Matrices and Molecular Vibrations

The flexibility matrix of a system is described and the normal modes of vibration of various simple ‘molecules’ are derived. Matrices which describe the geometrical symmetries of the molecules are shown to commute with the flexibility matrix, and this property assists the quick calculation of normal modes. Symmetry gives rise to degeneracy in the frequency spectrum, and this suggests practical ways of deciding which of various possible configurations a molecule actually has. The treatment is as simple as possible so that it can be used in the classroom.     

Existence of solutions to a new model of biological pattern formation

In this paper we study the existence of classical solutions to a new model of skeletal development in the vertebrate limb. The model incorporates a general term describing adhesion interaction between cells and fibronectin, an extracellular matrix molecule secreted by the cells, as well as two secreted, diffusible regulators of fibronectin production, the positively-acting differentiation factor (“activator”) TGF-β, and a negatively-acting factor (“inhibitor”). Together, these terms constitute a pattern forming system of equations. We analyze the conditions guaranteeing that smooth solutions exist globally in time. We prove that these conditions can be significantly relaxed if we add a diffusion term to the equation describing the evolution of fibronectin.     

Characterization of symmetric M-matrices as resistive inverses

We aim here at characterizing those nonnegative matrices whose inverse is an irreducible Stieltjes matrix. Specifically, we prove that any irreducible Stieltjes matrix is a resistive inverse. To do this we consider the network defined by the off-diagonal entries of the matrix and we identify the matrix with a positive definite Schrödinger operator whose ground state is determined by the lowest eigenvalue of the matrix and the corresponding positive eigenvector. We also analyze the case in which the operator is positive semidefinite which corresponds to the study of singular irreducible symmetric M-matrices.     

A tensor product matrix approximation problem in quantum physics

We consider a matrix approximation problem arising in the study of entanglement in quantum physics. This notion represents a certain type of correlations between subsystems in a composite quantum system. The states of a system are described by a density matrix, which is a positive semidefinite matrix with trace one. The goal is to approximate such a given density matrix by a so-called separable density matrix, and the distance between these matrices gives information about the degree of entanglement in the system. Separability here is expressed in terms of tensor products. We discuss this approximation problem for a composite system with two subsystems and show that it can be written as a convex optimization problem with special structure. We investigate related convex sets, and suggest an algorithm for this approximation problem which exploits the tensor product structure in certain subproblems. Finally some computational results and experiences are presented.     

Statistical inference of 2-type critical Galton–Watson processes with immigration

In this paper the asymptotic behavior of the conditional least squares estimators of the offspring mean matrix for a 2-type critical positively regular Galton–Watson branching process with immigration is described. We also study this question for a natural estimator of the spectral radius of the offspring mean matrix, which we call criticality parameter. We discuss the subcritical case as well.     

Second eigenvalue of transition matrix associated to iterated maps

We study the properties of the second eigenvalue of the transition matrix in unimodal and bimodal map’s families. We use in particular the relation with the mixing rate and apply this to classify families of isentropic bimodal maps. We present also a study which show the convergence of this quantity in those families.     

Expectations of Functions of Complex Wishart Matrix

In this article, we study lower and upper triangular factorizations of the complex Wishart matrix. Further, using these factorizations, we obtain several expected values of scalar and matrix valued functions of the complex Wishart matrix. We also generalize Muirhead’s identity for the complex case which gives a number of interesting special cases.     

Penalized Covariance Matrix Estimation Using a Matrix-Logarithm Transformation

For statistical inferences that involve covariance matrices, it is desirable to obtain an accurate covariance matrix estimate with a well-structured eigen-system. We propose to estimate the covariance matrix through its matrix logarithm based on an approximate log-likelihood function. We develop a generalization of the Leonard and Hsu log-likelihood approximation that no longer requires a nonsingular sample covariance matrix. The matrix log-transformation provides the ability to impose a convex penalty on the transformed likelihood such that the largest and smallest eigenvalues of the covariance matrix estimate can be regularized simultaneously. The proposed method transforms the problem of estimating the covariance matrix into the problem of estimating a symmetric matrix, which can be solved efficiently by an iterative quadratic programming algorithm. The merits of the proposed method are illustrated by a simulation study and two real applications in classification and portfolio optimization. Supplementary materials for this article are available online.     

On the extremal solutions for capacitated network problems

In this note we give a unifying approach to the problem of characterizing the extreme points of those convex matrix sets which correspond to the domains of various types of capacitated network problems. It is shown that we can determine whether a matrix is an extreme point of the sets by examining the pattern of a certain graph associated with it. We also study the extreme points of the convex matrix sets which are related to network problems free from capacity constraints by linking them up with certain capacitated network problem.     

Applications of Symmetry and Group Theory for the Investigation of Molecular Vibrations

The application of symmetry and mathematical group theory is a powerful tool for investigating the vibrations of molecules. In this paper, we present an overview of the methods utilized. First we briefly discuss the quantum mechanical nature of vibrations and the experimental methods used. We then present the principal concepts for applying group theory to molecules. The symmetry operations which are used to comprise groups are described and then used to determine the point groups of molecules. The properties of character tables are presented and the method for obtaining a reducible representation for all the motions of a molecule is detailed. This can then be broken down to obtain the irreducible representation which contains the symmetry species of the individual vibrations. The determination of symmetry adapted linear combinations is outlined and the basis for spectroscopic selection rules is presented. The paper concludes by examining how matrix algebra along with symmetry concepts simplifies calculations with molecular force constants.     

Relative asymptotics for orthogonal matrix polynomials

In this paper we study sequences of matrix polynomials that satisfy a non-symmetric recurrence relation. To study this kind of sequences we use a vector interpretation of the matrix orthogonality. In the context of these sequences of matrix polynomials we introduce the concept of the generalized matrix Nevai class and we give the ratio asymptotics between two consecutive polynomials belonging to this class. We study the generalized matrix Chebyshev polynomials and we deduce its explicit expression as well as we show some illustrative examples. The concept of a Dirac delta functional is introduced. We show how the vector model that includes a Dirac delta functional is a representation of a discrete Sobolev inner product. It also allows to reinterpret such perturbations in the usual matrix Nevai class. Finally, the relative asymptotics between a polynomial in the generalized matrix Nevai class and a polynomial that is orthogonal to a modification of the corresponding matrix measure by the addition of a Dirac delta functional is deduced.     

Character expansion method for the first order asymptotics of a matrix integral

The estimation of various matrix integrals as the size of the matrices goes to infinity is motivated by theoretical physics, geometry and free probability questions. On a rigorous ground, only integrals of one matrix or of several matrices with simple quadratic interaction (called AB interaction) could be evaluated so far (see e.g. [19], [17] or [9]). In this article, we follow an idea widely developed in the physics literature, which is based on character expansion, to study more complex interaction. In this context, we derive a large deviation principle for the empirical measure of Young tableaux. We then use it to study a matrix model defined in the spirit of the ‘dually weighted graph model’ introduced in [13], but with a cutoff function such that the matrix integral and its character expansion converge. We prove that the free energy of this model converges as the size of the matrices goes to infinity and study the critical points of the limit.     

General Moments of the Inverse Real Wishart Distribution and Orthogonal Weingarten Functions

We study a random positive definite symmetric matrix distributed according to a real Wishart distribution. We compute general moments of the random matrix and of its inverse explicitly. To do so, we employ the orthogonal Weingarten function, which was recently introduced in the study of Haar-distributed orthogonal matrices. As applications, we give formulas for moments of traces of a Wishart matrix and its inverse.     

On the use of dense matrix techniques within sparse simplex

In this paper we discuss some instances where dense matrix techniques can be utilized within a sparse simplex linear programming solver. The main emphasis is on the use of the Schur complement matrix as a part of the basis matrix representation. This approach enables to represent the basis matrix as an easily invertible sparse matrix and one or more dense Schur complement matrices. We describe our variant of this method which uses updating of the QR factorization of the Schur complement matrix. We also discuss some implementation issues of the LP software package which is based on this approach.     

Stability of Parallel Fluid Loaded Plates: A Nonlocal Approach

We consider the motion of a collection of fluid loaded elastic plates, situated horizontally in an infinitely long channel. We use a new, unified approach to boundary value problems, introduced by A.S. Fokas in the late 1990s, and show the problem is equivalent to a system of one‐parameter integral equations. We give a detailed study of the linear problem, providing explicit solutions and well‐posedness results in terms of standard Sobolev spaces. We show that the associated Cauchy problem is completely determined by a matrix, which depends solely on the mean separation of the plates and the horizontal velocity of each of the driving fluids. This matrix corresponds to the infinitesimal generator of the C₀ ‐semigroup for the evolution equations in Fourier space. By analyzing the properties of this matrix, we classify necessary and sufficient conditions for which the problem is asymptotically stable.     

A continuous variable neighborhood search heuristic for finding the three-dimensional structure of a molecule

We develop a continuous variable neighborhood search heuristic for minimizing the potential energy function of a molecule. Computing the global minimum of this function is very difficult because it has a large number of local minimizers which grows exponentially with molecule size. Experimental evidence shows that in the great majority of cases the global minimum potential energy of a given molecule corresponds to its three-dimensional structure and this structure is important because it dictates most of the properties of the molecule. Computational results for problems with up to 200 degrees of freedom are presented and favourable compared with other two existing methods from the literature.     

On Matrix Elements for the Quantized Cat Map Modulo Prime Powers

The quantum cat map is a model for a quantum system with underlying chaotic dynamics. In this paper we study the matrix elements of smooth observables in this model, when taking arithmetic symmetries into account. We give explicit formulas for the matrix elements as certain exponential sums. With these formulas we can show that there are sequences of eigenfunctions for which the matrix elements decay significantly slower then was previously expected. We also prove a limiting distribution for the fluctuation of the normalized matrix elements around their average. Submitted: March 3, 2008., Accepted: August 11, 2008. This material is based upon work supported by the National Science Foundation under agreement No. DMS-0635607. Any opinions, findings and conclusions or recommendations expressed in this material are those of the author and do not necessarily reflect the views of the National Science Foundation.     

New measures for comparing matrices and their application to image processing

In this work we present the class of matrix resemblance functions, i.e., functions that measure the difference between two matrices. We present two construction methods and study the properties that matrix resemblance functions satisfy, which suggest that this class of functions is an appropriate tool for comparing images. Hence, we present a comparison method for grayscale images whose result is a new image, which enables to locate the areas where both images are equally similar or dissimilar. Additionally, we propose some applications in which this comparison method can be used, such as defect detection in industrial manufacturing processes and video motion detection and object tracking.     

Free products of matrices

In this note we give some new examples of matrix groups which are free products. We use this in our study of the Burau representation in dimension four.