The development of a high-order Taylor expansion solution to the chemical rate equation for the simulation of complex biochemical systems

A numerical method for evaluating chemical rate equations ispresented. This method was developed by expressing the systemof coupled, first-degree, ordinary differential chemical rateequations as a single tensor equation. The tensorial rate equationis invariant in form for all reversible and irreversible reactionschemes that can be expressed as first- and second-order reactionsteps, and can accommodate any number of reactive components.The tensor rate equation was manipulated to obtain a simpleformula (in terms of rate constants and initial concentrations)for the power coefficients of the Taylor expansion of the chemicalrate equation. The Taylor expansion formula was used to developa FORTRAN algorithm for analysing the time development of chemicalsystems. A computational experiment was performed with a Michaelis-Mentenscheme in which step size and expansion order (to the 100thterm) were varied; the inclusion of high-order terms of theTaylor expansion was shown to reduce truncation and round-offerrors associated with Runge-Kutta methods and lead to increasedcomputational efficiency. Received on July 14, 1989; accepted on February 28, 1990     

Nonlocal weakly relativistic permittivity tensor of magnetized plasma near electron cyclotron resonances

Compact expressions are derived for the nonlocal permittivity tensor of weakly relativistic plasma in a 2D nonuniform magnetic field near the resonances at the second harmonic of the electron cyclotron frequency for an extraordinary wave and at the first harmonic for an ordinary wave. It is shown that the wave equation with allowance for the obtained thermal correction to the permittivity tensor in the form of a differential operator in transverse (with respect to the external magnetic field) coordinates possesses an integral in the form of the energy conservation law.     

M5 mesoscopic and macroscopic models for mesenchymal motion

In this paper mesoscopic (individual based) and macroscopic (population based) models for mesenchymal motion of cells in fibre networks are developed. Mesenchymal motion is a form of cellular movement that occurs in three-dimensions through tissues formed from fibre networks, for example the invasion of tumor metastases through collagen networks. The movement of cells is guided by the directionality of the network and in addition, the network is degraded by proteases. The main results of this paper are derivations of mesoscopic and macroscopic models for mesenchymal motion in a timely varying network tissue. The mesoscopic model is based on a transport equation for correlated random walk and the macroscopic model has the form of a drift-diffusion equation where the mean drift velocity is given by the mean orientation of the tissue and the diffusion tensor is given by the variance-covariance matrix of the tissue orientations. The transport equation as well as the drift-diffusion limit are coupled to a differential equation that describes the tissue changes explicitly, where we distinguish the cases of directed and undirected tissues. As a result the drift velocity and the diffusion tensor are timely varying. We discuss relations to existing models and possible applications.Dedicated to K.P. Hadeler, a great scientist, teacher, and friend.     

Calculation of Thermal Conductivity Coefficients of Electrons in Magnetized Dense Matter

The solution of Boltzmann equation for plasma in magnetic field with arbitrarily degenerate electrons and nondegenerate nuclei is obtained by Chapman?Enskog method. Functions generalizing Sonine polynomials are used for obtaining an approximate solution. Fully ionized plasma is considered. The tensor of the heat conductivity coefficients in nonquantized magnetic field is calculated. For nondegenerate and strongly degenerate plasma the asymptotic analytic formulas are obtained and compared with results of previous authors. The Lorentz approximation with neglecting of electron?electron encounters is asymptotically exact for strongly degenerate plasma. For the first time, analytical expressions for the heat conductivity tensor for nondegenerate electrons in the presence of a magnetic field are obtained in the three-polynomial approximation with account of electron?electron collisions. Account of the third polynomial improved substantially the precision of results. In the two-polynomial approximation, the obtained solution coincides with the published results. For strongly degenerate electrons, an asymptotically exact analytical solution for the heat conductivity tensor in the presence of a magnetic field is obtained for the first time. This solution has a considerably more complicated dependence on the magnetic field than those in previous publications and gives a several times smaller relative value of the thermal conductivity across the magnetic field at ωτ * 0.8.     

Frictional properties of nonspherical multisubunit structures. Application to tubules and cylinders

Methods are described for numerical calculation of the anisotropic components of the translational and rotational friction coefficient tensors and of the intrinsic viscosity for rigid multisubunit structures in dilute solution. The methods apply to assemblies of any shape, provided that translation–rotation coupling is negligible. Application is made to short cylindrical and tubular structures. Anomalous results arise when the Oseen tensor is used to describe the hydrodynamic interaction of the subunits, but these are corrected by use of a modified tensor. Transport coefficients for hollow tubules with typical supramolecular dimensions are found to be nearly the same as those for the corresponding solid cylinders. The Scheraga–Mandelkern equation is found to be useful for the determination of the molecular weights of such structures. For long hollow structures such as microtubules, use of the corresponding solid cylinder or wormlike chain equations should be adequate for interpreting hydrodynamic studies.     

Transport properties of particles with segmental flexibility. I. Hydrodynamic resistance and diffusion coefficients of a freely hinged particle

Expressions are derived for the hydrodynamic resistance tensor and the diffusion tensor of a particle consisting of two rigid subunits connected by a free hinge. No restrictions are placed on the shapes of the subunits. The resistance tensor is obtained by using two independent approaches: first, from the Rayleigh dissipation function and, second, from an examination of the generalized forces for the appropriate seven-dimensional coordinate system. For the derivation of the generalized Einstein equation connecting the diffusion and resistance tensors, the Brownian motion is treated as a stochastic process. That derivation is based on the assumption that the restoring force for bending is negligible, and the Einstein relation holds instantaneously only if that assumption is true. The relationship between these tensors and the macroscopically observable parameters is discussed, and it is shown that the separate measurement of resistance and diffusion coefficients can be used to detect macromolecular flexibility. One example is treated, the diffusion of a particle composed of two long rods joined at a free hinge. Those calculations are carried out with the first-order assumption of negligible hydrodynamic interactions between the subunits. For the hinged rod, the bending degree of freedom produces a 34% increase in the translational diffusion coefficient over that of a stiff rod of the same total length, while the rotational diffusion coefficient about the axis perpendicular to the plane of bending is increased by 125%.     

A new simplified bioheat equation for the effect of blood flow on local average tissue temperature

A new simplified three-dimensional bioheat equation is derived to describe the effect of blood flow on blood-tissue heat transfer. In two recent theoretical and experimental studies [1, 2] the authors have demonstrated that the so-called isotropic blood perfusion term in the existing bioheat equation is negligible because of the microvascular organization, and that the primary mechanism for blood-tissue energy exchange is incomplete countercurrent exchange in the thermally significant microvessels. The new theory to describe this basic mechanism shows that the vascularization of tissue causes it to behave as an anisotropic heat transfer medium. A remarkably simple expression is derived for the tensor conductivity of the tissue as a function of the local vascular geometry and flow velocity in the thermally significant countercurrent vessels. It is also shown that directed as opposed to isotropic blood perfusion between the countercurrent vessels can have a significant influence on heat transfer in regions where the countercurrent vessels are under 70-micron diameter. The new bioheat equation also describes this mechanism.     

Mass and Energy Transport Through Slit Pores: Application to Planar Poiseuille Flow

Abstract

We develop a simple, efficient and general statistical mechanical technique for calculating the pressure tensor and the heat flux vector in atomic fluids. The method is applied to the case of planar Poiseuille flow through a narrow slit pore and the results indicate that our technique is accurate and relatively efficient. A second method to calculate shear stress is derived from the momentum continuity equation. This mesoscopic method again is seen to be accurate with good computational efficiency.

We also find that the commonly used approximation to the Irving-Kirkwood expression for the heat flux and the pressure tensor (where the Irving-Kirkwood O_ij operator is set equal to unity-the so-called IK1 approximation), leads to incorrect results for highly inhomogeneous fluids. In such cases the pressure tensor and heat flux vector display spurious oscillations.

We calculate the spatially dependent viscosity across a narrow pore and find that it exhibits real but weak oscillations, a consequence of oscillations in the number density. Finally we point out that if the heat flux vector is coupled to the gradient of the square of the strain rate tensor such an effect will only affect the shape of the temperature profile. For planar Poiseuille flow, the temperature profile should deviate from the classical quartic form and include an additional quadratic component. The actual magnitude and shape of the heat flux vector remain exactly as they would if such a coupling did not exist.     

A Bimodular Theory for Finite Deformations: Comparison of Orthotropic Second-order and Exponential Stress Constitutive Equations for Articular Cartilage

Cartilaginous tissues, such as articular cartilage and the annulus fibrosus, exhibit orthotropic behavior with highly asymmetric tensile–compressive responses. Due to this complex behavior, it is difficult to develop accurate stress constitutive equations that are valid for finite deformations. Therefore, we have developed a bimodular theory for finite deformations of elastic materials that allows the mechanical properties of the tissue to differ in tension and compression. In this paper, we derive an orthotropic stress constitutive equation that is second-order in terms of the Biot strain tensor as an alternative to traditional exponential type equations. Several reduced forms of the bimodular second-order equation, with six to nine parameters, and a bimodular exponential equation, with seven parameters, were fit to an experimental dataset that captures the highly asymmetric and orthotropic mechanical response of cartilage. The results suggest that the bimodular second-order models may be appealing for some applications with cartilaginous tissues.     

Kinematics of plant growth.

Many of the concepts and equations which have been used in the study of compressible fluids can be applied to problems of plant development. Growth field variables, i.e. functions of position in the plant and of time, can be specified in either Eulerian (spatial) or Lagrangian (material) terms. The two specifications coincide only when the spatial distribution of the variable is steady, and steady patterns are most likely to emerge when an apex is chosen as origin of the co-ordinate system. The growth field itself can be described locally by the magnitude and orientation of the principal axes of the rate of strain tensor and by the vorticity tensor. Material derivatives can be calculated if the temporal and spatial variation in both growth velocity, u (rate of displacement from a material origin), and the variable of interest are known. The equation of continuity shows the importance of including both growth velocity, u, and growth rate, ▽ ·u in estimates of local biosynthesis and transport rates in expanding tissue, although the classical continuity equation must be modified to accommodate the compartmentalized distributions characteristic of plant tissue. Relatively little information on spatial variation in plant organs can be found in the botanical literature, but the current availability of interactive computer graphics equipment suggests that analysis of the spatial distribution of growth rates at least is no longer difficult.     

Comparing G: multivariate analysis of genetic variation in multiple populations

The additive genetic variance–covariance matrix (G) summarizes the multivariate genetic relationships among a set of traits. The geometry of G describes the distribution of multivariate genetic variance, and generates genetic constraints that bias the direction of evolution. Determining if and how the multivariate genetic variance evolves has been limited by a number of analytical challenges in comparing G-matrices. Current methods for the comparison of G typically share several drawbacks: metrics that lack a direct relationship to evolutionary theory, the inability to be applied in conjunction with complex experimental designs, difficulties with determining statistical confidence in inferred differences and an inherently pair-wise focus. Here, we present a cohesive and general analytical framework for the comparative analysis of G that addresses these issues, and that incorporates and extends current methods with a strong geometrical basis. We describe the application of random skewers, common subspace analysis, the 4th-order genetic covariance tensor and the decomposition of the multivariate breeders equation, all within a Bayesian framework. We illustrate these methods using data from an artificial selection experiment on eight traits in Drosophila serrata, where a multi-generational pedigree was available to estimate G in each of six populations. One method, the tensor, elegantly captures all of the variation in genetic variance among populations, and allows the identification of the trait combinations that differ most in genetic variance. The tensor approach is likely to be the most generally applicable method to the comparison of G-matrices from any sampling or experimental design.     

Calculation of poloidal velocity in the tokamak plasma with allowance for density inhomogeneity and diamagnetic drift of ions

A one-dimensional evolution equation for the angle-averaged poloidal momentum of the tokamak plasma is derived in the framework of reduced magnetohydrodynamics with allowance for density inhomogeneity and diamagnetic drift of ions. In addition to fluctuations of the E × B drift velocity, the resulting turbulent Reynolds stress tensor includes fluctuations of the ion density and ion pressure, as well as turbulent radial fluxes of particles and heat. It is demonstrated numerically by using a particular example that the poloidal velocity calculated using the refined one-dimensional evolution equation differs substantially from that provided by the simplified model. When passing to the new model, both the turbulent Reynolds force and the Stringer-Winsor force increase, which leads to an increase in the amplitude of the ion poloidal velocity. This, in turn, leads to a decrease in turbulent fluxes of particles and heat due to the effect of shear decorrelation.     

Wolff's law of trabecular architecture at remodeling equilibrium

An elastic constitutive relation for cancellous bone tissue is developed. This relationship involves the stress tensor T, the strain tensor E and the fabric tensor H for cancellous bone. The fabric tensor is a symmetric second rank tensor that is a quantitative stereological measure of the microstructural arrangement of trabeculae and pores in the cancellous bone tissue. The constitutive relation obtained is part of an algebraic formulation of Wolff's law of trabecular architecture in remodeling equilibrium. In particular, with the general constitutive relationship between T, H and E, the statement of Wolff's law at remodeling equilibrium is simply the requirement of the commutativity of the matrix multiplication of the stress tensor and the fabric tensor at remodeling equilibrium, T*H* = H*T*. The asterisk on the stress and fabric tensor indicates their values in remodeling equilibrium. It is shown that the constitutive relation also requires that E*H* = H*E*. Thus, the principal axes of the stress, strain and fabric tensors all coincide at remodeling equilibrium.     

A theoretical model for peripheral tissue heat transfer using the bioheat equation of Weinbaum and Jiji

In this paper the new bioheat equation derived in Weinbaum and Jiji is applied to the three layer conceptual model of microvascular surface tissue organization proposed in. A simplified one-dimensional quantitative model of peripheral tissue energy exchange is then developed for application in limb and whole body heat transfer studies. A representative vasculature is constructed for each layer and the enhancement in the local tensor conductivity of the tissue as a function of vascular geometry and blood flow is examined. Numerical solutions for the boundary value problem coupling the three layers are presented and these results used to study the thermal behavior of peripheral tissue for a wide variety of physiological conditions from supine resting state to maximum exercise.     

Optical anisotropy of polypeptide chains

Optical anisotropies γ² of N-t-butylacetamide (tBA), N-Methylacetamide (MA), and N, N-dimethylacetamide (DMA) have been determined from the Rayleigh ratios for depolarzed scattering by dilute solutions of the amides in p-dioxane. Traceless optical polarizability tensors \documentclass{article}\pagestyle{empty}\begin{document}$ \widehat{\rm \alpha } $\end{document} for the amides are derived from these results in conjunction with the Kerr constant for tBA determined by LeGèvre and co-workers. It is shown that the tensor \documentclass{article}\pagestyle{empty}\begin{document}$ \widehat{\rm \alpha } $\end{document}_i for the glycyle unit in a polypeptide chain may be identified with \documentclass{article}\pagestyle{empty}\begin{document}$ \widehat{\rm \alpha } $\end{document}MA . Methods for deriving corresponding tensors for other peptide units are indicated and the traceless polarizability tensor \documentclass{article}\pagestyle{empty}\begin{document}$ \widehat{\rm \alpha } $\end{document} for a polypeptide chain in any specified configuration is formulated.     

System of kinetic equations describing large-scale processes in collisionless space plasma

A system of kinetic equations describing relatively slow large-scale processes in collisionless magnetoplasma structures with a spatial resolution of about the characteristic gyroradius is derived. Plasma is assumed to be quasineutral, while the magnetic and electric fields are determined by the instantaneous distributions of the particle and current densities and the stress tensor of all plasma components in the longrange instantaneous interaction approximation. A special version of equations is derived for the case of magnetized electrons described by the Vlasov equation in the drift approximation. The obtained system of equations can be used to develop a global numerical kinetic model of the Earth’s magnetosphere with a spatial resolution of about 100 km, as well as local models of certain regions of the Earth’s magnetosphere with a higher resolution.