Chromatin: a tunable spring at work inside chromosomes

This paper focuses on mechanical aspects of chromatin biological functioning. Within a basic geometric modeling of the chromatin assembly, we give for the first time the complete set of elastic constants (twist and bend persistence lengths, stretch modulus and twist-stretch coupling constant) of the so-called 30-nm chromatin fiber, in terms of DNA elastic properties and geometric properties of the fiber assembly. The computation naturally embeds the fiber within a current analytical model known as the ``extensible worm-like rope'', allowing a straightforward prediction of the force-extension curves. We show that these elastic constants are strongly sensitive to the linker length, up to 1 bp, or equivalently to its twist, and might locally reach very low values, yielding a highly flexible and extensible domain in the fiber. In particular, the twist-stretch coupling constant, reflecting the chirality of the chromatin fiber, exhibits steep variations and sign changes when the linker length is varied. We argue that this tunable elasticity might be a key feature for chromatin function, for instance in the initiation and regulation of transcription.Comment: 38 pages 15 figure

On computing upper and lower bounds on the outputs of linear elasticity problems approximated by the smoothed finite element method

Verification of the computation of local quantities of interest, e.g. the displacements at a point, the stresses in a local area and the stress intensity factors at crack tips, plays an important role in improving the structural design for safety. In this paper, the smoothed finite element method (SFEM) is used for finding upper and lower bounds on the local quantities of interest that are outputs of the displacement field for linear elasticity problems, based on bounds on strain energy in both the primal and dual problems. One important feature of SFEM is that it bounds the strain energy of the structure from above without needing the solutions of different subproblems that are based on elements or patches but only requires the direct finite element computation. Upper and lower bounds on two linear outputs and one quadratic output related with elasticity—the local reaction, the local displacement and the J-integral—are computed by the proposed method in two different examples. Some issues with SFEM that remain to be resolved are also discussed

Lattice Resistance and Peierls Stress in Finite-size Atomistic Dislocation Simulations

Atomistic computations of the Peierls stress in fcc metals are relatively scarce. By way of contrast, there are many more atomistic computations for bcc metals, as well as mixed discrete-continuum computations of the Peierls-Nabarro type for fcc metals. One of the reasons for this is the low Peierls stresses in fcc metals. Because atomistic computations of the Peierls stress take place in finite simulation cells, image forces caused by boundaries must either be relaxed or corrected for if system size independent results are to be obtained. One of the approaches that has been developed for treating such boundary forces is by computing them directly and subsequently subtracting their effects, as developed by V. B. Shenoy and R. Phillips [Phil. Mag. A, 76 (1997) 367]. That work was primarily analytic, and limited to screw dislocations and special symmetric geometries. We extend that work to edge and mixed dislocations, and to arbitrary two-dimensional geometries, through a numerical finite element computation. We also describe a method for estimating the boundary forces directly on the basis of atomistic calculations. We apply these methods to the numerical measurement of the Peierls stress and lattice resistance curves for a model aluminum (fcc) system using an embedded-atom potential.Comment: LaTeX 47 pages including 20 figure

Classical and all-floating FETI methods for the simulation of arterial tissues

High-resolution and anatomically realistic computer models of biological soft tissues play a significant role in the understanding of the function of cardiovascular components in health and disease. However, the computational effort to handle fine grids to resolve the geometries as well as sophisticated tissue models is very challenging. One possibility to derive a strongly scalable parallel solution algorithm is to consider finite element tearing and interconnecting (FETI) methods. In this study we propose and investigate the application of FETI methods to simulate the elastic behavior of biological soft tissues. As one particular example we choose the artery which is - as most other biological tissues - characterized by anisotropic and nonlinear material properties. We compare two specific approaches of FETI methods, classical and all-floating, and investigate the numerical behavior of different preconditioning techniques. In comparison to classical FETI, the all-floating approach has not only advantages concerning the implementation but in many cases also concerning the convergence of the global iterative solution method. This behavior is illustrated with numerical examples. We present results of linear elastic simulations to show convergence rates, as expected from the theory, and results from the more sophisticated nonlinear case where we apply a well-known anisotropic model to the realistic geometry of an artery. Although the FETI methods have a great applicability on artery simulations we will also discuss some limitations concerning the dependence on material parameters.Comment: 29 page

Non-regularised inverse finite element analysis for 3D traction force microscopy

The tractions that cells exert on a gel substrate from the observed displacements is an increasingly attractive and valuable information in biomedical experiments. The computation of these tractions requires in general the solution of an inverse problem. Here, we resort to the discretisation with finite elements of the associated direct variational formulation, and solve the inverse analysis using a least square approach. This strategy requires the minimisation of an error functional, which is usually regularised in order to obtain a stable system of equations with a unique solution. In this paper we show that for many common threedimensional geometries, meshes and loading conditions, this regularisation is unnecessary. In these cases, the computational cost of the inverse problem becomes equivalent to a direct finite element problem. For the non-regularised functional, we deduce the necessary and sufficient conditions that the dimensions of the interpolated displacement and traction fields must preserve in order to exactly satisfy or yield a unique solution of the discrete equilibrium equations. We apply the theoretical results to some illustrative examples and to real experimental data. Due to the relevance of the results for biologists and modellers, the article concludes with some practical rules that the finite element discretisation must satisfy.Peer ReviewedPostprint (author's final draft

Optimal boundary geometry in an elasticity problem: a systematic adjoint approach

p. 509-524In different problems of Elasticity the definition of the optimal geometry of the boundary, according to a given objective function, is an issue of great interest. Finding the shape of a hole in the middle of a plate subjected to an arbitrary loading such that the stresses along the hole minimizes some functional or the optimal middle curved concrete vault for a tunnel along which a uniform minimum compression are two typical examples. In these two examples the objective functional depends on the geometry of the boundary that can be either a curve (in case of 2D problems) or a surface boundary (in 3D problems). Typically, optimization is achieved by means of an iterative process which requires the computation of gradients of the objective function with respect to design variables. Gradients can by computed in a variety of ways, although adjoint methods either continuous or discrete ones are the more efficient ones when they are applied in different technical branches. In this paper the adjoint continuous method is introduced in a systematic way to this type of problems and an illustrative simple example, namely the finding of an optimal shape tunnel vault immersed in a linearly elastic terrain, is presented.Garcia-Palacios, J.; Castro, C.; Samartin, A. (2009). Optimal boundary geometry in an elasticity problem: a systematic adjoint approach. Editorial Universitat Politècnica de València. http://hdl.handle.net/10251/654

Multiscale Surrogate Modeling and Uncertainty Quantification for Periodic Composite Structures

Computational modeling of the structural behavior of continuous fiber composite materials often takes into account the periodicity of the underlying micro-structure. A well established method dealing with the structural behavior of periodic micro-structures is the so- called Asymptotic Expansion Homogenization (AEH). By considering a periodic perturbation of the material displacement, scale bridging functions, also referred to as elastic correctors, can be derived in order to connect the strains at the level of the macro-structure with micro- structural strains. For complicated inhomogeneous micro-structures, the derivation of such functions is usually performed by the numerical solution of a PDE problem - typically with the Finite Element Method. Moreover, when dealing with uncertain micro-structural geometry and material parameters, there is considerable uncertainty introduced in the actual stresses experienced by the materials. Due to the high computational cost of computing the elastic correctors, the choice of a pure Monte-Carlo approach for dealing with the inevitable material and geometric uncertainties is clearly computationally intractable. This problem is even more pronounced when the effect of damage in the micro-scale is considered, where re-evaluation of the micro-structural representative volume element is necessary for every occurring damage. The novelty in this paper is that a non-intrusive surrogate modeling approach is employed with the purpose of directly bridging the macro-scale behavior of the structure with the material behavior in the micro-scale, therefore reducing the number of costly evaluations of corrector functions, allowing for future developments on the incorporation of fatigue or static damage in the analysis of composite structural components.Comment: Appeared in UNCECOMP 201