Ionomers, polymers containing a small fraction of covalently bound ionic groups, have potential as solid, single ion conducting electrolytes in future batteries. However, the ions tend to form aggregates, making counterion diffusion unacceptably slow. A key materials design question is how molecular properties affect ionic aggregation and counterion dynamics. Recent experimental advances have allowed synthesis and extensive characterization of ionomers with a precise, constant spacing of charged groups. Because the molecular architecture is controlled and these materials show increased ionic aggregate ordering versus their randomly spaced analogs, this set of experiments is ideal for direct comparisons with molecular simulations. We perform molecular dynamics simulations of coarse-grained ionomers with either periodically or randomly spaced charged beads. The charged beads are placed either in the polymer backbone (ionenes) or as pendants on the backbone. To understand the range of ionic aggregate morphologies possible in real materials, we vary the spacing of charges along the chain, degree of randomness (from periodic to random block to fully random), and dielectric constant. The well-known "ionomer peak" in the scattering is present in all cases. The peak is significantly more intense for pendant ions with a long periodic spacing of charged beads, which form roughly spherical aggregates. This morphology is in qualitative contrast to the extended aggregates of ionenes that show increased counterion diffusion. Depending on the degree of randomness in spacing of charged beads along the chain, counterion diffusion can increase or decrease versus that of the precisely spaced materials. Possible implications for ionomer electrolyte design will be discussed. Sandia National Laboratories is a multi-program laboratory operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.
Ionomers--polymers containing a small fraction of covalently bound ionic groups--have potential application as solid electrolytes in batteries. Understanding ion transport in ionomers is essential for such applications. Due to strong electrostatic interactions in these materials, the ions form aggregates, tending to slow counterion diffusion. A key question is how ionomer properties affect ionic aggregation and counterion dynamics on a molecular level. Recent experimental advances have allowed synthesis and extensive characterization of ionomers with a precise, constant spacing of charged groups, making them ideal for controlled measurement and more direct comparison with molecular simulation. We have used coarse-grained molecular dynamics to simulate such ionomers with regularly spaced charged beads. The charged beads are placed either in the polymer backbone or as pendants on the backbone. The polymers, along with the counterions, are simulated at melt densities. The ionic aggregate structure was determined as a function of the dielectric constant, spacing of the charged beads on the polymer, and the sizes of the charged beads and counterions. The pendant ion architecture can yield qualitatively different aggregate structures from those of the linear polymers. For small pendant ions, roughly spherical aggregates have been found above the glass transition temperature. The implications of these aggregates for ion diffusion will be discussed.
Cell membranes are dynamic substrates that achieve a diverse array of functions through multi-scale reconfigurations. We explore the morphological changes that occur upon protein interaction to model membrane systems that induce deformation of their planar structure to yield nanotube assemblies. In the two examples shown in this report we will describe the use of membrane adhesion and particle trajectory to form lipid nanotubes via mechanical stretching, and protein adsorption onto domains and the induction of membrane curvature through steric pressure. Through this work the relationship between membrane bending rigidity, protein affinity, and line tension of phase separated structures were examined and their relationship in biological membranes explored.
This highly interdisciplinary team has developed dual-color, total internal reflection microscopy (TIRF-M) methods that enable us to optically detect and track in real time protein migration and clustering at membrane interfaces. By coupling TIRF-M with advanced analysis techniques (image correlation spectroscopy, single particle tracking) we have captured subtle changes in membrane organization that characterize immune responses. We have used this approach to elucidate the initial stages of cell activation in the IgE signaling network of mast cells and the Toll-like receptor (TLR-4) response in macrophages stimulated by bacteria. To help interpret these measurements, we have undertaken a computational modeling effort to connect the protein motion and lipid interactions. This work provides a deeper understanding of the initial stages of cellular response to external agents, including dynamics of interaction of key components in the signaling network at the 'immunological synapse,' the contact region of the cell and its adversary.
We have conducted a molecular dynamics (MD) simulation study of water confined between methyl-terminated and carboxyl-terminated alkylsilane self-assembled monolayers (SAMs) on amorphous silica substrates. In doing so, we have investigated the dynamic and structural behavior of the water molecules when compressed to loads ranging from 20 to 950 MPa for two different amounts of water (27 and 58 water molecules/nm{sup 2}). Within the studied range of loads, we observe that no water molecules penetrate the hydrophobic region of the carboxyl-terminated SAMs. However, we observe that at loads larger than 150 MPa water molecules penetrate the methyl-terminated SAMs and form hydrogen-bonded chains that connect to the bulk water. The diffusion coefficient of the water molecules decreases as the water film becomes thinner and pressure increases. When compared to bulk diffusion coefficients of water molecules at the various loads, we found that the diffusion coefficients for the systems with 27 water molecules/nm{sup 2} are reduced by a factor of 20 at low loads and by a factor of 40 at high loads, while the diffusion coefficients for the systems with 58 water molecules/nm{sup 2} are reduced by a factor of 25 at all loads.
A molecular-scale interpretation of interfacial processes is often downplayed in the analysis of traditional water treatment methods. However, such an approach is critical for the development of enhanced performance in traditional desalination and water treatments. Water confined between surfaces, within channels, or in pores is ubiquitous in technology and nature. Its physical and chemical properties in such environments are unpredictably different from bulk water. As a result, advances in water desalination and purification methods may be accomplished through an improved analysis of water behavior in these challenging environments using state-of-the-art microscopy, spectroscopy, experimental, and computational methods.
A suite of experimental nuclear magnetic resonance (NMR) spectroscopy tools were developed to investigate lipid structure and dynamics in model membrane systems. By utilizing both multinuclear and multidimensional NMR experiments a range of different intra- and inter-molecular contacts were probed within the membranes. Examples on pure single component lipid membranes and on the canonical raft forming mixture of DOPC/SM/Chol are presented. A unique gel phase pretransition in SM was also identified and characterized using these NMR techniques. In addition molecular dynamics into the hydrogen bonding network unique to sphingomyelin containing membranes were evaluated as a function of temperature, and are discussed.
We have enhanced our parallel molecular dynamics (MD) simulation software LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator, lammps.sandia.gov) to include many new features for accelerated simulation including articulated rigid body dynamics via coupling to the Rensselaer Polytechnic Institute code POEMS (Parallelizable Open-source Efficient Multibody Software). We use new features of the LAMMPS software package to investigate rhodopsin photoisomerization, and water model surface tension and capillary waves at the vapor-liquid interface. Finally, we motivate the recipes of MD for practitioners and researchers in numerical analysis and computational mechanics.
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.
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.
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.