Forces in Biological Systems

Israelachvili, J. N., Intermolecular and Surface Forces, 2d ed., Academic Press, New York, 1991. (Undergraduate and graduate levels. The best reference available currently on the topic. Many examples of the application of surface forces in biological systems. The links between molecular forces and surface forces and the relation between molecular forces and bulk properties of materials are discussed in a manner accessible to advanced undergraduate students.)... 

Experimentally, rupture forces in biological systems can be measured with atomic force microscopy, surface force apparatus, optical tweezers, or the biomembrane force probe technique. Each of these methods operates on different time.scales and gives additional insights into the dynamics strength of biological bonds (see Ref. 75). Since none of these methods yields details on the atomic level, this is a nice application for molecular dynamics. 

Interactions between macromolecules (protems, lipids, DNA,.. . ) or biological structures (e.g. membranes) are considerably more complex than the interactions described m the two preceding paragraphs. The sum of all biological mteractions at the molecular level is the basis of the complex mechanisms of life. In addition to computer simulations, direct force measurements [98], especially the surface forces apparatus, represent an invaluable tool to help understand the molecular interactions in biological systems. 

Equations (l)-(3) in combination are a potential energy function that is representative of those commonly used in biomolecular simulations. As discussed above, the fonn of this equation is adequate to treat the physical interactions that occur in biological systems. The accuracy of that treatment, however, is dictated by the parameters used in the potential energy function, and it is the combination of the potential energy function and the parameters that comprises a force field. In the remainder of this chapter we describe various aspects of force fields including their derivation (i.e., optimization of the parameters), those widely available, and their applicability. 

The specific protein-DNA interactions described in this book are all with DNA in its regular B-form, or, in some cases with distorted B-DNA. In biological systems DNA appears not to adopt the A conformation, although double-stranded RNA does preferentially adopt this conformation in vivo. Whether or not Z-DNA occurs in nature is a matter of controversy. However, the formation of A-DNA and Z-DNA in vitro does illustrate the large structural changes that DNA can be forced to undergo. 

Mass transfer Irreversible and spontaneous transport of mass of a chemical component in a space with a non-homogeneous field of the chemical potential of the component. The driving force causing the transport can be the difference in concentration (in liquids) or partial pressures ( in gases) of the component. In biological systems. 

Many experimental results have been published, which deal with shear stress in biological systems. Most of them use laminar flow systems such as viscosimeters, flow channels or flasks and very small agitated vessels which are not relevant to technical reactor systems with fully developed turbulent flow. On the other hand the geometric and technical parameters are often not sufficiently described. Therefore it is not possible to explain the complex mechanism of force in bioreactors only on the basis of existing results from biological systems. 

Johnson, A.S., C.L. Nehl, M.G. Mason, and J.H. Hafner. 2003. Fluid electric force microscopy for charge density mapping in biological systems. Langmuir 19 10007-10010. 

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