Steven O. Nielsen

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This article presents a topical review of coarse grain simulation techniques. First, we motivate these techniques with illustrative examples from biology and materials science. Next, approaches in the literature for increasing the efficiency of atomistic simulations are mentioned. Considerations related to a specific coarse grain modelling approach are(More)
A cylindrical transmembrane molecule is constructed by linking hydrophobic sites selected from a coarse grain model. The resulting hollow tube assembly serves as a representation of a transmembrane channel, pore, or a carbon nanotube. The interactions of a coarse grain di-myristoyl-phosphatidyl-choline hydrated bilayer with both a purely hydrophobic tube(More)
Synthetic and natural peptide assemblies can possess transport or conductance activity across biomembranes through the formation of nanopores. The fundamental mechanisms of membrane insertion necessary for antimicrobial or synthetic pore formation are poorly understood. We observe a lipid-assisted mechanism for passive insertion into a model membrane from(More)
A coarse-grained intermolecular potential has been parametrized for phenyl-based molecules. The parametrization was accomplished by fitting to experimental thermodynamic data. Specifically, the intermolecular potentials, which were based on Lennard-Jones functional forms, were parametrized and validated using experimental surface tension, density, and(More)
In many multi-repeat proteins, linkers between repeats have little secondary structure and place few constraints on folding or unfolding. However, the large family of spectrin-like proteins, including alpha-actinin, spectrin, and dystrophin, share three-helix bundle, spectrin repeats that appear in crystal structures to be linked by long helices. All of(More)
The perturbations induced in a lipid bilayer by the presence of a transmembrane nanotube are investigated using coarse grained molecular dynamics. Meniscus formation by the lipids and tilting of the nanotube occur in response to hydrophobic mismatch, although these two effects do not compensate completely for the total mismatch. The lipid head-to-tail(More)
A DPD model of PEO-based block copolymer vesicles in water is developed by introducing a new density based coarse graining and by using experimental data for interfacial tension. Simulated as a membrane patch, the DPD model is in excellent agreement with experimental data for both the area expansion modulus and the scaling of hydrophobic core thickness with(More)
The physical properties of nanoscale materials often vary with their size, unlike the corresponding bulk material properties, which can only be changed by modifying the material composition. In particular, it is believed that hydration phenomena are length scale dependent. The manifestation of hydrophobicity over multiple length scales plays a crucial role(More)
The electronic properties of carbon nanotubes can be altered significantly by modifying the nanotube surface. In this study, single-walled carbon nanotubes (SWCNTs) were functionalized noncovalently using designed surfactant peptides, and the resultant SWCNT electronic properties were investigated. These peptides have a common amino acid sequence of(More)