Electrokinetic Lattice Boltzmann solver coupled to Molecular Dynamics: application to polymer translocation

We develop a theoretical and computational approach to deal with systems that involve a disparate range of spatio-temporal scales, such as those comprised of colloidal particles or polymers moving in a fluidic molecular environment. Our approach is based on a multiscale modeling that combines the slow dynamics of the large particles with the fast dynamics of the solvent into a unique framework. The former is numerically solved via Molecular Dynamics and the latter via a multi-component Lattice Boltzmann. The two techniques are coupled together to allow for a seamless exchange of information between the descriptions. Being based on a kinetic multi-component description of the fluid species, the scheme is flexible in modeling charge flow within complex geometries and ranging from large to vanishing salt concentration. The details of the scheme are presented and the method is applied to the problem of translocation of a charged polymer through a nanopores. In the end, we discuss the advantages and complexities of the approach

Variational Methods for Biomolecular Modeling

Structure, function and dynamics of many biomolecular systems can be characterized by the energetic variational principle and the corresponding systems of partial differential equations (PDEs). This principle allows us to focus on the identification of essential energetic components, the optimal parametrization of energies, and the efficient computational implementation of energy variation or minimization. Given the fact that complex biomolecular systems are structurally non-uniform and their interactions occur through contact interfaces, their free energies are associated with various interfaces as well, such as solute-solvent interface, molecular binding interface, lipid domain interface, and membrane surfaces. This fact motivates the inclusion of interface geometry, particular its curvatures, to the parametrization of free energies. Applications of such interface geometry based energetic variational principles are illustrated through three concrete topics: the multiscale modeling of biomolecular electrostatics and solvation that includes the curvature energy of the molecular surface, the formation of microdomains on lipid membrane due to the geometric and molecular mechanics at the lipid interface, and the mean curvature driven protein localization on membrane surfaces. By further implicitly representing the interface using a phase field function over the entire domain, one can simulate the dynamics of the interface and the corresponding energy variation by evolving the phase field function, achieving significant reduction of the number of degrees of freedom and computational complexity. Strategies for improving the efficiency of computational implementations and for extending applications to coarse-graining or multiscale molecular simulations are outlined.Comment: 36 page

Computational fluid dynamic modeling of fluidized bed polymerization reactors

Polyethylene is one of the most widely used plastics, and over 60 million tons are produced worldwide every year. Polyethylene is obtained by the catalytic polymerization of ethylene in gas and liquid phase reactors. The gas phase processes are more advantageous, and use fluidized bed reactors for production of polyethylene. Since they operate so close to the melting point of the polymer, agglomeration is an operational concern in all slurry and gas polymerization processes. Electrostatics and hot spot formation are the main factors that contribute to agglomeration in gas-phase processes. Electrostatic charges in gas phase polymerization fluidized bed reactors are known to influence the bed hydrodynamics, particle elutriation, bubble size, bubble shape etc. Accumulation of electrostatic charges in the fluidized-bed can lead to operational issues. In this work a first-principles electrostatic model is developed and coupled with a multifluid computational fluid dynamic (CFD) model to understand the effect of electrostatics on the dynamics of a fluidized-bed. The multifluid CFD model for gas-particle flow is based on the kinetic theory of granular flow closures. The electrostatic model is developed based on a fixed, size-dependent charge for each type of particle (catalyst, polymer, polymer fines) phase. The combined CFD model is first verified using simple test cases, validated with experiments and applied to a pilot-scale polymerization fluidized bed reactor. The CFD model reproduced qualitative trends in particle segregation and entrainment due to electrostatic charges observed in experiments. For the scale up of fluidized bed reactor, filtered models are developed and implemented on pilot scale reactor

Modeling electromechanical properties of layered electrets: Application of the finite-element method

We present calculations on the deformation of two- and three-layer electret systems. The electrical field is coupled with the stress-strain equations by means of the Maxwell stress tensor. In the simulations, two-phase systems are considered, and intrinsic relative dielectric permittivity and Young's modulus of the phases are altered. The numerically calculated electro-mechanical activity is compared to an analytical expression. Simulations are performed on two- and three-layer systems. Various parameters in the model are systematically varied and their influence on the resulting piezoelectricity is estimated. In three-layer systems with bipolar charge, the piezoelectric coefficients exhibit a strong dependence on the elastic moduli of the phases. However, with mono-polar charge, there is no significant piezoelectric effect. A two-dimensional simulation illustrated that higher piezoelectricity coefficients can be obtained for non-uniform surface charges and low Poisson's ratio of phases. Irregular structures considered exhibit low piezoelectric activity compared to two-layer structures.Comment: To be appaer in J Electrostatic

Controlled DNA compaction within chromatin: the tail-bridging effect

We study the mechanism underlying the attraction between nucleosomes, the fundamental packaging units of DNA inside the chromatin complex. We introduce a simple model of the nucleosome, the eight-tail colloid, consisting of a charged sphere with eight oppositely charged, flexible, grafted chains that represent the terminal histone tails. We demonstrate that our complexes are attracted via the formation of chain bridges and that this attraction can be tuned by changing the fraction of charged monomers on the tails. This suggests a physical mechanism of chromatin compaction where the degree of DNA condensation can be controlled via biochemical means, namely the acetylation and deacetylation of lysines in the histone tails.Comment: 4 pages, 5 figures, submitte

Structural prediction and in silico physicochemical characterization for mouse caltrin I and bovine caltrin proteins

It is known that caltrin (calcium transport inhibitor) protein binds to sperm cells during ejaculation and inhibits extracellular Ca2+ uptake. Although the sequence and some biological features of mouse caltrin I and bovine caltrin are known, their physicochemical properties and tertiary structure are mainly unknown. We predicted the 3D structures of mouse caltrin I and bovine caltrin by molecular homology modeling and threading. Surface electrostatic potentials and electric fields were calculated using the Poisson–Boltzmann equation. Several different bioinformatics tools and available web servers were used to thoroughly analyze the physicochemical characteristics of both proteins, such as their Kyte and Doolittle hydropathy scores and helical wheel projections. The results presented in this work significantly aid further understanding of the molecular mechanisms of caltrin proteins modulating physiological processes associated with fertilization.Fil: Grasso, Ernesto Javier. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones Biológicas y Tecnológicas. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas, Físicas y Naturales. Instituto de Investigaciones Biológicas y Tecnológicas; ArgentinaFil: Sottile, Adolfo Emiliano. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones Biológicas y Tecnológicas. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas, Físicas y Naturales. Instituto de Investigaciones Biológicas y Tecnológicas; ArgentinaFil: Coronel, Carlos Enrique. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones Biológicas y Tecnológicas. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas, Físicas y Naturales. Instituto de Investigaciones Biológicas y Tecnológicas; Argentin