A Renormalization Group Approach and the Phenomenological Theory of a Polymer Chain

Oono, Yoshitsugu; Oyama, Tomo o.

doi:10.1143/jpsj.44.301

Cited by 33 publications

(36 citation statements)

References 23 publications

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“…36; for a review, see Ref. 37) models. Most notably, any "cooperativity" found in the protein folding process must result as a specific consequence of a given thermodynamic condition and the interplay among It has been recently argued by Levitt and Sharon34 that molecular dynamics simulations that explicitly include the solvent molecules provide a more realistic description of dynamics in proteins.…”

Section: Construction Of the Modelmentioning

confidence: 99%

The nature of folded states of globular proteins

Honeycutt¹,

1992

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We suggest, using dynamical simulations of a simple heteropolymer modelling the alpha-carbon sequence in a protein, that generically the folded states of globular proteins correspond to statistically well-defined metastable states. This hypothesis, called the metastability hypothesis, states that there are several free energy minima separated by barriers of various heights such that the folded conformations of a polypeptide chain in each of the minima have similar structural characteristics but have different energies from one another. The calculated structural characteristics, such as bond angle and dihedral angle distribution functions, are assumed to arise from only those configurations belonging to a given minimum. The validity of this hypothesis is illustrated by simulations of a continuum model of a heteropolymer whose low temperature state is a well-defined beta-barrel structure. The simulations were done using a molecular dynamics algorithm (referred to as the "noisy" molecular dynamics method) containing both friction and noise terms. It is shown that for this model there are several distinct metastable minima in which the structural features are similar. Several new methods of analyzing fluctuations in structures belonging to two distinct minima are introduced. The most notable one is a dynamic measure of compactness that can in principle provide the time required for maximal compactness to be achieved. The analysis shows that for a given metastable state in which the protein has a well-defined folded structure the transition to a state of higher compactness occurs very slowly, lending credence to the notion that the system encounters a late barrier in the process of folding to the most compact structure. The examination of the fluctuations in the structures near the unfolding----folding transition temperature indicates that the transition state for the unfolding to folding process occurs closer to the folded state.

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Section: Construction Of the Modelmentioning

confidence: 99%

The nature of folded states of globular proteins

Honeycutt¹,

1992

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“…When estimating A values the maximum values of Flory parameters were used obtained in the approximation of preliminary averaging of Ozeen's hydrodynamic interactions tensor. In a number of works using Monte‐Carlo method and the theory of renormalization group33–35 the hydrodynamic behaviour of macromolecules without the preliminary averaging of Ozeen tensor was investigated which resulted in somewhat different extrapolated values of Φ 0 and P 0 parameters. This leads to some shift in the A values evaluations.…”

Section: Resultsmentioning

confidence: 99%

Conformational Parameters of Poly(N‐methyl‐N‐vinylacetamide) Molecules Through the Hydrodynamic Characteristics Studies

Pavlov

Okatova

Mikhailova

et al. 2010

Macromolecular Bioscience

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Water-soluble PMVA was synthesized by radical polymerization methods. A number of polymer samples were fractionated in the chloroform-diethyl ether system. Fractions were studied by molecular hydrodynamics methods (sedimentation velocity, translational isothermal diffusion and viscosity) in H(2)O and DMF. The molecular masses of fractions were determined and the Kuhn-Mark-Houwink-Sakurada relationships were obtained in the molecular mass range of 3.5 < M x 10(-3) g x mol(-1) <540. A negative temperature coefficient of the characteristic viscosity was obtained in both solvents. The Kuhn statistic segment length and the hydrodynamic diameter of the molecule were estimated for PMVA. The hydrodynamic volumes, occupied by the molecules of PMVA, poly(1-vinyl-2-pyrrolidone), poly(vinylformamide), and pullulan were compared.

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“…The relation between the bare and renormalized variables is defined, as customary, by the minimal subtraction method. [27][28][29] However, to lowest order in ⑀, the two sets of bare and renormalized quantities are equal to each other, respectively, so the details of the renormalization are unnecessary here. The factor of 1Ϫ⑀ 2 /4 is likewise not expanded in the renormalized version of Eq.…”

Section: ͑50͒mentioning

confidence: 99%

The concentration dependent cooperative friction coefficient of dilute polymer solutions at the theta point

Cherayil

Freed

1996

The Journal of Chemical Physics

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We combine multiple scattering and renormalization group methods to calculate the leading order dimensionless virial coefficient k s for the friction coefficient of dilute polymer solutions under conditions where the osmotic second virial coefficient vanishes ͑i.e., at the theta point T ͒. Our calculations are formulated in terms of coupled kinetic equations for the polymer and solvent, in which the polymers are modeled as continuous chains whose configurations evolve under the action of random forces in the velocity field of the solvent. To lowest order in ⑀ϭ4Ϫd, we find that k s ϭ1.06. This result compares satisfactorily with existing experimental estimates of k s , which are in the range 0.7-0.8. It is also in good agreement with other theoretical results on chains and suspensions at T . Our calculated k s is also found to be identical to the leading order virial coefficient of the tracer friction coefficient at the theta point. We discuss possible reasons for the difficulties encountered when attempting to evaluate k s by extrapolating prior renormalization group calculations from semidilute concentrations to the infinitely dilute limit.

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A Renormalization Group Approach and the Phenomenological Theory of a Polymer Chain

Cited by 33 publications

References 23 publications

The nature of folded states of globular proteins

The nature of folded states of globular proteins

Conformational Parameters of Poly(N‐methyl‐N‐vinylacetamide) Molecules Through the Hydrodynamic Characteristics Studies

The concentration dependent cooperative friction coefficient of dilute polymer solutions at the theta point

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