No / Scytalidium catalase is a homotetramer including heme d in each subunit. Its primary function is the dismutation of H2O2 to water and oxygen, but it is also able to oxidase various small organic compounds including catechol and phenol. The crystal structure of Scytalidium catalase reveals the presence of three linked channels providing access to the exterior like other catalases reported so far. The function of these channels has been extensively studied, revealing the possible routes for substrate flow and product release. In this report, we have focussed on the semi-conserved residue Val228, located near to the vinyl groups of the heme at the opening of the lateral channel. Its replacement with Ala, Ser, Gly, Cys, Phe and Ile were tested. We observed a significant decrease in catalytic efficiency in all mutants with the exception of a remarkable increase in oxidase activity when Val228 was mutated to either Ala, Gly or Ser. The reduced catalytic efficiencies are characterized in terms of the restriction of hydrogen peroxide as electron acceptor in the active centre resulting from the opening of lateral channel inlet by introducing the smaller side chain residues. On the other hand, the increased oxidase activity is explained by allowing the suitable electron donor to approach more closely to the heme. The crystal structures of V228C and V228I were determined at 1.41 and 1.47 Å resolution, respectively. The lateral channels of the V228C and V228I presented a broadly identical chain of arranged waters to that observed for wild-type enzyme.

<p>In recent years, multiple-input multiple-output (MIMO)systems appear to be very promising since they can provide highdata rates in environments with sucient scattering byexploiting the spatial domain. To design a real MIMO wirelesssystem and predict its performance under certain circumstances,it is necessary to have accurate MIMO wireless channel modelsfor dierent scenarios. This thesis presents dierent models forindoor MIMO radio propagation channels based on 5.2 GHz indoorMIMO channel measurements.The recent research on MIMO radio channel modeling isbriey reviewed in this thesis. The models are categorized intonon-physical and physical models. The non-physical modelsprimarily rely on the statistical characteristics of MIMOchannels obtained from the measured data while the physicalmodels describe the MIMO channel (or its distribution) via somephysical parameters. The relationships between dierent modelsare also discussed.For the narrowband case, a non line-of-sight (NLOS)indoor MIMO channel model is presented. The model is based on aKronecker structure of the channel covariance matrix and thefact that the channel is complex Gaussian. It is extended tothe line-of-sight (LOS) scenario by estimating and modeling thedominant component separately.As for the wideband case, two NLOS MIMO channel modelsare proposed. The rst model uses the power delay prole and theKronecker structure of the second order moments of each channeltap to model the wideband MIMO channel while the second modelcombines a simple single-input single-output (SISO) model withthe same Kronecker structure of the second order moments.Monte-Carlo simulations are used to generate indoor MIMOchannel realizations according to the above models. The resultsare compared with the measured data and good agreement has beenobserved.</p>

No description available.

Haemonchus contortus is a parasitic nematode that is controlled by several nematocides which target ion channels. We have identified two H. contortus ion channel genes, Hcounc- 49B and C that encode two GABA-gated chloride channel subunits. Electrophysiological analysis shows that the Hco-UNC-49B subunit forms a functional homomeric channel in Xenopus laevis oocytes that produces a robust response to GABA and is highly sensitive to picrotoxin. In contrast, Hco-UNC-49C alone does not respond to GABA but can assemble with Hco-UNC-49B to form a heteromeric channel with an increased sensitivity to GABA and a lower sensitivity to picrotoxin. To investigate the subunit requirements for high agonist sensitivity, we generated cross-assembled channels by co-expressing the H. contortus subunits with UNC-49 subunits from the nematode Caenorhabditis elegans (Cel-UNC-49). Co-expressing the Cel-UNC-49B with Hco- UNC-49C produced a heteromeric channel with a low sensitivity to GABA. In contrast, co-expressing Hco-UNC-49B with Cel-UNC-49C produced a heteromeric channel that was highly sensitive to GABA. These results suggest that the Hco-UNC-49B subunit is the key determinant for the high agonist sensitivity of heteromeric channels.

Enabling cooperation among nodes of a wireless network can significantly reduce the required transmit power as well as the induced intra-network interference. Due to the practical half-duplexity constraint of the cooperating nodes, they are prohibited to simultaneously transmit and receive data at the same time-frequency resource. The purpose of this dissertation is to illustrate the value of cooperation in such an environment. To understand how to cooperate efficiently, information theory is employed as a useful tool, which not only determines the fundamental limits of communication (i.e., capacity) over the considered network, but also provides insights into the design of a proper transmission scheme for that network. In this thesis, two simple but yet important types of wireless networks, namely Relay Channel, and Interference Channel are studied. In fact, these models constitute building blocks for larger networks. The first considered channel is a diamond-shaped relay channel consisting of a source, a destination, and two parallel relays. The second analyzed channel is an interference channel composed of two transmitter-receiver pairs with out-of-band transmitter cooperation, also referred to as conferencing encoders. While characterizing the capacity of these channels are difficult, a simpler and a more common approach is to find an achievable scheme for each channel that ensures a small gap from the capacity for all channel parameters. In chapter 2, the diamond relay channel is investigated in detail. Because of the half-duplex nature of the relays, each relay is either in transmit or receive mode, making four modes possible for the two-relay combination, specifically, 1) broadcast mode (both relays receive) 2,3) routing modes (one relay transmits, another receives) 4) multiple-access mode (both relays transmit). An appropriate scheduling ( i.e., timing over the modes) and transmission scheme based on the decode-and-forward strategy are proposed and shown to be able to achieve either the capacity for certain channel conditions or at most 3.6 bits below the capacity for general channel conditions. Particularly, by assuming each transmitter has a constant power constraint over all modes, a parameter Δ is defined, which captures some important features of the channel. It is proven that for Δ=0 the capacity of the channel can be attained by successive relaying, i.e., using modes 2 and 3 defined above in a successive manner. This strategy may have an infinite gap from the capacity of the channel when Δ≠0. To achieve rates as close as 0.71 bits to the capacity, it is shown that the cases of Δ>0 and Δ<0 should be treated differently. Using new upper bounds based on the dual problem of the linear program associated with the cut-set bounds, it is proven that the successive relaying strategy needs to be enhanced by an additional broadcast mode (mode 1), or multiple access mode (mode 4), for the cases of Δ<0 and Δ>0, respectively. Furthermore, it is established that under average power constraints the aforementioned strategies achieve rates as close as 3.6 bits to the capacity of the channel. In chapter 3, a two-user Gaussian Interference Channel (GIC) is considered, in which encoders are connected through noiseless links with finite capacities. The setup can be motivated by downlink cellular systems, where base stations are connected via infrastructure backhaul networks. In this setting, prior to each transmission block the encoders communicate with each other over the cooperative links. The capacity region and the sum-capacity of the channel are characterized within some constant number of bits for some special classes of symmetric and Z interference channels. It is also established that properly sharing the total limited cooperation capacity between the cooperative links may enhance the achievable region, even when compared to the case of unidirectional transmitter cooperation with infinite cooperation capacity. To obtain the results, genie-aided upper bounds on the sum-capacity and cut-set bounds on the individual rates are compared with the achievable rate region. The achievable scheme enjoys a simple type of Han-Kobayashi signaling, together with the zero-forcing, and basic relaying techniques.

Channel order estimation is an important problem in many fields including signal processing, communications, acoustics, and more. In this thesis, blind channel order estimation problem is considered for single-input, multi-output (SIMO) FIR systems. The problem is to estimate the effective channel order for the SIMO system given only the output samples corrupted by noise. Two new methods for channel order estimation are presented. These methods have several useful features compared to the currently known techniques. They are guaranteed to find the true channel order for noise free case and they perform significantly better for noisy observations. These algorithms show a consistent performance when the number of observations, channels and channel order are changed. The proposed algorithms are integrated with the least squares smoothing (LSS) algorithm for blind identification of the channel coefficients. LSS algorithm is selected since it is a deterministic algorithm and has some additional features suitable for order estimation. The proposed algorithms are compared with a variety of dierent algorithms including linear prediction (LP) based methods. LP approaches are known to be robust to channel order overestimation. In this thesis, it is shown that significant gain can be obtained compared to LP based approaches when the proposed techniques are used. The proposed algorithms are also compared with the oversampled single-input, single-output (SISO) system with a generic decision feedback equalizer, and better mean-square error performance is observed for the blind setting. Channel order estimation problem is also investigated for semi-blind systems where a pilot signal is used which is known at the receiver. In this case, two new methods are proposed which exploit the pilot signal in dierent ways. When both unknown and pilot symbols are used, a better estimation performance can be achieved compared to the proposed blind methods. The semi-blind approach is especially effective in terms of bit error rate (BER) evaluation thanks to the use of pilot symbols in better estimation of channel coecients. This approach is also more robust to ill-conditioned channels. The constraints for these approaches, such as synchronization, and the decrease in throughput still make the blind approaches a good alternative for channel order estimation. True and effective channel order estimation topics are discussed in detail and several simulations are done in order to show the significant performance gain achieved by the proposed methods.

Underwater acoustic channel models have been studied in the context of communication and sonar applications. Acoustic propagation channel in an underwater environment exhibits multipath, time-variability and Doppler eects. In this thesis, multipath fading channel models, underwater physical properties and sound propagation characteristics are studied. An underwater channel model for sonar applications is proposed. In the proposed model, the physical characteristics of underwater environment are considered in a comprehensive manner. Experiments /simulations were carried out using real-life data. Model parameters are estimated for a specific location, scenario and physical conditions. The channel response is approximated by fitting the model output to the recorded data. The optimization and estimation are conducted in frequency domain using Mean Square Error criterion.

Glycine receptors (GlyRs) are ligand-gated ion channels (LGICs) that, along with other members of the cys-loop superfamily of receptors, mediate a considerable portion of fast neurotransmission in the central nervous system (CNS). GlyRs are pentameric channels, organized quasi-symmetrically around an ion-conducting pore. Opening of the integral ion pore depends on ligand binding and transduction of this binding signal to the channel gate. Research presented in this dissertation describes a number of critical electrostatic interactions that play a role in conserving the closed-state stability of the receptor in the absence of ligand, ensuring that receptor activation occurs only upon neurotransmitter binding. These amino acids, aspartic acid at position 97 (D97), lysine 116 (K116), arginine 119 (R119) and arginine R131 (R131) are charged residues that interact with one another through electrostatic attraction. When D97 is replaced with any other amino acid this destabilizes the closed state of the channel and causes spontaneous GlyR channel opening. I show that restoration of this electrostatic interaction in GlyR bearing double mutations in which the charges are swapped (D97R/R119E and D97R/R131D) markedly decreases this spontaneous current. In addition, I investigate how these residues that interact at the interfaces between receptor subunits affect the efficacies of GlyR partial agonists. My work shows that the partial agonist taurine is converted into a full agonist at both D97R and R131D receptors. Furthermore, I analyzed the structure of the more extracellular part of the transmembrane (TM) 2 segment that lines the ion channel pore, showing that it is unlikely that this fragment (stretching from T13’ to S18’) is constrained in a true alpha helical conformation. From this work, using disulfide trapping and whole cell electrophysiology, I conclude that a significant level of flexibility characterizes this part of the TM2 domain. This segment includes residue S267, previously shown to be significant for alcohol and anesthetic actions, as well as residue Q266 that, when mutated, produces a hyperekplexia-like phenotype. The range of movement of residues in this region may therefore play an important role not only in channel gating but also in how modulators of GlyR function exert their actions. / text

Enabling cooperation among nodes of a wireless network can significantly reduce the required transmit power as well as the induced intra-network interference. Due to the practical half-duplexity constraint of the cooperating nodes, they are prohibited to simultaneously transmit and receive data at the same time-frequency resource. The purpose of this dissertation is to illustrate the value of cooperation in such an environment. To understand how to cooperate efficiently, information theory is employed as a useful tool, which not only determines the fundamental limits of communication (i.e., capacity) over the considered network, but also provides insights into the design of a proper transmission scheme for that network. In this thesis, two simple but yet important types of wireless networks, namely Relay Channel, and Interference Channel are studied. In fact, these models constitute building blocks for larger networks. The first considered channel is a diamond-shaped relay channel consisting of a source, a destination, and two parallel relays. The second analyzed channel is an interference channel composed of two transmitter-receiver pairs with out-of-band transmitter cooperation, also referred to as conferencing encoders. While characterizing the capacity of these channels are difficult, a simpler and a more common approach is to find an achievable scheme for each channel that ensures a small gap from the capacity for all channel parameters. In chapter 2, the diamond relay channel is investigated in detail. Because of the half-duplex nature of the relays, each relay is either in transmit or receive mode, making four modes possible for the two-relay combination, specifically, 1) broadcast mode (both relays receive) 2,3) routing modes (one relay transmits, another receives) 4) multiple-access mode (both relays transmit). An appropriate scheduling ( i.e., timing over the modes) and transmission scheme based on the decode-and-forward strategy are proposed and shown to be able to achieve either the capacity for certain channel conditions or at most 3.6 bits below the capacity for general channel conditions. Particularly, by assuming each transmitter has a constant power constraint over all modes, a parameter Δ is defined, which captures some important features of the channel. It is proven that for Δ=0 the capacity of the channel can be attained by successive relaying, i.e., using modes 2 and 3 defined above in a successive manner. This strategy may have an infinite gap from the capacity of the channel when Δ≠0. To achieve rates as close as 0.71 bits to the capacity, it is shown that the cases of Δ>0 and Δ<0 should be treated differently. Using new upper bounds based on the dual problem of the linear program associated with the cut-set bounds, it is proven that the successive relaying strategy needs to be enhanced by an additional broadcast mode (mode 1), or multiple access mode (mode 4), for the cases of Δ<0 and Δ>0, respectively. Furthermore, it is established that under average power constraints the aforementioned strategies achieve rates as close as 3.6 bits to the capacity of the channel. In chapter 3, a two-user Gaussian Interference Channel (GIC) is considered, in which encoders are connected through noiseless links with finite capacities. The setup can be motivated by downlink cellular systems, where base stations are connected via infrastructure backhaul networks. In this setting, prior to each transmission block the encoders communicate with each other over the cooperative links. The capacity region and the sum-capacity of the channel are characterized within some constant number of bits for some special classes of symmetric and Z interference channels. It is also established that properly sharing the total limited cooperation capacity between the cooperative links may enhance the achievable region, even when compared to the case of unidirectional transmitter cooperation with infinite cooperation capacity. To obtain the results, genie-aided upper bounds on the sum-capacity and cut-set bounds on the individual rates are compared with the achievable rate region. The achievable scheme enjoys a simple type of Han-Kobayashi signaling, together with the zero-forcing, and basic relaying techniques.

Delay is an important quality-of-service measure for the design of next-generation wireless networks. This dissertation considers the problem of delay-limited communication over block-fading channels, where the channel state information is available at the receiver but not at the transmitter. For this communication scenario, the difference between the ergodic capacity and the maximum achievable expected rate (the expected capacity) for coding over a finite number of coherent blocks represents a fundamental measure of the penalty incurred by the delay constraint. This dissertation introduces a notion of worst-case expected-capacity loss. Focusing on the slow-fading scenario (one-block delay), the worst-case additive and multiplicative expected-capacity losses are precisely characterized for the point-to- point fading channel. Extension to the problem of writing on fading paper is also considered, where both the ergodic capacity and the additive expected-capacity loss over one-block delay are characterized to within one bit per channel use. The problem with multiple-block delay is considerably more challenging. This dissertation presents two partial results. First, the expected capacity is precisely characterized for the point-to-point two-state fading channel with two-block delay. Second, the optimality of Gaussian superposition coding with indirect decoding is established for a two-parallel Gaussian broadcast channel with three receivers. Both results reveal some intrinsic complexity in characterizing the expected capacity with multiple-block delay.