Currently the treatment of alcohol use disorder is very difficult and often requires the combination of therapy and medications, with many who undertake treatment experiencing relapse over time. There is also no treatment in use to prevent the development of alcohol use disorder. It is the aim of this work to provide information that may be useful for the development of a preventative treatment for developing alcohol use disorder by elucidating more of the acute effects of alcohol use. It is known that these effects originate in the brain. Within the brain are circuits made up of neurons that communicate with each other through chemical synapses. These chemical synapses involve the release of neurotransmitters from one neuron that are detected by another neuron, which initiates its own response. It is known that ethanol can change how much neurotransmitter is released from a neuron, depending on the specific neuron tested, and many researchers have implicated the "release machinery" as a target. It is also known that alcohol can affect lipid membrane properties that are important for the fusion of the vesicle membrane, encapsulating the neurotransmitter, with the cell membrane for release of the neurotransmitter outside of the neuron. It is not known if alcohol directly affects the SNARE proteins ("release machinery") or the lipid membranes to initiate the change in neurotransmitter release previously observed. Within this work you will find a discussion of the steps of neurotransmitter release and the known effects of anesthetics on components of this process, as an introduction to the topic (Chapters 1 and 2). In Chapters 3-5 you will find studies that successively dive deeper and deeper into the effects of alcohol on the SNARE proteins and lipid membranes. We show that ethanol is effective at a dose of 0.4% v/v or 64 mM at increasing fusion probability in a model of neurotransmitter release that uses the 3 SNARE proteins to drive fusion of a vesicle with a supported membrane. We also show that alcohol has little direct effect on the SNARE proteins themselves. In addition, we provide evidence that alcohol alters fusion oppositely, depending on which membrane leaflet it has most direct access to. In Chapter 5 we show that alcohol increases the probability of lipid tail protrusion in silico. Previously it has been shown that protrusion of one fatty acid tail of one lipid can initiate fusion of that membrane with an apposing membrane. These data provide further insight into the effects of alcohol on a neuron and we would argue are valuable to research pursuing treatment and prevention of alcohol use disorder.

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The transport of a biomolecule through a nanopore occurs in many biological functions such as, DNA or RNA transport across nuclear pores and the translocation of proteins across the eukaryotic endoplasmic reticulum. In addition to the biological processes, it has potential applications in technology such as, drug delivery, gene therapy, and single molecule sensing. The DNA translocation through a synthetic nanopore device is considered as the basis for cheap and fast sequencing technology. Motivated by the experimental advances, many theoretical models have been developed. In this thesis, we explore the dynamics of driven translocation of a semiflexible polymer through a nanopore in two dimensions (2D) using Langevin dynamics (LD) simulation. By carrying out extensive simulation as a function of different parameters such as, driving force, length and rigidity of the chain, viscosity of the solvent, and diameter of the nanopore, we provide a detailed description of the translocation process. Our studies are relevant for fundamental understanding of the translocation process which is essential for making accurate nano-pore based devices.

Most of the computer simulations of molecules in Metal-Organic Frameworks (MOFs) to be found in the literature are done with rigid framework. But, Molecular Dynamics (MD) simulations of the self-diffusivity, Ds, of ethane within the one-dimensional 4.5 Å channels of the MOF type Zn(tbip)(H2 tbip = 5-tert-butyl isophthalic acid) presented in this work have shown not only quantitative, but also qualitative, differences in the Ds values for fixed and flexible lattices. Particularly, the dependence of Ds upon the concentration of molecules, c, is strongly influenced by the lattice flexibility. The reasons for this influence are investigated with the aid of probability density plots, free energy landscapes and barriers, along with a determination of the structural changes accompanying increasing c. It is found that for flexible lattices, the tighter, more constrained parts of the channels become wider at higher c; this allows more molecules to diffuse in the central region of the channels. The investigations for Zn(tbip) have been extended to three equimolar mixtures of ethane/ethane, CO2/ethane and CO2/methanol. The simulations take into account the lattice flexibility. The diffusional characteristics are discussed in relation to molecule properties and lattice geometry. The results show that Zn(tbip) may be a useful material for separating methane/ethane and CO2/ethane mixtures at low concentrations, and CO2/methanol mixtures at high concentrations. The temperature and concentration dependence of the self-diffusivity of propane diffusion in Zn(tbip) have been investigated as well by performing normal MD and hyper-MD with bias potential simulations. The obtained temperature dependence of the self-diffusivities is analyzed using an Arrhenius relationship, yielding the activation energy to be 9.53 kJ/mol and the pre-exponential factor to be 4.48×10-9 m2s-1. Using this hyper-MD method, interesting mechanisms of the propane molecules able to pass each other and exchange their sites in the channels can be observed. Because of mutual hindrance of propane molecules, the propane self-diffusivities decrease with increasing concentration.

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Most of the computer simulations of molecules in Metal-Organic Frameworks (MOFs) to be found in the literature are done with rigid framework. But, Molecular Dynamics (MD) simulations of the self-diffusivity, Ds, of ethane within the one-dimensional 4.5 Å channels of the MOF type Zn(tbip)(H2 tbip = 5-tert-butyl isophthalic acid) presented in this work have shown not only quantitative, but also qualitative, differences in the Ds values for fixed and flexible lattices. Particularly, the dependence of Ds upon the concentration of molecules, c, is strongly influenced by the lattice flexibility. The reasons for this influence are investigated with the aid of probability density plots, free energy landscapes and barriers, along with a determination of the structural changes accompanying increasing c. It is found that for flexible lattices, the tighter, more constrained parts of the channels become wider at higher c; this allows more molecules to diffuse in the central region of the channels. The investigations for Zn(tbip) have been extended to three equimolar mixtures of ethane/ethane, CO2/ethane and CO2/methanol. The simulations take into account the lattice flexibility. The diffusional characteristics are discussed in relation to molecule properties and lattice geometry. The results show that Zn(tbip) may be a useful material for separating methane/ethane and CO2/ethane mixtures at low concentrations, and CO2/methanol mixtures at high concentrations. The temperature and concentration dependence of the self-diffusivity of propane diffusion in Zn(tbip) have been investigated as well by performing normal MD and hyper-MD with bias potential simulations. The obtained temperature dependence of the self-diffusivities is analyzed using an Arrhenius relationship, yielding the activation energy to be 9.53 kJ/mol and the pre-exponential factor to be 4.48×10-9 m2s-1. Using this hyper-MD method, interesting mechanisms of the propane molecules able to pass each other and exchange their sites in the channels can be observed. Because of mutual hindrance of propane molecules, the propane self-diffusivities decrease with increasing concentration.

No description available.

No description available.