Molecular dynamics simulation of methane in sodium montmorillonite clay hydrates at elevated pressures and temperatures

Computer simulation has been used to study the structure and dynamics of methane in hydrated sodium montmorillonite clays under conditions encountered in sedimentary basins. Systems containing approximately one, two, three and four molecular layers of water have followed gradients of 150 bar km-1 and 30Kkm-1, to a maximum burial depth of 6 km (900 bar and 460 K). Methane is coordinated to approximately 19 oxygen atoms, of which typically 6 are provided by the clay surface. Only in the three- and four-layer hydrates is methane able to leave the clay surface. Diffusion depends strongly on the porosity (water content) and burial depth: self-diffusion coefficients are in the range 0.12 × 10-9m2s-1 for water and 0.04 × 10−9m2s−1 < D < 8.64 × 10−9m2s−1 for methane. Bearing in mind that porosity decreases with burial depth, it is estimated that maximum diffusion occurs at around 3 km. This is in good agreement with the known location of methane reservoirs in sedimentary basins.

Mode-locked semiconductor lasers with optical injection

We perform characterization of the pulse shape and noise properties of quantum dot passively mode-locked lasers (PMLLs). We propose a novel method to determine the RF linewidth and timing jitter, applicable to high repetition rate PMLLs, through the dependence of modal linewidth on the mode number. Complex electric field measurements show asymmetric pulses with parabolic phase close to threshold, with the appearance of waveform instabilities at higher currents. We demonstrate that the waveform instabilities can be overcome through optical injection-locking to the continues wave (CW) master laser, leading to time-bandwidth product (TBP) improvement, spectral narrowing, and spectral tunability. We discuss the benefits of single- and dual-tone master sources and demonstrate that dual-tone optical injection can additionally improve the noise properties of the slave laser with RF linewidth reduction below instrument limits (1 kHz) and integrated timing jitter values below 300 fs. Dual-tone injection allowed slave laser repetition rate control over a 25 MHz range with reduction of all modal optical linewidths to the master source linewidth, demonstrating phase-locking of all slave modes and coherence improvement.

Specialist contact lens fitting

What is meant by the term ‘specialist contact lens fitting’? Or put another way, what would be considered non-specialist contact lens fitting? Is there such a thing as routine contact lens fitting? Soft or silicone hydrogel fitting for daily wear would probably be considered as routine contact lens fitting, but would extended or flexible wear remain in the same category or would they be considered a specialist fit? Different eras will classify different products as being ‘specialist’. Certainly twenty years ago soft toric contact lenses were considered as being speciality lenses but today would be thought of as routine lenses. Conversely, gas permeable lenses were thought of as mainstream twenty years ago but now are considered as speciality lenses. Although this would not be the same globally, as in some countries (such as Netherlands, France and Japan) gas permeable lens fitting remains popular and is not on the decline as in other countries (Canada, Australia and Sweden) [1]. Bandage soft lenses applied after surface laser refractive procedures would be considered as therapeutic lenses but in reality they are just plano thin hydrogel lenses worn constantly for 3–4 days to allow the underlying epithelium to convalesce and are then removed [2]. Some patients find that wearing hydrogel lenses during periods when they suffer from seasonal allergies actually improves their ocular comfort as the contact lens acts as a barrier to the allergen [3] and [4]. Scleral lenses have long been considered speciality lenses, apart from a time when they were the only lenses available but at that time all contact lens work would have been considered speciality practice! Nowadays we see the advent of mini-scleral designs and we see large diameter gas permeable lenses too. It is possible that these lenses increase the popularity of gas permeable lenses again and they become more main stream. So it would seem that the lines between routine and speciality contact lens fitting are not clear. Whether a lens is classed a specialist fit or not would depend on the lens type, why it was fitted, where in the world the fitting was being done and even the era in which it was fitted. This begs the question as to what would be considered entry level knowledge in contact lens fitting. This may not be an issue for most BCLA members or CLAE readers but certainly would be for bodies such as the College of Optometrists (UK) or the Association of British Dispensing Opticians when they are planning the final registration examinations for budding practitioners or when planning the level of higher level qualifications such as College Certificates or Diplomas. Similarly for training institutions when they are planning their course content. This becomes even trickier when trying to devise a qualification that spans across many countries, like the European Diploma in Optometry and Optics. How do we know if the training and examination level is correct? One way would be to analyse things when they go wrong and if patterns of malpractice are seen then maybe that could be used as an indicator to more training being needed. There were 162 Fitness to Practice Hearing at the General Optical Council between 2001 and 2010. Forty-seven of these were clinically related case, 39 fraud related, and 76 others. Of the clinical ones only 3 were contact lens related. So it would appear that as whole, in the profession, contact lens clinical skills are not being questioned too often (although it seems a few of us can’t keep our hands out the cookie jar!).

Editorial

This time of year we look back at the year that has passed and make plans for the next year. I like to reflect on things that I have learnt and people that I have met, especially those who facilitated that learning. In 2009 I went to various conferences, The BCLA conference in Manchester, The Romanian Optical Society meeting in Brasov, Transylvania (where the university is actually on Vlad Tepes Street), The European Council for Optometry and Optics (ECOO) in Brno, Czech Republic, The American Academy of Optometry (AAO) in Orlando USA, The International Association of Contact Lens Educators (IACLE) meeting in Tianjin China and finally The Vereinigung Deutscher Contactlinsen-Spezialisten (VDCO) meeting in Jena. All were interesting places and thoroughly all were enjoyable conferences with their own highlights but I wanted to focus on Jena and one person I met there and his inspirational search for knowledge and the contributions he made in the field of contact lenses. Jena itself is a fascinating place and should be on the ‘must visit’ list of anyone involved in eye care. It is the birth place of Carl Zeiss of course and where he started his company. It is also the birth place of Ernst Abbe (physicist and optometrist and expert lens maker), and Otto Schott (chemist and technologist who made high quality glass. There are many road signs bearing witness to these famous pioneers. The optical museum is worth spending a few hours looking around too. I was invited to speak at the VDCO at the kind invitation from colleagues at the Jena School of Optometry, Professor Wolfgang Sickenberger and Professor Sebastian Marx. At this meeting I met 87-year-old Willi KAUE who was being awarded the Adolf Wilhelm Müller-Welt prize by the VDCO for contribution to contact lenses over his 60-year career. At the age of 15 Willi Kaue took up an apprenticeship to become an Optician in Germany in 1937. At this time he first heard about the scleral glass lenses made by the Carl Zeiss Company in Jena. This started his lifelong fascination which was to become his passion but not yet his career. During the war he was enlisted into military service but immediately after was back to his former career. In 1950 Willi corrected his own 3.5 dioptres of myopia with a plastic scleral lens. His fascination strengthened as for the first time he himself could experience a wider field of view than his spectacles gave him, less aberrations and less retinal minification. He also appreciated the fact that contact lenses did not cause pressure on the nose or ears and did not slide down his nose plus remained optically centred with his eye movements. He decided that form now on he would make fitting contact lenses his career. He travelled to London to learn more about contact lenses and how to fit them but initially did not find many willing teachers and to start with became largely self-taught. He wanted to know how to make scleral lenses. So far he only knew that pulverized polymethyl methacrylate (PMMA) was pressed and moulded. In 1951 he met Berlin optician Otto Marzock. He made his only scleral lenses from using military PMMA windshields. His process involved lathe cutting the lenses and resulted in lenses that were thinner than moulded ones. Willi developed a manufacturing method, using a rotary diamond drill, starting form the outer edge and towards the centre at a constant cut speed. This enabled him to make more reproducible lenses and in less time. His enthusiasm in the field was clear from the travels he made in the pursuit of advancement - travelling around Europe, South America, North America and Asia. In 1963 he visited George Nissel in Hemel Hempstead, England. Constantly thriving towards innovations Willi came across the new Naturalens from the USA made from HEMA at a congress in Marseille in 1969. Amongst his contributions to the field, was his own technique of fitting ocular prosthetics, using an alginate impression of the orbit. I was fortunate enough to have dinner with Willi Kaue and learnt more about his fascinating career through the patient interpreting skills of Hilmar Bussacker (the 2008 winner of the same award and the 2007 winner of the European Federation of the Contact Lens and IOL Industries Award). I look forward to 2010 with eager anticipation as to what I may learn and who I might meet!!! Copyright © 2009 British Contact Lens Association. Published by Elsevier Ltd. All rights reserved.

Signal processing for molecular and cellular biological physics:an emerging field

Recent advances in our ability to watch the molecular and cellular processes of life in action-such as atomic force microscopy, optical tweezers and Forster fluorescence resonance energy transfer-raise challenges for digital signal processing (DSP) of the resulting experimental data. This article explores the unique properties of such biophysical time series that set them apart from other signals, such as the prevalence of abrupt jumps and steps, multi-modal distributions and autocorrelated noise. It exposes the problems with classical linear DSP algorithms applied to this kind of data, and describes new nonlinear and non-Gaussian algorithms that are able to extract information that is of direct relevance to biological physicists. It is argued that these new methods applied in this context typify the nascent field of biophysical DSP. Practical experimental examples are supplied.

Structure and dynamics of multiple cationic vectors-siRNA complexation by all-atomic molecular dynamics simulations

Understanding the molecular mechanism of gene condensation is a key component to rationalizing gene delivery phenomena, including functional properties such as the stability of the gene-vector complex and the intracellular release of the gene. In this work, we adopt an atomistic molecular dynamics simulation approach to study the complexation of short strand duplex RNA with four cationic carrier systems of varying charge and surface topology at different charge ratios. At lower charge ratios, polymers bind quite effectively to siRNA, while at high charge ratios, the complexes are saturated and there are free polymers that are unable to associate with RNA. We also observed reduced fluctuations in RNA structures when complexed with multiple polymers in solution as compared to both free siRNA in water and the single polymer complexes. These novel simulations provide a much better understanding of key mechanistic aspects of gene-polycation complexation and thereby advance progress toward rational design of nonviral gene delivery systems.

Atomic structure of the two intermediate phase glasses SiSe4 and GeSe4

The microscopic origin of the intermediate phase in two prototypical covalently bonded AxB1-x network glass forming systems, where A=Ge or Si, B=Se, and 0=x=1, was investigated by combining neutron diffraction with first-principles molecular-dynamics methods. Specifically, the structure of glassy GeSe4 and SiSe4 was examined, and the calculated total structure factor and total pair-correlation function for both materials are in good agreement with experiment. The structure of both glasses differs markedly from a simple model comprising undefective AB4 corner-sharing tetrahedra in which all A atoms are linked by B2 dimers. Instead, edge-sharing tetrahedra occur and the twofold coordinated Se atoms form three distinct structural motifs, namely, Se-Se2, Se-SeGe (or Se-SeSi), and Se-Ge2 (or Se-Si2). This identifies several of the conformations that are responsible for the structural variability in GexSe1-x and SixSe1-x glasses, a quantity that is linked to the finite width of the intermediate phase window.

A molecular dynamics model of the atomic structure of dysprosium alumino-phosphate glass

Molecular dynamics (MD) has been used to identify the relative distribution of dysprosium in the phosphate glass DyAl0.30P3.05O9.62. The MD model has been compared directly with experimental data obtained from neutron diffraction to enable a detailed comparison beyond the total structure factor level. The MD simulation gives Dy ... Dy correlations at 3.80(5) and 6.40(5) angstrom with relative coordination numbers of 0.8(1) and 7.3(5), thus providing evidence of minority rare-earth clustering within these glasses. The nearest neighbour Dy-O peak occurs at 2.30 angstrom with each Dy atom having on average 5.8 nearest neighbour oxygen atoms. The MD simulation is consistent with the phosphate network model based on interlinked PO4 tetrahedra where the addition of network modifiers Dy3+ depolymerizes the phosphate network through the breakage of P-(O)-P bonds whilst leaving the tetrahedral units intact. The role of aluminium within the network has been taken into explicit account, and A1 is found to be predominantly (78 tetrahedrally coordinated. In fact all four A1 bonds are found to be to P (via an oxygen atom) with negligible amounts of Al-O-Dy bonds present. This provides an important insight into the role of Al additives in improving the mechanical properties of these glasses.

Potential for broad range multiplexing of fibre Bragg gratings in polymer optical fibres and operation in the 700-nm wavelength range

Refractive index and structural characteristics of optical polymers are strongly influenced by the thermal history of the material. Polymer optical fibres (POF) are drawn under tension, resulting in axial orientation of the polymer molecular chains due to their susceptibility to align in the fibre direction. This change in orientation from the drawing process results in residual strain in the fibre and also affects the transparency and birefringence of the material (1-3). PMMA POF has failure strain as high as over 100%. POF has to be drawn under low tension to achieve this value. The drawing tension affects the magnitude of molecular alignment along the fibre axis, thus affecting the failure strain. The higher the tension the lower the failure stain will be. However, the properties of fibre drawn under high tension can approach that of fibre drawn under low tension by means of an annealing process. Annealing the fibre can generally optimise the performance of POF while keeping most advantages intact. Annealing procedures can reduce index difference throughout the bulk and also reduce residual stress that may cause fracture or distortion. POF can be annealed at temperatures approaching the glass transition temperature (Tg) of the polymer to produce FBG with a permanent blue Bragg wave-length shift at room temperature. At this elevated temperature segmental motion in the structure results in a lower viscosity. The material softens and the molecular chains relax from the axial orientation causing shrinking of the fibre. The large attenuation of typically 1dB/cm in the 1550nm spectral region of PMMA POF has limited FBG lengths to less than 10cm. The more expensive fluorinated polymers with lower absorption have had no success as FBG waveguides. Bragg grating have been inscribed onto various POF in the 800nm spectral region using a 30mW continuous wave 325nm helium cadmium laser, with a much reduced attenuation coefficient of 10dB/m (5). Fabricating multiplexed FBGs in the 800nm spectral region in TOPAS and PMMA POF consistently has lead to fabrication of multiplexed FBG in the 700nm spectral region by a method of prolonged annealing. The Bragg wavelength shift of gratings fabricated in PMMA fibre at 833nm and 867nm was monitored whilst the POF was thermally annealed at 80°C. Permanent shifts exceeding 80nm into the 700nm spectral region was attained by both gratings on the fibre. The large permanent shift creates the possibility of multiplexed Bragg sensors operating over a broad range. -------------------------------------------------------------------------------------------------------------------- 1. Pellerin C, Prud'homme RE, Pézolet M. Effect of thermal history on the molecular orientation in polystyrene/poly (vinyl methyl ether) blends. Polymer. 2003;44(11):3291-7. 2. Dvoránek L, Machová L, Šorm M, Pelzbauer Z, Švantner J, Kubánek V. Effects of drawing conditions on the properties of optical fibers made from polystyrene and poly (methyl methacrylate). Die Angewandte Makromolekulare Chemie. 1990;174(1):25-39. 3. Dugas J, Pierrejean I, Farenc J, Peichot JP. Birefringence and internal stress in polystyrene optical fibers. Applied optics. 1994;33(16):3545-8. 4. Jiang C, Kuzyk MG, Ding JL, Johns WE, Welker DJ. Fabrication and mechanical behavior of dye-doped polymer optical fiber. Journal of applied physics. 2002;92(1):4-12. 5. Johnson IP, Webb DJ, Kalli K, Yuan W, Stefani A, Nielsen K, et al., editors. Polymer PCF Bragg grating sensors based on poly (methyl methacrylate) and TOPAS cyclic olefin copolymer2011: SPIE.

Effects of rare-earth co-doping on the local structure of rare-earth phosphate glasses using high and low energy X-ray diffraction

Rare-earth co-doping in inorganic materials has a long-held tradition of facilitating highly desirable optoelectronic properties for their application to the laser industry. This study concentrates specifically on rare-earth phosphate glasses, (R2O3)x(R'2O3)y(P2O5)1-(x+y), where (R, R') denotes (Ce, Er) or (La, Nd) co-doping and the total rare-earth composition corresponds to a range between metaphosphate, RP3O9, and ultraphosphate, RP5O14. Thereupon, the effects of rare-earth co-doping on the local structure are assessed at the atomic level. Pair-distribution function analysis of high-energy X-ray diffraction data (Qmax = 28 Å-1) is employed to make this assessment. Results reveal a stark structural invariance to rare-earth co-doping which bears testament to the open-framework and rigid nature of these glasses. A range of desirable attributes of these glasses unfold from this finding; in particular, a structural simplicity that will enable facile molecular engineering of rare-earth phosphate glasses with 'dial-up' lasing properties. When considered together with other factors, this finding also demonstrates additional prospects for these co-doped rare-earth phosphate glasses in nuclear waste storage applications. This study also reveals, for the first time, the ability to distinguish between P-O and PO bonding in these rare-earth phosphate glasses from X-ray diffraction data in a fully quantitative manner. Complementary analysis of high-energy X-ray diffraction data on single rare-earth phosphate glasses of similar rare-earth composition to the co-doped materials is also presented in this context. In a technical sense, all high-energy X-ray diffraction data on these glasses are compared with analogous low-energy diffraction data; their salient differences reveal distinct advantages of high-energy X-ray diffraction data for the study of amorphous materials. © 2013 The Owner Societies.

Potential for broad range multiplexing of fibre Bragg gratings in polymer optical fibres and operation in the 700-nm wavelength range

Refractive index and structural characteristics of optical polymers are strongly influenced by the thermal history of the material. Polymer optical fibres (POF) are drawn under tension, resulting in axial orientation of the polymer molecular chains due to their susceptibility to align in the fibre direction. This change in orientation from the drawing process results in residual strain in the fibre and also affects the transparency and birefringence of the material (1-3). PMMA POF has failure strain as high as over 100%. POF has to be drawn under low tension to achieve this value. The drawing tension affects the magnitude of molecular alignment along the fibre axis, thus affecting the failure strain. The higher the tension the lower the failure stain will be. However, the properties of fibre drawn under high tension can approach that of fibre drawn under low tension by means of an annealing process. Annealing the fibre can generally optimise the performance of POF while keeping most advantages intact. Annealing procedures can reduce index difference throughout the bulk and also reduce residual stress that may cause fracture or distortion. POF can be annealed at temperatures approaching the glass transition temperature (Tg) of the polymer to produce FBG with a permanent blue Bragg wave-length shift at room temperature. At this elevated temperature segmental motion in the structure results in a lower viscosity. The material softens and the molecular chains relax from the axial orientation causing shrinking of the fibre. The large attenuation of typically 1dB/cm in the 1550nm spectral region of PMMA POF has limited FBG lengths to less than 10cm. The more expensive fluorinated polymers with lower absorption have had no success as FBG waveguides. Bragg grating have been inscribed onto various POF in the 800nm spectral region using a 30mW continuous wave 325nm helium cadmium laser, with a much reduced attenuation coefficient of 10dB/m (5). Fabricating multiplexed FBGs in the 800nm spectral region in TOPAS and PMMA POF consistently has lead to fabrication of multiplexed FBG in the 700nm spectral region by a method of prolonged annealing. The Bragg wavelength shift of gratings fabricated in PMMA fibre at 833nm and 867nm was monitored whilst the POF was thermally annealed at 80°C. Permanent shifts exceeding 80nm into the 700nm spectral region was attained by both gratings on the fibre. The large permanent shift creates the possibility of multiplexed Bragg sensors operating over a broad range. -------------------------------------------------------------------------------------------------------------------- 1. Pellerin C, Prud'homme RE, Pézolet M. Effect of thermal history on the molecular orientation in polystyrene/poly (vinyl methyl ether) blends. Polymer. 2003;44(11):3291-7. 2. Dvoránek L, Machová L, Šorm M, Pelzbauer Z, Švantner J, Kubánek V. Effects of drawing conditions on the properties of optical fibers made from polystyrene and poly (methyl methacrylate). Die Angewandte Makromolekulare Chemie. 1990;174(1):25-39. 3. Dugas J, Pierrejean I, Farenc J, Peichot JP. Birefringence and internal stress in polystyrene optical fibers. Applied optics. 1994;33(16):3545-8. 4. Jiang C, Kuzyk MG, Ding JL, Johns WE, Welker DJ. Fabrication and mechanical behavior of dye-doped polymer optical fiber. Journal of applied physics. 2002;92(1):4-12. 5. Johnson IP, Webb DJ, Kalli K, Yuan W, Stefani A, Nielsen K, et al., editors. Polymer PCF Bragg grating sensors based on poly (methyl methacrylate) and TOPAS cyclic olefin copolymer2011: SPIE.

Mechanical actuation by responsive polyelectrolyte brushes and triblock gels

Progress in the development of actuating molecular devices based on responsive polymers is reviewed. The synthesis and characterization of "grafted from brushes and triblock copolymers is reported. The responsive nature of polyelectrolyte brushes, grown by surface initiated atomic transfer radical polymerization (ATRP), has been characterized by scanning force microscopy, neutron reflectometry, and single molecule force measurements. The molecular response is measured directly for the brushes in terms of both the brush height and composition and the force generated by a single molecule. Triblock copolymers, based on hydrophobic end blocks and polyacid midblock, have been used to produce polymer gels where the deformation of the molecules can be followed directly by small angle Xray scattering (SAXS), and a correlation between molecular shape change and macroscopic deformation has been established. A Landolt pHoscillator, based on bromate/sulfite/ferrocyanide, with a room temperature period of 20 min and a range of 3.1

Evidence-based nanoscopic and molecular framework for excipient functionality in compressed orally disintegrating tablets

The work investigates the adhesive/cohesive molecular and physical interactions together with nanoscopic features of commonly used orally disintegrating tablet (ODT) excipients microcrystalline cellulose (MCC) and D-mannitol. This helps to elucidate the underlying physico-chemical and mechanical mechanisms responsible for powder densification and optimum product functionality. Atomic force microscopy (AFM) contact mode analysis was performed to measure nano-adhesion forces and surface energies between excipient-drug particles (6-10 different particles per each pair). Moreover, surface topography images (100 nm2-10 μm2) and roughness data were acquired from AFM tapping mode. AFM data were related to ODT macro/microscopic properties obtained from SEM, FTIR, XRD, thermal analysis using DSC and TGA, disintegration testing, Heckel and tabletability profiles. The study results showed a good association between the adhesive molecular and physical forces of paired particles and the resultant densification mechanisms responsible for mechanical strength of tablets. MCC micro roughness was 3 times that of D-mannitol which explains the high hardness of MCC ODTs due to mechanical interlocking. Hydrogen bonding between MCC particles could not be established from both AFM and FTIR solid state investigation. On the contrary, D-mannitol produced fragile ODTs due to fragmentation of surface crystallites during compression attained from its weak crystal structure. Furthermore, AFM analysis has shown the presence of extensive micro fibril structures inhabiting nano pores which further supports the use of MCC as a disintegrant. Overall, excipients (and model drugs) showed mechanistic behaviour on the nano/micro scale that could be related to the functionality of materials on the macro scale. © 2014 Al-khattawi et al.

A hybrid molecular dynamics/fluctuating hydrodynamics method for modelling liquids at multiple scales in space and time

A new 3D implementation of a hybrid model based on the analogy with two-phase hydrodynamics has been developed for the simulation of liquids at microscale. The idea of the method is to smoothly combine the atomistic description in the molecular dynamics zone with the Landau-Lifshitz fluctuating hydrodynamics representation in the rest of the system in the framework of macroscopic conservation laws through the use of a single "zoom-in" user-defined function s that has the meaning of a partial concentration in the two-phase analogy model. In comparison with our previous works, the implementation has been extended to full 3D simulations for a range of atomistic models in GROMACS from argon to water in equilibrium conditions with a constant or a spatially variable function s. Preliminary results of simulating the diffusion of a small peptide in water are also reported.

Bioactive sol-gel glasses at the atomic scale:the complementary use of advanced probe and computer modeling methods

Sol-gel-synthesized bioactive glasses may be formed via a hydrolysis condensation reaction, silica being introduced in the form of tetraethyl orthosilicate (TEOS), and calcium is typically added in the form of calcium nitrate. The synthesis reaction proceeds in an aqueous environment; the resultant gel is dried, before stabilization by heat treatment. These materials, being amorphous, are complex at the level of their atomic-scale structure, but their bulk properties may only be properly understood on the basis of that structural insight. Thus, a full understanding of their structure-property relationship may only be achieved through the application of a coherent suite of leading-edge experimental probes, coupled with the cogent use of advanced computer simulation methods. Using as an exemplar a calcia-silica sol-gel glass of the kind developed by Larry Hench, in the memory of whom this paper is dedicated, we illustrate the successful use of high-energy X-ray and neutron scattering (diffraction) methods, magic-angle spinning solid-state NMR, and molecular dynamics simulation as components to a powerful methodology for the study of amorphous materials.