Publications

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This LDRD project has involved the development and application of Sandia's massively parallel materials modeling software to several significant biophysical systems. They have been successful in applying the molecular dynamics code LAMMPS to modeling DNA, unstructured proteins, and lipid membranes. They have developed and applied a coupled transport-molecular theory code (Tramonto) to study ion channel proteins with gramicidin A as a prototype. they have used the Towhee configurational bias Monte-Carlo code to perform rigorous tests of biological force fields. they have also applied the MP-Sala reacting-diffusion code to model cellular systems. Electroporation of cell membranes has also been studied, and detailed quantum mechanical studies of ion solvation have been performed. In addition, new molecular theory algorithms have been developed (in FasTram) that may ultimately make protein solvation calculations feasible on workstations. Finally, they have begun implementation of a combined molecular theory and configurational bias Monte-Carlo code. They note that this LDRD has provided a basis for several new internal (e.g. several new LDRD) and external (e.g. 4 NIH proposals and a DOE/Genomes to Life) proposals.

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Molecular dynamics simulations of a simple, bead-spring model of semiflexible polyelectrolytes such as DNA are performed. All charges are explicitly treated. Starting from extended, noncondensed conformations, condensed structures form in the simulations with tetravalent or trivalent counterions. No condensates form or are stable for divalent counterions. The mechanism by which condensates form is described. Briefly, condensation occurs because electrostatic interactions dominate entropy, and the favored Coulombic structure is a charge ordered state. Condensation is a generic phenomena and occurs for a variety of polyelectrolyte parameters. Toroids and rods are the condensate structures. Toroids form preferentially when the molecular stiffness is sufficiently strong.

The fracture of highly-crosslinked networks is investigated by molecular dynamics simulations. The network is modeled as a bead-spring polymer network between two solid surfaces. The network is dynamically formed by crosslinking an equilibrated liquid mixture. Tensile pull fracture is simulated as a function of the number of interracial bonds. The sequence of molecular structural deformations that lead to failure are determined, and the connectivity is found to strongly control the stress-strain response and failure modes. The failure strain is related to the minimal paths in the network that connect the two solid surfaces. The failure stress is a fraction of the ideal stress required to fracture all the interracial bonds, and is linearly proportional to the number of interracial bonds. By allowing only a single bond between a crosslinker and the surface, interracial failure always occurs. Allowing up to half of the crosslinker's bonds to occur with the surface, cohesive failure can occur.

For highly crosslinked, polymer networks bonded to a solid surface, the effect of interfacial bond density as well as system size on interfacial fracture is studied molecular dynamics simulations. The correspondence between the stress-strain curve and the sequence of molecular deformations is obtained. The failure strain for a fully bonded surface is equal to the strain necessary to make taut the average minimal path through the network from the bottom solid surface to the top surface. At bond coverages less than full, nanometer scale cavities form at the surface yielding an inhomogeneous strain profile. The failure strain and stress are linearly proportional to the number of bonds at the interface unless the number of bonds is so few that van der Waals interactions dominate. The failure is always interfacial due to fewer bonds at the interface than in the bulk.

The failure of thermosetting polymer adhesives is an important problem which particularly lacks understanding from the molecular viewpoint. While linear elastic fracture mechanics works well for such polymers far from the crack tip, the method breaks down near the crack tip where large plastic deformation occurs and the molecular details become important [1]. Results of molecular dynamics simulations of highly crosslinked polymer networks bonded to a solid surface are presented here. Epoxies are used as the guide for modeling. The focus of the simulations is the network connectivity and the interfacial strength. In a random network, the bond stress is expected to vary, and the most stressed bonds will break first [2]. Crack initiation should occur where a cluster of highly constrained bonds exists. There is no reason to expect crack initiation to occur at the interface. The results to be presented show that the solid surface limits the interfacial bonding resulting in stressed interfacial bonds and interfacial fracture. The bonds in highly-crosslinked random networks do not become stressed as expected. The sequence of molecular structural deformations that lead to failure has been determined and found to be strongly dependent upon the network connectivity. The structure of these networks and its influence on the stress-strain behavior will be discussed in general. A set of ideal, ordered networks have been constructed to manipulate the deformation sequence to achieve different fracture modes (i.e. cohesive vs. adhesive).

This report focuses on the relationship between the fundamental interactions acting across an interface and macroscopic engineering observable such as fracture toughness or fracture stress. The work encompasses experiment, theory, and simulation. The model experimental system is epoxy on polished silicon. The interfacial interactions between the substrate and the adhesive are varied continuously using self-assembling monolayer. Fracture is studied in two specimen geometries: a napkin-ring torsion geometry and a double cantilevered beam specimen. Analysis and modeling involves molecular dynamics simulations and continuum mechanics calculations. Further insight is gained from analysis of measurements in the literature of direct force measurements for various fundamental interactions. In the napkin-ring test, the data indicate a nonlinear relationship between interface strength and fracture stress. In particular, there is an abrupt transition in fracture stress which corresponds to an adhesive-to-cohesive transition. Such nonlinearity is not present in the MD simulations on the tens-of-nanometer scale, which suggests that the nonlinearity comes from bulk material deformation occurring on much larger length scales. We postulate that the transition occurs when the interface strength becomes comparable to the yield stress of the material. This postulate is supported by variation observed in the fracture stress curve with test temperature. Detailed modeling of the stress within the sample has not yet been attempted. In the DCB test, the relationship between interface strength and fracture toughness is also nonlinear, but the fracture mechanisms are quite different. The fracture does not transition from adhesive to cohesive, but remains adhesive over the entire range of interface strength. This specimen is modeled quantitatively by combining (i) continuum calculations relating fracture toughness to the stress at 90 {angstrom} from the crack tip, and (ii) a relationship from molecular simulations between fracture stress on a {approx} 90 {angstrom} scale and the fraction of surface sites which chemically bond. The resulting relationship between G{sub c} and fraction of bonding sites is then compared to the experimental data. This first order model captures the nonlinearity in the experimentally-determined relationship. A much more extensive comparison is needed (calculations extending to higher G{sub c} values, experimental data extending to lower G{sub c} values) to guide further model development.