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Full-Text Articles in Engineering
Short-Range Helical Ordering Of Isotactic Vinyl Polymers In The Liquid State, Gustavo Carri
Short-Range Helical Ordering Of Isotactic Vinyl Polymers In The Liquid State, Gustavo Carri
Gustavo A. Carri
Wide-angle x-ray scattering measurements on various vinyl polymer melts show that the main amorphous peak (at k˜1.5 A-1) in the structure factor initially broadens, and then forms a ``pre-peak'' that shifts to lower k as the size of the pendant group increases. To investigate this behavior we performed self-consistent PRISM calculations on isotactic polypropylene and polystyrene liquids. Good qualitative agreement was seen for the theoretical structure factors with scattering data. Analysis of the torsional angle distribution shows a significant amount of short-range helical content in the iPP and iPS melts. At 450^oK the average number of consecutive trans/gauche pairs along …
A Molecular Dynamics Simulation Of The Stability-Limited Growth Mechanism Of Peptide-Mediated Gold-Nanoparticle Synthesis, Gustavo Carri
A Molecular Dynamics Simulation Of The Stability-Limited Growth Mechanism Of Peptide-Mediated Gold-Nanoparticle Synthesis, Gustavo Carri
Gustavo A. Carri
The bindingof a 12-residue peptide to a Au {111} surface and nanoparticles with different sizes result in various equilibrium structures and stabilities due to the surface morphology. The equilibrium structures are represented by the distance of peptide atoms to Au surface and the stabilities of peptide residues are represented by the average change of dihedral angles.
Dynamics Of Lysozyme In A Glycerol-Water System, Gustavo Carri
Dynamics Of Lysozyme In A Glycerol-Water System, Gustavo Carri
Gustavo A. Carri
Bio-preservation of proteins is of great commercial and academic interest. A variety of sugars have been found to be effective in preserving the structure of proteins. This has been attributed and in some cases proved to their ability to form strong hydrogen bonds with proteins thus restricting their motion. The work presented here explores the hypothesis that glycerol, a tri-alcohol curbs the motion of protein. We have carried out a 10ns Molecular Dynamics simulation to study the phenomenon. The structure of Lysozyme (PDB code 193L) has been studied in three solutions of 10, 20 and 30 % by weight of …
Stretching Helical Macromolecules, Gustavo Carri
Stretching Helical Macromolecules, Gustavo Carri
Gustavo A. Carri
We study the elasticity of a homopolypeptide under extension using Monte Carlo simulations based on the Wang-Landau algorithm. The effect of external mechanical forces is described with an extension of a model for helical polymers (V. Varshney et. al., Macromolecules 2004, 37, 8794). We find that the application of a mechanical force first increases the helix-to-coil transition temperature and then decreases it. This non-monotonic behavior is a consequence of a change in the nature of the helix-coil transition which becomes a helix-extended-coil transition for strong forces. We also find that the force-elongation curve at constant temperature displays three different behaviors …
Fast Dynamics Of Binary Glass Formers And Its Role In The Cryo-Preservation Of Proteins. An Atomistic Molecular Dynamics Simulation Study., Gustavo Carri
Gustavo A. Carri
Bio-preservative agents such as trehalose and glycerol are commonly used to preserve biomolecules against denaturation and its consequent loss of activity. The molecular mechanisms that control the preservation ability of such bio-protective agents is not fully understood at present. Studies of the fast dynamic behavior of these agents, which is a consequence of the small-amplitude atomistic motions in the system, provide valuable information in understanding this phenomena. We present a molecular dynamics simulation study of the fast dynamics of trehalose-glycerol mixtures with different compositions and at different temperatures. We found that a mixture of five percent glycerol (a liquid) and …
Stretching Networks Of Helical Polymers, Gustavo Carri
Stretching Networks Of Helical Polymers, Gustavo Carri
Gustavo A. Carri
We present a computational study of the stress-strain behavior of a network of helical polymers. For this study, we employ a combination of Monte Carlo simulations based on the Wang-Landau algorithm and the traditional three-chain model of polymer networks. The helical polymers are described with a recently developed model (V. Varshney \textit{et. al}., \textit{Macromolecules} \textbf{2004}, 37, 8794) that has proven to capture the configurational, conformational and thermodynamic properties of single helical polymers correctly. In this talk, we will focus on the mechanical and thermodynamic properties of the network as a whole together with the conformational and configurational characteristics of a …
Thermodynamic Properties Of Gold Nanoparticles Described By Sutton-Chen Potential And Quantum Sutton-Chen Potential, Gustavo Carri
Thermodynamic Properties Of Gold Nanoparticles Described By Sutton-Chen Potential And Quantum Sutton-Chen Potential, Gustavo Carri
Gustavo A. Carri
Thermodynamic properties of gold nanoparticles (<1.6nm) have been investigated by atomistic Monte Carlo simulations with three different potential functions/parameterizations (Sutton-Chen potential, Sutton-Chen potential with Pawluk's parameterization, and Quantum Sutton-Chen potential). The melting temperature of gold nanoparticles is predicted and compared to other theoretical and experimental values. The agreement between the predicted melting temperatures and the experimental values was not satisfactory for any of the three potentials in the studied range of sizes. However, the Sutton-Chen potential showed very good agreement for nanoparticles larger than 1.3nm while the Quantum Sutton-Chen potential exhibited a trend of melting temperatures similar to the …
Modern Concepts And Methods In Polymer Physics-Introduction, Gustavo Carri
Modern Concepts And Methods In Polymer Physics-Introduction, Gustavo Carri
Gustavo A. Carri
No abstract provided.
Microscopic Insights Into The Dynamics Of Protein--Solvent Mixtures, Gustavo Carri
Microscopic Insights Into The Dynamics Of Protein--Solvent Mixtures, Gustavo Carri
Gustavo A. Carri
No abstract provided.
Coupling Between Protein And Solvent Dynamics, Gustavo Carri
Coupling Between Protein And Solvent Dynamics, Gustavo Carri
Gustavo A. Carri
No abstract provided.
On The Helix-Coil Transition Of Wormlike Polymers, Gustavo Carri
On The Helix-Coil Transition Of Wormlike Polymers, Gustavo Carri
Gustavo A. Carri
We present a geometric approach to the simulation of the Helix-Coil transition in wormlike polymer chains. Our method combines the original concepts proposed by Zimm, Bragg and others with the Monte Carlo method recently developed by Landau and Wang. The wormlike polymer is modeled with the Freely Rotating Chain Model where the beads interact via a hard-core repulsion. For each conformation of the chain, the value of the torsion on each bead was computed using finite differences. The difference between the computed torsion and the ideal torsion of the perfect helix was used as a criterion to determine the conformational …
Solvent-Induced Collapse Of A Helical Semiflexible Polymer, Gustavo Carri
Solvent-Induced Collapse Of A Helical Semiflexible Polymer, Gustavo Carri
Gustavo A. Carri
It has been stated that ``the class of materials richest in the occurrence of phase transitions are polymers'' (E. A. Di Marzio, \textit{Prog. Polym. Sci}. \textbf{24}, 329 (1999)). This wealth of phase transitions is unique to polymers and is a consequence of the myriad of possible ways of coupling the basic ten classes of polymeric phase transitions into pairs, triplets and so forth. Two of these transitions are the helix-coil and coil-globule transitions. In this talk we explore the coupling of these two transitions, its molecular origins and physical consequences. For this purpose, we extend a recently developed model of …
A Minimal Model For The Helix-Coil Transition Of Worm-Like Polymers, Gustavo Carri
A Minimal Model For The Helix-Coil Transition Of Worm-Like Polymers, Gustavo Carri
Gustavo A. Carri
We present a geometric approach to the simulation of the Helix-Coil transition in wormlike polymers. In our model, the polymer is treated as a Freely Rotating Chain with hard-core repulsion between beads. The conformational state (helix or coil) of each bead is determined by the value of its torsion. If the difference between the torsion of a bead and the one of the perfect helix is less than a cutoff value, then the bead is part of a helical domain and carries a negative energy, otherwise it is part of a random coil. We have simulated these concepts using the …