Article

# Diffusion-controlled first contact of the ends of a polymer: Crossover between two scaling regimes

Department of Physics, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1.

Physical Review E (Impact Factor: 2.29). 10/2005; 72(3 Pt 1):031804. DOI: 10.1103/PhysRevE.72.031804 Source: PubMed

**ABSTRACT**

We report on Monte Carlo simulations of loop formation of an ideal flexible polymer consisting of N bonds with two reactive ends. We determine the first-passage time associated with chain looping that yields a conformation in which the end monomers are separated by a distance a--the reaction radius. In particular, our numerical results demonstrate how this time scale crosses over from tau(first) approximately N(3/2)/a to the a-independent tau(first) approximately N2 as N is increased. The existence and characteristics, of the two scaling regimes and the crossover between the two, are further illuminated by a scaling argument.

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**ABSTRACT:**The thermodynamics and kinetics of ABAB pseudoknot formation owing to reversible intrachain reactions are investigated for a flexible polymer based on the off-lattice Monte Carlo simulations. The polymer is made of N hard spheres tethered by inextensible bonds and consists of two reactive pairs AA and BB with binding energies -epsilon1 and -epsilon2, respectively, and three loop lengths (l1, l2, and l3). Although two intermediate states, loops A and B, may be formed, the folding path goes mainly through the intermediate loop whose free energy reduction associated with coil-to-loop crossover is greater. The conformational entropy loss is found to follow DeltaS=alpha ln N+G, where alpha approximately 2.48 for coil-loop crossover and alpha approximately 2.43 for loop-pseudoknot crossover. The constant G depends on the three loop lengths and the two end-to-reactive site lengths (L1 and L2). For a given total loop length, G is maximum when the three loop lengths are equal (l1=l2=l3). When l1=l3, the entropy loss is minimum if l2=0. However, the condition l1 not equal l3 makes G even smaller. This consequence indicates that asymmetry in loop lengths is thermodynamically favorable and this fact is consistent with observations of pseudoknotted RNA structures. - [Show abstract] [Hide abstract]

**ABSTRACT:**Using Monte Carlo simulations, we study the diffusion-controlled dynamics of a polymer chain, which leads to the intrachain reaction of two reactive monomers. On the basis of the bond fluctuation lattice model, we computed the mean first-passage time and examined its scaling behavior as a function of the chain length and location of the reactive monomers, for five different types of polymer architectures. While the simulation results confirmed previous theoretical predictions for the free chain case, our measurements of the mean first-passage time also yielded new insights into the looping dynamics of end-grafted chains. -
##### Article: Renormalization group analysis of polymer cyclization with non-equilibrium initial conditions

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**ABSTRACT:**We develop a renormalization group approach for cyclizing polymers for the case when chain ends are initially close together (ring initial conditions). We analyze the behavior at times much shorter than the longest polymer relaxation time. In agreement with our previous work (Europhys. Lett. 73, 621 (2006)) we find that the leading time dependence of the reaction rate k(t) for ring initial conditions and equilibrium initial conditions are related, namely k ring(t) ∝ t -δ and k eq(t) ∝ t 1-δ for times less than the longest polymer relaxation time. Here δ is an effective exponent which approaches δ = 5/4 for very long Rouse chains. Our present analysis also suggests a “sub-leading” term proportional to (ln t)/t which should be particularly significant for smaller values of the renormalized reaction rate and early times. For Zimm dynamics, our RG analysis indicates that the leading time dependence for the reaction rate is k(t) ∼ 1/t for very long chains. The leading term is again consistent with the expected relation between ring and equilibrium initial conditions. We also find a logarithmic correction term which we “exponentiate” to a logarithmic form with a Landau pole. The presence of the logarithm is particularly important for smaller chains and, in the Zimm case, large values of the reaction rate.