Publications

Biophysical Journal

In 't Veld, Pieter J.; Stevens, Mark J.

We perform atomistic simulations on a single collagen molecule to determine its intrinsic molecular strength. A tensile pull simulation to determine the tensile strength and Young's modulus is performed, and a simulation that separates two of the three helices of collagen examines the internal strength of the molecule. The magnitude of the calculated tensile forces is consistent with the strong forces of bond stretching and angle bending that are involved in the tensile deformation. The triple helix unwinds with increasing tensile force. Pulling apart the triple helix has a smaller, oscillatory force. The oscillations are due to the sequential separation of the hydrogen-bonded helices. The force rises due to reorienting the residues in the direction of the separation force. The force drop occurs once the hydrogen bond between residues on different helices break and the residues separate. © 2008 by the Biophysical Society.

Grest, Gary S.; In 't Veld, Pieter J.; Lechman, Jeremy B.

Abstract not provided.

Molecular Physics

Ismail, Ahmed I.; In 't Veld, Pieter J.; Grest, Gary S.

Abstract not provided.

In 't Veld, Pieter J.; Ismail, Ahmed I.; Grest, Gary S.

Abstract not provided.

Horsch, Mark H.; Grest, Gary S.; In 't Veld, Pieter J.

Abstract not provided.

Journal of Chemical Physics

In 't Veld, Pieter J.; Ismail, Ahmed I.; Grest, Gary S.

Abstract not provided.

Holdych, David J.; Stevens, Mark J.; In 't Veld, Pieter J.

The purpose of this project is to develop tools to model and simulate the processes of self-assembly and growth in biological systems from the molecular to the continuum length scales. The model biological system chosen for the study is the tendon fiber which is composed mainly of Type I collagen fibrils. The macroscopic processes of self-assembly and growth at the fiber scale arise from microscopic processes at the fibrillar and molecular length scales. At these nano-scopic length scales, we employed molecular modeling and simulation method to characterize the mechanical behavior and stability of the collagen triple helix and the collagen fibril. To obtain the physical parameters governing mass transport in the tendon fiber we performed direct numerical simulations of fluid flow and solute transport through an idealized fibrillar microstructure. At the continuum scale, we developed a mixture theory approach for modeling the coupled processes of mechanical deformation, transport, and species inter-conversion involved in growth. In the mixture theory approach, the microstructure of the tissue is represented by the species concentration and transport and material parameters, obtained from fibril and molecular scale calculations, while the mechanical deformation, transport, and growth processes are governed by balance laws and constitutive relations developed within a thermodynamically consistent framework.