Kinesin’s processivity results from mechanical and chemical coordination between the ATP hydrolysis cycles of the two motor domains

Kinesin is a processive motor protein: A single molecule can walk continuously along a microtubule for several micrometers, taking hundreds of 8-nm steps without dissociating. To elucidate the biochemical and structural basis for processivity, we have engineered a heterodimeric one-headed kinesin and compared its biochemical properties to those of the wild-type two-headed molecule. Our construct retains the functionally important neck and tail domains and supports motility in high-density microtubule gliding assays, though it fails to move at the single-molecule level. We find that the ATPase rate of one-headed kinesin is 3–6 s−1 and that detachment from the microtubule occurs at a similar rate (3 s−1). This establishes that one-headed kinesin usually detaches once per ATP hydrolysis cycle. Furthermore, we identify the rate-limiting step in the one-headed hydrolysis cycle as detachment from the microtubule in the ADP⋅Pi state. Because the ATPase and detachment rates are roughly an order of magnitude lower than the corresponding rates for two-headed kinesin, the detachment of one head in the homodimer (in the ADP⋅Pi state) must be accelerated by the other head. We hypothesize that this results from internal strain generated when the second head binds. This idea accords with a hand-over-hand model for processivity in which the release of the trailing head is contingent on the binding of the forward head. These new results, together with previously published ones, allow us to propose a pathway that defines the chemical and mechanical cycle for two-headed kinesin.

Unified derivations of measurement-based schemes for quantum computation

We present unified, systematic derivations of schemes in the two known measurement-based models of quantum computation. The first model (introduced by Raussendorf and Briegel, [Phys. Rev. Lett. 86, 5188 (2001)]) uses a fixed entangled state, adaptive measurements on single qubits, and feedforward of the measurement results. The second model (proposed by Nielsen, [Phys. Lett. A 308, 96 (2003)] and further simplified by Leung, [Int. J. Quant. Inf. 2, 33 (2004)]) uses adaptive two-qubit measurements that can be applied to arbitrary pairs of qubits, and feedforward of the measurement results. The underlying principle of our derivations is a variant of teleportation introduced by Zhou, Leung, and Chuang, [Phys. Rev. A 62, 052316 (2000)]. Our derivations unify these two measurement-based models of quantum computation and provide significantly simpler schemes.

5,6-Dihydroxyindole-2-carboxylic acid: a first principles density functional study

We report first principles density functional calculations for 5,6-dihydroxyindole-2-carboxylic acid (DHICA) and several oxidised forms. DHICA and 5,6-dihydroxyindole (DHI) are believed to be the basic building blocks of the eumelanins. Our results show that carboxylation has a significant effect on the physical properties of the molecules. In particular, the relative stabilities and the highest occupied molecular orbital-lowest unoccupied molecular orbital gaps (calculated with the DeltaSCF method) of the various redox forms are strongly affected. We predict that, in contrast to DHI, the density of unpaired electrons, and hence the ESR signal, in DHICA is negligibly small. (C) 2004 Elsevier B.V. All rights reserved.

Optical Bloch equations and enhanced decay of Rabi oscillations in strong driving fields

Optical Bloch equations are widely used for describing dynamics in a system consisting molecules, electromagnetic waves, and a thermal bath. We analyze applicability of these equations to a single molecule imbedded in a solid matrix. Classical Bloch equations and the limits of their applicability are derived from more general master equations. Simple and intuitively appealing picture based on stochastic Bloch equations shows that at low temperatures, contrary to common believes, a strong driving field can not only suppress but can also increase decay rates of Rabi oscillations. A physical system where predicted effects can be observed experimentally is suggested. (c) 2005 Elsevier B.V. All rights reserved.

Simulation of optical fibre communication systems influenced by stimulated brillouin scattering

Boyd's SBS model which includes distributed thermal acoustic noise (DTAN) has been enhanced to enable the Stokes-spontaneous density depletion noise (SSDDN) component of the transmitted optical field to be simulated, probably for the first time, as well as the full transmitted field. SSDDN would not be generated from previous SBS models in which a Stokes seed replaces DTAN. SSDDN becomes the dominant form of transmitted SBS noise as model fibre length (MFL) is increased but its optical power spectrum remains independent of MFL. Simulations of the full transmitted field and SSDDN for different MFLs allow prediction of the optical power spectrum, or system performance parameters which depend on this, for typical communication link lengths which are too long for direct simulation. The SBS model has also been innovatively improved by allowing the Brillouin Shift Frequency (BS) to vary over the model fibre length, for the nonuniform fibre model (NFM) mode, or to remain constant, for the uniform fibre model (UFM) mode. The assumption of a Gaussian probability density function (pdf) for the BSF in the NFM has been confirmed by means of an analysis of reported Brillouin amplified power spectral measurements for the simple case of a nominally step-index single-mode pure silica core fibre. The BSF pdf could be modified to match the Brillouin gain spectra of other fibre types if required. For both models, simulated backscattered and output powers as functions of input power agree well with those from a reported experiment for fitting Brillouin gain coefficients close to theoretical. The NFM and UFM Brillouin gain spectra are then very similar from half to full maximum but diverge at lower values. Consequently, NFM and UFM transmitted SBS noise powers inferred for long MFLs differ by 1-2 dB over the input power range of 0.15 dBm. This difference could be significant for AM-VSB CATV links at some channel frequencies. The modelled characteristic of Carrier-to-Noise Ratio (CNR) as a function of input power for a single intensity modulated subcarrier is in good agreement with the characteristic reported for an experiment when either the UFM or NFM is used. The difference between the two modelled characteristics would have been more noticeable for a higher fibre length or a lower subcarrier frequency.

The role of science in policy making

This thesis aims to consider the role played by science in policy making. Firstly, two decision models are considered, synoptic rationality which depends heavily on formal information and comprehensive planning, and disjointed incrementalism, under which decisions are made in a fragmented and remedial manner via the interaction of interested partisans and with little necessity for formal information. Secondly, different descriptions of scientific activity are discussed and a broadly Kuhnian view of science is supported, with what is regarded as a `fact' being heavily influenced by social factors. It is suggested that scientific controversies are more likely to occur in policy related science but for reasons that are intrinsic to science rather than due to some correctable aberration. A number of case studies, including two `in-depth' studies into maternal deprivation and the relationship between hyperactivity and food additives, support this contention and also show that whilst scientific findings can raise issues they cannot aid in the resolution of these as the synoptic model suggests that they should. Instead information supports and legitimates value based policy views, with actual policy decisions arrived at via negotiation and aiming at a balancing of partisan pressures, as suggested by the incremental model. Not only does information not aid the resolution of policy disputes, it cannot do so. When policy is disputed, scientific findings are also likely to be disputed and further research merely attracts more highly destructive criticism. This is termed the over critical model. When policy is decided then there is reduced impetus to critically test scientific ideas; this is termed the under critical model. Both of these situations act to the detriment of science. The main conclusion drawn is that the belief that science is essential to decision making is misleading and may serve to mask rather than illuminate areas of dispute.

Analysis and modelling of immune cell behaviour in lymph nodes based on multi-photon imaging

This thesis presents quantitative studies of T cell and dendritic cell (DC) behaviour in mouse lymph nodes (LNs) in the naive state and following immunisation. These processes are of importance and interest in basic immunology, and better understanding could improve both diagnostic capacity and therapeutic manipulations, potentially helping in producing more effective vaccines or developing treatments for autoimmune diseases. The problem is also interesting conceptually as it is relevant to other fields where 3D movement of objects is tracked with a discrete scanning interval. A general immunology introduction is presented in chapter 1. In chapter 2, I apply quantitative methods to multi-photon imaging data to measure how T cells and DCs are spatially arranged in LNs. This has been previously studied to describe differences between the naive and immunised state and as an indicator of the magnitude of the immune response in LNs, but previous analyses have been generally descriptive. The quantitative analysis shows that some of the previous conclusions may have been premature. In chapter 3, I use Bayesian state-space models to test some hypotheses about the mode of T cell search for DCs. A two-state mode of movement where T cells can be classified as either interacting to a DC or freely migrating is supported over a model where T cells would home in on DCs at distance through for example the action of chemokines. In chapter 4, I study whether T cell migration is linked to the geometric structure of the fibroblast reticular network (FRC). I find support for the hypothesis that the movement is constrained to the fibroblast reticular cell (FRC) network over an alternative 'random walk with persistence time' model where cells would move randomly, with a short-term persistence driven by a hypothetical T cell intrinsic 'clock'. I also present unexpected results on the FRC network geometry. Finally, a quantitative method is presented for addressing some measurement biases inherent to multi-photon imaging. In all three chapters, novel findings are made, and the methods developed have the potential for further use to address important problems in the field. In chapter 5, I present a summary and synthesis of results from chapters 3-4 and a more speculative discussion of these results and potential future directions.

Properties of polycrystalline gas sensors based on d.c. and a.c. electrical measurements

Electrical properties of polycrystalline gas sensors are analyzed by d.c. and a.c. measurements. d.c. electrical conductivity values compared with those obtained by admittance spectroscopy methods help to obtain a detailed 'on line' analysis of conductivity-modulated gas sensors. The electrical behaviour of grain boundaries is obtained and a new design of sensors can be achieved by enhancing the activity of surface states in the detecting operation. A Schottky barrier model is used to explain the grain boundary action under the presence of surrounding gases. The height of this barrier is a function of gas concentration due to the trapping of excess charge generated by gas adsorption at the interface. A comparison between this dependence, and a plot of the real and imaginary components of the admittance versus frequency at different gas concentrations, provides information on the different parameters that play a role in the conduction mechanisms. These methods have been applied to the design of a CO sensor based on tin oxide films for domestic purposes, the characteristics of which are presented.

Developmentof engineering projects supported by BIM technology: internship report

Building Information Modeling (BIM) concept is able to reshape each AEC project and the industry in general, offering a comprehensive collaboration process over a model of structure with regularly actualized and synchronized information. This report presents an overview of BIM with focus on its core concepts, applications in the project life cycle and benefits for project stakeholders through four case studies carried out during the internship in the engineering office NEWTON - Engineering Consultancy Company. The aim of the four cases studies was to cover multidisciplinary and varied projects. The first case study highlights the engineering project’s workflow and presents a comparison of traditional procedures and BIM concepts applied on the rehabilitation of an existing building. In the second and third case study, attention is focused on the goals achieved, particularly by structural engineer, due to the implementation of the mentioned technology on a full-lifecycle BIM project of a small residence and a complex project of residential building in Porto and on its architectural integration. In addition, through the fourth case study, the spatial coordination of Mechanical, Electrical and Plumbing (MEP) systems at a large-scale hotel project has been analyzed and accomplished, highlighting merits of BIM at this project stage. Through a reduction of the space used for facilities and infrastructures and the ability to identify conflicts and to nullify the related costs, its advantage for a complex building was proved.

A methodological framework to assess the carbon balance of tropical managed forests.

Background: Managed forests are a major component of tropical landscapes. Production forests as designated by national forest services cover up to 400 million ha, i.e. half of the forested area in the humid tropics. Forest management thus plays a major role in the global carbon budget, but with a lack of unified method to estimate carbon fluxes from tropical managed forests. In this study we propose a new time- and spatially-explicit methodology to estimate the above-ground carbon budget of selective logging at regional scale. Results: The yearly balance of a logging unit, i.e. the elementary management unit of a forest estate, is modelled by aggregating three sub-models encompassing (i) emissions from extracted wood, (ii) emissions from logging damage and deforested areas and (iii) carbon storage from post-logging recovery. Models are parametrised and uncertainties are propagated through a MCMC algorithm. As a case study, we used 38 years of National Forest Inventories in French Guiana, northeastern Amazonia, to estimate the above-ground carbon balance (i.e. the net carbon exchange with the atmosphere) of selectively logged forests. Over this period, the net carbon balance of selective logging in the French Guianan Permanent Forest Estate is estimated to be comprised between 0.12 and 1.33 Tg C, with a median value of 0.64 Tg C. Uncertainties over the model could be diminished by improving the accuracy of both logging damage and large woody necromass decay submodels. Conclusions: We propose an innovating carbon accounting framework relying upon basic logging statistics. This flexible tool allows carbon budget of tropical managed forests to be estimated in a wide range of tropical regions

Double Gaussian distribution of barrier height observed in densely packed GaN nanorods over Si (111) heterostructures

GaN nanorods were grown by plasma assisted molecular beam epitaxy on intrinsic Si (111) substrates which were characterized by powder X-ray diffraction, field emission scanning electron microscopy, and photoluminescence. The current-voltage characteristics of the GaN nanorods on Si (111) heterojunction were obtained from 138 to 493K which showed the inverted rectification behavior. The I-V characteristics were analyzed in terms of thermionic emission model. The temperature variation of the apparent barrier height and ideality factor along with the non-linearity of the activation energy plot indicated the presence of lateral inhomogeneities in the barrier height. The observed two temperature regimes in Richardson's plot could be well explained by assuming two separate Gaussian distribution of the barrier heights. (C) 2014 AIP Publishing LLC.

Wnt activation of immortalized brain endothelial cells as a tool for generating a standardized model of the blood brain barrier in vitro

Reproducing the characteristics and the functional responses of the blood-brain barrier (BBB) in vitro represents an important task for the research community, and would be a critical biotechnological breakthrough. Pharmaceutical and biotechnology industries provide strong demand for inexpensive and easy-to-handle in vitro BBB models to screen novel drug candidates. Recently, it was shown that canonical Wnt signaling is responsible for the induction of the BBB properties in the neonatal brain microvasculature in vivo. In the present study, following on from earlier observations, we have developed a novel model of the BBB in vitro that may be suitable for large scale screening assays. This model is based on immortalized endothelial cell lines derived from murine and human brain, with no need for co-culture with astrocytes. To maintain the BBB endothelial cell properties, the cell lines are cultured in the presence of Wnt3a or drugs that stabilize β-catenin, or they are infected with a transcriptionally active form of β-catenin. Upon these treatments, the cell lines maintain expression of BBB-specific markers, which results in elevated transendothelial electrical resistance and reduced cell permeability. Importantly, these properties are retained for several passages in culture, and they can be reproduced and maintained in different laboratories over time. We conclude that the brain-derived endothelial cell lines that we have investigated gain their specialized characteristics upon activation of the canonical Wnt pathway. This model may be thus suitable to test the BBB permeability to chemicals or large molecular weight proteins, transmigration of inflammatory cells, treatments with cytokines, and genetic manipulation.

Heterogeneous model for gas transport in carbon molecular sieves

A dual resistance model with distribution of either barrier or pore diffusional activation energy is proposed in this work for gas transport in carbon molecular sieve (CMS) micropores. This is a novel approach in which the equilibrium is homogeneous, but the kinetics is heterogeneous. The model seems to provide a possible explanation for the concentration dependence of the thermodynamically corrected barrier and pore diffusion coefficients observed in previous studies from this laboratory on gas diffusion in CMS.(1.2) The energy distribution is assumed to follow the gamma distribution function. It is shown that the energy distribution model can fully capture the behavior described by the empirical model established in earlier studies to account for the concentration dependence of thermodynamically corrected barrier and pore diffusion coefficients. A methodology is proposed for extracting energy distribution parameters, and it is further shown that the extracted energy distribution parameters can effectively predict integral uptake and column breakthrough profiles over a wide range of operating pressures.

Effects of HNO3 molecular doping in graphene/Si Schottky barrier solar cells

Schottky barrier solar cells based on graphene/n-silicon heterojunction have been fabricated and characterized and the effect of graphene molecular doping by HNO3 on the solar cells performances have been analyzed. Different doping conditions and thermal annealing processes have been tested to asses and optimize the stability of the devices. The PCE of the cells increases after the treatment by HNO3 and reaches 5% in devices treated at 200 °C immediately before the exposition to the oxidant. Up to now our devices retain about 80% of efficiency over a period of two weeks, which represents a good stability result for similar devices.