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Full-Text Articles in Engineering
A Molecular Dynamics Simulation Of The Stability-Limited Growth Mechanism Of Peptide-Mediated Gold-Nanoparticle Synthesis, Jing Yu, Matthew Becker, Gustavo Carri
A Molecular Dynamics Simulation Of The Stability-Limited Growth Mechanism Of Peptide-Mediated Gold-Nanoparticle Synthesis, Jing Yu, Matthew Becker, 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.
Coupling Transitions In Helical Polymers: The Case Of The Helix-Coil And Coil-Globule Transitions, Gustavo Carri
Coupling Transitions In Helical Polymers: The Case Of The Helix-Coil And Coil-Globule Transitions, Gustavo Carri
Gustavo A. Carri
We explore the coupling between the helix-coil and coil-globule transitions of a helical polymer using Monte Carlo simulations. A very rich state diagram is found. Each state is characterized by a specific configuration of the chain which could be a helix, a random coil, an amorphous globule or one of various other globular states which carry residual helical strands. We study the boundaries between states and provide further insight into the physics of the system with a detailed analysis of the order parameter and other properties.
Design, Synthesis, And Traveling Wave Ion Mobility Mass Spectrometry Characterization Of Iron (Ii)--And Ruthenium (Ii)--Terpyridine Metallomacrocycles, Gustavo Carri
Gustavo A. Carri
New metallomacrocycles composed of 2,2':6',2″-terpyridine (tpy) ligands and Ru(II) or Fe(II) transition metal ions were prepared by stepwise directed assembly and characterized by 2D diffusion NMR spectroscopy (DOSY), electrospray ionization traveling wave ion mobility mass spectrometry (ESI TWIM MS), and molecular modeling. The supramolecular polymers synthesized include a homonuclear all-Ru hexamer as well as heteronuclear hexamer and nonamer with alternating Ru/Ru/Fe metal centers. ESI MS yields several charge states from each supramacromolecule. If ESI is interfaced with TWIM MS, overlapping charge states and the isomeric components of an individual charge state are separated based on their unique drift times through …
A Monte Carlo Simulation Study Of The Mechanical And Conformational Properties Of Networks Of Helical Polymers. I. General Concepts, Gustavo Carri
A Monte Carlo Simulation Study Of The Mechanical And Conformational Properties Of Networks Of Helical Polymers. I. General Concepts, Gustavo Carri
Gustavo A. Carri
We study the mechanical and conformational properties of networks of helical polymers with a combination of Monte Carlo simulations based on the Wang-Landau algorithm and the Three-chain Model. We find that the stress-strain behavior of these networks has novel features not observed in typical networks made of synthetic polymers. In particular, we find that as these networks are stretched they first strengthen, then soften and finally strengthen again. This non-monotonic behavior of the stress correlates with the one of the helical content and is rationalized by the elongation-induced formation and melting of the helical structure of the polymer. We complement …
A Minimal Model For The Helix-Coil Transition Of Wormlike Polymers. Insights From Monte Carlo Simulations And Theoretical Implications, Gustavo Carri
A Minimal Model For The Helix-Coil Transition Of Wormlike Polymers. Insights From Monte Carlo Simulations And Theoretical Implications, Gustavo Carri
Gustavo A. Carri
We present a geometric approach to the simulation of the helix−coil transition in wormlike polymers. Our approach has its foundations on a novel real-space realization of the concepts proposed by Zimm, Bragg, and other researchers. 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 …
Stretching Helical Semiflexible Polymers, Gustavo Carri
Stretching Helical Semiflexible Polymers, Gustavo Carri
Gustavo A. Carri
We study the elastic behavior of a helical semiflexible polymer under extension. The polymer is described with a coarse-grained model recently developed by us (V. Varshney, et al. Macromolecules 2004, 37, 8794) where the chain is modeled using the freely rotating chain model and each bead can be in one of two possible conformations, helix or coil, depending on the value of its torsion. In this study, we extend the original model to include the effect of external mechanical forces and solve it using a Monte Carlo simulation approach based on the Wang−Landau sampling scheme. We found that the application …
Separation And Characterization Of Metallosupramolecular Libraries By Ion Mobility Mass Spectrometry, Gustavo Carri
Separation And Characterization Of Metallosupramolecular Libraries By Ion Mobility Mass Spectrometry, Gustavo Carri
Gustavo A. Carri
The self-assembly of Zn(II) ions and bis(terpyridine) (tpy) ligands carrying 120° or 180° angles between their metal binding sites was utilized to prepare metallosupramolecular libraries with the connectivity. These combinatorial libraries were separated and characterized by ion mobility mass spectrometry (IM MS) and tandem mass spectrometry (MS(2)). The 180°-angle building blocks generate exclusively linear complexes, which were used as standards to determine the architectures of the assemblies resulting from the 120°-angle ligands. The latter ligand geometry promotes the formation of macrocyclic hexamers, but other n-mers with smaller (n = 5) or larger ring sizes (n = 7-9) were identified as …
Inertial Suppression Of Protein Dynamics In A Binary Glycerol-Trehalose Glass, Gustavo Carri
Inertial Suppression Of Protein Dynamics In A Binary Glycerol-Trehalose Glass, Gustavo Carri
Gustavo A. Carri
The traditional approach used to predict the ability of a glassy matrix to maximally preserve the activity of a protein solute is the glass transition temperature (T(g)) of the glass. Recently it has been shown that the addition of a low T(g) diluent (glycerol) can rigidify the structure of a high T(g) glassy matrix in binary glycerol-trehalose glasses. The optimal density of glycerol in trehalose minimizes the average mean square displacements of non-exchangeable protons in the glass samples. The amount of glycerol added to a trehalose glass coincides with the maximal recovery of biological activity in a separate study using …
Statistical Mechanics Of Wormlike Polymers From A New Generating Function. Ii. The Force-Elongation Relationship, Gustavo Carri
Statistical Mechanics Of Wormlike Polymers From A New Generating Function. Ii. The Force-Elongation Relationship, Gustavo Carri
Gustavo A. Carri
No abstract provided.
The Influence Of Amino Acid Sequence And Functionality On The Binding Process Of Peptides Onto Gold Surfaces, Gustavo Carri
The Influence Of Amino Acid Sequence And Functionality On The Binding Process Of Peptides Onto Gold Surfaces, Gustavo Carri
Gustavo A. Carri
We present a molecular dynamics study of the binding process of peptide A3 (AYSSGAPPMPPF) and other similar peptides onto gold surfaces, and identify the functions of many amino acids. Our results provide a clear picture of the separate regimes present in the binding process: diffusion, anchoring, crawling and binding. Moreover, we explored the roles of individual residues. We found that tyrosine, methionine, and phenylalanine are strong binding residues; serine serves as an effective anchoring residue; proline acts as a dynamic anchoring point, while glycine and alanine give flexibility to the peptide backbone. We then show that our findings apply to …