Outer endomorphisms of free metabelian Lie algebras

2000 Mathematics Subject Classification: 17B01, 17B30, 17B40.

The Berkovits Complex and Semi-free Extensions of Koszul Algebras

Peer reviewed

Efficient solution of two-sided nonlinear space-fractional diffusion equations using fast Poisson preconditioners

We develop a fast Poisson preconditioner for the efficient numerical solution of a class of two-sided nonlinear space fractional diffusion equations in one and two dimensions using the method of lines. Using the shifted Gr¨unwald finite difference formulas to approximate the two-sided(i.e. the left and right Riemann-Liouville) fractional derivatives, the resulting semi-discrete nonlinear systems have dense Jacobian matrices owing to the non-local property of fractional derivatives. We employ a modern initial value problem solver utilising backward differentiation formulas and Jacobian-free Newton-Krylov methods to solve these systems. For efficient performance of the Jacobianfree Newton-Krylov method it is essential to apply an effective preconditioner to accelerate the convergence of the linear iterative solver. The key contribution of our work is to generalise the fast Poisson preconditioner, widely used for integer-order diffusion equations, so that it applies to the two-sided space fractional diffusion equation. A number of numerical experiments are presented to demonstrate the effectiveness of the preconditioner and the overall solution strategy.

Calculations of the free energy of interaction of the c-Fos−c-Jun coiled coil: Effects of the solvation model and the inclusion of polarization effects

The leucine zipper region of activator protein-1 (AP-1) comprises the c-Jun and c-Fos proteins and constitutes a well-known coiled coil protein−protein interaction motif. We have used molecular dynamics (MD) simulations in conjunction with the molecular mechanics/Poisson−Boltzmann generalized-Born surface area [MM/PB(GB)SA] methods to predict the free energy of interaction of these proteins. In particular, the influence of the choice of solvation model, protein force field, and water potential on the stability and dynamic properties of the c-Fos−c-Jun complex were investigated. Use of the AMBER polarizable force field ff02 in combination with the polarizable POL3 water potential was found to result in increased stability of the c-Fos−c-Jun complex. MM/PB(GB)SA calculations revealed that MD simulations using the POL3 water potential give the lowest predicted free energies of interaction compared to other nonpolarizable water potentials. In addition, the calculated absolute free energy of binding was predicted to be closest to the experimental value using the MM/GBSA method with independent MD simulation trajectories using the POL3 water potential and the polarizable ff02 force field, while all other binding affinities were overestimated.

Free vibration of rectangular beams of arbitrary depth

The state space approach is extended to the two dimensional elastodynamic problems. The formulation is in a form particularly amenable to consistent reduction to obtain approximate theories of any desired order. Free vibration of rectangular beams of arbitrary depth is investigated using this approach. The method does not involve the concept of the shear coefficientk. It takes into account the vertical normal stress and the transverse shear stress. The frequency values are calculated using the Timoshenko beam theory and the present analysis for different values of Poisson's ratio and they are in good agreement. Four cases of beams with different end conditions are considered.Die Zustandsraum-Technik wird auf zweidimensionale elastodynamische Probleme ausgedehnt. Die Formulierung ist besonders geeignet für die Aufstellung von Näherungstheorien beliebigen Grades. Freie Schwingungen von Rechteckbalken beliebiger Höhe wurden mit Hilfe dieser Technik untersucht. Das Verfahren umgeht den Begriff des Schubbeiwertsk. Es berücksichtigt die senkrechte Normalbeanspruchung und die Querkraft. Die Frequenzwerte werden mit Hilfe der Balkentheorie von Timoshenko und der vorliegenden Analyse berechnet, und zwar für verschiedene Werte der Querdehnzahl. Die berechneten Werte befinden sich in guter Übereinstimmung. Vier Fälle von Balken mit verschiedenen Endbedingungen werden untersucht.

Docking and free energy simulations to predict conformational domains involved in hCG-LH receptor interactions using recombinant antibodies

Single chain fragment variables (ScFvs) have been extensively employed in studying the protein-protein interactions. ScFvs derived from phage display libraries have an additional advantage of being generated against a native antigen, circumventing loss of information on conformational epitopes. In the present study, an attempt has been made to elucidate human chorionic gonadotropin (hCG)-luteinizing hormone (LH) receptor interactions by using a neutral and two inhibitory ScFvs against hCG. The objective was to dock a computationally derived model of these ScFvs onto the crystal structure of hCG and understand the differential roles of the mapped epitopes in hCG-LH receptor interactions. An anti-hCG ScFv, whose epitope was mapped previously using biochemical tools, served as the positive control for assessing the quality of docking analysis. To evaluate the role of specific side chains at the hCG-ScFv interface, binding free energy as well as residue interaction energies of complexes in solution were calculated using molecular mechanics Poisson-Boltzmann/surface area method after performing the molecular dynamic simulations on the selected hCG-ScFv models and validated using biochemical and SPR analysis. The robustness of these calculations was demonstrated by comparing the theoretically determined binding energies with the experimentally obtained kinetic parameters for hCG-ScFv complexes. Superimposition of hCG-ScFv model onto a model of hCG complexed with the 51-266 residues of LH receptor revealed importance of the residues previously thought to be unimportant for hormone binding and response. This analysis provides an alternate tool for understanding the structure-function analysis of ligand-receptor interactions. Proteins 2011;79:3108-3122. (C) 2011 Wiley-Liss, Inc.

MODELING HETEROSTRUCTURES WITH SCHRODINGER-POISSON-NAVIER ITERATIVE SCHEMES, EFFECT OF CARRIER CHARGE, AND INFLUENCE OF ELECTROMECHANICAL COUPLING

This paper presents a detailed investigation of the erects of piezoelectricity, spontaneous polarization and charge density on the electronic states and the quasi-Fermi level energy in wurtzite-type semiconductor heterojunctions. This has required a full solution to the coupled Schrodinger-Poisson-Navier model, as a generalization of earlier work on the Schrodinger-Poisson problem. Finite-element-based simulations have been performed on a A1N/GaN quantum well by using both one-step calculation as well as the self-consistent iterative scheme. Results have been provided for field distributions corresponding to cases with zero-displacement boundary conditions and also stress-free boundary conditions. It has been further demonstrated by using four case study examples that a complete self-consistent coupling of electromechanical fields is essential to accurately capture the electromechanical fields and electronic wavefunctions. We have demonstrated that electronic energies can change up to approximately 0.5 eV when comparing partial and complete coupling of electromechanical fields. Similarly, wavefunctions are significantly altered when following a self-consistent procedure as opposed to the partial-coupling case usually considered in literature. Hence, a complete self-consistent procedure is necessary when addressing problems requiring more accurate results on optoelectronic properties of low-dimensional nanostructures compared to those obtainable with conventional methodologies.

An improved free surface modeling for incompressible SPH

In Incompressible Smooth Particle Hydrodynamics (ISPH), a pressure Poisson equation (PPE) is solved to obtain a divergence free velocity field. When free surfaces are simulated using this method a Dirichlet boundary condition for pressure at the free surface has to be applied. In existing ISPH methods this is achieved by identifying free surface particles using heuristically chosen threshold of a parameter such as kernel sum, density or divergence of the position, and explicitly setting their pressure values. This often leads to clumping of particles near the free surface and spraying off of surface particles during splashes. Moreover, surface pressure gradients in flows where surface tension is important are not captured well using this approach. We propose a more accurate semi-analytical approach to impose Dirichlet boundary conditions on the free surface. We show the efficacy of the proposed algorithm by using test cases of elongation of a droplet and dam break. We perform two dimensional simulations of water entry and validate the proposed algorithm with experimental results. Further, a three dimensional simulation of droplet splash is shown to compare well with the Volume-of-Fluid simulations. (C) 2014 Elsevier Ltd. All rights reserved.

An augmented method for free boundary problems with moving contact lines

An augmented immersed interface method (IIM) is proposed for simulating one-phase moving contact line problems in which a liquid drop spreads or recoils on a solid substrate. While the present two-dimensional mathematical model is a free boundary problem, in our new numerical method, the fluid domain enclosed by the free boundary is embedded into a rectangular one so that the problem can be solved by a regular Cartesian grid method. We introduce an augmented variable along the free boundary so that the stress balancing boundary condition is satisfied. A hybrid time discretization is used in the projection method for better stability. The resultant Helmholtz/Poisson equations with interfaces then are solved by the IIM in an efficient way. Several numerical tests including an accuracy check, and the spreading and recoiling processes of a liquid drop are presented in detail. (C) 2010 Elsevier Ltd. All rights reserved.

An analogue of the Magnus problem for associative algebras

We prove an analogue of Magnus theorem for associative algebras without unity over arbitrary fields. Namely, if an algebra is given by $n+k$ generators and $k$ relations and has an $n$-element system of generators, then this algebra is a free algebra of rank $n$.

Non-trivial stably free modules over crossed products

We consider the class of crossed products of noetherian domains with universal enveloping algebras of Lie algebras. For algebras from this class we give a sufficient condition for the existence of projective non-free modules. This class includes Weyl algebras and universal envelopings of Lie algebras, for which this question, known as noncommutative Serre's problem, was extensively studied before. It turns out that the method of lifting of non-trivial stably free modules from simple Ore extensions can be applied to crossed products after an appropriate choice of filtration. The motivating examples of crossed products are provided by the class of RIT algebras, originating in non-equilibrium physics.

SK1 of graded division algebras

The reduced Whitehead group $\SK$ of a graded division algebra graded by a torsion-free abelian group is studied. It is observed that the computations here are much more straightforward than in the non-graded setting. Bridges to the ungraded case are then established by the following two theorems: It is proved that $\SK$ of a tame valued division algebra over a henselian field coincides with $\SK$ of its associated graded division algebra. Furthermore, it is shown that $\SK$ of a graded division algebra is isomorphic to $\SK$ of its quotient division algebra. The first theorem gives the established formulas for the reduced Whitehead group of certain valued division algebras in a unified manner, whereas the latter theorem covers the stability of reduced Whitehead groups, and also describes $\SK$ for generic abelian crossed products.

Unitary SK1 of unitary and graded division algebras

The reduced unitary Whitehead group $\SK$ of a graded division algebra equipped with a unitary involution (i.e., an involution of the second kind) and graded by a torsion-free abelian group is studied. It is shown that calculations in the graded setting are much simpler than their nongraded counterparts. The bridge to the non-graded case is established by proving that the unitary $\SK$ of a tame valued division algebra wih a unitary involution over a henselian field coincides with the unitary $\SK$ of its associated graded division algebra. As a consequence, the graded approach allows us not only to recover results available in the literature with substantially easier proofs, but also to calculate the unitary $\SK$ for much wider classes of division algebras over henselian fields.

K-Theory of Azumaya Algebras over Schemes

Let X be a connected, noetherian scheme and A{script} be a sheaf of Azumaya algebras on X, which is a locally free O{script}-module of rank a. We show that the kernel and cokernel of K(X) ? K(A{script}) are torsion groups with exponent a for some m and any i = 0, when X is regular or X is of dimension d with an ample sheaf (in this case m = d + 1). As a consequence, K(X, Z/m) ? K(A{script}, Z/m), for any m relatively prime to a. © 2013 Copyright Taylor and Francis Group, LLC.

Hyperbolic unit groups and quaternion algebras

We classify the quadratic extensions K = Q[root d] and the finite groups G for which the group ring o(K)[G] of G over the ring o(K) of integers of K has the property that the group U(1)(o(K)[G]) of units of augmentation 1 is hyperbolic. We also construct units in the Z-order H(o(K)) of the quaternion algebra H(K) = (-1, -1/K), when it is a division algebra.