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.