Efficient global biopolymer sampling with end-transfer configurational bias Monte Carlo

We develop an "end-transfer configurational bias Monte Carlo" method for efficient thermodynamic sampling of complex biopolymers and assess its performance on a mesoscale model of chromatin (oligonucleosome) at different salt conditions compared to other Monte Carlo moves. Our method extends traditional configurational bias by deleting a repeating motif (monomer) from one end of the biopolymer and regrowing it at the opposite end using the standard Rosenbluth scheme. The method's sampling efficiency compared to local moves, pivot rotations, and standard configurational bias is assessed by parameters relating to translational, rotational, and internal degrees of freedom of the oligonucleosome. Our results show that the end-transfer method is superior in sampling every degree of freedom of the oligonucleosomes over other methods at high salt concentrations (weak electrostatics) but worse than the pivot rotations in terms of sampling internal and rotational sampling at low-to-moderate salt concentrations (strong electrostatics). Under all conditions investigated, however, the end-transfer method is several orders of magnitude more efficient than the standard configurational bias approach. This is because the characteristic sampling time of the innermost oligonucleosome motif scales quadratically with the length of the oligonucleosomes for the end-transfer method while it scales exponentially for the traditional configurational-bias method. Thus, the method we propose can significantly improve performance for global biomolecular applications, especially in condensed systems with weak nonbonded interactions and may be combined with local enhancements to improve local sampling.     

Multifrequency ESR and ENDOR studies of ionomers

We describe methods for determining the local environment of cations and the process of ionic clustering in ionomers, using electron magnetic resonance spectroscopy. The distance between Cu²⁺ cations in perfluorinated membranes (Nafion) containing terminal sulfonic groups and swollen by water has been deduced from an analysis of ESR spectra at L (1.25 GHz), S (2.36 GHz) and X (9.36 GHz) bands, in membranes containing cupric ion concentrations in the range 1–30 percent of the total amount needed to fully neutralize the pendant acid groups. At higher cation concentrations ESR spectra indicate the presence of aggregated cations. The intercation distance determination is based on the simulation of spectra from isolated cations using distribution widths δg₁₁ and δA₁₁ and extraction of the residual width ΔH^R, which is due to dipolar interactions. No aggregation is detected in membranes swollen by less polar solvents such as methanol, dimethylformamide (DMF) and tetrahydrofuran (THF); these results are in contrast to SAXS experiments in membranes swollen by methanol, which exhibit the “ionic peak”. Cu²⁺-Cu²⁺ and Ti³⁺-Ti³⁺ dimers have been detected in Nafion swollen by water, methanol, DMF and THF, and have been characterized by an analysis of the spin-forbidden half-field Δm_s=2 transition, and by computer simulations. The intercation distance in the cupric dimers, deduced from the intensity ratio of the Δm_s=2 and Δm_s=1 dimer transitions, is 5.0±0.2 Å. A model for the dimer has been proposed, which explains the crosslinking of the polymer chains by the metal cations. ENDOR signals from ¹H, ²H and ¹⁹F nuclei have been detected in Nafion neutralized by Ti³⁺. The ENDOR results allow determination of the local environment of the paramagnetic cations, to a distance of ∼10 Å.