GENIe - Global-problematique Education Network Initiative

Postprint (published version

A Plea for More Theory in Molecular Biology

The integrationist principles of systems theory have proven hugely successful in the physical sciences and engineering. It is an underlying assumption made in the systems approach to biology that they can also be used to understand biological phenomena at the level of an entire organism or organ. Within this holistic vision, the vastmajority of systems biology research projects investigate phenomena at the level of the cell, with the belief that unifying principles established at the most basic level can establish a framework within which we may understand phenomena at higher levels of organization. In this spirit, and to use a celestial analogy, if a disease effecting an organ or entire body is our universe of discourse, then the cell is the star we gaze at. In building an understanding of disease and the effect of drugs, systems biology makes an implicit assumption about direct causal entailment between cell function and physiology. A skeptic might argue that this is about the same as trying to predict the world economy from observations made at a local supermarket. However, assuming for the moment that the money and hope we are investing inmolecular biology, genomics, and systems biology is justified, how should this amazing 118 O. Wolkenhauer, M. Mesarovi´c, P. Wellstead intellectual achievement be possible? In this chapter we argue that an essential tool to progress is a systems theory that allows biological objects and their operational characteristics to be captured in a succinct yet general form. Armed with this conceptual framework, we construct mathematical representations of standard cellular and intercellular functions which can be integrated to describe more general processes of cell complexes, and potentially entire organ

Phenomenological constitutive model for a CNT turf

AbstractCarbon nanotubes (CNT), grown on a substrate, form a turf – a complex structure of intertwined, mostly nominally vertical tubes, cross-linked by adhesive contact and few bracing tubes. The turfs are compliant and good thermal and electrical conductors. In this paper, we consider the micromechanical analysis of the turf deformation reported earlier, and develop a phenomenological constitutive model of the turf. We benchmark the developed model using a finite element implementation and compare the model predictions to the results two different nanoindentation tests.The model includes: nonlinear elastic deformation, small Kelvin–Voigt type relaxation, caused by the thermally activated sliding of contacts, and adhesive contact between the turf and the indenter. The pre-existing (locked-in) strain energy of bent nanotubes produces a high initial tangent modulus, followed by an order of magnitude decrease in the tangent modulus with increasing deformation. The strong adhesion between the turf and indenter tip is due to the van der Waals interactions.The finite element simulations capture the results from the nanoindentation experiments, including the loading, unloading, viscoelastic relaxation during hold, and adhesive pull-off

Formal properties of recursive Virtual Machine architectures.

A formal model of hardware/software architectures is developed and applied to Virtual Machine Systems. Results are derived on the sufficient conditions that a machine architecture must verify in order to support VM systems. The model deals explicitly with resource mappings (protection) and with I/O devices. Some already published results are retrieved and other ones, more general, are obtained

Effects of crack tip geometry on dislocation emission and cleavage: A possible path to enhanced ductility

We present a systematic study of the effect of crack blunting on subsequent crack propagation and dislocation emission. We show that the stress intensity factor required to propagate the crack is increased as the crack is blunted by up to thirteen atomic layers, but only by a relatively modest amount for a crack with a sharp 60$^\circ$ corner. The effect of the blunting is far less than would be expected from a smoothly blunted crack; the sharp corners preserve the stress concentration, reducing the effect of the blunting. However, for some material parameters blunting changes the preferred deformation mode from brittle cleavage to dislocation emission. In such materials, the absorption of preexisting dislocations by the crack tip can cause the crack tip to be locally arrested, causing a significant increase in the microscopic toughness of the crack tip. Continuum plasticity models have shown that even a moderate increase in the microscopic toughness can lead to an increase in the macroscopic fracture toughness of the material by several orders of magnitude. We thus propose an atomic-scale mechanism at the crack tip, that ultimately may lead to a high fracture toughness in some materials where a sharp crack would seem to be able to propagate in a brittle manner. Results for blunt cracks loaded in mode II are also presented.Comment: 12 pages, REVTeX using epsfig.sty. 13 PostScript figures. Final version to appear in Phys. Rev. B. Main changes: Discussion slightly shortened, one figure remove

A New Biology: A Modern Perspective on the Challenge of Closing the Gap between the Islands of Knowledge

This paper discusses the rebirth of the old quest for the principles of biology along the discourse line of machine-organism disanalogy and within the context of biocomputation from a modern perspective. It reviews some new attempts to revise the existing body of research and enhance it with new developments in some promising fields of mathematics and computation. The major challenge is that the latter are expected to also answer the need for a new framework, a new language and a new methodology capable of closing the existing gap between the different levels of complex system organization

Wide Range Control of Microstructure and Mechanical Properties of Carbon Nanotube Forests: A Comparison Between Fixed and Floating Catalyst CVD Techniques

Vertically aligned carbon nanotube (CNT) forests may be used as miniature springs, compliant thermal interfaces, and shock absorbers, and for these and other applications it is vital to understand how to engineer their mechanical properties. Herein is investigated how the diameter and packing density within CNT forests govern their deformation behavior, structural stiffness, and elastic energy absorption properties. The mechanical behavior of low‐density CNT forests grown by fixed catalyst CVD methods and high‐density CNT forests grown by a floating catalyst CVD method are studied by in situ SEM compression testing and tribometer measurements of force‐displacement relationships. Low‐density and small‐diameter CNT columns (fixed catalyst) exhibit large plastic deformation and can be pre‐deformed to act as springs within a specified elastic range, whereas high‐density and large‐diameter CNT columns (floating catalyst) exhibit significant elastic recovery after deformation. In this work the energy absorption capacity of CNT forests is tuned over three orders of magnitude and it is shown that CNT forest density can be tuned over a range of conventional foam materials, but corresponding stiffness is ∼10× higher. It is proposed that the elastic behavior of CNT forests is analogous to open‐cell foams and a simple model is presented. It is also shown that this model can be useful as a first‐order design tool to establish design guidelines for the mechanical properties of CNT forests and selection of the appropriate synthesis method. Wide range stiffness tuning of carbon nanotube (CNT) forests over three orders of magnitude is presented by directly modifying the diameter and packing density of CNTs through the modulation of chemical vapor deposition (CVD) parameters. Fixed catalyst and floating catalyst CVD techniques exhibit significantly different deformation mechanisms and the open‐cell foam model predicts the stiffness ratio within one type of CVD method very well.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/94517/1/5028_ftp.pd