J. J. de Pablo

Monte Carlo simulations of Wyoming sodium montmorillonite hydrates

Monte Carlo simulations have been used to predict the interlayer basal separations of sodium-saturated Wyoming clays at constant stress (NPzzT ensemble) and at constant chemical potential (μVT ensemble). These simulations use the Ewald summation technique to incorporate long-range Coulombic interactions in the calculation of the total potential energy and the pressure tensor. A comparison is made between the use of one, two, and three sheets of clay. It is shown that, for small separations, at least two separate clay sheets must be used to avoid system-size effects. The stable interlamellar separations are determined by combining results from isostress–isothermal and grand canonical simulations. It is shown that, consistent with experiments, at the temperature and pressure studied here, the cations in the interlayer are hydrated, except at the smallest basal separations.

A Mesoscale Model of DNA and Its Renaturation

A mesoscale model of DNA is presented (3SPN.1), extending the scheme previously developed by our group. Each nucleotide is mapped onto three interaction sites. Solvent is accounted for implicitly through a medium-effective dielectric constant and electrostatic interactions are treated at the level of Debye-Hückel theory. The force field includes a weak, solvent-induced attraction, which helps mediate the renaturation of DNA. Model parameterization is accomplished through replica exchange molecular dynamics simulations of short oligonucleotide sequences over a range of composition and chain length. The model describes the melting temperature of DNA as a function of composition as well as ionic strength, and is consistent with heat capacity profiles from experiments. The dependence of persistence length on ionic strength is also captured by the force field. The proposed model is used to examine the renaturation of DNA. It is found that a typical renaturation event occurs through a nucleation step, whereby an interplay between repulsive electrostatic interactions and colloidal-like attractions allows the system to undergo a series of rearrangements before complete molecular reassociation occurs.

Polymer-particle mixtures: Depletion and packing effects

The structure of polymers in the vicinity of spherical colloids is investigated by Monte Carlo simulations and integral equation theory. Polymers are represented by a simple bead-spring model; only repulsive Lennard-Jones interactions are taken into account. Using advanced trial moves that alter chain connectivity, depletion and packing effects are analyzed as a function of chain length and density, both at the bond and the chain level. Chain ends segregate to the colloidal surface and polymer bonds orient parallel to it. In the dilute regime, the polymer chain length governs the range of depletion and has a negligible influence on monomer packing in dense polymer melts. Polymers adopt an ellipsoidal shape, with the larger axis parallel to the surface of the particle, as they approach larger colloids. The dimensions are perturbed within the range of the depletion layer.

Liquid-crystal-mediated self-assembly at nanodroplet interfaces

Technological applications of liquid crystals have generally relied on control of molecular orientation at a surface or an interface. Such control has been achieved through topography, chemistry and the adsorption of monolayers or surfactants. The role of the substrate or interface has been to impart order over visible length scales and to confine the liquid crystal in a device. Here, we report results from a computational study of a liquid-crystal-based system in which the opposite is true: the liquid crystal is used to impart order on the interfacial arrangement of a surfactant. Recent experiments on macroscopic interfaces have hinted that an interfacial coupling between bulk liquid crystal and surfactant can lead to a two-dimensional phase separation of the surfactant at the interface, but have not had the resolution to measure the structure of the resulting phases. To enhance that coupling, we consider the limit of nanodroplets, the interfaces of which are decorated with surfactant molecules that promote local perpendicular orientation of mesogens within the droplet. In the absence of surfactant, mesogens at the interface are all parallel to that interface. As the droplet is cooled, the mesogens undergo a transition from a disordered (isotropic) to an ordered (nematic or smectic) liquid-crystal phase. As this happens, mesogens within the droplet cause a transition of the surfactant at the interface, which forms new ordered nanophases with morphologies dependent on surfactant concentration. Such nanophases are reminiscent of those encountered in block copolymers, and include circular, striped and worm-like patterns.

Self-assembling resists for nanolithography

In this paper we present our approach for integrating block copolymers into the lithographic process so as to enable molecular-level control over the dimensions and shapes of nanoscale patterned resist features and simultaneously retain essential process attributes such as pattern perfection, registration, and the ability to create non-regular device-oriented structures. Combining self-assembling materials with advanced lithographic tools may allow current manufacturing techniques to be extended to the scale of 10 nm and below and meet the long-term requirements detailed in the International Technology Roadmap for Semiconductors (2004)

Potential of mean force between two nanometer-scale particles in a polymer solution

Expanded ensemble density-of-states simulations and a connectivity altering algorithm are used to investigate the effective interactions that arise between nanoparticles suspended in polymer solutions. Our calculations with systems of long polymeric chains reveal oscillations in the effective polymer-induced interactions between the particles, even at low concentrations. The range of these interactions is considerably longer than originally anticipated, and their origin is traced back to the chain-end effects and density fluctuations that were absent in previous treatments of these systems.

Engineering tissue from human embryonic stem cells

•  Stem cell tissue engineering –  Potential cell sources –  Incorporation of hESCs •  Undifferentiated hESC culture engineering •  Ectodermal tissues –  Skin –  Cornea –  Neural lineages •  Mesodermal tissues –  Heart –  Bone and cartilage –  Circulatory system •  Endodermal tissues –  Pancreas –  Liver •  Future challenges

Quenched disorder in a liquid-crystal biosensor: Adsorbed nanoparticles at confining walls

We analyze the response of a nematic liquid-crystal film, confined between parallel walls, to the presence of nanoscopic particles adsorbed at the walls. This is done for a variety of patterns of adsorption (random and periodic) and operational conditions of the system that can be controlled in experimental liquid-crystal-based devices. We compute simulated optical textures and the total optical output of the sensor between crossed polars, as well as the correlation function for the liquid-crystal tensor order parameter; we use these observables to discuss the gradual destruction of the original uniform orientation. For large concentrations of particles adsorbed in random patterns, the liquid crystal at the center of the sensor adopts a multidomain state, characterized by a small correlation length of the tensor order parameter, and also by a loss of optical anisotropy under observation through crossed polars. In contrast, for particles adsorbed in periodic patterns, the nematic at the center of the cell can remain in a monodomain orientation state, provided the patterns in opposite walls are synchronized.

A two-dimensional model of the deformation of photoresist structures using elastoplastic polymer properties

A model was developed for predicting the collapse behavior of photoresist structures due to the drying of rinse liquids during wet chemical processing. The magnitude of the capillary forces was estimated using the classical thermodynamics of surface tension, and the deformation of the structure was modeled using beam bending mechanics that accounts for both elastic and plastic modes of deformation. The two-dimensional model can predict the critical beam height of collapse as a function of the wetting behavior of the rinse liquid on the beam, the elastic and plastic mechanical properties of the polymeric photoresist, and the beam dimensions. Collapse behavior was predicted for polymer nanostructures with elastoplastic mechanical properties similar to those of bulk poly(methyl methacrylate). We have compared the collapse predictions from our model with the results of models that account only for elastic or plastic deformation behavior. Regimes in the elastic-plastic mechanical property space for which it is...

Bond‐bias simulation of phase equilibria for strongly associating fluids

In this work a novel Monte Carlo method is developed to simulate the equilibrium thermodynamic properties of strongly associating fluids. The highly anisotropic nature of intermolecular interactions in these fluids makes conventional simulation techniques of little use. By introducing biased sampling techniques we are able to explore configuration space efficiently, thereby obtaining reliable estimates for the thermodynamic properties, including phase equilibria, of model systems. The results of our simulations are used to assess the accuracy and validity of various theories for associating fluids.