Robert Yaris

Washington University in St. Louis, San Luis, Missouri, United States

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Publications (51)209.88 Total impact

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    Macromolecules 04/2002; 18(3). DOI:10.1021/ma00145a012 · 5.93 Impact Factor
  • Jeffrey Skolnick, Robert Yaris
    Macromolecules 04/2002; 18(8). DOI:10.1021/ma00150a020 · 5.93 Impact Factor
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    Accounts of Chemical Research 04/2002; 20(9). DOI:10.1021/ar00141a006 · 24.35 Impact Factor
  • John T. Bendler, Robert Yaris
    Macromolecules 04/2002; 11(4). DOI:10.1021/ma60064a007 · 5.93 Impact Factor
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    Macromolecules 04/2002; 17(11). DOI:10.1021/ma00141a023 · 5.93 Impact Factor
  • Macromolecules 04/2002; 19(10). DOI:10.1021/ma00164a018 · 5.93 Impact Factor
  • J. Skolnick, Robert Yaris
    Macromolecules 04/2002; 16(2). DOI:10.1021/ma00236a021 · 5.93 Impact Factor
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    ABSTRACT: To investigate the character of local chain packing in a globally amorphous polymer melt, Monte Carlo simulations were performed on model systems consisting of polymers confined to a diamond lattice. The necessary condition for the existence of locally ordered domains is shown to be the presence of local chain stiffness, which in these systems is manifested by the energetic preference of trans (t) over gauche (g) states. These locally parallel domains are not unique static structures but rather are defined only in a statistical sense and exist over a rather broad temperature range. The local domain structure appears to be insensitive to the molecular weight, provided that the chain length exceeds the domain size. It is also found that, to a very good approximation, within a given chain, two subchains belonging to two different domains are statistically independent. The local domain structure becomes enhanced, at fiied chain stiffness, by inclusion of attractive interactions between nonbonded nearest neighbors and/or by increasing the polymer density. The locally ordered melt is shown to be globally disordered over a broad temperature range, with the dimensions of an individual chain very close to those obtained from ideal chain statistics. Various quantities characterizing the character of local ordering in these model systems are examined, and the applicability of these results to real polymer systems is discussed.
    Macromolecules 04/2002; 19(10). DOI:10.1021/ma00164a017 · 5.93 Impact Factor
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    ABSTRACT: In order to investigate further the mechanism of the phenyl ring motion put forth by Schaefer et al. (Schaefer, J.; Stejskal, E. 0.; Perchak, D.; Skolnick, J.; Yaris, R. Macromolecules 1985,18,368), Brownian dynamics computer simulations on two-dimensional lattices of interacting benzene rings have been performed. Two versions of this model were studied. One was a "rigid" lattice, which only allowed rotational motions of the rings, and the other was a "flexible" lattice, where vibrational motion of the rings was also allowed in the lattice plane. Consistent with the conjecture of Schaefer et al., for the simple models studied, flexibility in the lattice provided the mechanism that allowed rings to flip.
    Macromolecules 04/2002; 20(1). DOI:10.1021/ma00167a021 · 5.93 Impact Factor
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    J. Skolnick, Robert Yaris
    Macromolecules 04/2002; 15(4). DOI:10.1021/ma00232a017 · 5.93 Impact Factor
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    Macromolecules 04/2002; 20(2). DOI:10.1021/ma00168a039 · 5.93 Impact Factor
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    Macromolecules 04/2002; 18(2). DOI:10.1021/ma00144a023 · 5.93 Impact Factor
  • Duane R. Whitney, Robert Yaris
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    ABSTRACT: In order to obtain the mechanism for the infrequent phenyl ring π-flips in glassy polycarbonate, a generalized Langevin dynamics simulation was performed on a reduced model consisting of a flipping ring and its keeper ring. The frequency of π-flips and activation energy for π-flips obtained from the simulation are in agreement with experiment. A phenyl ring π-flip occurs when there is an increase in the separation distance between the ring and its nearest neighbor ring on another chain, accompanied by, and in synchrony with, an increase in its rotational kinetic energy.
    Macromolecules 03/1997; 30(6):1741-1751. DOI:10.1021/ma9611432 · 5.93 Impact Factor
  • Piotr Romiszowski, Robert Yaris
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    ABSTRACT: It is shown that both the full simulation and the generalized Langevin dynamics simulation π flips in a two-dimensional array of interacting benzene rings [P. Romiszowski and R. Yaris, J. Chem. Phys. XX, xxxx (1991)] satisfy Poisson statistics.
    The Journal of Chemical Physics 11/1991; 95(9):7013-7014. DOI:10.1063/1.461048 · 3.12 Impact Factor
  • Piotr Romiszowski, Robert Yaris
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    ABSTRACT: Our method [P. Romiszowski and R. Yaris, J. Chem. Phys. 94, 6751, (1991)] of simulating infrequent motions by using an equation of motion with the uninteresting degrees of freedom suppressed—the generalized Langevin equation—has been extended to enable us to obtain the mechanism for the gated transition. The model problem is a two-dimensional array of benzene rings interacting with nearest neighbor potentials and we are looking for the mechanism of the π-flip transition of the central benzene ring. Thus we retain only the angular coordinates of the central ring and its four nearest neighbors in the generalized Langevin equation. The mechanism obtained for the gating by the nearest neighbor rings is the same both qualitatively and quantitatively in the simulation with a reduced number of degrees of freedom and in the full simulation.
    The Journal of Chemical Physics 11/1991; 95(9):6738-6744. DOI:10.1063/1.461512 · 3.12 Impact Factor
  • Piotr Romiszowski, Robert Yaris
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    ABSTRACT: In order to be able to simulate slow or infrequent motions which require extremely long (or sometimes impossibly long) simulations, a method of simulation using an equation of motion with the uninteresting degrees of freedom suppressed—the generalized Langevin equation—has been used. This method obtains the memory function and effective potential used in the generalized Langevin equation by fitting to the fast motion behavior of a full simulation with all of the degrees of freedom retained. Hence, only a relatively short time full simulation is necessary. The method was tested on two model problems: a two‐dimensional potential model designed to mimic conformational transitions and a two‐dimensional array of ellipsoids (representing benzene rings) interacting with nearest‐neighbor potentials. In both cases, the results obtained simulating with a reduced number of degrees of freedom are in good agreement with the results of the full simulation.
    The Journal of Chemical Physics 05/1991; 94(10):6751-6761. DOI:10.1063/1.460726 · 3.12 Impact Factor
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    ABSTRACT: In the context of dynamic Monte Carlo simulations on a model protein confined to a tetrahedral lattice, the interplay of protein size and tertiary structure, and the requirements for an all-or-none transition to a unique native state, are investigated. Small model proteins having a primary sequence consisting of a central bend neutral region flanked by two tails having an alternating hydrophobic/hydrophilic pattern of residues are seen to undergo a continuous transition to a beta-hairpin collapsed state. On increasing the length of the tails, the beta-hairpin structural motif is found to be in equilibrium with a four-member beta-barrel. Further increase of the tail length results in the shift of the structural equilibrium to the four-member beta-barrel. The random coil to beta-barrel transition is of an all-or-none character, but while the central turn is always the desired native bend, the location of the turns involving the two external strands is variable. That is, beta-barrels having the external stands that are two residues out of register are also observed in the transition region. Introduction into the primary sequence of two additional regions that are at the very least neutral toward turn formation produces an all-or-none transition to the unique, native, four-member beta-barrel. Various factors that can augment the stability of the native conformation are explored. Overall, these folding simulations strongly indicate that the general rules of globular protein folding are rather robust--namely, one requires a general pattern of hydrophobic/hydrophilic residues that allow the protein to have a well-defined interior and exterior and the presence of regions in the amino acid sequence that at the very least are locally indifferent to turn formation. Since no site-specific interactions between hydrophobic and hydrophilic residues are required to produce a unique four-member beta-barrel, these simulations strongly suggest that site specificity is involved in structural fine-tuning.
    Biopolymers 06/1989; 28(6):1059-1095. DOI:10.1002/bip.360280604 · 2.29 Impact Factor
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    ABSTRACT: To help elucidate the general rules of equilibrium globular protein folding, dynamic Monte Carlo simulations of a model beta-barrel globular protein having the six-stranded Greek key motif characteristic of real globular proteins were undertaken. The model protein possesses a typical beta-barrel amino acid sequence; however, all residues of a given type (e.g. hydrophobic residues) are identical. Even in the absence of site-specific interactions, starting from a high-temperature denatured state, these models undergo an all-or-none transition to a structurally unique six-stranded beta-barrel. These simulations suggest that the general rules of globular protein folding are rather robust in that the overall tertiary structure is determined by the general pattern of hydrophobic, hydrophilic, and turn-type residues, with site-specific interactions mainly involved in structural fine tuning of a given topology. Finally, these studies suggest that loops may play an important role in producing a unique native state. Depending on the stability of the native conformation of the long loop in the Greek key, the conformational transition can be described by a two-state, three-state, or even larger number of multiple equilibrium states model.
    Proceedings of the National Academy of Sciences 03/1989; 86(4):1229-33. DOI:10.1073/pnas.86.4.1229 · 9.81 Impact Factor
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    ABSTRACT: A model of polymer melt diffusion recently proposed by Skolnick, Yaris, and Kolinski and which does not invoke reptation as the dominant mechanism of polymer melt motion is used to fit polymer self-diffusion constant data measured by Antonietti, Fölsch, and Sillescu for a homopolymeric melt as well as for a probe in a larger molecular weight matrix. The quality of fit of the data indicates that reptation theory cannot be verified by simple comparison to diffusion constant measurements.
    Journal of Polymer Science Part B Polymer Physics 01/1989; 27(1):151-154. DOI:10.1002/polb.1989.090270109 · 2.22 Impact Factor
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    ABSTRACT: A particularly interesting problem in polymer physics is the mechanism by which an individual polymer chain moves in a polymer melt or concentrated polymer solution. The first rather successful model of polymer dynamics was the reptation model of de Gennes which asserts that due to the effect of entanglements a polymer finds itself confined to a tube. Thus, the dominant long wavelength motion of the chain should be slithering out the ends of the tube. In order to examine the validity of the reptation model, a series of dynamic Monte Carlo simulations were performed. Although the simulations are on chains sufficiently long that agreement with the experimentally observed scaling with degree of polymerization n of the self diffusion constant and terminal relaxation time is observed, reptation does not appear to be the dominant mechanism of long distance motion. Rather the motion is isotropic, with the slowdown from dilute solution behavior arising from the formation of dynamic entanglements — rare long lived contacts where a given chain drags another chain through the melt for times on the order of longest internal relaxation time. Motivated by the simulations results, a phenomenological theory for the diffusive and viscoelastic behavior is developed that is consistent with both simulations and experiment and which does not invoke reptation. The major conclusions arising from the theoretical approach are described, and comparison is made with experiment.
    International Journal of Modern Physics B 01/1989; 3(01):33-64. DOI:10.1142/S0217979289000038 · 0.46 Impact Factor