Inverse Problem in Vibration of Lumped Non Conservative Systems Generating Symmetric Coefficient Matrices

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Molecular mechanisms of the coupling of gating to voltage sensing in transmembrane proteins

Voltage gated potassium ion (Kv) channels regulate action potentials of the nervous system by responding to changes in transmembrane voltage, enabling K+ transport across the membrane to restore cells to their resting potential. Comprised of four identical subunits, Kv channels contain four voltage sensing domains arranged on the periphery of a central pore domain. Each voltage sensor is comprised of four transmembrane helices, numbered S1 through S4. The S4 helix, containing four to six highly-conserved, positively-charged arginine or lysine residues, is responsible for voltage sensitivity in Kv channels. The pore domain consists of two transmembrane helices, S5 and S6. The S5 helix constitutes the periphery of the pore domain and is believed to be relatively immobile. The S6 helices, lining the interior of the channel, gate the protein and regulate K+ permeation. Because each subunit of Kv channels contains six transmembrane helices, they are often referred to as 6TM Kv channels. The depolarization of an action potential is initiated as sodium ions enter the cell. At the cellular resting potential of -70 mV, potassium ion channels are closed, and the S4 helix is in its “down” state. As the electrochemical gradient changes, the S4 helices of Kv channels begin to reorient within the membrane. At the peak of the action potential (roughly +20 mV), the S4 helices exist in their “up” state. This conformational transition of the S4 helix is coupled to the pore domain via the S4-S5 linker, a short, amphipathic helix along the intracellular membrane-water interface. By bridging the C-terminus of the voltage sensor to the N-terminus of the pore domain, the S4-S5 linker couples the voltage sensitivity of the voltage sensor to K+ conduction in the pore domain. Because they begin opening at voltages less than 0 mV, all crystal structures of Kv channels contain an open pore domain. With no structure in the closed conformation, the mechanism of gating in Kv channels remains unclear. Nevertheless, significant biophysical studies have revealed insights into both the closed conformation and the gating transition itself. In this dissertation, I will explore questions relevant to the gating mechanism in voltage gated potassium ion channels through fully-atomistic molecular dynamics (MD) simulations. First, in Chapter 2, I will address the potential role of the 310 helical conformation found in the C-terminal end of S4 in the crystal structures of Kv channels. Spanning eight or more residues, these 310 helices are both uncharacteristically long and conserved in K+ channel crystal structures. By simulating the Kv1.2/2.1 chimera channel’s voltage sensor embedded in a lipid bilayer, I find that an alpha to 310 helical interconversion of the S4 helix reproduces many experimental measurements of the open and closed states of Kv channels. In Chapter 3, I perform molecular dynamics simulations of the entire Kv1.2/2.1 chimera channel. First, I examine the impact of an alpha to 310 helical interconversion of the S4 helix on the pore domain of the channel. Though the results are consistent with the results in Chapter 2 (and the corresponding experimental measurements), I find that this secondary structural modification is insufficient to influence the pore domain of the channel on the timescale of my simulations. In the second half of Chapter 3, I use molecular dynamics simulations to generate a closed state model of the Kv1.2/2.1 chimera from luminescence resonance energy transfer (LRET) measurements of the closed conformation of KvAP. The resulting structure is indeed closed, and also recapitulates a number of experimentally determined measurements of the closed channel. In Chapter 4, I focus on the pore domain. First, using targeted molecular dynamics simulations, I generate a transition between a closed model of the KvAP linker and pore domain to the open conformation. Then, using an umbrella sampling method, I quantify the energetics of the gating transition in KvAP and assess the physiological implications. In agreement with experimental studies of Kv channel energetics, I find that the open pore is roughly 2.7 kcal/mol lower in free energy than the closed conformation. The targeted molecular dynamics and umbrella sampling simulations reveal additional insights into the gating mechanism of KvAP. Lastly, in Chapter 5, I use MD simulations to gain insights into the binding mechanism of VSTx1, a Kv channel inhibitor. By using the experimentally determined neutron scattering density profile of the VSTx1 toxin bound to a lipid bilayer as a restraint for molecular dynamics simulations, I recreate the experimental scattering density profile, and also offer insight into the binding of VSTx1 to a lipid membrane

Legged Robot Using Hydro-Muscles

Multiple hydraulically actuated muscles (HAM) can be recruited in parallel to exert a greater force than a single muscle is capable of producing. Many of these “muscle groups” can be used to equip a system for high force output applications. The hopping biped system uses four muscle groups attached to the legs of the biped apparatus to perform a single jumping action actuated. Two muscle groups are attached to the lower section of the apparatus to act similarly to Gastrocnemius muscles, while the other two muscle groups are attached to the upper section of the apparatus to act similarly to Quadriceps muscles. The height reached by the biped system demonstrates the high force output capabilities of HAM and the apparatus will serve as a test-bed for future studies of legged hopping dynamics

Employment politics while employing people with health handicaps in the Czech Republic

Nowadays significant topic is the employment of people with handicaps, not only for HR. Even though, the state is visibly supporting and motivating employers to offer jobs to people with handicaps, this group of job seekers is still at significant risk due to their health handicaps and unequal changes in the job market. The main aim of this article is to collect the views of employees and to understand their opinions on the employment of people with a handicap. Primarily, we are interested in the opinions of HR employees. In training for HR, workers participated 252 HR workers presented to 172 companies. Based on the answers about company politics towards employment of people with health handicaps we can formulate the hypothesis that people with health handicaps are more likely to employ companies which have employment of these people of the mission, vision, or culture of the company

Level Design in a Music Education Video Game

In both video games and teaching practices, the way that information is presented and experienced by the user is an important factor in information retention, immersion, and other components. This project examined the role of level design in an educational video game that introduces musical concepts to kids in an informal manner. I developed a prototype game demo that embodied the level design theory outlined In my background research, and administered a survey to a select group of past WPI music students to gather information about specific aspects of the level design in the game prototype. This validated that the world I created achieved its goals, but still has much room for improvement

The effects of 2-methoxyethanol and 2-ethoxyethanol on hematological changes induced by 2-butoxyethanol

Background: Alkoxyethanols (ethylene glycol alkyl ethers) are used as mixtures in a variety of industrial and household products. The aim of this study has been to evaluate the effects of 2-methoxyethanol (ME) and 2-ethoxyethanol (EE) on hematological changes induced by 2-butoxyethanol (BE) in rats. Material and Methods: Experiments were performed on male Wistar rats treated subcutaneously with BE, ME, and EE alone (in the dose of 0.75 mM/kg/day and 1.25 mM/kg/day) and their mixtures with the molar ratio 1:1, for 4 weeks. Hematological analyses were performed on the day 0, 4, 11, 18, and 29. Hemoglobin (HGB) concentration in the urine was also determined in the rats treated with BE alone and co-exposed to BE and ME and also BE and EE. Results: The rats co-exposed to BE and ME or BE and EE demonstrated significantly less pronounced hematological changes in comparison with animals treated with BE alone at the beginning of exposure. At the later period the hematological alterations in the same animals were markedly pronounced and progressing with exposure time. The rats co-exposed to BE and ME or BE and EE did not demonstrate hemoglobinuria. Conclusions: ME or EE co-administered to rats with BE lead to the amelioration in the majority of the hematological parameters at the beginning of the exposure. The hematological changes at the end of the co-exposure to BE and ME or BE and EE were markedly pronounced. The effects observed in this study appear to be related with metabolic interactions of the examined ether. Med Pr 2015;66(3):303–31