Layer-by-layer formation of oligoelectrolyte multilayers: a combined experimental and computational study

For the first time, the combination of experimental preparation and results of fully atomistic simulations of an oligoelectrolyte multilayer (OEM) made of poly(diallyl dimethyl ammonium chloride)/poly(styrene sulfonate sodium salt) (PDADMAC/PSS) is presented. The layer-by-layer growth was carried out by dipping silica substrates in oligoelectrolyte solutions and was modeled by means of atomistic molecular dynamics simulations with a protocol that mimics the experimental procedure up to the assembly of four layers. Measurements of OEM thickness, surface roughness and amount of adsorbed oligoelectrolyte chains obtained from both approaches are compared. A good agreement between simulated and experimental results was found, with some deviations due to intrinsic limitations of both methods. However, the combination of information extracted from simulations to support the analysis of experimental data can overcome such restrictions and improve the interpretation of experimental results. On the other hand, processes dominated by slower kinetics, like the destabilization of adsorbed layers upon equilibration with the surrounding environment, are out of reach for the simulation modeling approach, but they can be investigated by monitoring in situ the oligoelectrolyte adsorption during the assembly process. This demonstrates how the synergistic use of simulation and experiments improves the knowledge of OEM properties down to the molecular scale

Mapping atomistic to coarse-grained polymer models using automatic simplex optimization to fit structural properties

We develop coarse-grained force fields for poly (vinyl alcohol) and poly (acrylic acid) oligomers. In both cases, one monomer is mapped onto a coarse-grained bead. The new force fields are designed to match structural properties such as radial distribution functions of various kinds derived by atomistic simulations of these polymers. The mapping is therefore constructed in a way to take into account as much atomistic information as possible. On the technical side, our approach consists of a simplex algorithm which is used to optimize automatically non-bonded parameters as well as bonded parameters. Besides their similar conformation (only the functional side group differs), poly (acrylic acid) was chosen to be in aqueous solution in contrast to a poly (vinyl alcohol) melt. For poly (vinyl alcohol) a non-optimized bond angle potential turns out to be sufficient in connection with a special, optimized non-bonded potential. No torsional potential has to be applied here. For poly (acrylic acid), we show that each peak of the radial distribution function is usually dominated by some specific model parameter(s). Optimization of the bond angle parameters is essential. The coarse-grained forcefield reproduces the radius of gyration of the atomistic model. As a first application, we use the force field to simulate longer chains and compare the hydrodynamic radius with experimental data.Comment: 34 pages, 3 tables, 16 figure

Investigating Interactions of Biomembranes and Alcohols: A Multiscale Approach

We study the interaction of lipid bilayers with short chain alcohols using molecular dynamics on different length scales. We use detailed atomistic modeling and modeling on the length scale where an alcohol is just an amphiphilic dimer. Our strategy is to calibrate a coarse--grained model against the detailed model at selected state points at low alcohol concentration and then perform a wider range of simulations using the coarse--grained model. We get semiquantitative agreement with experiment for the major observables such as order parameter and area per molecule. We find a linear increase of area per molecule with alcohol concentration. The alcohol molecules in both system descriptions are in close contact with the glycerol backbone. Butanol molecules can enter the bilayer to some extent in contrast to the behavior of shorter alcohols. At very high alcohol concentrations we find clearly increased interdigitation between leaflets.Comment: 14 pages, 6 figure

Open Boundary Simulations of Proteins and Their Hydration Shells by Hamiltonian Adaptive Resolution Scheme

The recently proposed Hamiltonian Adaptive Resolution Scheme (H-AdResS) allows to perform molecular simulations in an open boundary framework. It allows to change on the fly the resolution of specific subset of molecules (usually the solvent), which are free to diffuse between the atomistic region and the coarse-grained reservoir. So far, the method has been successfully applied to pure liquids. Coupling the H-AdResS methodology to hybrid models of proteins, such as the Molecular Mechanics/Coarse-Grained (MM/CG) scheme, is a promising approach for rigorous calculations of ligand binding free energies in low-resolution protein models. Towards this goal, here we apply for the first time H-AdResS to two atomistic proteins in dual-resolution solvent, proving its ability to reproduce structural and dynamic properties of both the proteins and the solvent, as obtained from atomistic simulations.Comment: This document is the Accepted Manuscript version of a Published Work that appeared in final form in Journal of Chemical Theory and Computation, copyright \c{opyright} American Chemical Society after peer review and technical editing by the publishe

Hierarchical approach to 'atomistic' 3-D MOSFET simulation

We present a hierarchical approach to the 'atomistic' simulation of aggressively scaled sub-0.1-μm MOSFETs. These devices are so small that their characteristics depend on the precise location of dopant atoms within them, not just on their average density. A full-scale three-dimensional drift-diffusion atomistic simulation approach is first described and used to verify more economical, but restricted, options. To reduce processor time and memory requirements at high drain voltage, we have developed a self-consistent option based on a solution of the current continuity equation restricted to a thin slab of the channel. This is coupled to the solution of the Poisson equation in the whole simulation domain in the Gummel iteration cycles. The accuracy of this approach is investigated in comparison to the full self-consistent solution. At low drain voltage, a single solution of the nonlinear Poisson equation is sufficient to extract the current with satisfactory accuracy. In this case, the current is calculated by solving the current continuity equation in a drift approximation only, also in a thin slab containing the MOSFET channel. The regions of applicability for the different components of this hierarchical approach are illustrated in example simulations covering the random dopant-induced threshold voltage fluctuations, threshold voltage lowering, threshold voltage asymmetry, and drain current fluctuations