Via dissipative particle dynamics (DPD), we simulate the self-assembly of end-functionalized, amphiphilic nanotubes and lipids in a hydrophilic solvent. Each nanotube encompasses a hydrophobic stalk and two hydrophilic ends, which are functionalized with end-tethered chains. With a relatively low number of the nanotubes in solution, the components self-assemble into stable lipid-nanotube vesicles. As the number of nanotubes is increased, the system exhibits a vesicle-to-bicelle transition, resulting in stable hybrid bicelle. Moreover, our results reveal that the nanotubes cluster into distinct tripod-like structures within the vesicles and aggregate into a ring-like assembly within the bicelles. For both the vesicles and bicelles, the nanotubes assume trans-membrane orientations, with the tethered hairs extending into the surrounding solution or the encapsulated fluid. Thus, the hairs provide a means of regulating the transport of species through the self-assembled structures. Our findings provide guidelines for creating nanotube clusters with distinctive morphologies that might be difficult to achieve through more conventional means. The results also yield design rules for creating synthetic cell-like objects or microreactors that can exhibit biomimetic functionality.

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In this work, the modeling and control of a batch crystallization process used to produce tetragonal hen egg white lysozyme crystals are studied. Two processes are considered, crystal nucleation and growth. Crystal nucleation rates are obtained from previous experiments. The growth of each crystal progresses via kinetic Monte Carlo simulations comprising of adsorption, desorption, and migration on the (110) and (101) faces. The expressions of the rate equations are similar to Durbin and Feher. To control the nucleation and growth of the protein crystals and produce a crystal population with desired shape and size, a model predictive control (MPC) strategy is implemented. Specifically, the steady‐state growth rates for the (110) and (101) faces are computed and their ratio is expressed in terms of the temperature and protein concentration via a nonlinear algebraic equation. The MPC method is shown to successfully regulate both the crystal size and shape distributions to different set‐point values. © 2013 American Institute of Chemical Engineers AIChE J, 59: 2317–2327, 2013

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CAl4 2−/− (D4h, 1A1g) is a cluster ion that has been established to be planar, aromatic, and contain a tetracoordinate planar C atom. Valence isoelectronic substitution of C with Si and Ge in this cluster leads to a radical change of structure toward distorted pentagonal species. We find that this structural change goes together with the cluster acquiring partial covalency of bonding between Si/Ge and Al4, facilitated by hybridization of the atomic orbitals (AOs). Counter intuitively, for the AAl4 2−/− (A = C, Si, Ge) clusters, hybridization in the dopant atom is strengthened from C, to Si, and to Ge, even though typically AOs are more likely to hybridize if they are closer in energy (i.e. in earlier elements in the Periodic Table). The trend is explained by the better overlap of the hybrids of the heavier dopants with the orbitals of Al4. From the thus understood trend, it is inferred that covalency in such clusters can be switched off, by varying the relative sizes of the AOs of the main element and the dopant. Using this mechanism, we then successfully killed covalency in Si, and predicted a new aromatic cluster ion containing a tetracoordinate square planar Si, SiIn4 2−/−.

The fluid-solid transition of the Lennard-Jones model is analyzed along a supercritical isotherm. The analysis is implemented via a simulation method which is based on a modification of the constrained cell model of Hoover and Ree. In the context of hard-sphere freezing, Hoover and Ree simulated the solid phase using a constrained cell model in which each particle is confined within its own Wigner-Seitz cell. Hoover and Ree also proposed a modified cell model by considering the effect of an external field of variable strength. High-field values favor configurations with a single particle per Wigner-Seitz cell and thus stabilize the solid phase. In previous work, a simulation method for freezing transitions, based on constant-pressure simulations of the modified cell model, was developed and tested on a system of hard spheres. In the present work, this method is used to determine the freezing transition of a Lennard-Jones model system on a supercritical isotherm at a reduced temperature of 2. As in the case of hard spheres, constant-pressure simulations of the fully occupied constrained cell model of a system of Lennard-Jones particles indicate a point of mechanical instability at a density which is approximately 70% of the density at close packing. Furthermore, constant-pressure simulations of the modified cell model indicate that as the strength of the field is reduced, the transition from the solid to the fluid is continuous below the mechanical instability point and discontinuous above. The fluid-solid transition of the Lennard-Jones system is obtained by analyzing the field-induced fluid-solid transition of the modified cell model in the high-pressure, zero-field limit. The simulations are implemented under constant pressure using tempering and histogram reweighting techniques. The coexistence pressure and densities are determined through finite-size scaling techniques for first-order phase transitions which are based on analyzing the size-dependent behavior of susceptibilities and dimensionless moment ratios of the order parameter.

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Despite recent advances, precise simulation of freezing transitions continues to be a challenging task. In this work, a simulation method for fluid-solid transitions is developed. The method is based on a modification of the constrained cell model which was proposed by Hoover and Ree [J. Chem. Phys. 47, 4873 (1967)]10.1063/1.1701730. In the constrained cell model, each particle is confined in a single Wigner-Seitz cell. Hoover and Ree pointed out that the fluid and solid phases can be linked together by adding an external field of variable strength. High values of the external field favor single occupancy configurations and thus stabilize the solid phase. In the present work, the modified cell model is simulated in the constant-pressure ensemble using tempering and histogram reweighting techniques. Simulation results on a system of hard spheres indicate that as the strength of the external field is reduced, the transition from solid to fluid is continuous at low and intermediate pressures and discontinuous at high pressures. Fluid-solid coexistence for the hard-sphere model is established by analyzing the phase transition of the modified model in the limit in which the external field vanishes. The coexistence pressure and densities are in excellent agreement with current state-of-the-art techniques.