper(II) oxide cluster-surface-modified titanium(IV) oxide on visible- and UV-light activities

Cu(acac)2 is chemisorbed on TiO2 particles [P-25 (anatase/rutile = 4/1 w/w), Degussa] via coordination by surface Ti–OH groups without elimination of the acac ligand. Post-heating of the Cu(acac)2-adsorbed TiO2 at 773 K yields molecular scale copper(II) oxide clusters on the surface (CuO/TiO2). The copper loading amount (Γ/Cu ions nm–2) is controlled in a wide range by the Cu(acac)2 concentration and the chemisorption–calcination cycle number. Valence band (VB) X-ray photoelectron and photoluminescence spectroscopy indicated that the VB maximum of TiO2 rises up with increasing Γ, while vacant midgap levels are generated. The surface modification gives rise to visible-light activity and concomitant significant increase in UV-light activity for the degradation of 2-naphthol and p-cresol. Prolonging irradiation time leads to the decomposition to CO2, which increases in proportion to irradiation time. The photocatalytic activity strongly depends on the loading, Γ, with an optimum value of Γ for the photocatalytic activity. Electrochemical measurements suggest that the surface CuO clusters promote the reduction of adsorbed O2. First principles density functional theory simulations clearly show that, at Γ < 1, unoccupied Cu 3d levels are generated in the midgap region, and at Γ > 1, the VB maximum rises and the unoccupied Cu 3d levels move to the conduction band minimum of TiO2. These results suggest that visible-light excitation of CuO/TiO2 causes the bulk-to-surface interfacial electron transfer at low coverage and the surface-to-bulk interfacial electron transfer at high coverage. We conclude that the surface CuO clusters enhance the separation of photogenerated charge carriers by the interfacial electron transfer and the subsequent reduction of adsorbed O2 to achieve the compatibility of high levels of visible and UV-light activities.

A first principles analysis of the effect of hydrogen concentration in hydrogenated amorphous silicon on the formation of strained Si-Si bonds and the optical and mobility gaps

In this paper, we use a model of hydrogenated amorphous silicon generated from molecular dynamics with density functional theory calculations to examine how the atomic geometry and the optical and mobility gaps are influenced by mild hydrogen oversaturation. The optical and mobility gaps show a volcano curve as the hydrogen content varies from undersaturation to mild oversaturation, with largest gaps obtained at the saturation hydrogen concentration. At the same time, mid-gap states associated with dangling bonds and strained Si-Si bonds disappear at saturation but reappear at mild oversaturation, which is consistent with the evolution of optical gap. The distribution of Si-Si bond distances provides the key to the change in electronic properties. In the undersaturation regime, the new electronic states in the gap arise from the presence of dangling bonds and strained Si-Si bonds, which are longer than the equilibrium Si-Si distance. Increasing hydrogen concentration up to saturation reduces the strained bonds and removes dangling bonds. In the case of mild oversaturation, the mid-gap states arise exclusively from an increase in the density of strained Si-Si bonds. Analysis of our structure shows that the extra hydrogen atoms form a bridge between neighbouring silicon atoms, thus increasing the Si-Si distance and increasing disorder in the sample.

Effect of reaction mechanism on precursor exposure time in atomic layer deposition of silicon oxide and silicon nitride

Atomic layer deposition (ALD) of highly conformal, silicon-based dielectric thin films has become necessary because of the continuing decrease in feature size in microelectronic devices. The ALD of oxides and nitrides is usually thought to be mechanistically similar, but plasma-enhanced ALD of silicon nitride is found to be problematic, while that of silicon oxide is straightforward. To find why, the ALD of silicon nitride and silicon oxide dielectric films was studied by applying ab initio methods to theoretical models for proposed surface reaction mechanisms. The thermodynamic energies for the elimination of functional groups from different silicon precursors reacting with simple model molecules were calculated using density functional theory (DFT), explaining the lower reactivity of precursors toward the deposition of silicon nitride relative to silicon oxide seen in experiments, but not explaining the trends between precursors. Using more realistic cluster models of amine and hydroxyl covered surfaces, the structures and energies were calculated of reaction pathways for chemisorption of different silicon precursors via functional group elimination, with more success. DFT calculations identified the initial physisorption step as crucial toward deposition and this step was thus used to predict the ALD reactivity of a range of amino-silane precursors, yielding good agreement with experiment. The retention of hydrogen within silicon nitride films but not in silicon oxide observed in FTIR spectra was accounted for by the theoretical calculations and helped verify the application of the model.

Ground and Electronic Excited States from Pairing Matrix Fluctuation and Particle-Particle Random Phase Approximation

The accurate description of ground and electronic excited states is an important and challenging topic in quantum chemistry. The pairing matrix fluctuation, as a counterpart of the density fluctuation, is applied to this topic. From the pairing matrix fluctuation, the exact electron correlation energy as well as two electron addition/removal energies can be extracted. Therefore, both ground state and excited states energies can be obtained and they are in principle exact with a complete knowledge of the pairing matrix fluctuation. In practice, considering the exact pairing matrix fluctuation is unknown, we adopt its simple approximation --- the particle-particle random phase approximation (pp-RPA) --- for ground and excited states calculations. The algorithms for accelerating the pp-RPA calculation, including spin separation, spin adaptation, as well as an iterative Davidson method, are developed. For ground states correlation descriptions, the results obtained from pp-RPA are usually comparable to and can be more accurate than those from traditional particle-hole random phase approximation (ph-RPA). For excited states, the pp-RPA is able to describe double, Rydberg, and charge transfer excitations, which are challenging for conventional time-dependent density functional theory (TDDFT). Although the pp-RPA intrinsically cannot describe those excitations excited from the orbitals below the highest occupied molecular orbital (HOMO), its performances on those single excitations that can be captured are comparable to TDDFT. The pp-RPA for excitation calculation is further applied to challenging diradical problems and is used to unveil the nature of the ground and electronic excited states of higher acenes. The pp-RPA and the corresponding Tamm-Dancoff approximation (pp-TDA) are also applied to conical intersections, an important concept in nonadiabatic dynamics. Their good description of the double-cone feature of conical intersections is in sharp contrast to the failure of TDDFT. All in all, the pairing matrix fluctuation opens up new channel of thinking for quantum chemistry, and the pp-RPA is a promising method in describing ground and electronic excited states.