A Study of Multiprocessor Systems using the Picoblaze 8-bit Microcontroller Implemented on Field Programmable Gate Arrays

As Field Programmable Gate Arrays (FPGAs) are becoming more capable of implementing complex logic circuits, designers are increasingly choosing them over traditional microprocessor-based systems for implementing digital controllers and digital signal processing applications. Indeed, as FPGAs are being built using state-of-the-art deep submicron CMOS processes, the increased amount of logic and memory resources allows such FPGA-based implementations to compete in terms of speed, complexity, and power dissipation with most custom-built chips, but at a fraction of the development costs. The modern FPGA is now capable of implementing multiple instances of configurable processors that are completely specified by a high-level descriptor language. Such arrays of soft processor cores have opened up new design possibilities that include complex embedded systems applications that were previously implemented by custom multiprocessor chips. As the FPGA-based multiprocessor system is completely configurable by the user, it can be optimized for speed and power dissipation to fit a given application. The goal of this thesis is to investigate design methods for implementing an array of soft processor cores using the Xilinx FPGA-based 8-bit microcontroller known as PicoBlaze. While development tools exist for the larger 32-bit processor from Xilinx known as MicroBlaze, no such resources are currently available for the PicoBlaze microcontroller. PicoBlaze benefits in applications that requires only less data bits (less than 8 bits). For example, consider the gene sequencing or DNA sequencing in which the processing requires only 2 to 5 bits. In such an application, PicoBlaze can be a simple processor to produce the results. Also, the PicoBlaze unit offers a finer level of granularity and hence consumes fewer resources than the larger 32-bit MicroBlaze processor. Hence, the former will find applications in embedded systems requiring a complex design to be partitioned over several processors but where only an 8-bit datapath is required

Structural Basis for Asymmetric Conductance of the Influenza M2 Proton Channel Investigated by Solid-State NMR Spectroscopy

The influenza M2 protein forms an acid-activated proton channel that is essential for virus replication. The transmembrane H37 selects for protons under low external pH while W41 ensures proton conduction only from the N terminus to the C terminus and prevents reverse current under low internal pH. Here, we address the molecular basis for this asymmetric conduction by investigating the structure and dynamics of a mutant channel, W41F, which permits reverse current under low internal pH. Solid-state NMR experiments show that W41F M2 retains the pH-dependent α-helical conformations and tetrameric structure of the wild-type (WT) channel but has significantly altered protonation and tautomeric equilibria at H37. At high pH, the H37 structure is shifted toward the π tautomer and less cationic tetrads, consistent with faster forward deprotonation to the C terminus. At low pH, the mutant channel contains more cationic tetrads than the WT channel, consistent with faster reverse protonation from the C terminus.15N NMR spectra allow the extraction of four H37 pKas and show that the pKas are more clustered in the mutant channel compared to WT M2. Moreover, binding of the antiviral drug, amantadine, at the N-terminal pore at low pH did not convert all histidines to the neutral state, as seen in WT M2, but left half of all histidines cationic, unambiguously demonstrating C-terminal protonation of H37 in the mutant. These results indicate that asymmetric conduction in WT M2 is due to W41 inhibition of C-terminal acid activation by H37. When Trp is replaced by Phe, protons can be transferred to H37 bidirectionally with distinct rate constants. Keywords: magic-angle-spinning NMR; tautomeric equilibrium; proton dissociation equilibrium; ion channels; gatingNational Institutes of Health (U.S.) (Grant GM088204

A Targeted Enrichment Strategy for Massively Parallel Sequencing of Angiosperm Plastid Genomes

Premise of the study: We explored a targeted enrichment strategy to facilitate rapid and low-cost next-generation sequencing (NGS) of numerous complete plastid genomes from across the phylogenetic breadth of angiosperms

Structure and dynamics of influenza M2 proton channels from solid-state NMR

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Chemistry, February, 2021Cataloged from the official PDF of thesis.Includes bibliographical references.The A and B strains of influenza virus places a substantial burden on health, causing around 30 million illnesses, several hundred thousand hospitalizations, and a few tens of thousands of deaths every year in the United States alone. Developing novel antiviral and vaccines against influenza requires understanding the proteins employed by these infectious virions. The matrix-2 protein (M2) is an essential viral protein that conducts protons in the endosomes of infected host cells and induces membrane curvature to facilitate virus budding. M2's proton channel activity is encapsulated by a transmembrane domain (TM) that is targeted by the FDA-approved antiviral drugs amantadine and rimantadine to inhibit viral replication. Proton conduction by M2's TM is mediated by a His-xxx-Trp motif conserved in the otherwise disparate M2 from influenza A (AM2) and influenza B (BM2) strains.The histidine selects for protons and activates the channel at low pH, while the tryptophan is responsible for gating and unidirectional conduction from the N-terminus (outside) to the C-terminus (inside). M2 conducts protons across lipid bilayers at a moderate rate of ca. 10-1000 s⁻¹. AM2 is well characterized and several high-resolution structures in a variety of membrane and membrane-mimetic environments are available, yet the mechanism of gating and the rate-limiting step of proton conduction are unknown. A gating-deficient mutant was utilized to determine that asymmetric conduction in AM2 is due to tryptophan blocking activation of histidine from the C-terminal side under low pH. Further, in phospholipid bilayers, AM2 shows two discrete conformations that interconvert on the proton conduction timescale, providing the first experimental evidence for a transporter-like mechanism.In contrast to AM2, BM2 is relatively poorly studied and no high-resolution structures in membranes is available. BM2 shares little sequence homology with AM2, is not inhibited by the antiviral drugs targeting influenza, and conducts protons faster but more bidirectionally than AM2. The first high-resolution structures of membrane-embedded BM2 in the closed and open states are reported. In contrast to the transporter-like motion of AM2, BM2 undergoes a subtler channel-like scissor opening motion, that allows for more efficient proton conduction at the expense of some bidirectional current.by Venkata Shiva Mandala.Ph. D.Ph.D. Massachusetts Institute of Technology, Department of Chemistr

High-sensitivity protein solid-state NMR spectroscopy

© 2019 Elsevier Ltd The sensitivity of solid-state nuclear magnetic resonance (SSNMR) spectroscopy for structural biology is significantly increased by 1H detection under fast magic-angle spinning (MAS) and by dynamic nuclear polarization (DNP) from electron spins to nuclear spins. The former allows studies of the structure and dynamics of small quantities of proteins under physiological conditions, while the latter permits studies of large biomolecular complexes in lipid membranes and cells, protein intermediates, and protein conformational distributions. We highlight recent applications of these two emerging SSNMR technologies and point out areas for future development

Cloud Computing Organizational Benefits : A Managerial concern

Context: Software industry is looking for new methods and opportunities to reduce the project management problems and operational costs. Cloud Computing concept is providing answers to these problems. Cloud Computing is made possible with the availability of high internet bandwidth. Cloud Computing is providing wide range of various services to varied customer base. Cloud Computing has some key elements such as on-demand services, large pool of configurable computing resources and minimal management effort to the users. The software organizations are looking for cloud benefits to address the project management problems. Objectives: The study is to identify various cloud benefits for addressing project management problems faced by software industry. The study is also investigates various challenges or problems faced by the organizations while using cloud computing environment. The solutions or suggestions to overcome these identified cloud challenges are also produced in this study. Cloud benefits across different cloud types also found during this study. Methods: Systematic literature review is conducted across eight databases to find different cloud benefits and challenges for the organizations to address the project management problems. Interview study is conducted across industrial experts working in cloud computing environment. Interview study is to check the status of cloud benefits and challenges found through systematic literature review and find new additions. The solutions and suggestions are also found to address the cloud challenges through both methodologies. Results: A total of 21 cloud benefits and 12 challenges found across 43 primary studies through systematic literature review. 26 cloud benefits and 14 cloud challenges found through interview study among 7 cloud computing industry experts. 6 cloud benefits and 2 cloud challenges found through this study are not available in existing literature. Cloud benefits across different types are also discussed in this study. Conclusion: This study identifies various cloud benefits and cloud challenges for organizations to address project management problems. Cloud utilizing organization has to differentiate its project management problems for identifying cloud type. Cloud utilizing organization has to take care of the challenges at the time of writing Service Level Agreements (SLAs) with the help of third party organization

Determination of long-range distances by fast magic-angle-spinning radiofrequency-driven 19 F-19 F dipolar recoupling NMR

Nanometer-range distances are important for restraining the three-dimensional structure and oligomeric assembly of proteins and other biological molecules. Solid-state NMR determination of protein structures typically utilizes 13C-13C and 13C-15N distance restraints, which can only be measured up to ∼7 Å because of the low gyromagnetic ratios of these nuclear spins. To extend the distance reach of NMR, one can harvest the power of 19F, whose large gyromagnetic ratio in principle allows distances up to 2 nm to be measured. However, 19F possesses large chemical shift anisotropies (CSAs) as well as large isotropic chemical shift dispersions, which pose challenges to dipolar coupling measurements. Here, we demonstrate 19F-19F distance measurements at high magnetic fields under fast magic-angle spinning (MAS) using radiofrequency-driven dipolar recoupling (RFDR). We show that 19F-19F cross-peaks for distances up to 1 nm can be readily observed in two-dimensional 19F-19F correlation spectra using less than 5 ms of RFDR mixing. This efficient 19F-19F dipolar recoupling is achieved using practically accessible MAS frequencies of 15-55 kHz, moderate 19F radio frequency field strengths, and no 1H decoupling. Experiments and simulations show that the fastest polarization transfer for aromatic fluorines with the highest distance accuracy is achieved using either fast MAS (e.g., 60 kHz) with large pulse duty cycles (>50%) or slow MAS with strong 19F pulses. Fast MAS considerably reduces relaxation losses during the RFDR π-pulse train, making finite-pulse RFDR under fast-MAS the method of choice. Under intermediate MAS frequencies (25-40 kHz) and intermediate pulse duty cycles (15-30%), the 19F CSA tensor orientation has a quantifiable effect on the polarization transfer rate; thus, the RFDR buildup curves encode both distance and orientation information. At fast MAS, the impact of CSA orientation is minimized, allowing pure distance restraints to be extracted. We further investigate how relayed transfer and dipolar truncation in multifluorine environments affect polarization transfer. This fast-MAS 19F RFDR approach is complementary to 19F spin diffusion for distance measurements and will be the method of choice under high-field fast-MAS conditions that are increasingly important for protein structure determination by solid-state NMR.German National Academy of Sciences (grant no. LPDS-2017-14)NIH (grant no. GM088204

Cloud Computing Organizational Benefits : A Managerial concern

Context: Software industry is looking for new methods and opportunities to reduce the project management problems and operational costs. Cloud Computing concept is providing answers to these problems. Cloud Computing is made possible with the availability of high internet bandwidth. Cloud Computing is providing wide range of various services to varied customer base. Cloud Computing has some key elements such as on-demand services, large pool of configurable computing resources and minimal management effort to the users. The software organizations are looking for cloud benefits to address the project management problems. Objectives: The study is to identify various cloud benefits for addressing project management problems faced by software industry. The study is also investigates various challenges or problems faced by the organizations while using cloud computing environment. The solutions or suggestions to overcome these identified cloud challenges are also produced in this study. Cloud benefits across different cloud types also found during this study. Methods: Systematic literature review is conducted across eight databases to find different cloud benefits and challenges for the organizations to address the project management problems. Interview study is conducted across industrial experts working in cloud computing environment. Interview study is to check the status of cloud benefits and challenges found through systematic literature review and find new additions. The solutions and suggestions are also found to address the cloud challenges through both methodologies. Results: A total of 21 cloud benefits and 12 challenges found across 43 primary studies through systematic literature review. 26 cloud benefits and 14 cloud challenges found through interview study among 7 cloud computing industry experts. 6 cloud benefits and 2 cloud challenges found through this study are not available in existing literature. Cloud benefits across different types are also discussed in this study. Conclusion: This study identifies various cloud benefits and cloud challenges for organizations to address project management problems. Cloud utilizing organization has to differentiate its project management problems for identifying cloud type. Cloud utilizing organization has to take care of the challenges at the time of writing Service Level Agreements (SLAs) with the help of third party organization

Structure and dynamics of membrane proteins from solid-state NMR

Solid-state nuclear magnetic resonance (SSNMR) spectroscopy elucidates membrane protein structures and dynamics in atomic detail to yield mechanistic insights. By interrogating membrane proteins in phospholipid bilayers that closely resemble biological membranes, SSNMR spectroscopists have revealed ion conduction mechanisms, substrate transport dynamics, and oligomeric interfaces of seven-transmembrane helix proteins. Research has also identified conformational plasticity underlying virus-cell membrane fusions by complex protein machineries, and β-sheet folding and assembly by amyloidogenic proteins bound to lipid membranes. These studies collectively show that membrane proteins exhibit extensive structural plasticity to carry out their functions. Because of the inherent dependence of NMR frequencies on molecular orientations and the sensitivity of NMR frequencies to dynamical processes on timescales from nanoseconds to seconds, SSNMR spectroscopy is ideally suited to elucidate such structural plasticity, local and global conformational dynamics, protein-lipid and protein-ligand interactions, and protonation states of polar residues. New sensitivity-enhancement techniques, resolution enhancement by ultrahigh magnetic fields, and the advent of 3D and 4D correlation NMR techniques are increasingly aiding these mechanistically important structural studies

Transport-Relevant Protein Conformational Dynamics and Water Dynamics on Multiple Time Scales in an Archetypal Proton Channel: Insights from Solid-State NMR

The influenza M2 protein forms a tetrameric proton channel that conducts protons from the acidic endosome into the virion by shuttling protons between water and a transmembrane histidine. Previous NMR studies have shown that this histidine protonates and deprotonates on the microsecond time scale. However, M2’s proton conduction rate is 10–1000 s^–1, more than 2 orders of magnitude slower than the histidine-water proton-exchange rate. M2 is also known to be conformationally plastic. To address the disparity between the functional time scale and the time scales of protein conformational dynamics and water dynamics, we have now investigated a W41F mutant of the M2 transmembrane domain using solid-state NMR. ¹³C chemical shifts of the membrane-bound peptide indicate the presence of two distinct tetramer conformations, whose concentrations depend exclusively on pH and hence the charge-state distribution of the tetramers. High-temperature 2D correlation spectra indicate that these two conformations interconvert at a rate of ∼400 s^–1 when the +2 and +3 charge states dominate, which gives the first experimental evidence of protein conformational motion on the transport time scale. Protein ¹³C-detected water ¹H T₂ relaxation measurements show that channel water relaxes an order of magnitude faster than bulk water and membrane-associated water, indicating that channel water undergoes nanosecond motion in a pH-independent fashion. These results connect motions on three time scales to explain M2’s proton-conduction mechanism: picosecond-to-nanosecond motions of water molecules facilitate proton Grotthuss hopping, microsecond motions of the histidine side chain allow water–histidine proton transfer, while millisecond motions of the entire four-helix bundle constitute the rate-limiting step, dictating the number of protons released into the virion