Molecular Dynamics Simulation of Microstructure of Nanocrystalline Copper

The microstructure of computer generated nanocrystalline coppers is simulated by using molecular dynamics with the Finnis-Sinclair potential, analysed by means of radial distribution functions, coordination number, atomic energy and local crystalline order. The influence of the grain size on the nanocrystalline structure is studied. The results reveal that as the grain size is reduced, the grain boundary shows no significant structural difference, but the grain interior becomes more disordered, and their structural difference diminishes gradually; however, the density and the atomic average energy of the grain boundary present different tendencies from those of the grain interior.

Building the perfect 3D hologram

A new liquid crystal device structure has been developed using a vertically grown Multi-Wall Carbon NanoTube (MWCNT) as a 3D electrode structure, which allows complicated phase only hologram to be displayed using conventional liquid crystal materials. The nanotubes act as an individual electrode sites that generate an electric field profile, dictating the refractive index profile with the liquid crystal cell. Changing the electric field applied makes it possible to tune the properties to modulate the light in an ideal kinoform. A perfect 3D image can be generated by a computer generated hologram by using the diffraction of the light from the hologram pixels to create an optical wave front that appears to come from 3D object. A multilevel phase modulating device based on nematic LC's is also under progress, which will be used with the LC/CNT devices on an LCOS backplane to project a full 3D image from the kinoform.

Field of view expansion for 3-D holographic display using a single spatial light modulator with scanning reconstruction light

Increasing the field of view of a holographic display while maintaining adequate image size is a difficult task. To address this problem, we designed a system that tessellates several sub-holograms into one large hologram at the output. The sub-holograms we generate is similar to a kinoform but without the paraxial approximation during computation. The sub-holograms are loaded onto a single spatial light modulator consecutively and relayed to the appropriate position at the output through a combination of optics and scanning reconstruction light. We will review the method of computer generated hologram and describe the working principles of our system. Results from our proof-of-concept system are shown to have an improved field of view and reconstructed image size. ©2009 IEEE.

The modulated grating hologram

A phase and amplitude, off-axis hologram has been synthesized from three computer-generated transmission masks, using a multiple-exposure holographic recording method. Each of the masks controls one fixed-phase component of the complex hologram transmittance. The basic grating is generated optically, relieving the computer of the burden of drawing details the size of each fringe. The maximum information capacity of the computer plotting device can then be applied to the generation of the grating modulation function. By this method large digital holograms (25 mm by 25 mm) have been synthesized in dichromated gelatin. The recording method is applicable to virtually any holographic medium.

The modulated grating hologram was designed primarily for the application of spatial filtering, in which the requirement is a hologram with large dynamic range and large free spectral range. Choice of a low-noise, high-efficiency medium such as dichromated gelatin will allow exceptionally large dynamic range. Independence of the optically-generated carrier grating from the computer-generated modulation functions allows arbitrarily large free spectral range.

The performance of a holographic spatial filter will be limited ultimately by noise originating from imperfections in the holographic medium. The characteristics of this noise are analyzed, and in the case of a high diffraction efficiency hologram are shown to differ significantly from previous analyses. The dominant noise source in holograms of high diffraction efficiency will be scattering of the first order or imaging wave by deformations in the hologram surface or other effects of low spatial frequency. Experimental measurements in various low-noise holographic media verify these predictions.

Influence of composition on the structure, electric and magnetic properties of Pd-Mn-P and Pd-Co-P amorphous alloys

The influence of composition on the structure and on the electric and magnetic properties of amorphous Pd-Mn-P and Pd-Co-P prepared by rapid quenching techniques were investigated in terms of (1) the 3d band filling of the first transition metal group, (2) the phosphorus concentration effect which acts as an electron donor and (3) the transition metal concentration.

The structure is essentially characterized by a set of polyhedra subunits essentially inverse to the packing of hard spheres in real space. Examination of computer generated distribution functions using Monte Carlo random statistical distribution of these polyhedra entities demonstrated tile reproducibility of the experimentally calculated atomic distribution function. As a result, several possible "structural parameters" are proposed such as: the number of nearest neighbors, the metal-to-metal distance, the degree of short-range order and the affinity between metal-metal and metal-metalloid. It is shown that the degree of disorder increases from Ni to Mn. Similar behavior is observed with increase in the phosphorus concentration.

The magnetic properties of Pd-Co-P alloys show that they are ferromagnetic with a Curie temperature between 272 and 399°K as the cobalt concentration increases from 15 to 50 at.%. Below 20 at.% Co the short-range exchange interactions which produce the ferromagnetism are unable to establish a long-range magnetic order and a peak in the magnetization shows up at the lowest temperature range . The electric resistivity measurements were performed from liquid helium temperatures up to the vicinity of the melting point (900°K). The thermomagnetic analysis was carried out under an applied field of 6.0 kOe. The electrical resistivity of Pd-Co-P shows the coexistence of a Kondo-like minimum with ferromagnetism. The minimum becomes less important as the transition metal concentration increases and the coefficients of ℓn T and T^2 become smaller and strongly temperature dependent. The negative magnetoresistivity is a strong indication of the existence of localized moment.

The temperature coefficient of resistivity which is positive for Pd- Fe-P, Pd-Ni-P, and Pd-Co-P becomes negative for Pd-Mn-P. It is possible to account for the negative temperature dependence by the localized spin fluctuation model and the high density of states at the Fermi energy which becomes maximum between Mn and Cr. The magnetization curves for Pd-Mn-P are typical of those resulting from the interplay of different exchange forces. The established relationship between susceptibility and resistivity confirms the localized spin fluctuation model. The magnetoresistivity of Pd-Mn-P could be interpreted in tenns of a short-range magnetic ordering that could arise from the Rudennan-Kittel type interactions.

Symmetry of the Talbot effect and its applications

The Talbot effect is one of the most basic optical phenomena that has received extensive investigations both because its new results provide us more understanding of the fundamental Fresnel diffraction and also because of its wide applications. We summarize our recent results on this subject. Symmetry of the Talbot effect, which was reported in Optics Communications in 1995, is now realized as the key to reveal other rules for explanation of the Talbot effect for array illumination. The regularly rearranged-neighboring-phase-differences (RRNPD) rule, a completely new set of analytic phase equations (Applied Optics, 1999), and the prime-number decomposing rule (Applied Optics, 2001) are the newly obtained results that reflect the symmetry of the Talbot effect in essence. We also reported our results on the applications of the Talbot effect. Talbot phase codes are the orthogonal codes that can be used for phase coding of holographic storage. A new optical scanner based on the phase codes for Talbot array illumination has unique advantages. Furthermore, a novel two-layered multifunctional computer-generated hologram based on the fractional Talbot effect was proposed and implemented (Optics Letters, 2003). We believe that these new results should bring us more new understanding of the Talbot effect and help us to design novel optical devices that should benefit practical applications. (C) 2004 Society of Photo-Optical Instrumentation Engineers.

A molecular dynamics study of the microscopic properties of simple dense fluids

The microscopic properties of a two-dimensional model dense fluid of Lennard-Jones disks have been studied using the so-called "molecular dynamics" method. Analyses of the computer-generated simulation data in terms of "conventional" thermodynamic and distribution functions verify the physical validity of the model and the simulation technique.

The radial distribution functions g(r) computed from the simulation data exhibit several subsidiary features rather similar to those appearing in some of the g(r) functions obtained by X-ray and thermal neutron diffraction measurements on real simple liquids. In the case of the model fluid, these "anomalous" features are thought to reflect the existence of two or more alternative configurations for local ordering.

Graphical display techniques have been used extensively to provide some intuitive insight into the various microscopic phenomena occurring in the model. For example, "snapshots" of the instantaneous system configurations for different times show that the "excess" area allotted to the fluid is collected into relatively large, irregular, and surprisingly persistent "holes". Plots of the particle trajectories over intervals of 2.0 to 6.0 x 10^-12 sec indicate that the mechanism for diffusion in the dense model fluid is "cooperative" in nature, and that extensive diffusive migration is generally restricted to groups of particles in the vicinity of a hole.

A quantitative analysis of diffusion in the model fluid shows that the cooperative mechanism is not inconsistent with the statistical predictions of existing theories of singlet, or self-diffusion in liquids. The relative diffusion of proximate particles is, however, found to be retarded by short-range dynamic correlations associated with the cooperative mechanism--a result of some importance from the standpoint of bimolecular reaction kinetics in solution.

A new, semi-empirical treatment for relative diffusion in liquids is developed, and is shown to reproduce the relative diffusion phenomena observed in the model fluid quite accurately. When incorporated into the standard Smoluchowski theory of diffusion-controlled reaction kinetics, the more exact treatment of relative diffusion is found to lower the predicted rate of reaction appreciably.

Finally, an entirely new approach to an understanding of the liquid state is suggested. Our experience in dealing with the simulation data--and especially, graphical displays of the simulation data--has led us to conclude that many of the more frustrating scientific problems involving the liquid state would be simplified considerably, were it possible to describe the microscopic structures characteristic of liquids in a concise and precise manner. To this end, we propose that the development of a formal language of partially-ordered structures be investigated.

Influência dos receptores opioides no efeito hipotensor arterial do propofol em humanos

O propofol é uma droga hipnótico-sedativa, amplamente utilizada em anestesiologia, devido à sua elevada eficácia hipnótica e ao seu despertar rápido e praticamente isento de efeitos residuais. A depressão cardiovascular, que é o efeito adverso mais importante e indesejável do propofol, parece estar intimamente relacionada à dose administrada, à velocidade de injeção do medicamento, à idade e ao estado físico dos pacientes, assim como, às condições de volemia e de reserva cardiovascular dos mesmos, podendo ser intensificada, ainda, pela associação de uma droga opioide ao propofol. A hipotensão arterial induzida pelo propofol parece possuir uma origem multifatorial, pois já foi evidenciada a participação de diversos sistemas nos efeitos produzidos pelo propofol, inclusive, a participação da via opioide no efeito antinociceptivo da droga. Portanto, o objetivo desse estudo foi investigar a participação dos receptores opioides no efeito hipotensor arterial do propofol. A pesquisa foi do tipo randomizada, transversal, aberta e comparativa. Foram estudados 40 pacientes estado físico ASA 1, submetidos a anestesia geral para cirurgias eletivas. Os desfechos avaliados neste estudo foram as pressões arteriais sistólica (PAS), diastólica (PAD) e média (PAM), a pressão venosa central (PVC) e a frequência cardíaca (FC). Portanto, após a monitorização contínua dos pacientes com cardioscopia com análise de ST, pressão arterial invasiva, pressão venosa central, oxicapnometria, análise eletroencefalográfica bispectral (BIS) e gasimetrias arteriais e venosas, estes foram divididos aleatoriamente através de programa de distribuição aleatória gerada por computador, de acordo com os 5 grupos existentes (n = 8 para todos os grupos). Foram 3 grupos de pacientes pré-medicados intravenosamente (iv) com naloxona 1 μg/Kg (PN1) ou 3 μg/Kg (PN3), ou com salina para controle (CP), 2 minutos antes da administração iv de propofol (2,5 mg/Kg). Outros 2 grupos controle da naloxona foram pré-medicados com naloxona 1 μg/Kg (CN1) ou 3 μg/Kg (CN3), mas não receberam propofol. Os resultados demonstraram que há mais de um mecanismo envolvido no efeito hipotensor arterial do propofol, que é composto por uma rápida redução inicial da PAM opioide-independente e uma lenta redução final da PAM, que foi dependente, ao menos parcialmente, de ação opioide. O propofol, na dose de 2,5 mg/Kg, reduziu a PAS, PAD e PAM de forma significativa e independente do efeito hipnótico do anestésico, dos valores iniciais de PVC e de modificações na FC dos pacientes, apesar de ter sido evidenciada a inibição do baroreflexo induzida pelo anestésico. A hipotensão induzida pelo propofol pôde ser parcialmente reduzida, de forma significativa e dose-dependente, pela prévia administração iv de naloxona de 3 μg/Kg, menor dose efetiva. Este efeito da naloxona ocorreu, principalmente, através de um aumento significativo da PAD, sem importar em modificações significativas da PAS, FC, PVC, BIS ou do ECG. Foi concluído que a hipotensão arterial induzida pelo propofol possui uma origem multifatorial, sendo produzida parcialmente por um mecanismo que é opioide-dependente e sensível ao pré-tratamento dos pacientes com a naloxona. Nosso estudo não recebeu nenhum financiamento externo.

Compact holographic optical interconnections using nematic liquid crystal spatial light modulators

In a fibre-optic communication network, the wavelength-division multiplexing (WDM) technique enables an expansion of the data-carrying capacity of optical fibres. This can be achieved by transmitting different channels on a single optical fibre, with each channel modulating a different wavelength. In order to access and manipulate these channels at a node of the network, a compact holographic optical switch is designed, modelled, and constructed. The structure of such a switch consists of a series of optical components which are used to collimate the beam from the input, de-multiplex each individual wavelength into separated channels, manipulate the separated channels, and reshape the beam to the output. A spatial light modulator (SLM) is crucial in this system, offering control and flexibility at the channel manipulation stage, and providing the ability to redirect light into the desired output fibre. This is achieved by the use of a 2-D analogue phase computer generated hologram (CGH) based on liquid crystal on silicon (LCOS) technology. © 2011 Copyright Society of Photo-Optical Instrumentation Engineers (SPIE).

Design of a compact reconfigurable optical interconnection using nematic liquid crystal spatial light modulator

The wavelength-division multiplexing (WDM) has been proposed as a promising technology to efficiently use the available bandwidth of a single optical fibre. This can be achieved by transmitting different channels on the optical fibre with each channel modulating a different wavelength. The aim of this paper is to propose a compact design (35 mm×65 mm) of a reconfigurable holographic optical switch in order to access and manipulate 4 channels at a node of a fibre-optic communication network. A vital component of such a switch is a nematic liquid crystal spatial light modulator offering control and flexibility at the channel manipulation stage and providing the ability to redirect light into the desired output fibre. This is achieved by the use of a 2-D analogue phase computer generated hologram (CGH) based on liquid crystal on silicon (LCOS) technology. © 2012 SPIE.

High resolution electron microscopy study of single chain single crystals of gutta percha

Single chain single crystals (SCSC) of gutta percha (GP) were prepared by a dilute-solution spraying method. Electron diffraction (ED) patterns revealed that the single chain single crystal was of a new crystalline modification, the delta form. The images of SCSC of GP obtained with a high resolution electron microscope (HREM) showed a two dimensional periodic structure. Most of the images consisted of lattice fringes derived from the (001) zone. This is the first time that the single chain single crystal images of GP have been observed at a molecular level. Micrographs were image processed using optical filtering methods to improve the signal-to-noise ratio, and were compared with computer-generated simulations of the images. From the viewpoint of the defects seen in high resolution images, the crystal formation and melting processes are discussed. (C) 1998 Elsevier Science Ltd. All rights reserved.

Optical micro- and nanofibres: Higher mode generation and particle manipulation studies

This thesis is centred on two experimental fields of optical micro- and nanofibre research; higher mode generation/excitation and evanescent field optical manipulation. Standard, commercial, single-mode silica fibre is used throughout most of the experiments; this generally produces high-quality, single-mode, micro- or nanofibres when tapered in a flame-heated, pulling rig in the laboratory. Single mode fibre can also support higher transverse modes, when transmitting wavelengths below that of their defined single-mode regime cut-off. To investigate this, a first-order Laguerre-Gaussian beam, LG01 of 1064 nm wavelength and doughnut-shaped intensity profile is generated free space via spatial light modulation. This technique facilitates coupling to the LP11 fibre mode in two-mode fibre, and convenient, fast switching to the fundamental mode via computer-generated hologram modulation. Following LP11 mode loss when exponentially tapering 125μm diameter fibre, two mode fibre with a cladding diameter of 80μm is selected fir testing since it is more suitable for satisfying the adiabatic criteria for fibre tapering. Proving a fruitful endeavour, experiments show a transmission of 55% of the original LP11 mode set (comprising TE01, TM01, HE21e,o true modes) in submicron fibres. Furthermore, by observing pulling dynamics and progressive mode-lass behaviour, it is possible to produce a nanofibre which supports only the TE01 and TM01 modes, while suppressing the HE21e,o elements of the LP11 group. This result provides a basis for experimental studies of atom trapping via mode-interference, and offers a new set of evanescent field geometries for sensing and particle manipulation applications. The thesis highlights the experimental results of the research unit’s Cold Atom subgroup, who successfully integrated one such higher-mode nanofibre into a cloud of cold Rubidium atoms. This led to the detection of stronger signals of resonance fluorescence coupling into the nanofibre and for light absorption by the atoms due to the presence of higher guided modes within the fibre. Theoretical work on the impact of the curved nanofibre surface on the atomic-surface van der Waals interaction is also presented, showing a clear deviation of the potential from the commonly-used flat-surface approximation. Optical micro- and nanofibres are also useful tools for evanescent-field mediated optical manipulation – this includes propulsion, defect-induced trapping, mass migration and size-sorting of micron-scale particles in dispersion. Similar early trapping experiments are described in this thesis, and resulting motivations for developing a targeted, site-specific particle induction method are given. The integration of optical nanofibres into an optical tweezers is presented, facilitating individual and group isolation of selected particles, and their controlled positioning and conveyance in the evanescent field. The effects of particle size and nanofibre diameter on pronounced scattering is experimentally investigated in this systems, as are optical binding effects between adjacent particles in the evanescent field. Such inter-particle interactions lead to regulated self-positioning and particle-chain speed enhancements.

A structural basis for different antifreeze protein roles

Antifreeze proteins (AFPs) are produced by a variety of organisms to either protect them from freezing or help them tolerate being frozen. Recent structural work has shown that AFPs bind to ice using ordered surface waters on a particular surface of the protein called the ice-binding site (IBS). These 'anchored clathrate' waters fuse to particular planes of an ice crystal and hence irreversibly bind the AFP to its ligand. An AFP isolated from the perennial ryegrass, Lolium perenne (LpAFP) was previously modelled as a right-handed beta helix with two proposed IBSs. Steric mutagenesis, where small side chains were replaced with larger ones, determined that only one of the putative IBSs was responsible for binding ice. The mutagenesis work also partly validated the fold of the computer-generated model of this AFP. In order to determine the structure of the protein, LpAFP was crystallized and solved to 1.4 Å resolution. The protein folds as an untwisted left-handed beta-helix, of opposite handedness to the model. The IBS identified by mutagenesis is remarkably flat, but less regular than the IBS of most other AFPs. Furthermore, several of the residues constituting the IBS are in multiple conformations. This irregularity may explain why LpAFP causes less thermal hysteresis than many other AFPs. Its imperfect IBS is also argued to be responsible for LpAFP's heightened ice-recrystallization inhibition activity. The structure of LpAFP is the first for a plant AFP and for a protein responsible for providing freeze tolerance rather than freeze resistance. To help understand what constitutes an IBS, a non-ice-binding homologue of type III AFP, sialic acid synthase (SAS), was engineered for ice binding. Point mutations were made to the germinal IBS of SAS to mimic key features seen in type III AFP. The crystal structures of some of the mutant proteins showed that the potential IBS became less charged and flatter as the mutations progressed, and ice affinity was gained. This proof-of-principle study highlights some of the difficulties in AFP engineering.

Investigating shape-from-shading illusions using solid objects

Recent growth in the shape-from-shading psychophysics literature has been paralled by an increasing availability of computer graphics hardware and software, to the extent that most psychophysical studies in this area now employ computer lighting algorithms. The most widely used of algorithms is shape-from-shading psychophysics is the Phong lighting model. This model, and other shading models of its genre, produce readily ineterpretable imiages of three-dimensional scenes. However, such algorithms are only approximations of how light interacts with real objects in the natural environment. Nevertheless, the results from psychophysical experiments using these techniques have been used to infer the processes underlying the perception of shape-from-shading in natural environments. It is important to establish whether this substitution is ever valid. We report a series of experiments investigating whether two recently reported illusions seen computer-generated, Phond shaded images occur for solid objects under real illuminants. The two illusions investigated are three-dimensional curvature contrast and the illuminant-position effect on perceived curvature. We show that both effects do occur for solid objects, and that the magnitude of these effects are equivalent regardless of whether subjects are presented with ray traced or solid objects.

Validation of membrane protein topology models by oxidative labeling and mass spectrometry

Computer-assisted topology predictions are widely used to build low-resolution structural models of integral membrane proteins (IMPs). Experimental validation of these models by traditional methods is labor intensive and requires modifications that might alter the IMP native conformation. This work employs oxidative labeling coupled with mass spectrometry (MS) as a validation tool for computer-generated topology models. ·OH exposure introduces oxidative modifications in solvent-accessible regions, whereas buried segments (e.g., transmembrane helices) are non-oxidizable. The Escherichia coli protein WaaL (O-antigen ligase) is predicted to have 12 transmembrane helices and a large extramembrane domain (Pérez et al., Mol. Microbiol. 2008, 70, 1424). Tryptic digestion and LC-MS/MS were used to map the oxidative labeling behavior of WaaL. Met and Cys exhibit high intrinsic reactivities with ·OH, making them sensitive probes for solvent accessibility assays. Overall, the oxidation pattern of these residues is consistent with the originally proposed WaaL topology. One residue (M151), however, undergoes partial oxidation despite being predicted to reside within a transmembrane helix. Using an improved computer algorithm, a slightly modified topology model was generated that places M151 closer to the membrane interface. On the basis of the labeling data, it is concluded that the refined model more accurately reflects the actual topology of WaaL. We propose that the combination of oxidative labeling and MS represents a useful strategy for assessing the accuracy of IMP topology predictions, supplementing data obtained in traditional biochemical assays. In the future, it might be possible to incorporate oxidative labeling data directly as constraints in topology prediction algorithms.