Redox-linked proton transfer by cytochrome c oxidase

The respiratory chain is found in the inner mitochondrial membrane of higher organisms and in the plasma membrane of many bacteria. It consists of several membrane-spanning enzymes, which conserve the energy that is liberated from the degradation of food molecules as an electrochemical proton gradient across the membrane. The proton gradient can later be utilized by the cell for different energy requiring processes, e.g. ATP production, cellular motion or active transport of ions. The difference in proton concentration between the two sides of the membrane is a result of the translocation of protons by the enzymes of the respiratory chain, from the negatively charged (N-side) to the positively charged side (P-side) of the lipid bilayer, against the proton concentration gradient. The endergonic proton transfer is driven by the flow of electrons through the enzymes of the respiratory chain, from low redox-potential electron donors to acceptors of higher potential, and ultimately to oxygen. Cytochrome c oxidase is the last enzyme in the respiratory chain and catalyzes the reduction of dioxygen to water. The redox reaction is coupled to proton transport across the membrane by a yet unresolved mechanism. Cytochrome c oxidase has two proton-conducting pathways through which protons are taken up to the interior part of the enzyme from the N-side of the membrane. The K-pathway transfers merely substrate protons, which are consumed in the process of water formation at the catalytic site. The D-pathway transfers both substrate protons and protons that are pumped to the P-side of the membrane. This thesis focuses on the role of two conserved amino acids in proton translocation by cytochrome c oxidase, glutamate 278 and tryptophan 164. Glu278 is located at the end of the D-pathway and is thought to constitute the branching point for substrate and pumped protons. In this work, it was shown that although Glu278 has an important role in the proton transfer mechanism, its presence is not an obligatory requirement. Alternative structural solutions in the area around Glu278, much like the ones present in some distantly related heme-copper oxidases, could in the absence of Glu278 support the formation of a long hydrogen-bonded water chain through which proton transfer from the D-pathway to the catalytic site is possible. The other studied amino acid, Trp164, is hydrogen bonded to the ∆-propionate of heme a3 of the catalytic site. Mutation of this amino acid showed that it may be involved in regulation of proton access to a proton acceptor, a pump site, from which the proton later is expelled to the P-side of the membrane. The ion pair that is formed by the ∆-propionate of heme a3 and arginine 473 is likely to form a gate-like structure, which regulates proton mobility to the P-side of the membrane. The same gate may also be part of an exit path through which water molecules produced at the catalytically active site are removed towards the external side of the membrane. Time-resolved optical and electrometrical experiments with the Trp164 to phenylalanine mutant revealed a so far undetected step in the proton pumping mechanism. During the A to PR transition of the catalytic cycle, a proton is transferred from Glu278 to the pump site, located somewhere in the vicinity of the ∆-propionate of heme a3. A mechanism for proton pumping by cytochrome c oxidase is proposed on the basis of the presented results and the mechanism is discussed in relation to some relevant experimental data. A common proton pumping mechanism for all members of the heme-copper oxidase family is moreover considered.

Indoor air quality and energy management through real–time sensing in commercial buildings

Rapid growth in the global population requires expansion of building stock, which in turn calls for increased energy demand. This demand varies in time and also between different buildings, yet, conventional methods are only able to provide mean energy levels per zone and are unable to capture this inhomogeneity, which is important to conserve energy. An additional challenge is that some of the attempts to conserve energy, through for example lowering of ventilation rates, have been shown to exacerbate another problem, which is unacceptable indoor air quality (IAQ). The rise of sensing technology over the past decade has shown potential to address both these issues simultaneously by providing high–resolution tempo–spatial data to systematically analyse the energy demand and its consumption as well as the impacts of measures taken to control energy consumption on IAQ. However, challenges remain in the development of affordable services for data analysis, deployment of large–scale real–time sensing network and responding through Building Energy Management Systems. This article presents the fundamental drivers behind the rise of sensing technology for the management of energy and IAQ in urban built environments, highlights major challenges for their large–scale deployment and identifies the research gaps that should be closed by future investigations.

Free energy calculations of glycosaminoglycan - Protein interactions

Glycosaminoglycans (GAGs) are complex highly charged linear polysaccharides that have a variety of roles in biological processes. We report the first use of molecular dynamics (MD) free energy calculations using the MM/PBSA method to investigate the binding of GAGs to protein molecules, namely the platelet endothelial cell adhesion molecule 1 (PECAM-1) and annexin A2. Calculations of the free energy of the binding of heparin fragments of different sizes reveal the existence of a region of low GAG-binding affinity in domains 5-6 of PECAM-1 and a region of high affinity in domains 2-3, consistent with experimental data and ligand-protein docking studies. A conformational hinge movement between domains 2 and 3 was observed, which allows the binding of heparin fragments of increasing size (pentasaccharides to octasaccharides) with an increasingly higher binding affinity. Similar simulations of the binding of a heparin fragment to annexin A2 reveal the optimization of electrostatic and hydrogen bonding interactions with the protein and protein-bound calcium ions. In general, these free energy calculations reveal that the binding of heparin to protein surfaces is dominated by strong electrostatic interactions for longer fragments, with equally important contributions from van der Waals interactions and vibrational entropy changes, against a large unfavorable desolvation penalty due to the high charge density of these molecules.

Inflammation-driven bone formation in a mouse model of ankylosing spondylitis: Sequential not parallel processes

Background Ankylosing spondylitis (AS) is an immune-mediated arthritis particularly targeting the spine and pelvis and is characterised by inflammation, osteoproliferation and frequently ankylosis. Current treatments that predominately target inflammatory pathways have disappointing efficacy in slowing disease progression. Thus, a better understanding of the causal association and pathological progression from inflammation to bone formation, particularly whether inflammation directly initiates osteoproliferation, is required. Methods The proteoglycan-induced spondylitis (PGISp) mouse model of AS was used to histopathologically map the progressive axial disease events, assess molecular changes during disease progression and define disease progression using unbiased clustering of semi-quantitative histology. PGISp mice were followed over a 24-week time course. Spinal disease was assessed using a novel semi-quantitative histological scoring system that independently evaluated the breadth of pathological features associated with PGISp axial disease, including inflammation, joint destruction and excessive tissue formation (osteoproliferation). Matrix components were identified using immunohistochemistry. Results Disease initiated with inflammation at the periphery of the intervertebral disc (IVD) adjacent to the longitudinal ligament, reminiscent of enthesitis, and was associated with upregulated tumor necrosis factor and metalloproteinases. After a lag phase, established inflammation was temporospatially associated with destruction of IVDs, cartilage and bone. At later time points, advanced disease was characterised by substantially reduced inflammation, excessive tissue formation and ectopic chondrocyte expansion. These distinct features differentiated affected mice into early, intermediate and advanced disease stages. Excessive tissue formation was observed in vertebral joints only if the IVD was destroyed as a consequence of the early inflammation. Ectopic excessive tissue was predominantly chondroidal with chondrocyte-like cells embedded within collagen type II- and X-rich matrix. This corresponded with upregulation of mRNA for cartilage markers Col2a1, sox9 and Comp. Osteophytes, though infrequent, were more prevalent in later disease. Conclusions The inflammation-driven IVD destruction was shown to be a prerequisite for axial disease progression to osteoproliferation in the PGISp mouse. Osteoproliferation led to vertebral body deformity and fusion but was never seen concurrent with persistent inflammation, suggesting a sequential process. The findings support that early intervention with anti-inflammatory therapies will be needed to limit destructive processes and consequently prevent progression of AS.

Simulation of laminar flow in a three-dimensional lid-driven cavity by lattice Boltzmann method

Purpose - The purpose of this paper is to apply lattice Boltzmann equation method (LBM) with multiple relaxation time (MRT) model, to investigate lid-driven flow in a three-dimensional (3D), rectangular cavity, and compare the results with flow in an equivalent two-dimensional (2D) cavity. Design/methodology/approach - The second-order MRT model is implemented in a 3D LBM code. The flow structure in cavities of different aspect ratios (0.25-4) and Reynolds numbers (0.01-1000) is investigated. The LBM simulation results are compared with those from numerical solution of Navier-Stokes (NS) equations and with available experimental data. Findings - The 3D simulations demonstrate that 2D models may predict the flow structure reasonably well at low Reynolds numbers, but significant differences with experimental data appear at high Reynolds numbers. Such discrepancy between 2D and 3D results are attributed to the effect of boundary layers near the side-walls in transverse direction (in 3D), due to which the vorticity in the core-region is weakened in general. Secondly, owing to the vortex stretching effect present in 3D flow, the vorticity in the transverse plane intensifies whereas that in the lateral plane decays, with increase in Reynolds number. However, on the symmetry-plane, the flow structure variation with respect to cavity aspect ratio is found to be qualitatively consistent with results of 2D simulations. Secondary flow vortices whose axis is in the direction of the lid-motion are observed; these are weak at low. Reynolds numbers, but become quite strong at high Reynolds numbers. Originality/value - The findings will be useful in the study of variety of enclosed fluid flows.

Universalization of access to modern energy services in Indian households-Economic and policy analysis

Provision of modern energy services for cooking (with gaseous fuels)and lighting (with electricity) is an essential component of any policy aiming to address health, education or welfare issues; yet it gets little attention from policy-makers. Secure, adequate, low-cost energy of quality and convenience is core to the delivery of these services. The present study analyses the energy consumption pattern of Indian domestic sector and examines the urban-rural divide and income energy linkage. A comprehensive analysis is done to estimate the cost for providing modern energy services to everyone by 2030. A public-private partnership-driven business model, with entrepreneurship at the core, is developed with institutional, financing and pricing mechanisms for diffusion of energy services. This approach, termed as EMPOWERS (entrepreneurship model for provision of wholesome energy-related basic services), if adopted, can facilitate large-scale dissemination of energy-efficient and renewable technologies like small-scale biogas/biofuel plants, and distributed power generation technologies to provide clean, safe, reliable and sustainable energy to rural households and urban poor. It is expected to integrate the processes of market transformation and entrepreneurship development involving government, NGOs, financial institutions and community groups as stakeholders. (C) 2009 Elsevier Ltd. All rights reserved.

The tired foot. The effects of physical activity, energy expenditure and sleep on the diabetic foot population

Background The most common pathway to development of diabetes foot ulcers is repetitive daily activity stress on the plantar surface of the neuropathic foot. Studies suggest an association between different diabetic foot complications and physical activity. However, to the best of the authors knowledge the steps/day and sleep patterns of people with diabetic foot ulcers has yet to be investigated. This observational study aims to investigate the physical activity and sleep patterns of three groups of adults with type 2 diabetes and different foot complications Methods Participants with type 2 diabetes were recruited into three groups: 1. those with no reported foot complications (DNIL), 2. those with diagnosis of neuropathy (DPN) and 3. those with a neuropathic ulcer (DFU). Exclusion criteria included peripheral arterial disease and mobility aid use. Participants wore a SenseWear Pro 3 Armband continuously for 7 days and completed an Epworth Sleepiness Scale. The Armband is a validated automated measure of activity (walking steps, average Metabolic Equivalent Task (MET), physical activity (>3 METs) duration), energy expenditure(kJ) (total and physical activity (>3 METs)) and sleep (duration). Data on age, sex, BMI, diabetes duration and HbA1c were also collected. Results Sixty-Six (14 DNIL, 22 DPN and 30 DFU's participants were recruited; 71% males, mean age 61(±12) years, diabetes duration 13(±9) years, HbA1c 8.3(±2.8), BMI 32.6(±5.9), average METs 1.2(0.2). Significant differences were reported in mean(SD) steps/day (5,859(±2,381) in DNIL; 5,007(±3,349) in DPN and 3,271(±2,417) in DFU's and daily energy expenditure (10,868(±1,307)kJ in DNIL; 11,060(±1,916)kJ in DPN and 13,006(± 3,559) in DFU's(p <0.05). No significant differences were reported for average METs, physical activity duration or energy expenditure, sleep time or Epworth score (p>0.1). Conclusions Preliminary findings suggest people with diabetes are sedentary. Results indicate that patients with a diabetic foot ulcer work significantly less than those with neuropathy or nil complications and use significantly more energy to do so. Sleep Parameters showed no differences. Recruitment is still on going.

A Search for Energy Minimized Sequences of Proteins

In this paper, we present numerical evidence that supports the notion of minimization in the sequence space of proteins for a target conformation. We use the conformations of the real proteins in the Protein Data Bank (PDB) and present computationally efficient methods to identify the sequences with minimum energy. We use edge-weighted connectivity graph for ranking the residue sites with reduced amino acid alphabet and then use continuous optimization to obtain the energy-minimizing sequences. Our methods enable the computation of a lower bound as well as a tight upper bound for the energy of a given conformation. We validate our results by using three different inter-residue energy matrices for five proteins from protein data bank (PDB), and by comparing our energy-minimizing sequences with 80 million diverse sequences that are generated based on different considerations in each case. When we submitted some of our chosen energy-minimizing sequences to Basic Local Alignment Search Tool (BLAST), we obtained some sequences from non-redundant protein sequence database that are similar to ours with an E-value of the order of 10(-7). In summary, we conclude that proteins show a trend towards minimizing energy in the sequence space but do not seem to adopt the global energy-minimizing sequence. The reason for this could be either that the existing energy matrices are not able to accurately represent the inter-residue interactions in the context of the protein environment or that Nature does not push the optimization in the sequence space, once it is able to perform the function.

A Slotted Aloha joint MAC-cum-Routing protocol for data gathering sensor network applications

In this paper we have proposed and implemented a joint Medium Access Control (MAC) -cum- Routing scheme for environment data gathering sensor networks. The design principle uses node 'battery lifetime' maximization to be traded against a network that is capable of tolerating: A known percentage of combined packet losses due to packet collisions, network synchronization mismatch and channel impairments Significant end-to-end delay of an order of few seconds We have achieved this with a loosely synchronized network of sensor nodes that implement Slotted-Aloha MAC state machine together with route information. The scheme has given encouraging results in terms of energy savings compared to other popular implementations. The overall packet loss is about 12%. The battery life time increase compared to B-MAC varies from a minimum of 30% to about 90% depending on the duty cycle.

A universal relation for the cohesive energy of nanoparticles

A universal relation between the cohesive energy and the particle size has been predicted based on the liquid-drop model. The universal relation is well supported by other theoretical models and the available experimental data. The universal relations for intermediate size range as well as for particles with very few atoms are discussed. A comparison of onset temperature of evaporation also establishes a universal relation.

Gibbs Energy of Formation of MnO: Measurement and Assessment

Based on the measurements of Alcock and Zador, Grundy et al. estimated an uncertainty of the order of +/- 5 kJ mol(-1) for the standard Gibbs energy of formation of MnO in a recent assessment. Since the evaluation of thermodynamic data for the higher oxides Mn3O4, Mn2O3, and MnO2 depends on values for MnO, a redetermination of its Gibbs energy of formation was undertaken in the temperature range from 875 to 1300 K using a solid-state electrochemical cell incorporating yttria-doped thoria (YDT) as the solid electrolyte and Fe + Fe1-delta O as the reference electrode. The cell can be presented as Pt, Mn + MnO/YDT/Fe + Fe1+delta O, Pt Since the metals Fe and Mn undergo phase transitions in the temperature range of measurement, the reversible emf of the cell is represented by the three linear segments. Combining the emf with the oxygen potential for the reference electrode, the standard Gibbs energy of formation of MnO from alpha-Mn and gaseous diatomic oxygen in the temperature range from 875 to 980 K is obtained as: Delta G(f)(o)/Jmol(-1)(+/- 250) = -385624 + 73.071T From 980 to 1300 K the Gibbs energy of formation of MnO from beta-Mn and oxygen gas is given by: Delta G(f)(o)/Jmol(-1)(+/- 250) = -387850 + 75.36T The new data are in excellent agreement with the earlier measurements of Alcock and Zador. Grundy et al. incorrectly analyzed the data of Alcock and Zador showing relatively large difference (+/- 5 kJ mol(-1)) in Gibbs energies of MnO from their two cells with Fe + Fe1-delta O and Ni + NiO as reference electrodes. Thermodynamic data for MnO is reassessed in the light of the new measurements. A table of refined thermodynamic data for MnO from 298.15 to 2000 K is presented.

Fracture process zone size and true fracture energy of concrete using acoustic emission

Acoustic emission (AE) energy, instead of amplitude, associated with each of the event is used to estimate the fracture process zone (FPZ) size. A steep increase in the cumulative AE energy of the events with respect to time is correlated with the formation of FPZ. Based on the AE energy released during these events and the locations of the events, FPZ size is obtained. The size-independent fracture energy is computed using the expressions given in the boundary effect model by least squares method since over-determined system of equations are obtained when data from several specimens are used. Instead of least squares method a different method is suggested in which the transition ligament length, measured from the plot of histograms of AE events plotted over the un-cracked ligament, is used directly to obtain size-independent fracture energy. The fracture energy thus calculated seems to be size-independent.

Quantitative photoacoustic tomography from boundary pressure measurements: noniterative recovery of optical absorption coefficient from the reconstructed absorbed energy map

We describe a noniterative method for recovering optical absorption coefficient distribution from the absorbed energy map reconstructed using simulated and noisy boundary pressure measurements. The source reconstruction problem is first solved for the absorbed energy map corresponding to single- and multiple-source illuminations from the side of the imaging plane. It is shown that the absorbed energy map and the absorption coefficient distribution, recovered from the single-source illumination with a large variation in photon flux distribution, have signal-to-noise ratios comparable to those of the reconstructed parameters from a more uniform photon density distribution corresponding to multiple-source illuminations. The absorbed energy map is input as absorption coefficient times photon flux in the time-independent diffusion equation (DE) governing photon transport to recover the photon flux in a single step. The recovered photon flux is used to compute the optical absorption coefficient distribution from the absorbed energy map. In the absence of experimental data, we obtain the boundary measurements through Monte Carlo simulations, and we attempt to address the possible limitations of the DE model in the overall reconstruction procedure.

Geant4 Hadronic Cascade Models and CMS Data Analysis : Computational Challenges in the LHC era

This work belongs to the field of computational high-energy physics (HEP). The key methods used in this thesis work to meet the challenges raised by the Large Hadron Collider (LHC) era experiments are object-orientation with software engineering, Monte Carlo simulation, the computer technology of clusters, and artificial neural networks. The first aspect discussed is the development of hadronic cascade models, used for the accurate simulation of medium-energy hadron-nucleus reactions, up to 10 GeV. These models are typically needed in hadronic calorimeter studies and in the estimation of radiation backgrounds. Various applications outside HEP include the medical field (such as hadron treatment simulations), space science (satellite shielding), and nuclear physics (spallation studies). Validation results are presented for several significant improvements released in Geant4 simulation tool, and the significance of the new models for computing in the Large Hadron Collider era is estimated. In particular, we estimate the ability of the Bertini cascade to simulate Compact Muon Solenoid (CMS) hadron calorimeter HCAL. LHC test beam activity has a tightly coupled cycle of simulation-to-data analysis. Typically, a Geant4 computer experiment is used to understand test beam measurements. Thus an another aspect of this thesis is a description of studies related to developing new CMS H2 test beam data analysis tools and performing data analysis on the basis of CMS Monte Carlo events. These events have been simulated in detail using Geant4 physics models, full CMS detector description, and event reconstruction. Using the ROOT data analysis framework we have developed an offline ANN-based approach to tag b-jets associated with heavy neutral Higgs particles, and we show that this kind of NN methodology can be successfully used to separate the Higgs signal from the background in the CMS experiment.

Studies of solar and stellar flares using multi-instrument data

Solar flares were first observed by plain eye in white light by William Carrington in England in 1859. Since then these eruptions in the solar corona have intrigued scientists. It is known that flares influence the space weather experienced by the planets in a multitude of ways, for example by causing aurora borealis. Understanding flares is at the epicentre of human survival in space, as astronauts cannot survive the highly energetic particles associated with large flares in high doses without contracting serious radiation disease symptoms, unless they shield themselves effectively during space missions. Flares may be at the epicentre of man s survival in the past as well: it has been suggested that giant flares might have played a role in exterminating many of the large species on Earth, including dinosaurs. Having said that prebiotic synthesis studies have shown lightning to be a decisive requirement for amino acid synthesis on the primordial Earth. Increased lightning activity could be attributed to space weather, and flares. This thesis studies flares in two ways: in the spectral and the spatial domain. We have extracted solar spectra using three different instruments, namely GOES (Geostationary Operational Environmental Satellite), RHESSI (Reuven Ramaty High Energy Solar Spectroscopic Imager) and XSM (X-ray Solar Monitor) for the same flares. The GOES spectra are low resolution obtained with a gas proportional counter, the RHESSI spectra are higher resolution obtained with Germanium detectors and the XSM spectra are very high resolution observed with a silicon detector. It turns out that the detector technology and response influence the spectra we see substantially, and are important to understanding what conclusions to draw from the data. With imaging data, there was not such a luxury of choice available. We used RHESSI imaging data to observe the spatial size of solar flares. In the present work the focus was primarily on current solar flares. However, we did make use of our improved understanding of solar flares to observe young suns in NGC 2547. The same techniques used with solar monitors were applied with XMM-Newton, a stellar X-ray monitor, and coupled with ground based Halpha observations these techniques yielded estimates for flare parameters in young suns. The material in this thesis is therefore structured from technology to application, covering the full processing path from raw data and detector responses to concrete physical parameter results, such as the first measurement of the length of plasma flare loops in young suns.