Browsing by Subject "MD simulation"
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Item How trehalose protects DNA in the dry state: a molecular dynamics simulation(Texas A&M University, 2008-10-10) Fu, XuebingMolecular dynamics simulations were conducted on a system consisting of a decamer DNA solvated by trehalose and water (molecular ratio= 1:2), to mimic a relatively dry state for the DNA molecule. Simulations were performed at two different temperatures, 300 K and 450 K. The B-form DNA structure was shown to be stable at both temperatures. The analysis of hydrogen bonds between trehalose/water and DNA revealed that trehalose and backbone DNA formed the largest number of hydrogen bonds and thus constituted the major effect of structural protection for DNA. The number of hydrogen bonds formed by each OH group of trehalose with the backbone DNA was compared. Different types of trehalose-DNA interactions were analyzed, with no prevalent pattern recognized. Diffusion constants for trehalose and water were also calculated, suggesting a glassy/viscose state of the simulation system. It is believed that trehalose protects DNA in the dry state through the network of hydrogen bonds built by the sugars, which reduces the structural fluctuations of DNA and prevents its denaturation.Item Molecular Simulation Study of Diverting Materials Used in Matrix Acidizing(2010-10-12) Sultan, Abdullah S.Recently there has been a great deal of attention in the oilfield industry focused on the phenomenal properties of viscoelastic surfactants (VES). The interest is motivated by their applications as switchable smart fluids, their surface tension, and their thickening and rheology enhancement in aqueous solution. Surfactant molecules in solution are known for their ability to assemble spontaneously into complex structures. Under certain thermodynamic conditions, temperature and electrolyte concentrations, wormlike micelles are formed. These micelles share similar equilibrium and dynamic properties with polymer solutions, However, micellar chains can break and recombine spontaneously which make them part of the more general class of living polymers. It is vital to understand the properties of viscoelastic wormlike micelles with regard to their flow in porous media. The overall objective of this study is to establish a better understanding of counterion effect on behavior of VES. The dependence of macroscopic properties on intermolecular interactions of complex fluid systems such as VES is an enormous challenge. To achieve our objective, we use first-principle calculations and molecular dynamics (MD) simulations to resolve the full chemical details in order to study how the structure of the micellar and solution properties depends on the chemical structure of the surfactant head group (HG) and type of counterion. In particular, we run simulations for different structures in gas-phase and aqueous solutions together with their salt counterions at room temperature and atmospheric pressure. For this purpose, we consider four types of surfactant HG (anionic, cationic, betaine and amidoamine oxide) together with the most common ions present in the acidizing fluid of a carbonate reservoir such as Ca2+, Mg2+, Fe2+, Fe3+, Mn2+ and Zn2+, Cl-, OH- and HS-. Hydration of ions as well as interactions with surfactant the HG are studied using density functional theory (DFT). The results give important insight into the links between molecular details of VES HG structure and observed solution properties. This study proposes for the first time the possible mechanisms that explain the exotic behavior of VES at high Fe(III) concentration. Also, our MD simulation suggests that distribution of chloride ion around surfactant molecules is responsible for their viscosity behavior in HCl solution. We believe that our results are an important step to develop more systematic procedures for the molecular design and formulation of more effective and efficient VES systems.Item Numerical Investigation of the Effect of Chirality of Carbon Nanotube on the Interfacial Thermal Resistance(2014-06-05) Hu, YuzhuConcentrated Solar Power (CSP) systems are used widely as a stable and reliable renewable source of energy. However, intermittency of this power source and the variability in demand for electrical power creates challenges that necessitate the integration with energy storage for reliable dispatch of power. Thermal Energy Storage (TES) systems provide a cheap, cost-effective and reliable option for energy storage in renewable power delivery systems. Due to their low vapor pressures at elevated temperatures, molten salts and their eutectics are used in conventional high temperature thermal energy storage (TES) systems and also as coolants for energy conversion, such as in power tower configurations that are typically used in CSP applications. A major drawback of the molten salts is their relatively poor thermo-physical properties, which may lead to lower systemic efficiencies in CSP/TES. Recent reports in the literature have shown that doping molten salts with nanoparticles at minute concentrations (typically less than 5% mass fraction and ideally at less than 1-2% mass fraction) can significantly enhance the thermo-physical properties of these nanomaterial (also termed as ?nanocomposites? in solid state and ?nanofluids? in liquid state). The dominant factor that controls the resultant thermo-physical properties of these nanomaterials is the interfacial thermal resistance (or Kapitza Resistance ?R_(k)?) that impedes the heat transfer between the nanoparticle surface and the bulk solvent molecules. In this study, the interfacial thermal resistance between a carbon nanotube (CNT) and carbonate molten salt eutectics were calculated by using numerical models that were then implemented in Molecular Dynamics (MD) simulations. The estimates for ?R_(k)? obtained from these simulations enabled the prediction of the optimum dimensions of the nanoparticles for maximizing the thermo-physical properties of the mixture, i.e. thermal conductivity and specific heat capacity values of these nanomaterial. The simulations were restricted to the carbonate salt eutectic, which is composed of a molar ratio of 62:38 for lithium carbonate (Li_(2)CO_(3)) and potassium carbonate (K_(2)CO_(3)). In this study, parametric simulations were performed to estimate the values of ?R_(k)? by varying the chirality of a single walled CNT (i.e, for armchair, chiral, and zig-zag CNT). The results show that the Kapitza resistance of the CNT is significantly affected by the change in the chirality of the CNT.Item Protein dynamics in sequence and conformational spaces(2016-08) Chen, Szu-Hua; Elber, Ron; Ren, Pengyu; Johnson, Kenneth A.; Ellington, Andrew; Makarov, Dmitrii E.Proteins are biological macromolecules that are involved in a wide range of cellular processes. The diverse functions of proteins are closely related to their dynamics and structures. Structures are frequently coded in a complex manner in the amino acid sequences. In this dissertation I discuss the dynamics of a special class of proteins through studies of their sequences and structures. These proteins are “switches,” which are made of highly similar sequences that fold to dramatically different structures. The existence of protein switches provides a great challenge to structure prediction algorithms as well as to our understanding of the process of protein structure evolution. To identify protein switches, we developed methods that assign switch sequences to structures with high accuracy. One method uses short MD simulations to enrich structural ensembles of protein switches in the neighborhood of their initial conformations for scoring by contact maps. The other method uses evolutionary profiles and contact maps of the wild-type proteins. Both methods were first tested against a series of experimentally engineered proteins in a switching system and then applied to examine a large number of computationally sampled protein switches for a particular pair of structures in sequence space. From the sampled switch sequences we found that making a point mutation near the N- and C-termini of the sequences is more likely to make the proteins switch between structures. To study the conformational change of a protein switch with a fixed sequence between two metastable states in conformational space, we proposed a new algorithm, named “Chain Growth”, to calculate reaction pathways. Unlike commonly used methods that require an initial guess of a path and minimize the energy of the path by local quenching, our method propagates the path in small segments and optimizes the whole path globally. These features avoid the problems of generating very distorted initial structures that other methods frequently encounter and allow more efficient minimization of the path. We provided computational examples of using Chain Growth to calculate the minimum energy path on the Müller potential energy surface as well as to the studies of conformational changes of alanine dipeptide and folding of tryptophan zipper.