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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.
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 …
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.
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 …
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 …
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.
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 …
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 …
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.
On The Generalized Borel Transform And Its Application To The Statistical Mechanics Of Macromolecules, Marcelo Marucho, Gustavo A. Carri
On The Generalized Borel Transform And Its Application To The Statistical Mechanics Of Macromolecules, Marcelo Marucho, Gustavo A. Carri
Gustavo A. Carri
We present a new integral transform called the generalized Borel transform (GBT) and show how to use it to compute distribution functions used to describe the statistical mechanics of macromolecules. For this purpose, we choose the random flight model (RFM) of macromolecules and show that the application of the GBT to this model leads to the exact expression of the polymer propagator (two-point correlation function) from which all the statistical properties of the model can be obtained. We also discuss the mathematical simplicity of the GBT and its applicability to macromolecules with other topologies. (C) 2003 American Institute of Physics.
Coupling Between Helix-Coil And Coil-Globule Transitions In Helical Polymers, Vikas Varshney, Gustavo A. Carri
Coupling Between Helix-Coil And Coil-Globule Transitions In Helical Polymers, Vikas Varshney, Gustavo A. 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.
Role Of Hydrogen Bonds In The Fast Dynamics Of Binary Glasses Of Trehalose And Glycerol: A Molecular Dynamics Simulation Study, Taner E. Dirama, Gustavo A. Carri, Alexei P. Sokolov
Role Of Hydrogen Bonds In The Fast Dynamics Of Binary Glasses Of Trehalose And Glycerol: A Molecular Dynamics Simulation Study, Taner E. Dirama, Gustavo A. Carri, Alexei P. Sokolov
Gustavo A. Carri
Trehalose-glycerol mixtures are known to be effective in the long time preservation of proteins. However, the microscopic mechanism of their effective preservation abilities remains unclear. In this article we present a molecular dynamics simulation study of the short time, less than 1 ns, dynamics of four trehalose-glycerol mixtures at temperatures below the glass transition temperature. We found that a mixture of 5% glycerol and 95% trehalose has the most suppressed short time dynamics (fast dynamics). This result agrees with the experimental analysis of the mean-square displacement of the hydrogen atoms, as measured via neutron scattering, and correlates with the experimentally …
Coupling Between Lysozyme And Glycerol Dynamics: Microscopic Insights From Molecular-Dynamics Simulations, Taner E. Dirama, Gustavo A. Carri, Alexei P. Sokolov
Coupling Between Lysozyme And Glycerol Dynamics: Microscopic Insights From Molecular-Dynamics Simulations, Taner E. Dirama, Gustavo A. Carri, Alexei P. Sokolov
Gustavo A. Carri
We explore possible molecular mechanisms behind the coupling of protein and solvent dynamics using atomistic molecular-dynamics simulations. For this purpose, we analyze the model protein lysozyme in glycerol, a well-known protein-preserving agent. We find that the dynamics of the hydrogen bond network between the solvent molecules in the first shell and the surface residues of the protein controls the structural relaxation (dynamics) of the whole protein. Specifically, we find a power-law relationship between the relaxation time of the aforementioned hydrogen bond network and the structural relaxation time of the protein obtained from the incoherent intermediate scattering function. We demonstrate that …
How Does The Coupling Of Secondary And Tertiary Interactions Control The Folding Of Helical Macromolecules?, Vikas Varshney, Gustavo A. Carri
How Does The Coupling Of Secondary And Tertiary Interactions Control The Folding Of Helical Macromolecules?, Vikas Varshney, Gustavo A. Carri
Gustavo A. Carri
The authors study how the simultaneous presence of short-range secondary and long-range tertiary interactions controls the folding and collapse behavior of a helical macromolecule. The secondary interactions stabilize the helical conformation of the chain, while the tertiary interactions govern its overall three-dimensional shape. The authors have carried out Monte Carlo simulations to study the effect of chain length on the folding and collapse behavior of the chain. They have calculated state diagrams for four chain lengths and found that the physics is very rich with a plethora of stable conformational states. In addition to the helix-coil and coil-globule transitions, their …
Statistical Mechanics Of Worm-Like Polymers From A New Generating Function, Gustavo A. Carri, Marcelo Marucho
Statistical Mechanics Of Worm-Like Polymers From A New Generating Function, Gustavo A. Carri, Marcelo Marucho
Gustavo A. Carri
We present a mathematical approach to the worm-like chain model of semiflexible polymers. Our method is built on a novel generating function from which all the properties of the model can be derived. Moreover, this approach satisfies the local inextensibility constraint exactly. In this paper, we focus on the lowest order contribution to the generating function and derive explicit analytical expressions for the characteristic function, polymer propagator, single chain structure factor, and mean square end-to-end distance. These analytical expressions are valid for polymers with any degree of stiffness and contour length. We find that our calculations are able to capture …
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 …
Coupling Between Lysozyme And Trehalose Dynamics: Microscopic Insights From Molecular-Dynamics Simulations, Taner E. Dirama, Joseph E. Curtis, Gustavo A. Carri, Alexei P. Sokolov
Coupling Between Lysozyme And Trehalose Dynamics: Microscopic Insights From Molecular-Dynamics Simulations, Taner E. Dirama, Joseph E. Curtis, Gustavo A. Carri, Alexei P. Sokolov
Gustavo A. Carri
We have carried out molecular-dynamics simulations on fully flexible all-atom models of the protein lysozyme immersed in trehalose, an effective biopreservative, with the purpose of exploring the nature and extent of the dynamical coupling between them. Our study shows a strong coupling over a wide range of temperatures. We found that the onset of anharmonic behavior was dictated by changes in the dynamics and relaxation processes in the trehalose glass. The physical origin of protein-trehalose coupling was traced to the hydrogen bonds formed at the interface between the protein and the solvent. Moreover, protein-solvent hydrogen bonding was found to control …
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 …