Proteins in silico-modeling and sampling

Proteins are linear chain molecules made out of amino acids. Only when they fold to their native states, they become functional. This dissertation aims to model the solvent (environment) effect and to develop & implement enhanced sampling methods that enable a reliable study of the protein folding problem in silico. We have developed an enhanced solvation model based on the solution to the Poisson-Boltzmann equation in order to describe the solvent effect. Following the quantum mechanical Polarizable Continuum Model (PCM), we decomposed net solvation free energy into three physical terms– Polarization, Dispersion and Cavitation. All the terms were implemented, analyzed and parametrized individually to obtain a high level of accuracy. In order to describe the thermodynamics of proteins, their conformational space needs to be sampled thoroughly. Simulations of proteins are hampered by slow relaxation due to their rugged free-energy landscape, with the barriers between minima being higher than the thermal energy at physiological temperatures. In order to overcome this problem a number of approaches have been proposed of which replica exchange method (REM) is the most popular. In this dissertation we describe a new variant of canonical replica exchange method in the context of molecular dynamic simulation. The advantage of this new method is the easily tunable high acceptance rate for the replica exchange. We call our method Microcanonical Replica Exchange Molecular Dynamic (MREMD). We have described the theoretical frame work, comment on its actual implementation, and its application to Trp-cage mini-protein in implicit solvent. We have been able to correctly predict the folding thermodynamics of this protein using our approach.

Post-Depositional Movement of Methanesulphonic Acid at Law Dome, Antarctica, and the Influence of Accumulation Rate

A series of ice cores from sites with different snow-accumulation rates across Law Dome, East Antarctica, was investigated for methanesulphonic acid (MSA) movement. The precipitation at these sites (up to 35 km apart) is influenced by the same air masses, the principal difference being the accumulation rate. At the low-accumulation-rate W20k site (0.17 in ice equivalent), MSA was completely relocated from the summer to winter layer. Moderate movement was observed at the intermediate-accumulation-rate site (0.7 in ice equivalent), Dome Summit South (DSS), while there was no evidence of movement at the high-accumulation-rate DE08 site (1.4 in ice equivalent). The main DSS record of MSA covered the epoch AD 1727-2000 and was used to investigate temporal post-depositional changes. Co-deposition of MSA and sea-salt ions was observed of the surface layers, outside of the main summer MSA peak, which complicates interpretation of these peaks as evidence of movement in deeper layers. A seasonal study of the 273 year DSS record revealed MSA migration predominantly from summer into autumn (in the up-core direction), but this migration was suppressed during the Tambora (1815) and unknown (1809) volcanic eruption period, and enhanced during an epoch (1770-1800) with high summer nitrate levels. A complex interaction between the gradients in nss-sulphate, nitrate and sea salts (which are influenced by accumulation rate) is believed to control the rate and extent of movement of MSA.

Bilateral uterine vessel ligation as a model of intrauterine growth restriction in mice

BACKGROUND Intrauterine growth restriction (IUGR) occurs in up to 10% of pregnancies and is considered as a major risk to develop various diseases in adulthood, such as cardiovascular diseases, insulin resistance, hypertension or end stage kidney disease. Several IUGR models have been developed in order to understand the biological processes linked to fetal growth retardation, most of them being rat or mouse models and nutritional models. In order to reproduce altered placental flow, surgical models have also been developed, and among them bilateral uterine ligation has been frequently used. Nevertheless, this model has never been developed in the mouse, although murine tools display multiple advantages for biological research. The aim of this work was therefore to develop a mouse model of bilateral uterine ligation as a surgical model of IUGR. RESULTS In this report, we describe the set up and experimental data obtained from three different protocols (P1, P2, P3) of bilateral uterine vessel ligation in the mouse. Ligation was either performed at the cervical end of each uterine horn (P1) or at the central part of each uterine horn (P2 and P3). Time of surgery was E16 (P1), E17 (P2) or E16.5 (P3). Mortality, maternal weight and abortion parameters were recorded, as well as placentas weights, fetal resorption, viability, fetal weight and size. Results showed that P1 in test animals led to IUGR but was also accompanied with high mortality rate of mothers (50%), low viability of fetuses (8%) and high resorption rate (25%). P2 and P3 improved most of these parameters (decreased mortality and improved pregnancy outcomes; improved fetal viability to 90% and 27%, respectively) nevertheless P2 was not associated to IUGR contrary to P3. Thus P3 experimental conditions enable IUGR with better pregnancy and fetuses outcomes parameters that allow its use in experimental studies. CONCLUSIONS Our results show that bilateral uterine artery ligation according to the protocol we have developed and validated can be used as a surgical mouse model of IUGR.

(Table 1) Maceral composition and organic carbon chemistry of ODP Leg 104 samples

The Cenozoic sediments sampled in ODP Leg 104 on the Vøring Plateau show a distinct variability of the total organic carbon content (TOC) and the accumulation rates of TOC. Based on the geochemical and organic-petrographic characterization of the sedimentary organic matter (OM), the allochthonous and autochthonous proportion of the OM could be quantified. The results clearly demonstrate that high TOC percentages and TOC accumulation rates in Cenozoic sediment sections display a generally high input of allochthonous organic matter. Oxidized and partly well-rounded organic particles built up the main portion of OM within the Miocene, TOC-rich sediments. The most probable source of this oxidized OM are reworked sediments from the Scandinavian shelf. Changes in the input of these organic particles are to some degree correlative with sea-level changes. The Cenozoic accumulation of autochthonous OM is low and does not reveal a clear variation during the Miocene and early Pliocene. In spite of a high accumulation rate of biogenic opal during the Early Miocene, the accumulation rate of autochthonous TOC is low. The autochthonous particle assemblage is dominated by relatively inert OM, like dinoflagellate cysts. This points to an intensive biological and/or early diagenetic degradation of the marine OM under well oxidized bottom water conditions during the last 23 Myr. Nevertheless, a continuation of marine OM degradation during later stages of diagenesis cannot be excluded. A prominent dominance of allochthonous OM over autochthonous is documented with the beginning of the Pliocene. At 2.45 Ma the episodic occurrence of ice-rafted, thermally mature OM reflects the onset of the glacial erosion of Mesozoic, coal and black shale bearing sediments on the Scandinavian and Barents Sea shelves. The first occurrence of these, in view of the actual burial depth, thermally overmature OM particles is, therefore, a marker for the beginning of the strong Scandinavian glaciation and the advance of the glacial front toward the shelves.

Integrated learning of computer applications for production engineering

A high productivity rate in Engineering is related to an efficient management of the flow of the large quantities of information and associated decision making activities that are consubstantial to the Engineering processes both in design and production contexts. Dealing with such problems from an integrated point of view and mimicking real scenarios is not given much attention in Engineering degrees. In the context of Engineering Education, there are a number of courses designed for developing specific competencies, as required by the academic curricula, but not that many in which integration competencies are the main target. In this paper, a course devoted to that aim is discussed. The course is taught in a Marine Engineering degree but the philosophy could be used in any Engineering field. All the lessons are given in a computer room in which every student can use each all the treated software applications. The first part of the course is dedicated to Project Management: the students acquire skills in defining, using Ms-PROJECT, the work breakdown structure (WBS), and the organization breakdown structure (OBS) in Engineering projects, through a series of examples of increasing complexity, ending up with the case of vessel construction. The second part of the course is dedicated to the use of a database manager, Ms-ACCESS, for managing production related information. A series of increasing complexity examples is treated ending up with the management of the pipe database of a real vessel. This database consists of a few thousand of pipes, for which a production timing frame is defined, which connects this part of the course with the first one. Finally, the third part of the course is devoted to the work with FORAN, an Engineering Production package of widespread use in the shipbuilding industry. With this package, the frames and plates where all the outfitting will be carried out are defined through cooperative work by the studens, working simultaneously in the same 3D model. In the paper, specific details about the learning process are given. Surveys have been posed to the students in order to get feed-back from their experience as well as to assess their satisfaction with the learning process. Results from these surveys are discussed in the paper

Hardware timestamping for image acquisition system based on FlexRIO and IEEE 1588 v2 Standard

Current fusion devices consist of multiple diagnostics and hundreds or even thousands of signals. This situation forces on multiple occasions to use distributed data acquisition systems as the best approach. In this type of distributed systems, one of the most important issues is the synchronization between signals, so that it is possible to have a temporal correlation as accurate as possible between the acquired samples of all channels. In last decades, many fusion devices use different types of video cameras to provide inside views of the vessel during operations and to monitor plasma behavior. The synchronization between each video frame and the rest of the different signals acquired from any other diagnostics is essential in order to know correctly the plasma evolution, since it is possible to analyze jointly all the information having accurate knowledge of their temporal correlation. The developed system described in this paper allows timestamping image frames in a real-time acquisition and processing system using 1588 clock distribution. The system has been implemented using FPGA based devices together with a 1588 synchronized timing card (see Fig.1). The solution is based on a previous system [1] that allows image acquisition and real-time image processing based on PXIe technology. This architecture is fully compatible with the ITER Fast Controllers [2] and offers integration with EPICS to control and monitor the entire system. However, this set-up is not able to timestamp the frames acquired since the frame grabber module does not present any type of timing input (IRIG-B, GPS, PTP). To solve this lack, an IEEE1588 PXI timing device its used to provide an accurate way to synchronize distributed data acquisition systems using the Precision Time Protocol (PTP) IEEE 1588 2008 standard. This local timing device can be connected to a master clock device for global synchronization. The timing device has a buffer timestamp for each PXI trigger line and requires tha- a software application assigns each frame the corresponding timestamp. The previous action is critical and cannot be achieved if the frame rate is high. To solve this problem, it has been designed a solution that distributes the clock from the IEEE 1588 timing card to all FlexRIO devices [3]. This solution uses two PXI trigger lines that provide the capacity to assign timestamps to every frame acquired and register events by hardware in a deterministic way. The system provides a solution for timestamping frames to synchronize them with the rest of the different signals.

Optimization and evaluation in space conditions of multi-GHz optical modulators

Among the different optical modulator technologies available such as polymer, III-V semiconductors, Silicon, the well-known Lithium Niobate (LN) offers the best trade-off in terms of performances, ease of use, and power handling capability [1-9]. The LN technology is still widely deployed within the current high data rate fibre optic communications networks. This technology is also the most mature and guarantees the reliability which is required for space applications [9].In or der to fulfil the target specifications of opto-microwave payloads, an optimization of the design of a Mach-Zehnder (MZ) modulator working at the 1500nm telecom wavelength was performed in the frame of the ESA-ARTES "Multi GigaHertz Optical Modulator" (MGOM) project in order to reach ultra-low optical insertion loss and low effective driving voltage in the Ka band. The selected modulator configuration was the X-cut crystal orientation, associated to high stability Titanium in-diffusion process for the optical waveguide. Starting from an initial modulator configuration exhibiting 9 V drive voltage @ 30 GHz, a complete redesign of the coplanar microwave electrodes was carried out in order to reach a 6 V drive voltage @ 30GHz version. This redesign was associated to an optimization of the interaction between the optical waveguide and the electrodes. Following the optimisation steps, an evaluation program was applied on a lot of 8 identical modulators. A full characterisation was carried out to compare performances, showing small variations between the initial and final functional characteristics. In parallel, two similar modulators were submitted to both gamma (10-100 krad) and proton irradiation (10.109 p/cm²) with minor performance degradation.

Mutation in bone morphogenetic protein receptor-IB is associated with increased ovulation rate in Booroola Mérino ewes

Ewes from the Booroola strain of Australian Mérino sheep are characterized by high ovulation rate and litter size. This phenotype is due to the action of the FecBB allele of a major gene named FecB, as determined by statistical analysis of phenotypic data. By genetic analysis of 31 informative half-sib families from heterozygous sires, we showed that the FecB locus is situated in the region of ovine chromosome 6 corresponding to the human chromosome 4q22–23 that contains the bone morphogenetic protein receptor IB (BMPR-IB) gene encoding a member of the transforming growth factor-β (TGF-β) receptor family. A nonconservative substitution (Q249R) in the BMPR-IB coding sequence was found to be associated fully with the hyperprolificacy phenotype of Booroola ewes. In vitro, ovarian granulosa cells from FecBB/FecBB ewes were less responsive than granulosa cells from FecB+/FecB+ ewes to the inhibitory effect on steroidogenesis of GDF-5 and BMP-4, natural ligands of BMPR-IB. It is suggested that in FecBB/FecBB ewes, BMPR-IB would be inactivated partially, leading to an advanced differentiation of granulosa cells and an advanced maturation of ovulatory follicles.

Live cell imaging of heavy-ion-induced radiation responses by beamline microscopy

To study the dynamics of protein recruitment to DNA lesions, ion beams can be used to generate extremely localized DNA damage within restricted regions of the nuclei. This inhomogeneous spatial distribution of lesions can be visualized indirectly and rapidly in the form of radiation-induced foci using immunocytochemical detection or GFP-tagged DNA repair proteins. To analyze faster protein translocations and a possible contribution of radiation-induced chromatin movement in DNA damage recognition in live cells, we developed a remote-controlled system to obtain high-resolution fluorescence images of living cells during ion irradiation with a frame rate of the order of seconds. Using scratch replication labeling, only minor chromatin movement at sites of ion traversal was observed within the first few minutes of impact. Furthermore, time-lapse images of the GFP-coupled DNA repair protein aprataxin revealed accumulations within seconds at sites of ion hits, indicating a very fast recruitment to damaged sites. Repositioning of the irradiated cells after fixation allowed the comparison of live cell observation with immunocytochemical staining and retrospective etching of ion tracks. These results demonstrate that heavy-ion radiation-induced changes in sub-nuclear structures can be used to determine the kinetics of early protein recruitment in living cells and that the changes are not dependent on large-scale chromatin movement at short times postirradiation. © 2005 by Radiation Research Society.

Ocular surface temperature:a review

Purpose. To review the evolution in ocular temperature measurement during the last century and examine the advantages and applications of the latest noncontact techniques. The characteristics and source of ocular surface temperature are also discussed. Methods. The literature was reviewed with regard to progress in human thermometry techniques, the parallel development in ocular temperature measurement, the current use of infrared imaging, and the applications of ocular thermography. Results. It is widely acknowledged that the ability to measure ocular temperature accurately will increase the understanding of ocular physiology. There is a characteristic thermal profile across the anterior eye, in which the central area appears coolest. Ocular surface temperature is affected by many factors, including inflammation. In thermometry of the human eye, contact techniques have largely been superseded by infrared imaging, providing a noninvasive and potentially more accurate method of temperature measurement. Ocular thermography requires high resolution and frame rate: features found in the latest generation of cameras. Applications have included dry eye, contact lens wear, corneal sensitivity, and refractive surgery. Conclusions. Interest in the temperature of the eye spans almost 130 years. It has been an area of research largely driven by prevailing technology. Current instrumentation offers the potential to measure ocular surface temperature with more accuracy, resolution, and speed than previously possible. The use of dynamic ocular thermography offers great opportunities for monitoring the temperature of the anterior eye. © 2005 Contact Lens Association of Ophthalmologists, Inc.

Optimal span length in high-speed transmission systems with hybrid Raman-erbium-doped fiber amplification

We show, using nonlinearity management, that the optimal performance in high-bit-rate dispersion-managed fiber systems with hybrid amplification is achieved for a specific amplifier spacing that is different from the asymptotically vanishing length corresponding to ideally distributed amplification [Opt. Lett. 15, 1064 (1990)]. In particular, we prove the existence of a nontrivial optimal span length for 40-Gbit/s wavelength-division transmission systems with Raman-erbium-doped fiber amplification. Optimal amplifier lengths are obtained for several dispersion maps based on commonly used transmission fibers. © 2005 Optical Society of America.

Hierarchical, ultrathin single-crystal nanowires of CdS conveniently produced in laser-induced thermal field

Hierarchical nanowires (HNWs) exhibit unique properties and have wide applications, while often suffering from imperfect structure. Herein, we report a facile strategy toward ultrathin CdS HNWs with monocrystal structure, where a continuous-wave (CW) Nd:YAG laser is employed to irradiate an oleic acid (OA) solution containing precursors and a light absorber. The high heating rate and large temperature gradient generated by the CW laser lead to the rapid formation of tiny zinc-blende CdS nanocrystals which then line up into nanowires with the help of OA molecules. Next, the nanowires experience a phase transformation from zinc-blende to wurtzite structure, and the transformation-induced stress creates terraces on their surface, which promotes the growth of side branches and eventually results in monocrystal HNWs with an ultrathin diameter of 24 nm. The one-step synthesis of HNWs is conducted in air and completes in just 40 s, thus being very simple and rapid. The prepared CdS HNWs display photocatalytic performance superior to their nanoparticle counterparts, thus showing promise for catalytic applications in the future.

Microstructure characterization of 316L deformed at high strain rates using EBSD

Specimens from split Hopkinson pressure bar experiments, at strain rates between ~ 1000–9000 s− 1 at room temperature and 500 °C, have been studied using electron backscatter diffraction. No significant differences in the microstructures were observed at different strain rates, but were observed for different strains and temperatures. Size distribution for subgrains with boundary misorientations > 2° can be described as a bimodal lognormal area distribution. The distributions were found to change due to deformation. Part of the distribution describing the large subgrains decreased while the distribution for the small subgrains increased. This is in accordance with deformation being heterogeneous and successively spreading into the undeformed part of individual grains. The variation of the average size for the small subgrain distribution varies with strain but not with strain rate in the tested interval. The mean free distance for dislocation slip, interpreted here as the average size of the distribution of small subgrains, displays a variation with plastic strain which is in accordance with the different stages in the stress-strain curves. The rate of deformation hardening in the linear hardening range is accurately calculated using the variation of the small subgrain size with strain.

Plasma diagnostics and ITO film deposition by RF-assisted closed-field dual magnetron system

Deposition of indium tin oxide (ITO) among various transparent conductive materials on flexible organic substrates has been intensively investigated among academics and industrials for a whole new array of imaginative optoelectronic products. One critical challenge coming with the organic materials is their poor thermal endurances, considering that the process currently used to produce industry-standard ITO usually involves relatively high substrate temperature in excess of 200°C and post-annealing. A lower processing temperature is thus demanded, among other desires of high deposition rate, large substrate area, good uniformity, and high quality of the deposited materials. For this purpose, we developed an RF-assisted closed-field dual magnetron sputtering system. The “prototype” system consists of a 3-inch unbalanced dual magnetron operated at a closed-field configuration. An RF coil was fabricated and placed between the two magnetron cathodes to initiate a secondary plasma. The concept is to increase the ionization faction with the RF enhancement and utilize the ion energy instead of thermal energy to facilitate the ITO film growth. The closed-field unbalanced magnetrons create a plasma in the intervening region rather than confine it near the target, thus achieving a large-area processing capability. An RF-compensated Langmuir probe was used to characterize and compare the plasmas in mirrored balanced and closed-field unbalanced magnetron configurations. The spatial distributions of the electron density ne and electron temperature Te were measured. The density profiles reflect the shapes of the plasma. Rather than intensively concentrated to the targets/cathodes in the balanced magnetrons, the plasma is more dispersive in the closed-field mode with a twice higher electron density in the substrate region. The RF assistance significantly enhances ne by one or two orders of magnitude higher. The effect of various other parameters, such as pressure, on the plasma was also studied. The ionization fractions of the sputtered atoms were measured using a gridded energy analyzer (GEA) combined with a quartz crystal microbalance (QCM). The presence of the RF plasma effectively increases the ITO ionization fraction to around 80% in both the balanced and closed-field unbalanced configurations. The ionization fraction also varies with pressure, maximizing at 5-10 mTorr. The study of the ionization not only facilitates understanding the plasma behaviors in the RF-assisted magnetron sputtering, but also provides a criterion for optimizing the film deposition process. ITO films were deposited on both glass and plastic (PET) substrates in the 3-inch RF-assisted closed-field magnetrons. The electrical resistivity and optical transmission transparency of the ITO films were measured. Appropriate RF assistance was shown to dramatically reduce the electrical resistivity. An ITO film with a resistivity of 1.2×10-3 Ω-cm and a visible light transmittance of 91% was obtained with a 225 W RF enhancement, while the substrate temperature was monitored as below 110°C. X-ray photoelectron spectroscopy (XPS) was employed to confirm the ITO film stoichiometry. The surface morphology of the ITO films and its effect on the film properties were studied using atomic force microscopy (AFM). The prototype of RF-assisted closed-field magnetron was further extended to a larger rectangular shaped dual magnetron in a flat panel display manufacturing system. Similar improvement of the ITO film conductivities by the auxiliary RF was observed on the large-area PET substrates. Meanwhile, significant deposition rates of 25-42 nm/min were achieved.

Holistic Design In High-Speed Optical Interconnects

Integrated circuit scaling has enabled a huge growth in processing capability, which necessitates a corresponding increase in inter-chip communication bandwidth. As bandwidth requirements for chip-to-chip interconnection scale, deficiencies of electrical channels become more apparent. Optical links present a viable alternative due to their low frequency-dependent loss and higher bandwidth density in the form of wavelength division multiplexing. As integrated photonics and bonding technologies are maturing, commercialization of hybrid-integrated optical links are becoming a reality. Increasing silicon integration leads to better performance in optical links but necessitates a corresponding co-design strategy in both electronics and photonics. In this light, holistic design of high-speed optical links with an in-depth understanding of photonics and state-of-the-art electronics brings their performance to unprecedented levels. This thesis presents developments in high-speed optical links by co-designing and co-integrating the primary elements of an optical link: receiver, transmitter, and clocking.

In the first part of this thesis a 3D-integrated CMOS/Silicon-photonic receiver will be presented. The electronic chip features a novel design that employs a low-bandwidth TIA front-end, double-sampling and equalization through dynamic offset modulation. Measured results show -14.9dBm of sensitivity and energy efficiency of 170fJ/b at 25Gb/s. The same receiver front-end is also used to implement source-synchronous 4-channel WDM-based parallel optical receiver. Quadrature ILO-based clocking is employed for synchronization and a novel frequency-tracking method that exploits the dynamics of IL in a quadrature ring oscillator to increase the effective locking range. An adaptive body-biasing circuit is designed to maintain the per-bit-energy consumption constant across wide data-rates. The prototype measurements indicate a record-low power consumption of 153fJ/b at 32Gb/s. The receiver sensitivity is measured to be -8.8dBm at 32Gb/s.

Next, on the optical transmitter side, three new techniques will be presented. First one is a differential ring modulator that breaks the optical bandwidth/quality factor trade-off known to limit the speed of high-Q ring modulators. This structure maintains a constant energy in the ring to avoid pattern-dependent power droop. As a first proof of concept, a prototype has been fabricated and measured up to 10Gb/s. The second technique is thermal stabilization of micro-ring resonator modulators through direct measurement of temperature using a monolithic PTAT temperature sensor. The measured temperature is used in a feedback loop to adjust the thermal tuner of the ring. A prototype is fabricated and a closed-loop feedback system is demonstrated to operate at 20Gb/s in the presence of temperature fluctuations. The third technique is a switched-capacitor based pre-emphasis technique designed to extend the inherently low bandwidth of carrier injection micro-ring modulators. A measured prototype of the optical transmitter achieves energy efficiency of 342fJ/bit at 10Gb/s and the wavelength stabilization circuit based on the monolithic PTAT sensor consumes 0.29mW.

Lastly, a first-order frequency synthesizer that is suitable for high-speed on-chip clock generation will be discussed. The proposed design features an architecture combining an LC quadrature VCO, two sample-and-holds, a PI, digital coarse-tuning, and rotational frequency detection for fine-tuning. In addition to an electrical reference clock, as an extra feature, the prototype chip is capable of receiving a low jitter optical reference clock generated by a high-repetition-rate mode-locked laser. The output clock at 8GHz has an integrated RMS jitter of 490fs, peak-to-peak periodic jitter of 2.06ps, and total RMS jitter of 680fs. The reference spurs are measured to be –64.3dB below the carrier frequency. At 8GHz the system consumes 2.49mW from a 1V supply.