Mark J. Stevens

The nature of flexible linear polyelectrolytes in salt free solution: A molecular dynamics study

We present results of molecular dynamics simulations of linear polyelectrolytes in solution. The fundamental model for polyelectrolytes in solution is studied. Specifically, simulations are performed for multichain systems of a flexible chain model of charged polymers. The full Coulomb interactions of the monomers and counterions are treated explicitly. Experimental measurements of the osmotic pressure and the structure factor are reproduced. The simulations reveal a new picture of the chain structure based on calculations of the structure factor, persistence length, end‐to‐end distance, etc. We present a detailed discussion of the chain structure and a comparison with present theories. In contrast to the predicted dilute limit of rodlike chains, we find that the chains have significant bending at very low densities. Furthermore, the chains contract significantly before they overlap. We also show that counterion condensation dramatically alters the chain structure.

Simple Simulations of DNA Condensation

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 phenomenon 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.

Coarse-grained simulations of lipid bilayers

A minimal model of lipid molecules consisting of bead-spring representation is developed. The basic interactions are hydrophobic and polar interactions. Essential physical features of lipid bilayers are maintained using this model, and relatively long times can be simulated in comparison to atomistic models. Self-assembly from a random starting configuration to a bilayer can readily be followed using molecular dynamics simulations. The diffusion of lipid molecules well beyond their nearest neighbors is attained. As a basis for description of the model, the area per lipid, the bending modulus, and the area compressibility as a function of temperature and tail length are calculated. A liquid to gel transition is observed and quantitatively characterized. Both saturated and unsaturated lipids are treated.

Capillary waves at the liquid-vapor interface and the surface tension of water

Capillary waves occurring at the liquid-vapor interface of water are studied using molecular dynamics simulations. In addition, the surface tension, determined thermodynamically from the difference in the normal and tangential pressure at the liquid-vapor interface, is compared for a number of standard three- and four-point water models. We study four three-point models (SPC/E, TIP3P, TIP3P-CHARMM, and TIP3P-Ew) and two four-point models (TIP4P and TIP4P-Ew). All of the models examined underestimate the surface tension; the TIP4P-Ew model comes closest to reproducing the experimental data. The surface tension can also be determined from the amplitude of capillary waves at the liquid-vapor interface by varying the surface area of the interface. The surface tensions determined from the amplitude of the logarithmic divergence of the capillary interfacial width and from the traditional thermodynamic method agree only if the density profile is fitted to an error function instead of a hyperbolic tangent function.

Comparison of shear flow of hexadecane in a confined geometry and in bulk

We examine the shear flow of hexadecane confined between plates with separation of 1–10 nm using molecular dynamics simulations. We also performed non-equilibrium molecular dynamics (NEMD) simulations of bulk hexadecane to compare with the simulations in the confined geometry. The stiffness of hexadecane and its high melting temperature result in a tendency to crystallize at room temperature or large load. We find that when confined between hydrocarbon walls, shearing hexadecane exhibits a velocity profile with substantial slip at the wall and essentially constant velocity over most of the interior space between the walls. As the strength of the wall-fluid interaction increases the amount of slip decreases, but slip always occurs at the boundary for the range of parameters studied. The results are compared with recent surface force apparatus experiments on hexadecane and with similar simulations of model bead-spring fluids.

Simulations of Nanotribology with Realistic Probe Tip Models

We present the results of massively parallel molecular dynamics simulations aimed at understanding the nanotribological properties of alkylsilane self-assembled monolayers (SAMs) on amorphous silica. In contrast to studies with opposing flat plates, as found in the bulk of the simulation literature, we use a model system with a realistic AFM tip (radius of curvature ranging from 3 to 30 nm) in contact with a SAM-coated silica substrate. We compare the differences in response between systems in which chains are fully physisorbed, fully chemisorbed, and systems with a mixture of the two. Our results demonstrate that the ubiquitous JKR and DMT models do not accurately describe the contact mechanics of these systems. In shear simulations, we find that the chain length has minimal effects on both the friction force and coefficient. The tip radius affects the friction force only (i.e., the coefficient is unchanged) by a constant shift in magnitude due to the increase in pull-off force with increasing radius. We also find that at extremely low loads, on the order of 10 nN, shearing from the tip causes damage to the physisorbed monolayers by removal of molecules.

Interactions between charged spherical macroions

Monte Carlo (MC) simulations were used to study the screened interactions between charged spherical macroions surrounded by discrete counterions, and to test previous theories of screening. The simulations were performed in the primitive cell of the bcc lattice, and in the spherical Wigner–Seitz cell that is commonly used in approximate calculations. We found that the Wigner–Seitz approximation is valid even at high volume fractions φ and large macroion charges Z, because the macroion charge becomes strongly screened. Pressures calculated from Poisson–Boltzmann theory and local density functional theory deviate from MC values as φ and Z increase, but continue to provide upper and lower bounds for the MC results. While Debye–Huckel (DH) theory fails badly when the bare charge is used, MC pressures can be fit with an effective DH charge, ZDH, that is nearly independent of volume fraction. As Z diverges, ZDH saturates at zψmaxRm/λ, where z is the counterion charge, Rm is the macroion radius, λ is the Bjerrum...

Ionic Aggregate Structure in Ionomer Melts: Effect of Molecular Architecture on Aggregates and the Ionomer Peak

We perform a comprehensive set of coarse-grained molecular dynamics simulations of ionomer melts with varying polymer architectures and compare the results to experiments in order to understand ionic aggregation on a molecular level. The model ionomers contain periodically or randomly spaced charged beads, placed either within or pendant to the polymer backbone, with the counterions treated explicitly. The ionic aggregate structure was determined as a function of the spacing of charged beads and also depends on whether the charged beads are in the polymer backbone or pendant to the backbone. The low wavevector ionomer peak in the counterion scattering is observed for all systems, and it is sharpest for ionomers with periodically spaced pendant charged beads with a large spacing between charged beads. Changing to a random or a shorter spacing moves the peak to lower wavevector. We present new experimental X-ray scattering data on Na(+)-neutralized poly(ethylene-co-acrylic acid) ionomers that show the same two trends in the ionomer peak, for similarly structured ionomers. The order within and between aggregates, and how this relates to various models used to fit the ionomer peak, is quantified and discussed.

Effect of mono- and multivalent salts on angle-dependent attractions between charged rods.

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.

Simulation of the Mechanical Strength of a Single Collagen Molecule

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 Youngs 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.