Protein-Ion Binding Process on Finite Macromolecular Concentration. A Poisson-Boltzmann and Monte Carlo Study

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

pK determination. A mean field, Poisson-Boltzmann approach

A model describing dissociation of monoprotonic acid and a method for the determination of its pK value are presented. The model is based on a mean field approximation. The Poisson-Boltzmann equation, adopting spherical symmetry, is numerically solved, and the solution of its linearized form is written. By use of the pH values of a dilution experiment of galacturonic acid as the entry data, the proposed method allowed estimation of the value of pK = 3.25 at a temperature of 25 degrees C. Values for the complex dimensions and dissociation degree are calculated using experimental pH values for solution concentration values ranging from 0.1 to 60 mM. The present analysis leads to the conclusion that the Poisson-Boltzmann equation or its linear form is equally suited for the description of such systems.

Aplicação da equação de Paisson-Boltzmann com condição de contorno para regulação carga-potencial a sistemas polieletrolíticos

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Thermal fluctuations and boundary conditions in the lattice Boltzmann method

The lattice Boltzmann method is a popular approach for simulating hydrodynamic interactions in soft matter and complex fluids. The solvent is represented on a discrete lattice whose nodes are populated by particle distributions that propagate on the discrete links between the nodes and undergo local collisions. On large length and time scales, the microdynamics leads to a hydrodynamic flow field that satisfies the Navier-Stokes equation. In this thesis, several extensions to the lattice Boltzmann method are developed. In complex fluids, for example suspensions, Brownian motion of the solutes is of paramount importance. However, it can not be simulated with the original lattice Boltzmann method because the dynamics is completely deterministic. It is possible, though, to introduce thermal fluctuations in order to reproduce the equations of fluctuating hydrodynamics. In this work, a generalized lattice gas model is used to systematically derive the fluctuating lattice Boltzmann equation from statistical mechanics principles. The stochastic part of the dynamics is interpreted as a Monte Carlo process, which is then required to satisfy the condition of detailed balance. This leads to an expression for the thermal fluctuations which implies that it is essential to thermalize all degrees of freedom of the system, including the kinetic modes. The new formalism guarantees that the fluctuating lattice Boltzmann equation is simultaneously consistent with both fluctuating hydrodynamics and statistical mechanics. This establishes a foundation for future extensions, such as the treatment of multi-phase and thermal flows. An important range of applications for the lattice Boltzmann method is formed by microfluidics. Fostered by the "lab-on-a-chip" paradigm, there is an increasing need for computer simulations which are able to complement the achievements of theory and experiment. Microfluidic systems are characterized by a large surface-to-volume ratio and, therefore, boundary conditions are of special relevance. On the microscale, the standard no-slip boundary condition used in hydrodynamics has to be replaced by a slip boundary condition. In this work, a boundary condition for lattice Boltzmann is constructed that allows the slip length to be tuned by a single model parameter. Furthermore, a conceptually new approach for constructing boundary conditions is explored, where the reduced symmetry at the boundary is explicitly incorporated into the lattice model. The lattice Boltzmann method is systematically extended to the reduced symmetry model. In the case of a Poiseuille flow in a plane channel, it is shown that a special choice of the collision operator is required to reproduce the correct flow profile. This systematic approach sheds light on the consequences of the reduced symmetry at the boundary and leads to a deeper understanding of boundary conditions in the lattice Boltzmann method. This can help to develop improved boundary conditions that lead to more accurate simulation results.

Two dimensional Lattice Boltzmann simulation of fluid flow through an idealized micro-structure of disordered media

This technical report discusses the application of Lattice Boltzmann Method (LBM) in the fluid flow simulation through porous filter-wall of disordered media. The diesel particulate filter (DPF) is an example of disordered media. DPF is developed as a cutting edge technology to reduce harmful particulate matter in the engine exhaust. Porous filter-wall of DPF traps these soot particles in the after-treatment of the exhaust gas. To examine the phenomena inside the DPF, researchers are looking forward to use the Lattice Boltzmann Method as a promising alternative simulation tool. The lattice Boltzmann method is comparatively a newer numerical scheme and can be used to simulate fluid flow for single-component single-phase, single-component multi-phase. It is also an excellent method for modelling flow through disordered media. The current work focuses on a single-phase fluid flow simulation inside the porous micro-structure using LBM. Firstly, the theory concerning the development of LBM is discussed. LBM evolution is always related to Lattice gas Cellular Automata (LGCA), but it is also shown that this method is a special discretized form of the continuous Boltzmann equation. Since all the simulations are conducted in two-dimensions, the equations developed are in reference with D2Q9 (two-dimensional 9-velocity) model. The artificially created porous micro-structure is used in this study. The flow simulations are conducted by considering air and CO2 gas as fluids. The numerical model used in this study is explained with a flowchart and the coding steps. The numerical code is constructed in MATLAB. Different types of boundary conditions and their importance is discussed separately. Also the equations specific to boundary conditions are derived. The pressure and velocity contours over the porous domain are studied and recorded. The results are compared with the published work. The permeability values obtained in this study can be fitted to the relation proposed by Nabovati [8], and the results are in excellent agreement within porosity range of 0.4 to 0.8.

Carnot Cycles: Traditional and Stefan Boltzmann, and the First Planck Argument

The Stefan Boltzmann equation is obtained using a non-traditional Carnot Engine. In addition, the original Planck argument for radiation density is given.

Lattice Boltzmann method for flow and heat transfer in microgeometries

Recent technological developments have made it possible to design various microdevices where fluid flow and heat transfer are involved. For the proper design of such systems, the governing physics needs to be investigated. Due to the difficulty to study complex geometries in micro scales using experimental techniques, computational tools are developed to analyze and simulate flow and heat transfer in microgeometries. However, conventional numerical methods using the Navier-Stokes equations fail to predict some aspects of microflows such as nonlinear pressure distribution, increase mass flow rate, slip flow and temperature jump at the solid boundaries. This necessitates the development of new computational methods which depend on the kinetic theory that are both accurate and computationally efficient. In this study, lattice Boltzmann method (LBM) was used to investigate the flow and heat transfer in micro sized geometries. The LBM depends on the Boltzmann equation which is valid in the whole rarefaction regime that can be observed in micro flows. Results were obtained for isothermal channel flows at Knudsen numbers higher than 0.01 at different pressure ratios. LBM solutions for micro-Couette and micro-Poiseuille flow were found to be in good agreement with the analytical solutions valid in the slip flow regime (0.01 < Kn < 0.1) and direct simulation Monte Carlo solutions that are valid in the transition regime (0.1 < Kn < 10) for pressure distribution and velocity field. The isothermal LBM was further extended to simulate flows including heat transfer. The method was first validated for continuum channel flows with and without constrictions by comparing the thermal LBM results against accurate solutions obtained from analytical equations and finite element method. Finally, the capability of thermal LBM was improved by adding the effect of rarefaction and the method was used to analyze the behavior of gas flow in microchannels. The major finding of this research is that, the newly developed particle-based method described here can be used as an alternative numerical tool in order to study non-continuum effects observed in micro-electro-mechanical-systems (MEMS).

Lattice Boltzmann Method for Flow and Heat Transfer in Microgeometries

Recent technological developments have made it possible to design various microdevices where fluid flow and heat transfer are involved. For the proper design of such systems, the governing physics needs to be investigated. Due to the difficulty to study complex geometries in micro scales using experimental techniques, computational tools are developed to analyze and simulate flow and heat transfer in microgeometries. However, conventional numerical methods using the Navier-Stokes equations fail to predict some aspects of microflows such as nonlinear pressure distribution, increase mass flow rate, slip flow and temperature jump at the solid boundaries. This necessitates the development of new computational methods which depend on the kinetic theory that are both accurate and computationally efficient. In this study, lattice Boltzmann method (LBM) was used to investigate the flow and heat transfer in micro sized geometries. The LBM depends on the Boltzmann equation which is valid in the whole rarefaction regime that can be observed in micro flows. Results were obtained for isothermal channel flows at Knudsen numbers higher than 0.01 at different pressure ratios. LBM solutions for micro-Couette and micro-Poiseuille flow were found to be in good agreement with the analytical solutions valid in the slip flow regime (0.01 < Kn < 0.1) and direct simulation Monte Carlo solutions that are valid in the transition regime (0.1 < Kn < 10) for pressure distribution and velocity field. The isothermal LBM was further extended to simulate flows including heat transfer. The method was first validated for continuum channel flows with and without constrictions by comparing the thermal LBM results against accurate solutions obtained from analytical equations and finite element method. Finally, the capability of thermal LBM was improved by adding the effect of rarefaction and the method was used to analyze the behavior of gas flow in microchannels. The major finding of this research is that, the newly developed particle-based method described here can be used as an alternative numerical tool in order to study non-continuum effects observed in micro-electro-mechanical-systems (MEMS).

Spatially averaged model of complex-plasma discharge with self-consistent electron energy distribution

A global, or averaged, model for complex low-pressure argon discharge plasmas containing dust grains is presented. The model consists of particle and power balance equations taking into account power loss on the dust grains and the discharge wall. The electron energy distribution is determined by a Boltzmann equation. The effects of the dust and the external conditions, such as the input power and neutral gas pressure, on the electron energy distribution, the electron temperature, the electron and ion number densities, and the dust charge are investigated. It is found that the dust subsystem can strongly affect the stationary state of the discharge by dynamically modifying the electron energy distribution, the electron temperature, the creation and loss of the plasma particles, as well as the power deposition. In particular, the power loss to the dust grains can take up a significant portion of the input power, often even exceeding the loss to the wall.

A kinetic model for an argon plasma containing dust grains

A complex low-pressure argon discharge plasma containing dust grains is studied using a Boltzmann equation for the electrons and fluid equations for the ions. Local effects, such as the spatial distribution of the dust density and external electric field, are included, and their effect on the electron energy distribution, the electron and ion number densities, the electron temperature, and the dust charge are investigated. It is found that dust particles can strongly affect the plasma parameters by modifying the electron energy distribution, the electron temperature, the creation and loss of plasma particles, as well as the spatial distributions of the electrons and ions. In particular, for sufficiently high grain density and/or size, in a low-pressure argon glow discharge, the Druyvesteyn-like electron distribution in pristine plasmas can become nearly Maxwellian. Electron collection by the dust grains is the main cause for the change in the electron distribution function.

Dynamics of a dilute sheared inelastic fluid. II. The effect of correlations

The effect of correlations on the viscosity of a dilute sheared inelastic fluid is analyzed using the ring-kinetic equation for the two-particle correlation function. The leading-order contribution to the stress in an expansion in epsilon=(1-e)(1/2) is calculated, and it is shown that the leading-order viscosity is identical to that obtained from the Green-Kubo formula, provided the stress autocorrelation function in a sheared steady state is used in the Green-Kubo formula. A systemmatic extension of this to higher orders is also formulated, and the higher-order contributions to the stress from the ring-kinetic equation are determined in terms of the terms in the Chapman-Enskog solution for the Boltzmann equation. The series is resummed analytically to obtain a renormalized stress equation. The most dominant contributions to the two-particle correlation function are products of the eigenvectors of the conserved hydrodynamic modes of the two correlated particles. In Part I, it was shown that the long-time tails of the velocity autocorrelation function are not present in a sheared fluid. Using those results, we show that correlations do not cause a divergence in the transport coefficients; the viscosity is not divergent in two dimensions, and the Burnett coefficients are not divergent in three dimensions. The equations for three-particle and higher correlations are analyzed diagrammatically. It is found that the contributions due to the three-particle and higher correlation functions to the renormalized viscosity are smaller than those due to the two-particle distribution function in the limit epsilon -> 0. This implies that the most dominant correlation effects are due to the two-particle correlations.

Electron attachment in binary mixtures of electronegative and buffer gases

The ratio of the electron attachment coefficient eta to the gas pressure p (reduced to 0 degrees C) evaluated from the Townsend current growth curves in binary mixtures of electronegative gases (SF6, CCl2F2, CO2) and buffer gases (N2, Ar, air) clearly indicate that the eta /p ratios do not scale as the partial pressure of electronegative gas in the mixture. Extensive calculations carried out using data experimentally obtained have shown that the attachment coefficient of the mixture eta mix can be expressed as eta mix= eta (1-exp- beta F/(100-F)) where eta is the attachment coefficient of the 100% electronegative gas, F is the percentage of the electronegative gas in the mixture and beta is a constant. The results of this analysis explain to a high degree of accuracy the data obtained in various mixtures and are in very good agreement with the data deduced by Itoh and co-workers (1980) using the Boltzmann equation method.

Multicarrier analysis of magnetotransport data at low and high electric fields

We present some results on multicarrier analysis of magnetotransport data, Both synthetic as well as data from narrow gap Hg0.8Cd0.2Te samples are used to demonstrate applicability of various algorithms vs. nonlinear least square fitting, Quantitative Mobility Spectrum Analysis (QMSA) and Maximum Entropy Mobility Spectrum Analysis (MEMSA). Comments are made from our experience oil these algorithms, and, on the inversion procedure from experimental R/sigma-B to S-mu specifically with least square fitting as an example. Amongst the conclusions drawn are: (i) Experimentally measured resistivity (R-xx, R-xy) should also be used instead of just the inverted conductivity (sigma(xx), sigma(xy)) to fit data to semiclassical expressions for better fits especially at higher B. (ii) High magnetic field is necessary to extract low mobility carrier parameters. (iii) Provided the error in data is not large, better estimates to carrier parameters of remaining carrier species can be obtained at any stage by subtracting highest mobility carrier contribution to sigma from the experimental data and fitting with the remaining carriers. (iv)Even in presence of high electric field, an approximate multicarrier expression can be used to guess the carrier mobilities and their variations before solving the full Boltzmann equation.

Rheology of dense sheared granular flows

Rapid granular flows are defined as flows in which the time scales for the particle interactions are small compared to the inverse of the strain rate, so that the particle interactions can be treated as instantaneous collisions. We first show, using Discrete Element simulations, that even very dense flows of sand or glass beads with volume fraction between 0.5 and 0.6 are rapid granular flows. Since collisions are instantaneous, a kinetic theory approach for the constitutive relations is most appropriate, and we present kinetic theory results for different microscopic models for particle interaction. The significant difference between granular flows and normal fluids is that energy is not conserved in a granular flow. The differences in the hydrodynamic modes caused by the non-conserved nature of energy are discussed. Going beyond the Boltzmann equation, the effect of correlations is studied using the ring kinetic approximation, and it is shown that the divergences in the viscometric coefficients, which are present for elastic fluids, are not present for granular flows because energy is not conserved. The hydrodynamic model is applied to the flow down an inclined plane. Since energy is not a conserved variable, the hydrodynamic fields in the bulk of a granular flow are obtained from the mass and momentum conservation equations alone. Energy becomes a relevant variable only in thin 'boundary layers' at the boundaries of the flow where there is a balance between the rates of conduction and dissipation. We show that such a hydrodynamic model can predict the salient features of a chute flow, including the flow initiation when the angle of inclination is increased above the 'friction angle', the striking lack of observable variation of the volume fraction with height, the observation of a steady flow only for certain restitution coefficients, and the density variations in the boundary layers.

Coherent quasiparticle approximation cQPA and nonlocal coherence

We show that the dynamical Wigner functions for noninteracting fermions and bosons can have complex singularity structures with a number of new solutions accompanying the usual mass-shell dispersion relations. These new shell solutions are shown to encode the information of the quantum coherence between particles and antiparticles, left and right moving chiral states and/or between different flavour states. Analogously to the usual derivation of the Boltzmann equation, we impose this extended phase space structure on the full interacting theory. This extension of the quasiparticle approximation gives rise to a self-consistent equation of motion for a density matrix that combines the quantum mechanical coherence evolution with a well defined collision integral giving rise to decoherence. Several applications of the method are given, for example to the coherent particle production, electroweak baryogenesis and study of decoherence and thermalization.