Biological Meaning of Nonlinear Mapping of Substitution Matrices in Metric Spaces

Abstract-Based on the Information Theory, a distance function between amino acids is induced to model the affinity relationship between them. Tables with mapping coordinates have been obtained by using nonlinear multidimensional scaling for different dimensions. These mapping coordinates are meaningless virtual data, but a high relationship with physical and chemical properties is found. The main conclusion is that the number of effective characteristics involved in substitution matrices is low. The hypothesis that hydrophobicity and secondary structure propensities are very important characteristics involved in substitution matrices is reinforced by the analysis of the results

About Robust Stability of Dynamic Systems with Time Delays through Fixed Point Theory

This paper investigates the global asymptotic stability independent of the sizes of the delays of linear time-varying systems with internal point delays which possess a limiting equation via fixed point theory. The error equation between the solutions of the limiting equation and that of the current one is considered as a perturbation equation in the fixed- point and stability analyses. The existence of a unique fixed point which is later proved to be an asymptotically stable equilibrium point is investigated. The stability conditions are basically concerned with the matrix measure of the delay-free matrix of dynamics to be negative and to have a modulus larger than the contribution of the error dynamics with respect to the limiting one. Alternative conditions are obtained concerned with the matrix dynamics for zero delay to be negative and to have a modulus larger than an appropriate contributions of the error dynamics of the current dynamics with respect to the limiting one. Since global stability is guaranteed under some deviation of the current solution related to the limiting one, which is considered as nominal, the stability is robust against such errors for certain tolerance margins.</p

Sensory Motor Remapping of Space in Human-Machine Interfaces

Studies of adaptation to patterns of deterministic forces have revealed the ability of the motor control system to form and use predictive representations of the environment. These studies have also pointed out that adaptation to novel dynamics is aimed at preserving the trajectories of a controlled endpoint, either the hand of a subject or a transported object. We review some of these experiments and present more recent studies aimed at understanding how the motor system forms representations of the physical space in which actions take place. An extensive line of investigations in visual information processing has dealt with the issue of how the Euclidean properties of space are recovered from visual signals that do not appear to possess these properties. The same question is addressed here in the context of motor behavior and motor learning by observing how people remap hand gestures and body motions that control the state of an external device. We present some theoretical considerations and experimental evidence about the ability of the nervous system to create novel patterns of coordination that are consistent with the representation of extrapersonal space. We also discuss the perspective of endowing human–machine interfaces with learning algorithms that, combined with human learning, may facilitate the control of powered wheelchairs and other assistive devices

Geometry of logarithmic strain measures in solid mechanics

We consider the two logarithmic strain measures$$\omega_{\rm iso}=\|\mathrm{dev}_n\log U\|=\|\mathrm{dev}_n\log \sqrt{F^TF}\|\quad\text{ and }\quad \omega_{\rm vol}=|\mathrm{tr}(\log U)|=|\mathrm{tr}(\log\sqrt{F^TF})|\,,$$which are isotropic invariants of the Hencky strain tensor $\log U$, and show that they can be uniquely characterized by purely geometric methods based on the geodesic distance on the general linear group $\mathrm{GL}(n)$. Here, $F$ is the deformation gradient, $U=\sqrt{F^TF}$ is the right Biot-stretch tensor, $\log$ denotes the principal matrix logarithm, $\|.\|$ is the Frobenius matrix norm, $\mathrm{tr}$ is the trace operator and $\mathrm{dev}_n X$ is the $n$-dimensional deviator of $X\in\mathbb{R}^{n\times n}$. This characterization identifies the Hencky (or true) strain tensor as the natural nonlinear extension of the linear (infinitesimal) strain tensor $\varepsilon=\mathrm{sym}\nabla u$, which is the symmetric part of the displacement gradient $\nabla u$, and reveals a close geometric relation between the classical quadratic isotropic energy potential $$\mu\,\|\mathrm{dev}_n\mathrm{sym}\nabla u\|^2+\frac{\kappa}{2}\,[\mathrm{tr}(\mathrm{sym}\nabla u)]^2=\mu\,\|\mathrm{dev}_n\varepsilon\|^2+\frac{\kappa}{2}\,[\mathrm{tr}(\varepsilon)]^2$$in linear elasticity and the geometrically nonlinear quadratic isotropic Hencky energy$$\mu\,\|\mathrm{dev}_n\log U\|^2+\frac{\kappa}{2}\,[\mathrm{tr}(\log U)]^2=\mu\,\omega_{\rm iso}^2+\frac\kappa2\,\omega_{\rm vol}^2\,,$$where $\mu$ is the shear modulus and $\kappa$ denotes the bulk modulus. Our deduction involves a new fundamental logarithmic minimization property of the orthogonal polar factor $R$, where $F=R\,U$ is the polar decomposition of $F$. We also contrast our approach with prior attempts to establish the logarithmic Hencky strain tensor directly as the preferred strain tensor in nonlinear isotropic elasticity

Evaluating the connectivity, continuity and distance norm in mathematical models for community ecology, epidemiology and multicellular pathway prediction

The main global threats of the biosphere on our planet, such as a global biodiversity impairment, global health issues in the developing countries, associated with an environmental decay, unnoticed in previous eras, the rise of greenhouse gasses and global warming, urge for a new evaluation of the applicability of mathematical modelling in the physical sciences and its benefits for society. In this paper, we embark on a historical review of the mathematical models developed in the previous century, that were devoted to the study of the geographical spread of biological infections. The basic notions of connectivity, continuity and distance norm as applied by successive bio-mathematicians, starting with the names of Volterra, Turing and Kendall, are highlighted in order to demonstrate their usefulness in several new areas of bio-mathematical research. These new areas include the well-known fields of community ecology and epidemiology, but also the less well-known field of multicellular pathway prediction. The biological interpretation of these abstract mathematical notions, as well as the methodological criteria for these interpretative schemes and their corroboration with empirical evidence are discussed. In particular, we will focus on the boundedness norm in polynomial Lyapunov functions and its application in Markovian models for community assembly and in models f

Swim-like motion of bodies immersed in an ideal fluid

The connection between swimming and control theory is attracting increasing attention in the recent literature. Starting from an idea of Alberto Bressan [A. Bressan, Discrete Contin. Dyn. Syst. 20 (2008) 1\u201335]. we study the system of a planar body whose position and shape are described by a finite number of parameters, and is immersed in a 2-dimensional ideal and incompressible fluid in terms of gauge field on the space of shapes. We focus on a class of deformations measure preserving which are diffeomeorphisms whose existence is ensured by the Riemann Mapping Theorem. After making the first order expansion for small deformations, we face a crucial problem: the presence of possible non vanishing initial impulse. If the body starts with zero initial impulse we recover the results present in literature (Marsden, Munnier and oths). If instead the body starts with an initial impulse different from zero, the swimmer can self-propel in almost any direction if it can undergo shape changes without any bound on their velocity. This interesting observation, together with the analysis of the controllability of this system, seems innovative. Mathematics Subject Classification. 74F10, 74L15, 76B99, 76Z10. Received June 14, 2016. Accepted March 18, 2017. 1. Introduction In this work we are interested in studying the self-propulsion of a deformable body in a fluid. This kind of systems is attracting an increasing interest in recent literature. Many authors focus on two different type of fluids. Some of them consider swimming at micro scale in a Stokes fluid [2,4\u20136,27,35,40], because in this regime the inertial terms can be neglected and the hydrodynamic equations are linear. Others are interested in bodies immersed in an ideal incompressible fluid [8,18,23,30,33] and also in this case the hydrodynamic equations turn out to be linear. We deal with the last case, in particular we study a deformable body -typically a swimmer or a fish- immersed in an ideal and irrotational fluid. This special case has an interesting geometric nature and there is an attractive mathematical framework for it. We exploit this intrinsically geometrical structure of the problem inspired by [32,39,40], in which they interpret the system in terms of gauge field on the space of shapes. The choice of taking into account the inertia can apparently lead to a more complex system, but neglecting the viscosity the hydrodynamic equations are still linear, and this fact makes the system more manageable. The same fluid regime and existence of solutions of these hydrodynamic equations has been studied in [18] regarding the motion of rigid bodies