Monte Carlo and molecular dynamics simulations of methane in potassium montmorillonite clay hydrates at elevated pressures and temperatures

The structure and dynamics of methane in hydrated potassium montmorillonite clay have been studied under conditions encountered in sedimentary basin and compared to those of hydrated sodium montmorillonite clay using computer simulation techniques. The simulated systems contain two molecular layers of water and followed gradients of 150 barkm-1 and 30 Kkm-1 up to a maximum burial depth of 6 km. Methane particle is coordinated to about 19 oxygen atoms, with 6 of these coming from the clay surface oxygen. Potassium ions tend to move away from the center towards the clay surface, in contrast to the behavior observed with the hydrated sodium form. The clay surface affinity for methane was found to be higher in the hydrated K-form. Methane diffusion in the two-layer hydrated K-montmorillonite increases from 0.39×10-9 m2s-1 at 280 K to 3.27×10-9 m2s-1 at 460 K compared to 0.36×10-9 m2s-1 at 280 K to 4.26×10-9 m2s-1 at 460 K in Na-montmorillonite hydrate. The distributions of the potassium ions were found to vary in the hydrates when compared to those of sodium form. Water molecules were also found to be very mobile in the potassium clay hydrates compared to sodium clay hydrates. © 2004 Elsevier Inc. All All rights reserved.

Histidine hydrogen bonding in MHC at pH 5 and pH 7 modeled by molecular docking and molecular dynamics simulations

Hydrogen bonds play important roles in maintaining the structure of proteins and in the formation of most biomolecular protein-ligand complexes. All amino acids can act as hydrogen bond donors and acceptors. Among amino acids, Histidine is unique, as it can exist in neutral or positively charged forms within the physiological pH range of 5.0 to 7.0. Histidine can thus interact with other aromatic residues as well as forming hydrogen bonds with polar and charged residues. The ability of His to exchange a proton lies at the heart of many important functional biomolecular interactions, including immunological ones. By using molecular docking and molecular dynamics simulation, we examine the influence of His protonation/deprotonation on peptide binding affinity to MHC class II proteins from locus HLA-DP. Peptide-MHC interaction underlies the adaptive cellular immune response, upon which the next generation of commercially-important vaccines will depend. Consistent with experiment, we find that peptides containing protonated His residues bind better to HLA-DP proteins than those with unprotonated His. Enhanced binding at pH 5.0 is due, in part, to additional hydrogen bonds formed between peptide His+ and DP proteins. In acidic endosomes, protein His79β is predominantly protonated. As a result, the peptide binding cleft narrows in the vicinity of His79β, which stabilizes the peptide - HLA-DP protein complex. © 2014 Bentham Science Publishers.

Ground and Electronic Excited States from Pairing Matrix Fluctuation and Particle-Particle Random Phase Approximation

The accurate description of ground and electronic excited states is an important and challenging topic in quantum chemistry. The pairing matrix fluctuation, as a counterpart of the density fluctuation, is applied to this topic. From the pairing matrix fluctuation, the exact electron correlation energy as well as two electron addition/removal energies can be extracted. Therefore, both ground state and excited states energies can be obtained and they are in principle exact with a complete knowledge of the pairing matrix fluctuation. In practice, considering the exact pairing matrix fluctuation is unknown, we adopt its simple approximation --- the particle-particle random phase approximation (pp-RPA) --- for ground and excited states calculations. The algorithms for accelerating the pp-RPA calculation, including spin separation, spin adaptation, as well as an iterative Davidson method, are developed. For ground states correlation descriptions, the results obtained from pp-RPA are usually comparable to and can be more accurate than those from traditional particle-hole random phase approximation (ph-RPA). For excited states, the pp-RPA is able to describe double, Rydberg, and charge transfer excitations, which are challenging for conventional time-dependent density functional theory (TDDFT). Although the pp-RPA intrinsically cannot describe those excitations excited from the orbitals below the highest occupied molecular orbital (HOMO), its performances on those single excitations that can be captured are comparable to TDDFT. The pp-RPA for excitation calculation is further applied to challenging diradical problems and is used to unveil the nature of the ground and electronic excited states of higher acenes. The pp-RPA and the corresponding Tamm-Dancoff approximation (pp-TDA) are also applied to conical intersections, an important concept in nonadiabatic dynamics. Their good description of the double-cone feature of conical intersections is in sharp contrast to the failure of TDDFT. All in all, the pairing matrix fluctuation opens up new channel of thinking for quantum chemistry, and the pp-RPA is a promising method in describing ground and electronic excited states.

Bridging the Scale Gap from Leaf to Canopy in Biosphere-Atmosphere Gas and Particle Exchanges

Terrestrial ecosystems, occupying more than 25% of the Earth's surface, can serve as

`biological valves' in regulating the anthropogenic emissions of atmospheric aerosol

particles and greenhouse gases (GHGs) as responses to their surrounding environments.

While the signicance of quantifying the exchange rates of GHGs and atmospheric

aerosol particles between the terrestrial biosphere and the atmosphere is

hardly questioned in many scientic elds, the progress in improving model predictability,

data interpretation or the combination of the two remains impeded by

the lack of precise framework elucidating their dynamic transport processes over a

wide range of spatiotemporal scales. The diculty in developing prognostic modeling

tools to quantify the source or sink strength of these atmospheric substances

can be further magnied by the fact that the climate system is also sensitive to the

feedback from terrestrial ecosystems forming the so-called `feedback cycle'. Hence,

the emergent need is to reduce uncertainties when assessing this complex and dynamic

feedback cycle that is necessary to support the decisions of mitigation and

adaptation policies associated with human activities (e.g., anthropogenic emission

controls and land use managements) under current and future climate regimes.

With the goal to improve the predictions for the biosphere-atmosphere exchange

of biologically active gases and atmospheric aerosol particles, the main focus of this

dissertation is on revising and up-scaling the biotic and abiotic transport processes

from leaf to canopy scales. The validity of previous modeling studies in determining

iv

the exchange rate of gases and particles is evaluated with detailed descriptions of their

limitations. Mechanistic-based modeling approaches along with empirical studies

across dierent scales are employed to rene the mathematical descriptions of surface

conductance responsible for gas and particle exchanges as commonly adopted by all

operational models. Specically, how variation in horizontal leaf area density within

the vegetated medium, leaf size and leaf microroughness impact the aerodynamic attributes

and thereby the ultrane particle collection eciency at the leaf/branch scale

is explored using wind tunnel experiments with interpretations by a porous media

model and a scaling analysis. A multi-layered and size-resolved second-order closure

model combined with particle

uxes and concentration measurements within and

above a forest is used to explore the particle transport processes within the canopy

sub-layer and the partitioning of particle deposition onto canopy medium and forest

oor. For gases, a modeling framework accounting for the leaf-level boundary layer

eects on the stomatal pathway for gas exchange is proposed and combined with sap

ux measurements in a wind tunnel to assess how leaf-level transpiration varies with

increasing wind speed. How exogenous environmental conditions and endogenous

soil-root-stem-leaf hydraulic and eco-physiological properties impact the above- and

below-ground water dynamics in the soil-plant system and shape plant responses

to droughts is assessed by a porous media model that accommodates the transient

water

ow within the plant vascular system and is coupled with the aforementioned

leaf-level gas exchange model and soil-root interaction model. It should be noted

that tackling all aspects of potential issues causing uncertainties in forecasting the

feedback cycle between terrestrial ecosystem and the climate is unrealistic in a single

dissertation but further research questions and opportunities based on the foundation

derived from this dissertation are also brie

y discussed.

Level-resolved quantum statistical theory of electron capture into many-electron compound resonances in highly charged ions

The strong mixing of many-electron basis states in excited atoms and ions with open f shells results in very large numbers of complex, chaotic eigenstates that cannot be computed to any degree of accuracy. Describing the processes which involve such states requires the use of a statistical theory. Electron capture into these “compound resonances” leads to electron-ion recombination rates that are orders of magnitude greater than those of direct, radiative recombination and cannot be described by standard theories of dielectronic recombination. Previous statistical theories considered this as a two-electron capture process which populates a pair of single-particle orbitals, followed by “spreading” of the two-electron states into chaotically mixed eigenstates. This method is similar to a configuration-average approach because it neglects potentially important effects of spectator electrons and conservation of total angular momentum. In this work we develop a statistical theory which considers electron capture into “doorway” states with definite angular momentum obtained by the configuration interaction method. We apply this approach to electron recombination with W²⁰⁺, considering 2×10⁶ doorway states. Despite strong effects from the spectator electrons, we find that the results of the earlier theories largely hold. Finally, we extract the fluorescence yield (the probability of photoemission and hence recombination) by comparison with experiment.

Simulation of Oil Shale Semi-Coke Particle Cold Transportation in a Spouted Bed Using CPFD Method

The spouted bed was widely used due to its good mixing of particles and effective phase transferability between the gas and solid phase. In this paper, the transportation process of particles in a 3D spouted bed was studied using the Computational Particle Fluid Dynamics (CPFD) numerical method. Experiments were conducted to verify the validity of the simulation results. Distributions of the pressure, velocities and particle concentration of transportation devices were investigated. The motion state and characteristics of multiphase flows in the transportation device were demonstrated under various operating conditions. The results showed that a good consistency was obtained between the simulated results and the experimental results. The motion characteristics of the gas-solid two-phase flow in the device was effectively predicted, which could assist the optimal operating condition estimation for the spouted transportation process.

Photochemical dynamics of laser-irradiated semiconductor nanostructures

Thesis (Ph.D.)--University of Washington, 2016-08

Holographic Tools for Probing the Dynamics of Strongly Coupled Field Theories

Thesis (Ph.D.)--University of Washington, 2016-08

Ionisation and discharge in cloud-forming atmospheres of brown dwarfs and extrasolar planets

Brown dwarfs and giant gas extrasolar planets have cold atmospheres with rich chemical compositions from which mineral cloud particles form. Their properties, like particle sizes and material composition, vary with height, and the mineral cloud particles are charged due to triboelectric processes in such dynamic atmospheres. The dynamics of the atmospheric gas is driven by the irradiating host star and/or by the rotation of the objects that changes during its lifetime. Thermal gas ionisation in these ultra-cool but dense atmospheres allows electrostatic interactions and magnetic coupling of a substantial atmosphere volume. Combined with a strong magnetic field , a chromosphere and aurorae might form as suggested by radio and x-ray observations of brown dwarfs. Non-equilibrium processes like cosmic ray ionisation and discharge processes in clouds will increase the local pool of free electrons in the gas. Cosmic rays and lighting discharges also alter the composition of the local atmospheric gas such that tracer molecules might be identified. Cosmic rays affect the atmosphere through air showers in a certain volume which was modelled with a 3D Monte Carlo radiative transfer code to be able to visualise their spacial extent. Given a certain degree of thermal ionisation of the atmospheric gas, we suggest that electron attachment to charge mineral cloud particles is too inefficient to cause an electrostatic disruption of the cloud particles. Cloud particles will therefore not be destroyed by Coulomb explosion for the local temperature in the collisional dominated brown dwarf and giant gas planet atmospheres. However, the cloud particles are destroyed electrostatically in regions with strong gas ionisation. The potential size of such cloud holes would, however, be too small and might occur too far inside the cloud to mimic the effect of, e.g. magnetic field induced star spots.

Shape and chemically anisotropic colloidal particles: A theoretical study of their structure, phase behavior, and slow dynamics

A detailed non-equilibrium state diagram of shape-anisotropic particle fluids is constructed. The effects of particle shape are explored using Naive Mode Coupling Theory (NMCT), and a single particle Non-linear Langevin Equation (NLE) theory. The dynamical behavior of non-ergodic fluids are discussed. We employ a rotationally frozen approach to NMCT in order to determine a transition to center of mass (translational) localization. Both ideal and kinetic glass transitions are found to be highly shape dependent, and uniformly increase with particle dimensionality. The glass transition volume fraction of quasi 1- and 2- dimensional particles fall monotonically with the number of sites (aspect ratio), while 3-dimensional particles display a non-monotonic dependence of glassy vitrification on the number of sites. Introducing interparticle attractions results in a far more complex state diagram. The ideal non-ergodic boundary shows a glass-fluid-gel re-entrance previously predicted for spherical particle fluids. The non-ergodic region of the state diagram presents qualitatively different dynamics in different regimes. They are qualified by the different behaviors of the NLE dynamic free energy. The caging dominated, repulsive glass regime is characterized by long localization lengths and barrier locations, dictated by repulsive hard core interactions, while the bonding dominated gel region has short localization lengths (commensurate with the attraction range), and barrier locations. There exists a small region of the state diagram which is qualified by both glassy and gel localization lengths in the dynamic free energy. A much larger (high volume fraction, and high attraction strength) region of phase space is characterized by short gel-like localization lengths, and long barrier locations. The region is called the attractive glass and represents a 2-step relaxation process whereby a particle first breaks attractive physical bonds, and then escapes its topological cage. The dynamic fragility of fluids are highly particle shape dependent. It increases with particle dimensionality and falls with aspect ratio for quasi 1- and 2- dimentional particles. An ultralocal limit analysis of the NLE theory predicts universalities in the behavior of relaxation times, and elastic moduli. The equlibrium phase diagram of chemically anisotropic Janus spheres and Janus rods are calculated employing a mean field Random Phase Approximation. The calculations for Janus rods are corroborated by the full liquid state Reference Interaction Site Model theory. The Janus particles consist of attractive and repulsive regions. Both rods and spheres display rich phase behavior. The phase diagrams of these systems display fluid, macrophase separated, attraction driven microphase separated, repulsion driven microphase separated and crystalline regimes. Macrophase separation is predicted in highly attractive low volume fraction systems. Attraction driven microphase separation is charaterized by long length scale divergences, where the ordering length scale determines the microphase ordered structures. The ordering length scale of repulsion driven microphase separation is determined by the repulsive range. At the high volume fractions, particles forgo the enthalpic considerations of attractions and repulsions to satisfy hard core constraints and maximize vibrational entropy. This results in site length scale ordering in rods, and the sphere length scale ordering in Janus spheres, i.e., crystallization. A change in the Janus balance of both rods and spheres results in quantitative changes in spinodal temperatures and the position of phase boundaries. However, a change in the block sequence of Janus rods causes qualitative changes in the type of microphase ordered state, and induces prominent features (such as the Lifshitz point) in the phase diagrams of these systems. A detailed study of the number of nearest neighbors in Janus rod systems reflect a deep connection between this local measure of structure, and the structure factor which represents the most global measure of order.

Exotic dynamics in a firing rate model of neural tissue with threshold accommodation

Many of the equations describing the dynamics of neural systems are written in terms of firing rate functions, which themselves are often taken to be threshold functions of synaptic activity. Dating back to work by Hill in 1936 it has been recognized that more realistic models of neural tissue can be obtained with the introduction of state-dependent dynamic thresholds. In this paper we treat a specific phenomenological model of threshold accommodation that mimics many of the properties originally described by Hill. Importantly we explore the consequences of this dynamic threshold at the tissue level, by modifying a standard neural field model of Wilson-Cowan type. As in the case without threshold accommodation classical Mexican-Hat connectivity is shown to allow for the existence of spatially localized states (bumps) in both one and two dimensions. Importantly an analysis of bump stability in one dimension, using recent Evans function techniques, shows that bumps may undergo instabilities leading to the emergence of both breathers and traveling waves. Moreover, a similar analysis for traveling pulses leads to the conditions necessary to observe a stable traveling breather. In the regime where a bump solution does not exist direct numerical simulations show the possibility of self-replicating bumps via a form of bump splitting. Simulations in two space dimensions show analogous localized and traveling solutions to those seen in one dimension. Indeed dynamical behavior in this neural model appears reminiscent of that seen in other dissipative systems that support localized structures, and in particular those of coupled cubic complex Ginzburg-Landau equations. Further numerical explorations illustrate that the traveling pulses in this model exhibit particle like properties, similar to those of dispersive solitons observed in some three component reaction-diffusion systems. A preliminary account of this work first appeared in S Coombes and M R Owen, Bumps, breathers, and waves in a neural network with spike frequency adaptation, Physical Review Letters 94 (2005), 148102(1-4).