In this work, an extension is proposed to the standard iterative Boltzmann inversion (IBI) method used to derive coarse-grained potentials. It is shown that the inclusion of target data from multiple states yields a less state-dependent potential, and is thus better suited to simulate systems over a range of thermodynamic states than the standard IBI method. The inclusion of target data from multiple states forces the algorithm to sample regions of potential phase space that match the radial distribution function at multiple state points, thus producing a derived potential that is more representative of the underlying interactions. It is shown that the algorithm is able to converge to the true potential for a system where the underlying potential is known. It is also shown that potentials derived via the proposed method better predict the behavior of n-alkane chains than those derived via the standard IBI method. Additionally, through the examination of alkane monolayers, it is shown that the relative weight given to each state in the fitting procedure can impact bulk system properties, allowing the potentials to be further tuned in order to match the properties of reference atomistic and/or experimental systems.

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We perform Brownian dynamics simulations on model 3-D systems of mono-tethered nanospheres (TNS) to study the equilibrium morphologies formed by their self-assembly in a selective solvent. We predict that in contrast to flexible amphiphiles the nanospheres are locally ordered and there is an increase in the local order with an increase in concentration or relative nanoparticle diameter. We present the temperature vs concentration phase diagram for a system of TNS and propose a dimensionless scaling factor F(v) (headgroup volume/tether volume) that allows a comparison between the morphologies formed from TNS and traditional surfactants.

We present results of simulations that predict the phases formed by the self-assembly of model nanospheres functionalized with a single polymer "tether," including double gyroid, perforated lamella, and crystalline bilayer phases. We show that microphase separation of the immiscible tethers and nanospheres causes confinement of the nanoparticles, which promotes local icosahedral packing that in turn stabilizes the gyroid. We present a new metric for determining the local arrangement of particles based on spherical harmonic "fingerprints," which we use to quantify the extent of icosahedral ordering.

Ceramides are known to be a key component of the stratum corneum, the outermost protective layer of the skin that controls barrier function. In this work, molecular dynamics simulations are used to examine the behavior of ceramide bilayers, focusing on non-hydroxy sphingosine (NS) and non-hydroxy phytosphingosine (NP) ceramides. Here, we propose a modified version of the CHARMM force field for ceramide simulation, which is directly compared to the more commonly used GROMOS-based force field of Berger (Biophys. J. 1997, 72); while both force fields are shown to closely match experiment from a structural standpoint at the physiological temperature of skin, the modified CHARMM force field is better able to capture the thermotropic phase transitions observed in experiment. The role of ceramide chemistry and its impact on structural ordering is examined by comparing ceramide NS to NP, using the validated CHARMM-based force field. These simulations demonstrate that changing from ceramide NS to NP results in changes to the orientation of the OH groups in the lipid headgroups. The arrangement of OH groups perpendicular to the bilayer normal for ceramide NP, verse parallel for NS, results in the formation of a distinct hydrogen bonding network, that is ultimately responsible for shifting the gel-to-liquid phase transition to higher temperature, in direct agreement with experiment.

We use Brownian dynamics (BD), molecular dynamics, and dissipative particle dynamics to study the phase behavior of diblock copolymer melts and to determine if hydrodynamics is required in the formation of phases with greater than one-dimensional periodicity. We present a phase diagram for diblock copolymers predicted by BD and provide a relationship between the inverse dimensionless temperature epsilon/k(B)T and the Flory-Huggins chi parameter, allowing for a quantitative comparison between methods and to mean field predictions. Our results concerning phase behavior are in good qualitative agreement with the theoretical predictions of Matsen and Bates [M. W. Matsen and F. S. Bates, Macromolecules 29, 1091 (1996)]; however, fluctuation effects arising from finite polymer lengths substantially alter the phase boundaries. Our results pertaining to the hydrodynamics are in contrast to earlier work by Groot et al. [R. D. Groot, T. J. Madden, and D. J. Tildesley, J. Chem. Phys. 110, 9739 (1999); D. Frenkel and B. Smit, Understanding Molecular Simulation, 2nd ed. (Academic, New York, 2001)]. In particular, we obtain the hexagonal ordered cylinder phase with BD, a method that does not include hydrodynamics.

We report the results from a computational study of the self-assembly of amphiphilic ditethered nanospheres using molecular simulation. As a function of the interaction strength and directionality of the tether-tether interactions, we predict the formation of four highly ordered phases not previously reported for nanoparticle systems. We find a double diamond structure comprised of a zinc blende (binary diamond) arrangement of spherical micelles with a complementary diamond network of nanoparticles (ZnS/D), a phase of alternating spherical micelles in a NaCl structure with a complementary simple cubic network of nanoparticles to form an overall crystal structure identical to that of AlCu2Mn (NaCl/SC), an alternating tetragonal ordered cylinder phase with a tetragonal mesh of nanoparticles described by the [8,8,4] Archimedean tiling (TC/T), and an alternating diamond phase in which both diamond networks are formed by the tethers (AD) within a nanoparticle matrix. We compare these structures with those observed in linear and star triblock copolymer systems.

Lipid bilayers composed of non-hydroxy sphingosine ceramide (CER NS), cholesterol (CHOL), and free fatty acids (FFAs), which are components of the human skin barrier, are studied via molecular dynamics simulations. Since mixtures of these lipids exist in dense gel phases with little molecular mobility at physiological conditions, care must be taken to ensure that the simulations become decorrelated from the initial conditions. Thus, we propose and validate an equilibration protocol based on simulated tempering, in which the simulation takes a random walk through temperature space, allowing the system to break out of metastable configurations and hence become decorrelated from its initial configuration. After validating the equilibration protocol, which we refer to as random-walk molecular dynamics, the effects of the lipid composition and ceramide tail length on bilayer properties are studied. Systems containing pure CER NS, CER NS + CHOL, and CER NS + CHOL + FFA, with the CER NS fatty acid tail length varied within each CER NS-CHOL-FFA composition, are simulated. The bilayer thickness is found to depend on the structure of the center of the bilayer, which arises as a result of the tail-length asymmetry between the lipids studied. The hydrogen bonding between the lipid headgroups and with water is found to change with the overall lipid composition, but is mostly independent of the CER fatty acid tail length. Subtle differences in the lateral packing of the lipid tails are also found as a function of CER tail length. Overall, these results provide insight into the experimentally observed trend of altered barrier properties in skin systems where there are more CERs with shorter tails present.