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Moreno N.,National University of Colombia | Perilla J.E.,National University of Colombia | Colina C.M.,Pennsylvania State University | Lisal M.,Czech Institute of Chemical Process Fundamentals | Lisal M.,rkinje University
Molecular Physics

Dissipative particle dynamics, a meso-scale particle-based model, was used to study the aggregation of mucins in aqueous solutions. Concentration, strength of the mucin-water interactions, as well as the effects of size, shape, and composition of the model molecules were studied. Model proteins were represented as rod-like objects formed by coarse-grained beads. In the first model, only one type of beads formed the mucin. It was found that all the surfaces were available to form aggregates and the conformation of the aggregates was a function of the strength of the mucin-water interaction. With this model, the number of aggregates was unaffected by the initial position of the mucins in the simulation box, except for the lowest mucin concentration. In a more refined mucin model, two kinds of beads were used in the molecule in order to represent the existence of cysteine-like terminal groups in the actual molecule. With this new scheme, aggregation took place by the interaction of the terminal groups between model molecules. The kinetic analysis of the evolution of the number of aggregates with time was also studied for both mucin models. © 2015 Taylor & Francis. Source

Petrus P.,rkinje University | Petrus P.,Czech Institute of Chemical Process Fundamentals | Lisal M.,Czech Institute of Chemical Process Fundamentals | Brennan J.K.,U.S. Army

We present a dissipative particle dynamics simulation study on the formation of nanostructures of symmetric diblock copolymers confined between planar surfaces with and without nanopattems. The nanopatterned surface is mimicked by alternating portions of the surface that interact differently with the diblock copolymers. The formation of the diblock.-copolymer nanostructures confined between the planar surfaces is investigated and characterized by varying the separation width and the strength of the interaction between the surfaces and the diblock copolymers. For surfaces with nanopattems, we also vary both the mutual area and location of the nanopatterns, where we consider nanopatterns on the opposing surfaces that are vertically (a) aligned, (b) staggered, and (c) partially staggered. In the case of planar slits without nanopattems, we observe the formation of perpendicular and parallel lamellar phases with different numbers of lamellae. In addition, the symmetric diblock copolymers self-assemble into adsorbed layer and adsorbed layer-parallel lamellar phases and a mixed lamellar phase when the opposing surfaces of the planar slits are modeled by different types of wall beads. In the case of nanopatterned planar slits, we observe novel nanostructures and attempt to rationalize the diblock copolymer self-assembly on the basis of the behavior that we observed in the planar slits without nanopattems. In particular, we investigate the applicability of predicting the structures formed in the nanopatterned slits by a superposition of the observed structures in slits without nanopatterns. © 2009 American Chemical Society. Source

Sirk T.W.,U.S. Army | Slizoberg Y.R.,U.S. Army | Brennan J.K.,U.S. Army | Lisal M.,Czech Institute of Chemical Process Fundamentals | And 2 more authors.
Journal of Chemical Physics

We develop an alternative polymer model to capture entanglements within the dissipative particle dynamics (DPD) framework by using simplified bond-bond repulsive interactions to prevent bond crossings. We show that structural and thermodynamic properties can be improved by applying a segmental repulsive potential (SRP) that is a function of the distance between the midpoints of the segments, rather than the minimum distance between segments. The alternative approach, termed the modified segmental repulsive potential (mSRP), is shown to produce chain structures and thermodynamic properties that are similar to the softly repulsive, flexible chains of standard DPD. Parameters for the mSRP are determined from topological, structural, and thermodynamic considerations. The effectiveness of the mSRP in capturing entanglements is demonstrated by calculating the diffusion and mechanical properties of an entangled polymer melt. © 2012 American Institute of Physics. Source

Fuentes-Paniagua E.,University of Alcala | Fuentes-Paniagua E.,CIBER ISCIII | Hernandez-Ros J.M.,University of Alcala | Sanchez-Milla M.,University of Alcala | And 11 more authors.
RSC Advances

Cationic carbosilane dendrimers of generations 1-3 have been synthesized employing thiol-ene click chemistry. The obtained dendrimers present three different types of ammonium functions, two of them with the charge at the surface, -NH3 + and -NMe3 +, and other with the charge internalized by the presence of ethylalcohol moieties, -[NMe2(CH2CH2OH)]+. The influence of -NMe3 + and -[NMe2(CH2CH 2OH)]+ in dendrimer structure have been studied by molecular dynamics. The antibacterial properties of these families of dendrimers have been evaluated against Gram-positive (Staphylococcus aureus CECT 240) and Gram-negative (Escherichia coli CECT 515) bacterial strains, and the results have been compared with those obtained for related cationic carbosilane dendrimers functionalized by hydrosilylation reactions. These data show the relevance of the sulfur atom versus the silicon atom close to the dendrimer surface and the outer charge versus the inner charge. Finally, the stability of the most active first generation dendrimers vs. pH and temperature has also been studied. © 2014 The Royal Society of Chemistry. Source

Lisal M.,Czech Institute of Chemical Process Fundamentals | Lisal M.,rkinje University
Journal of Chemical Physics

We present molecular-level insight into the liquid/gas interface of two chiral room-temperature ionic liquids (RTILs) derived from 1-n-butyl-3- methylimidazolium bromide ([bmim][Br]); namely, (R)-1-butyl-3-(3-hydroxy-2- methylpropyl)imidazolium bromide (hydroxypropyl) and 1-butyl-3-[(1R)-nopyl] imidazolium bromide (nopyl). We use our currently developed force field which was validated against the experimental bulk density, heat of vaporization, and surface tension of [bmim][Br]. The force field for the RTILs adopts the Chemistry at Harvard Molecular Mechanics (CHARMM) parameters for the intramolecular and repulsion-dispersion interactions along with the reduced partial atomic charges based on ab initio calculations. The net charges of the ions are around ±0.8e, which mimic the anion to cation charge transfer and many-body effects. Molecular dynamics simulations in the slab geometry combined with the intrinsic interface analysis are employed to provide a detailed description of the RTIL/gas interface in terms of the structural and dynamic properties of the interfacial, sub-interfacial, and central layers at a temperature of 300 K. The focus is on the comparison of the liquid/gas interface for the chiral RTILs with the interface for parent [bmim][Br]. The structure of the interface is elucidated by evaluating the surface roughness, intrinsic atomic density profiles, and orientation ordering of the cations. The dynamics of the ions at the interfacial region is characterized by computing the survival probability, and normal and lateral self-diffusion coefficients in the layers. © 2013 AIP Publishing LLC. Source

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