A bead and spring model for the stiffness of DNA

Using theory and computation to model nanoscale properties

This article provides an overview of the use of theory and computation to describe the structural, thermodynamic, mechanical, and optical properties of nanoscale materials. Nanoscience provides important opportunities for theory and computation to lead in the discovery process because the experimental tools often provide an incomplete picture of the structure and/or function of nanomaterials, and theory can often fill in missing features crucial to understanding what is being measured. However, there are important challenges to using theory as well, as the systems of interest are usually too large, and the time scales too long, for a purely atomistic level theory to be useful. At the same time, continuum theories that are appropriate for describing larger-scale (micrometer) phenomena are often not accurate for describing the nanoscale. Despite these challenges, there has been important progress in a number of areas, and there are exciting opportunities that we can look forward to as the capabilities of computational facilities continue to expand. Some specific applications that are discussed in this paper include: self-assembly of supramolecular structures, the thermal properties of nanoscale molecular systems (DNA melting and nanoscale water meniscus formation), the mechanical properties of carbon nanotubes and diamond crystals, and the optical properties of silver and gold nanoparticles.

Macromolecular organization of collagen fibres in natural and tanned basement membrane

The elastic constants and ultrastructure of natural and tanned basement membrane of the crystalline lens of the adult rat have been investigated. Sonicated and negatively stained specimens of both membranes show parallel filaments that have similar spacing of 3.5(+/- 0.1) nm and a different periodicity. In natural membrane the periodicity is 3.7(+/- 0.13) nm, whilst in tanned basement membrane the periodicity is 3.2(+/- 0.15) nm. The periodicity ratio of tanned membrane to natural membrane was 0.86 +/- 0.04, whilst the elongation ratio of tanned membrane compared with natural membrane was 0.88 +/- 0.05. In contrast to this, the thickness ratio of tanned to natural membrane was 1.098 +/- 0.045. Tanned basement membrane showed a shrinkage of 12% in length but an increase in thickness of about 10%. These data suggest, firstly, that the degree of extension of the superhelices of the filaments follows closely the degree of extension of the intact membrane and, secondly, that the coiled superhelices of tanned membrane have an angle of tilt of about 42 degrees compared with those of natural membrane, where the angle is about 50 degrees. The Young's modulus of elasticity and ultimate stress of tanned basement membrane are, respectively, eight times greater and one-third as great as natural membrane. The entropy change in basement membrane was calculated from the external work necessary to extend the tanned membrane, and was estimated to be -13.5(+/- 2.4) J K-1 mol-1. An estimate of the change in entropy from thermodynamic measurements made on a suspension of collagen tanned with glutaraldehyde was found to be -30.1(+/- 9.5) J K-1 mol-1. The two different estimates of the change in entropy of collagen following tanning suggest that in basement membrane only about 45% of the collagenous protein has an extensile helical structure.