Publications

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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.

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.

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Using molecular dynamics simulations we examine the effective interactions between two like-charged rods as a function of angle and separation. In particular, we determine how the competing electrostatic repulsions and multivalent-ion-induced attractions depend upon concentrations of simple and multivalent salts. We find that with increasing multivalent salt, the stable configuration of two rods evolves from isolated rods to aggregated perpendicular rods to aggregated parallel rods; at sufficiently high concentration, additional multivalent salt reduces the attraction. Monovalent salt enhances the attraction near the onset of aggregation and reduces it at a higher concentration of multivalent salt.

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.

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The fracture behavior of binary Lennard-Jones (LJ) glasses is studied by extensive molecular dynamics simulations. These LJ glasses represent a nonbond limit of polymer network glasses. We determine that the low strain behavior of the LJ and polymer glasses is similar. Two different LJ glasses are fractured under tensile strain without any preexisting crack. Void formation and resulting growth as strain increases is the mechanism through which the system fails. Void formation initiates at the yield strain of [Formula presented] which is approximately the same strain at which the yielding behavior is first observed in cross-linked network models of polymer adhesives. The yield stress increased only by small amounts with increased strain rate and with increased system size (from [Formula presented] atoms to [Formula presented] atoms). Within the ranges tested, the stress-strain behavior of these systems is independent of the temperature drop during quench and the initial molecular configuration. © 2003 The American Physical Society.

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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.

For highly cross-linked polymer networks bonded to a solid surface, the effect of interfacial bond density and system size on interfacial fracture is studied using molecular dynamics simulations. Results for tensile and shear mode simulations are given. 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 of the minimal paths through the network from a bonded site on the bottom solid surface to a bonded site on the top surface. At fractional interfacial bond densities, cavities form above the nonbonded surface, yielding an inhomogeneous strain profile and a smaller failure strain. The failure strain and stress are linearly proportional to the number of bonds at the interface except in the tensile mode when number of bonds is so few that van der Waals interactions dominate. The failure mode is successfully constructed to be interracial by limiting the interfacial bond density to be less than the bulk bond density.

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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.

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.

By studying model polymeric networks which only differ in their connectivity, the connectivity is shown to strongly control the stress-strain response and failure modes. The sequence of molecular structural deformations that lead to failure are strongly dependent upon the network connectivity. A set of ideal, ordered networks are constructed to manipulate the deformation sequence to achieve a variety of adhesive qualities. Compared to random, dynamically formed networks, these ideal networks can be made to have either much larger or smaller failure stresses and strains. Unlike the random networks, the failure stress of an ideal network can be made close to the ideal stress equal to breaking all bonds to the substrate. By varying the number of bonds to the surface, the failure mode can be controlled to be either adhesive or cohesive.

This set of view graphs outline the simulation of the behavior of polyelectrolytes.

Stiff polyelectrolytes are found to spontaneously form oriented bundles. Conditions under which bundling occurs are found. Molecular dynamics simulations show that divalent counterions are necessary, and the chains must be sufficiently long and stiff. No aggregation occurs for monovalent counterions. For flexible or short chains, aggregation occurs but bundle formation does not. Because of dynamical constraints, the systems tend to order into a network of connected bundles, not a single bundle. © 1999 The American Physical Society.