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Center for the Study of Systems Biology

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Now showing 1 - 3 of 3
  • Item
    The collapse transition of semiflexible polymers. A Monte Carlo simulation of a model system
    (Georgia Institute of Technology, 1986-09-15) Kolinski, Andrzej ; Skolnick, Jeffrey ; Yaris, Robert
    Monte Carlo simulations have been performed on a diamond lattice model of semiflexible polymers for a range of flexibilities and a range of chain lengths from 50 to 800 segments. The model includes both repulsive (excluded volume) and attractive segment–segment interactions. It is shown that the polymers group into two classes, "flexible" and "stiff." The flexible polymers exhibit decreasing chain dimensions as the temperature decreases with a gradual collapse from a loose random coil, high temperature state to a dense random coil, low temperature state. The stiffer polymers, on the other hand, exhibit increasing chain dimensions with decreasing temperature until at a critical temperature there is a sudden collapse to an ordered high density, low temperature state. This difference is due to the relative strength of the segment–segment attractive interactions compared to the energetic preference for a trans conformational state over a gauche state. When the attractive interaction is relatively strong (flexible case) the polymer starts to collapse before rotational degrees of freedom freeze out, leading to a disordered dense state. When the attractive interaction is relatively weak (stiff case) the polymer starts to freeze out rotational degrees of freedom before it finally collapses to a highly ordered dense state.
  • Item
    On the short time dynamics of dense polymeric systems and the origin of the glass transition: A model system
    (Georgia Institute of Technology, 1986-02-01) Kolinski, Andrzej ; Skolnick, Jeffrey ; Yaris, Robert
    In order to model the short time (and distance) scale motions for dense polymeric systems, we have performed dynamic Monte Carlo simulations of chains on a diamond lattice at considerably greater densities than those done previously. Chain dynamics were simulated by a random sequence of three- and four-bond kink motions and end moves. For times shorter than the chain diffusion time, the single bead autocorrelation function g(t) exhibits three distinct regimes: a short time Rouse-like regime where g(t)~t[superscript ½]; a mid-region where g(t)~t β, followed by a longer time, Rouse-like regime where g(t)~t1/2. There is a smooth crossover from Rouse-like dynamics, β =1/2, at low density to smaller values of β at higher density, and β =0 at the glass transition density (Φ[subscript G] =0.92±0.01). It is shown that the major motion of the chains is transverse to the chain contour rather than along the chain. The observed motion is successfully analyzed in terms of the motion of defects (holes) through the sample. It is shown that the glass transition at Φ[subscript G] ±0.92 is caused by the shutting down of the orientation changing four-bond motions.
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    Monte Carlo dynamics of diamond-lattice multichain systems
    (Georgia Institute of Technology, 1986-01-30) Kolinski, Andrzej ; Skolnick, Jeffrey ; Yaris, Robert
    We present preliminary results of Monte Carlo studies on the dynamics of multichain diamond-lattice systems at considerably greater densities than those done previously. Chain dynamics were simulated by a random sequence of three or four bond kink motions. The single bead autocorrelation function exhibits "slow" mode relaxation behavior with a g(t)∝ tβ. There is a smooth crossover from Rouse-like dynamics, β=1/2, at low density to smaller values of β at higher density and β=0 at the glass transition density (φG≅0.92). The simulation provides a self-diffusion coefficient D ∝ n-2, with n the number of beads, in agreement with experiment. A phenomenological model, different from the widely accepted reptation picture, is proposed.