Adaptive tree multigrids and simplified spherical harmonics approximation in deterministic neutral and charged particle transport

A new deterministic three-dimensional neutral and charged particle transport code, MultiTrans, has been developed. In the novel approach, the adaptive tree multigrid technique is used in conjunction with simplified spherical harmonics approximation of the Boltzmann transport equation. The development of the new radiation transport code started in the framework of the Finnish boron neutron capture therapy (BNCT) project. Since the application of the MultiTrans code to BNCT dose planning problems, the testing and development of the MultiTrans code has continued in conventional radiotherapy and reactor physics applications. In this thesis, an overview of different numerical radiation transport methods is first given. Special features of the simplified spherical harmonics method and the adaptive tree multigrid technique are then reviewed. The usefulness of the new MultiTrans code has been indicated by verifying and validating the code performance for different types of neutral and charged particle transport problems, reported in separate publications.

Measurements of the top-quark mass using charged particle tracking

We present three measurements of the top-quark mass in the lepton plus jets channel with approximately 1.9 fb-1 of integrated luminosity collected with the CDF II detector using quantities with minimal dependence on the jet energy scale. One measurement exploits the transverse decay length of b-tagged jets to determine a top-quark mass of 166.9+9.5-8.5 (stat) +/- 2.9 (syst) GeV/c2, and another the transverse momentum of electrons and muons from W-boson decays to determine a top-quark mass of 173.5+8.8-8.9 (stat) +/- 3.8 (syst) GeV/c2. These quantities are combined in a third, simultaneous mass measurement to determine a top-quark mass of 170.7 +/- 6.3 (stat) +/- 2.6 (syst) GeV/c2.

Search for Long-Lived Massive Charged Particles in 1.96 TeV pp̅ Collisions

We performed a signature-based search for long-lived charged massive particles (CHAMPs) produced in 1.0 $\rm{fb}^{-1}$ of $\bar{p}p$ collisions at $\sqrt{s}=1.96$ TeV, collected with the CDF II detector using a high transverse-momentum ($p_T$) muon trigger. The search used time-of-flight to isolate slowly moving, high-$p_T$ particles. One event passed our selection cuts with an expected background of $1.9 \pm 0.2$ events. We set an upper bound on the production cross section, and, interpreting this result within the context of a stable scalar top quark model, set a lower limit on the particle mass of 249 GeV/$c^2$ at 95% C.L.

Search for Charged Higgs Bosons in Decays of Top Quarks in pp̅ Collisions at √s=1.96 TeV

We report the recent charged Higgs search in top quark decays in 2.2/fb CDF data. This is the first attempt to search for charged Higgs using fully reconstructed mass assuming H->c-sbar in small tan beta region. No evidence of a charged Higgs is observed in the CDF data, hence 95% upper limits are placed at B(t->H+b)

Measurements of the top-quark mass using charged particle tracking

We present three measurements of the top-quark mass in the lepton plus jets channel with approximately 1.9 fb-1 of integrated luminosity collected with the CDF II detector using quantities with minimal dependence on the jet energy scale. One measurement exploits the transverse decay length of b-tagged jets to determine a top-quark mass of 166.9+9.5-8.5 (stat) +/- 2.9 (syst) GeV/c2, and another the transverse momentum of electrons and muons from W-boson decays to determine a top-quark mass of 173.5+8.8-8.9 (stat) +/- 3.8 (syst) GeV/c2. These quantities are combined in a third, simultaneous mass measurement to determine a top-quark mass of 170.7 +/- 6.3 (stat) +/- 2.6 (syst) GeV/c2.

Transverse momentum and pseudorapidity distributions of charged hadrons in pp collisions at sqrt(s) = 0.9 and 2.36 TeV

Measurements of inclusive charged-hadron transverse-momentum and pseudorapidity distributions are presented for proton-proton collisions at sqrt(s) = 0.9 and 2.36 TeV. The data were collected with the CMS detector during the LHC commissioning in December 2009. For non-single-diffractive interactions, the average charged-hadron transverse momentum is measured to be 0.46 +/- 0.01 (stat.) +/- 0.01 (syst.) GeV/c at 0.9 TeV and 0.50 +/- 0.01 (stat.) +/- 0.01 (syst.) GeV/c at 2.36 TeV, for pseudorapidities between -2.4 and +2.4. At these energies, the measured pseudorapidity densities in the central region, dN(charged)/d(eta) for |eta|

Turning the Kaleidoscope - (E)FL Educational Experience and Inquiry as Auto/biography

This book is a study on learning, teaching/counselling, and research on the two. My quest has been to find a pedagogically-motivated way of researching learning and teaching interaction, and in particular counselling, in an autonomous language-learning environment. I have tried to develop a method that would make room for lived experience, meaning-making and narrating, because in my view these all characterise learning encounters between language learners and counsellors, and learners and their peers. Lived experience as a source of meaning, telling and co-telling becomes especially significant when we try to listen to the diverse personal and academic voices of the past as expressed in autobiographical narratives. I have aimed at researching various ALMS dialogues (Autonomous Learning Modules, University of Helsinki Language Centre English course and programme), and autobiographical narratives within them, in a way that shows respect for the participants, and that is relevant, reflective and, most importantly, self-reflexive. My interest has been in autobiographical telling in (E)FL [(English as a) foreign language], both in students first-person written texts on their language- learning histories and in the sharing of stories between learners and a counsellor. I have turned to narrative inquiry in my quest and have written the thesis as an experiential narrative. In particular, I have studied learners and counsellors in one and the same story, as characters in one narrative, in an attempt to avoid the impression that I am telling yet another separate, anecdotal story, retrospectively. Through narrative, I have shed light on the subjective dimensions of language learning and experience, and have come closer to understanding the emotional aspects of learning encounters. I have questioned and rejected a distanced and objective approach to describing learning and teaching/counselling. I have argued for a holistic and experiential approach to (E)FL encounters in which there is a need to see emotion and cognition as intertwined, and thus to appreciate learners and counsellors emotionally-charged experiences as integral to their identities. I have also argued for a way of describing such encounters as they are situated in history, time, autobiography, and the learning context. I have turned my gaze on various constellations of lived experience: the data was collected on various occasions and in various settings during one course and consists of videotaped group sessions, individual counselling sessions between students and their group counsellor, biographic narrative interviews with myself, open-ended personally-inspired reflection texts written by the students about their language-learning histories, and student logs and diaries. I do not consider data collection an unproblematic occasion, or innocent practice, and I defend the integrity of the research process. Research writing cannot be separated from narrative field work and analysing and interpreting the data. The foci in my work have turned to be the following: 1) describing ALMS encounters and specifying their narrative aspects; 2) reconceptualising learner and teacher autonomy in ALMS and in (E)FL; 2) developing (E)FL methodologically through a teacher-researcher s identity work; 4) research writing as a dialogical narrative process, and the thesis as an experiential narrative. Identity and writing as inquiry, and the deeply narrative and autobiographical nature of the (E)FL teaching/counselling/researching have come to the fore in this research. Research writing as a relational activity and its implications for situated ways of knowing and knowledge turned out to be important foci. I have also focussed on the context-bound and local teacher knowledge and ways of knowing about being a teacher, and I have argued for personal ways of knowing about, and learning and studying foreign languages. I discuss research as auto/biography: as a practising counsellor I use my own life and (E)FL experience to understand and interpret the stories of the research participants even though I was not involved in their course work. The supposedly static binaries of learner/teacher, and also learner autonomy/teacher autonomy, are thus brought into the discussion. I have highlighted the infinite variability and ever-changing nature of learning and teaching English, but the book is also of relevance to foreign language education in general.

On the functional ordering of biomembranes : Implications for drug binding

Cells are packed with membrane structures, defining the inside and outside, and the different subcellular compartments. These membranes consisting mainly of phospholipids have a variety of functions in addition to providing a permeability barrier for various compounds. These functions involve cellular signaling, where lipids can act as second messengers, or direct regulation of membrane associating proteins. The first part of this study focuses on relating some of the physicochemical properties of membrane lipids to the association of drug compounds to membranes. A fluorescence based method is described allowing for determination of the membrane association of drugs. This method was subsequently applied to a novel drug, siramesine, previously shown to have anti-cancer activity. Siramesine was found to associate with anionic lipids. Especially interesting is its strong affinity for a second messenger lipid phosphatidic acid. This is the first example of a small molecule drug compound specifically interacting with a cellular lipid. Phosphatidic acid in cells is required for the activation of many signaling pathways mediating growth and proliferation. This provides an intriguing possibility for a simple molecular mechanism of the observed anti-cancer activity of siramesine. In the second part the thermal behavior and self assembly of charged and uncharged membrane assemblies was studied. Strong inter-lamellar co-operativity was observed for multilamellar DPPC vesicles using fluorescence techniques together with calorimetry. The commonly used membrane models, large unilamellar vesicles (LUV) and multilamellar vesicles (MLV) were found to possess different biophysical properties as interlamellar interactions of MLVs drive segregation of a pyrene labeled lipid analogue into clusters. The effect of a counter-ion lattice on the self assembly of a cationic gemini surfactant was studied. The presence of NaCl strongly influenced the thermal phase behavior of M-1 vesicles, causing formation of giant vesicles upon exceeding a phase transition temperature, followed by a subsequent transition into a more homogenous dispersion. Understanding the underlying biophysical aspects of cellular membranes is of fundamental importance as the complex picture of the structure and function of cells is evolving. Many of the cellular reactions take place on membranes and membranes are known to regulate the activity of many peripheral and intergral membrane associating proteins. From the point of view of drug design and gene technology, membranes can provide an interesting target for future development of drugs, but also a vehicle sensitive for environmental changes allowing for encapsulating drugs and targeting them to the desired site of action.

Biochemical and structural properties of Potato virus A VPg

The potato virus A (PVA) genome linked protein (VPg) is a multifunctional protein that takes part in vital infection cycle events such as replication and movement of the virus from cell to cell. VPg is attached to the 5´ end of the genome and is carried in the tip structure of the filamentous virus particle. VPg is also the last protein to be cleaved from the polyprotein. VPg interacts with several viral and host proteins and is phosphorylated at several positions. These features indicate a central role in virus epidemiology and a requirement for an efficient but flexible mechanism for switching between different functions. -- This study examines some of the key VPg functions in more detail. Mutations in the positively charged region from Ala38 to Lys44 affected the NTP binding, uridylylation, and in vitro translation inhibition activities of VPg, whereas in vivo translation inhibition was not affected. Some of the data generated in this study implicated the structural flexibility of the protein in functional activities. VPg lacks a rigid structure, which could allow it to adapt conformationally to different functions as needed. A major finding of this study is that PVA VPg belongs to the class of ´intrinsically disordered proteins´ (IDPs). IDPs are a novel protein class that has helped to explain the observed lack of structure. The existence of IDPs clearly shows that proteins can be functional and adapt a native fold without a rigid structure. Evidence for the intrinsic disorder of VPg was provided by CD spectroscopy, NMR, fluorescence spectroscopy, bioinformatic analysis, and limited proteolytic digestion. The structure of VPg resembles that of a molten globule-type protein and has a hydrophobic core domain. Approximately 50% of the protein is disordered and an α-helical stabilization of these regions has been hypothesized. Surprisingly, VPg structure was stabilized in the presence of anionic lipid vesicles. The stabilization was accompanied by a change in VPg structure and major morphological modifications of the vesicles, including a pronounced increase in the size and appearance of pore or plaque like formations on the vesicle surface. The most likely scenario seems to be an α-helical stabilization of VPg which induces formation of a pore or channel-like structure on the vesicle surface. The size increase is probably due to fusion or swelling of the vesicles. The latter hypothesis is supported by the evident disruption of the vesicles after prolonged incubation with VPg. A model describing the results is presented and discussed in relation to other known properties of the protein.

Use of non-specific and specific interactions in the analysis of testosterone and related compounds by capillary electromigration techniques

Determination of testosterone and related compounds in body fluids is of utmost importance in doping control and the diagnosis of many diseases. Capillary electromigration techniques are a relatively new approach for steroid research. Owing to their electrical neutrality, however, separation of steroids by capillary electromigration techniques requires the use of charged electrolyte additives that interact with the steroids either specifically or non-specifically. The analysis of testosterone and related steroids by non-specific micellar electrokinetic chromatography (MEKC) was investigated in this study. The partial filling (PF) technique was employed, being suitable for detection by both ultraviolet spectrophotometry (UV) and electrospray ionization mass spectrometry (ESI-MS). Efficient, quantitative PF-MEKC UV methods for steroid standards were developed through the use of optimized pseudostationary phases comprising surfactants and cyclodextrins. PF-MEKC UV proved to be a more sensitive, efficient and repeatable method for the steroids than PF-MEKC ESI-MS. It was discovered that in PF-MEKC analyses of electrically neutral steroids, ESI-MS interfacing sets significant limitations not only on the chemistry affecting the ionization and detection processes, but also on the separation. The new PF-MEKC UV method was successfully employed in the determination of testosterone in male urine samples after microscale immunoaffinity solid-phase extraction (IA-SPE). The IA-SPE method, relying on specific interactions between testosterone and a recombinant anti-testosterone Fab fragment, is the first such method described for testosterone. Finally, new data for interactions between steroids and human and bovine serum albumins were obtained through the use of affinity capillary electrophoresis. A new algorithm for the calculation of association constants between proteins and neutral ligands is introduced.

Intermolecular Interactions of Noble-Gas-Containing Species

The importance of intermolecular interactions to chemistry, physics, and biology is difficult to overestimate. Without intermolecular forces, condensed phase matter could not form. The simplest way to categorize different types of intermolecular interactions is to describe them using van der Waals and hydrogen bonded (H-bonded) interactions. In the H-bond, the intermolecular interaction appears between a positively charged hydrogen atom and electronegative fragments and it originates from strong electrostatic interactions. H-bonding is important when considering the properties of condensed phase water and in many biological systems including the structure of DNA and proteins. Vibrational spectroscopy is a useful tool for studying complexes and the solvation of molecules. Vibrational frequency shift has been used to characterize complex formation. In an H-bonded system A∙∙∙H-X (A and X are acceptor and donor species, respectively), the vibrational frequency of the H-X stretching vibration usually decreases from its value in free H-X (red-shift). This frequency shift has been used as evidence for H-bond formation and the magnitude of the shift has been used as an indicator of the H-bonding strength. In contrast to this normal behavior are the blue-shifting H-bonds, in which the H-X vibrational frequency increases upon complex formation. In the last decade, there has been active discussion regarding these blue-shifting H-bonds. Noble-gases have been considered inert due to their limited reactivity with other elements. In the early 1930 s, Pauling predicted the stable noble-gas compounds XeF6 and KrF6. It was not until three decades later Neil Bartlett synthesized the first noble-gas compound, XePtF6, in 1962. A renaissance of noble-gas chemistry began in 1995 with the discovery of noble-gas hydride molecules at the University of Helsinki. The first hydrides were HXeCl, HXeBr, HXeI, HKrCl, and HXeH. These molecules have the general formula of HNgY, where H is a hydrogen atom, Ng is a noble-gas atom (Ar, Kr, or Xe), and Y is an electronegative fragment. At present, this class of molecules comprises 23 members including both inorganic and organic compounds. The first and only argon-containing neutral chemical compound HArF was synthesized in 2000 and its properties have since been investigated in a number of studies. A helium-containing chemical compound, HHeF, was predicted computationally, but its lifetime has been predicted to be severely limited by hydrogen tunneling. Helium and neon are the only elements in the periodic table that do not form neutral, ground state molecules. A noble-gas matrix is a useful medium in which to study unstable and reactive species including ions. A solvated proton forms a centrosymmetric NgHNg+ (Ng = Ar, Kr, and Xe) structure in a noble-gas matrix and this is probably the simplest example of a solvated proton. Interestingly, the hypothetical NeHNe+ cation is isoelectronic with the water-solvated proton H5O2+ (Zundel-ion). In addition to the NgHNg+ cations, the isoelectronic YHY- (Y = halogen atom or pseudohalogen fragment) anions have been studied with the matrix-isolation technique. These species have been known to exist in alkali metal salts (YHY)-M+ (M = alkali metal e.g. K or Na) for more than 80 years. Hydrated HF forms the FHF- structure in aqueous solutions, and these ions participate in several important chemical processes. In this thesis, studies of the intermolecular interactions of HNgY molecules and centrosymmetric ions with various species are presented. The HNgY complexes show unusual spectral features, e.g. large blue-shifts of the H-Ng stretching vibration upon complexation. It is suggested that the blue-shift is a normal effect for these molecules, and that originates from the enhanced (HNg)+Y- ion-pair character upon complexation. It is also found that the HNgY molecules are energetically stabilized in the complexed form, and this effect is computationally demonstrated for the HHeF molecule. The NgHNg+ and YHY- ions also show blue-shifts in their asymmetric stretching vibration upon complexation with nitrogen. Additionally, the matrix site structure and hindered rotation (libration) of the HNgY molecules were studied. The librational motion is a much-discussed solid state phenomenon, and the HNgY molecules embedded in noble-gas matrices are good model systems to study this effect. The formation mechanisms of the HNgY molecules and the decay mechanism of NgHNg+ cations are discussed. A new electron tunneling model for the decay of NgHNg+ absorptions in noble-gas matrices is proposed. Studies of the NgHNg+∙∙∙N2 complexes support this electron tunneling mechanism.

Spirituality of Finnish peacekeepers

The previous academic research on Finnish peacekeeping has clarified the operative and historical aspects of Finnish peacekeeping lacking the view of an individual who does the actual peacekeeping work. This research is based on the underlying theoretical assumption of human beings possessing different kinds of talents and intelligences creating a holistic entity. In this broad perspective spirituality was explored as an umbrella concept, as a holistic ability or talent, that can be explored as the deepest aspect of defining what it means to be human. The theoretical framework incorporated the concept of an intelligence, which is defined in Gardner's theory of multiple intelligences as the ability to solve problems, or to create products, that are valued within one or more cultural settings (Gardner, 1993, x). The viability of this theory was studied in the sample of Finnish peacekeepers. Spirituality in the theoretical and conceptual horizon was viewed as an extension of Gardner's theory of intelligences as one potential Gardnerian intelligence candidate. In addition to Gardner's theory, spirituality was explored as sensitivity which includes capacities such as sensing awareness, sensing mystery and sensing value (Hay, 1998). Also the practical aspects of spirituality were taken in account as shown in our everyday lives giving us the direction and influencing our social responsibilities and concerns (Bradford, 1995). Spirituality was explored also involving the element of the peacekeepers' community, the element of personal moral orientations and in the domain of religion and coping. The purpose of this research aimed in two dimensions. First, the aim was to outline the intelligence profile and the spiritual sensitivity profile of peacekeepers. Second, the aim was to understand qualitatively the nature of peacekeepers' spirituality The research interests were studied with different kinds of peacekeepers. Applying the mixed methods approach the research was conducted in two phases: first the former SFOR peacekeepers (N=6) were interviewed and the data was analysed. Inspired by the primary findings of these interviews, the data for the case-study of one peacekeeper was collected in co-operation with one former SFOR peacekeeper (N=1). In the second phase the data was collected from KFOR peacekeepers through the quantitative MI-Survey and the spiritual sensitivity survey (N=195). The quantitative method was used to outline the intelligence profile and the spiritual sensitivity profile of peacekeepers (N=195). In the mixed methods approach this method highlighted the general overview of intelligence traits and spiritual sensitivity of peacekeepers. In the mixed methods approach the qualitative method including interviews (N=6) and a case-study of one peacekeeper (N=1) increased subjective, qualitative information of spirituality of peacekeepers. The intelligence profile of peacekeepers highlighted the bodily-kinesthetic and interpersonal dimensions as the practical and social aspects of peacekeepers. Strong inter-item dependencies in the intrapersonal intelligence profile meant that peacekeepers possess a self-reflection and self-knowledge component and they reflect on deep psychological and philosophical issues. Regarding the spiritual sensitivity, peacekeepers found awareness-sensing, mystery-sensing, value-sensing and community-sensing important. The community-sensing emphasised a strong will to advance peace and to help people who are in need: things that are close to the heart of the peacekeepers. These results depicted practicality, being socially capable, and reflecting one's inner world as essential to peacekeepers. Moreover, spirituality as peacekeepers' moral endeavour became clearer because the sub-model of their community-sensing described morally charged destinations: advancing peace and helping people in need. In the qualitative findings peacekeepers articulated justice orientation and rule-following characterising the nature of peacekeepers' moral attitude and moral call (Kohlberg, 1969). An ethic of care (Gilligan, 1982) describes mainly female moral orientation, but the findings revealed that an ethic of care is also an important agent supporting strongly male peacekeepers in their aim to carry out qualitatively good peacekeeping work. The moral endeavour was voiced, when the role of religion in coping meant the assessment of the a way of life, a way of conduct, a way of being truthful to one's own values in confusing surroundings. The practical level of spiritual and religious contemplation was voiced as morally charged inner motivation to fulfil one's duties and at the same time to cope with various peacekeeping challenges. The results of different data sets were combined and interpreted as the moral endeavour, which characterises peacekeepers' spirituality. As the combining result, the perspective of peacekeepers' spirituality is considered moral or at least morally charged.

Bending the Rules of Cell Protrusions : Molecular Mechanisms and Biological Roles of Inverse-BAR Proteins in Cell Morphogenesis

Plasma membrane adopts myriad of different shapes to carry out essential cellular processes such as nutrient uptake, immunological defence mechanisms and cell migration. Therefore, the details how different plasma membrane structures are made and remodelled are of the upmost importance. Bending of plasma membrane into different shapes requires substantial amount of force, which can be provided by the actin cytoskeleton, however, the molecules that regulate the interplay between the actin cytoskeleton and plasma membrane have remained elusive. Recent findings have placed new types of effectors at sites of plasma membrane remodelling, including BAR proteins, which can directly bind and deform plasma membrane into different shapes. In addition to their membrane-bending abilities, BAR proteins also harbor protein domains that intimately link them to the actin cytoskeleton. The ancient BAR domain fold has evolved into at least three structurally and functionally different sub-groups: the BAR, F-BAR and I-BAR domains. This thesis work describes the discovery and functional characterization of the Inverse-BAR domains (I-BARs). Using synthetic model membranes, we have shown that I-BAR domains bind and deform membranes into tubular structures through a binding-surface composed of positively charged amino acids. Importantly, the membrane-binding surface of I-BAR domains displays an inverse geometry to that of the BAR and F-BAR domains, and these structural differences explain why I-BAR domains induce cell protrusions whereas BAR and most F-BAR domains induce cell invaginations. In addition, our results indicate that the binding of I-BAR domains to membranes can alter the spatial organization of phosphoinositides within membranes. Intriguingly, we also found that some I-BAR domains can insert helical motifs into the membrane bilayer, which has important consequences for their membrane binding/bending functions. In mammals there are five I-BAR domain containing proteins. Cell biological studies on ABBA revealed that it is highly expressed in radial glial cells during the development of the central nervous system and plays an important role in the extension process of radial glia-like C6R cells by regulating lamellipodial dynamics through its I-BAR domain. To reveal the role of these proteins in the context of animals, we analyzed MIM knockout mice and found that MIM is required for proper renal functions in adult mice. MIM deficient mice displayed a severe urine concentration defect due to defective intercellular junctions of the kidney epithelia. Consistently, MIM localized to adherens junctions in cultured kidney epithelial cells, where it promoted actin assembly through its I-BAR andWH2 domains. In summary, this thesis describes the mechanism how I-BAR proteins deform membranes and provides information about the biological role of these proteins, which to our knowledge are the first proteins that have been shown to directly deform plasma membrane to make cell protrusions.

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.