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.
There are many important biological processes involving lipid bilayers on times scales beyond that accessible by atomistic simulations. We have developed coarse-grained, bead-spring models of lipid molecules to treat membrane fusion, domain formation and the general physical characteristics of lipid bilayers. A key aspect of these coarse-grained models is that the liquid nature of a bilayer is explicitly present in the simulations; the lipids diffuse far beyond their neighbors in contrast to atomistic simulations. With these models self-assembly into a bilayer starting from a random configuration of lipids and solvent is readily simulated. We have performed extensive simulations to characterize these lipid models in single component lipid bilayers. For a variety of tail lengths, the area per lipid as a function of temperature has been calculated; the liquid-gel transition has been characterized. Models have been developed for a variety of lipids including double bonds in the lipid tails. Simulation results will be presented for fusion and domain formation.
In this study, we perform molecular dynamics simulations of adhesive contact and friction between alkylsilane Si(OH){sub 3}(CX{sub 2}){sub 10}CX{sub 3} and alkoxylsilane Si(OH){sub 2}(CX{sub 2}){sub 10}CX{sub 3} (where X = H or F) self-assembled monolayers (SAMs) on an amorphous silica substrate. The alkylsilane SAMs are primarily hydrogen-bonded or physisorbed to the surface. The alkoxylsilane SAMs are covalently bonded or chemisorbed to the surface. Previously, we studied the chemisorbed systems. In this work, we study the physisorbed systems and compare the tribological properties with the chemisorbed systems. Furthermore, we examine how water at the interface of the SAMs and substrate affects the tribological properties of the physisorbed systems. When less than a third of a monolayer is present, very little difference in the microscopic friction coefficient {mu} or shear stresses is observed. For increasing amounts of water, the values of {mu} and the shear stresses decrease; this effect is somewhat more pronounced for fluorocarbon alkylsilane SAMs than for the hydrocarbon SAMs. The observed decrease in friction is a consequence of a slip plane that occurs in the water as the amount of water is increased. We studied the frictional behavior using relative shear velocities ranging from v = 2 cm/s to 2 m/s. Similar to previously reported results for alkoxylsilane SAMs, the values of the measured stress and {mu} for the alkylsilane SAM systems decrease monotonically with v.
Understanding the dynamics of the membrane protein rhodopsin will have broad implications for other membrane proteins and cellular signaling processes. Rhodopsin (Rho) is a light activated G-protein coupled receptor (GPCR). When activated by ligands, GPCRs bind and activate G-proteins residing within the cell and begin a signaling cascade that results in the cell's response to external stimuli. More than 50% of all current drugs are targeted toward G-proteins. Rho is the prototypical member of the class A GPCR superfamily. Understanding the activation of Rho and its interaction with its Gprotein can therefore lead to a wider understanding of the mechanisms of GPCR activation and G-protein activation. Understanding the dark to light transition of Rho is fully analogous to the general ligand binding and activation problem for GPCRs. This transition is dependent on the lipid environment. The effect of lipids on membrane protein activity in general has had little attention, but evidence is beginning to show a significant role for lipids in membrane protein activity. Using the LAMMPS program and simulation methods benchmarked under the IBIG program, we perform a variety of allatom molecular dynamics simulations of membrane proteins.
Lee, Kun C.; Borukhov, Itamar; Gelbart, William M.; Liu, Andrea J.; Stevens, Mark J.
The effective interactions between two like-charged rods were examined as a function of angle and separation using molecular dynamics simulations. The effect of concentrations of simple and multivalent salts on the electrostatic repulsions and multivalent-ion-induced attractions were determined. It was found that the stable configuration of two rods evolves from isolated rods to aggregated perpendicular rods to aggregated parallel rods as a result of an increase in the multivalent salt. Monovalent salt was found to enhance the attraction near the onset of aggregation, and reduce it at a higher concentration.
The effect of cross-linker functionality and interfacial bond density on the fracture behavior of highly cross-linked polymer networks bonded to a solid surface is studied using large-scale molecular dynamics simulations. Three different cross-linker functionalities (f = 3, 4, and 6) are considered. The polymer networks are created between two solid surfaces with the number of bonds to the surfaces varying from zero to full bonding to the network. Stress?strain curves are determined for each system from tensile pull and shear deformations. At full interfacial bond density the failure mode is cohesive. The cohesive failure stress is almost identical for shear and tensile modes. The simulations directly show that cohesive failure occurs when the number of interfacial bonds is greater than in the bulk. Decreasing the number of interfacial bonds results in cohesive to adhesive transition consistent with recent experimental results. The correspondence between the stress?strain curves at different f and the sequence of molecular deformations is obtained. The failure stress decreases with smaller f while failure strain increases with smaller f.