arXiv subjects

Rikkert J. Nap

Publications and source records attributed to Rikkert J. Nap.

3 recordsLinked to original sources

arXiv2024

Local Volume Concentration, Packing Domains and Scaling Properties of Chromatin

We propose the Self Returning Excluded Volume (SR-EV) model for the structure of chromatin based on stochastic rules and physical interactions. The SR-EV rules of return generate conformationally-defined domains observed by single cell imaging techniques. From nucleosome to chromosome scales, the model captures the overall chromatin organization as a corrugated system, with dense and dilute regions alternating in a manner that resembles the mixing of two disordered bi-continuous phases. This particular organizational topology is a consequence of the multiplicity of interactions and processes occurring in the nuclei, and mimicked by the proposed return rules. Single configuration properties and ensemble averages show a robust agreement between theoretical and experimental results including chromatin volume concentration, contact probability, packing domain identification and size characterization, and packing scaling behavior. Model and experimental results suggest that there is an inherent chromatin organization regardless of the cell character and resistant to an external forcing such as Rad21 degradation.

physics.bio-ph↗

arXiv2018

Association Free Energies of Metal Cations with Mesylate and Acetate in Brine Calculated via Molecular Dynamics Simulation

Here we report results from fully-atomistic molecular dynamics simulations and present the calculated binding free energies of the associations between metal cations and anionic functional groups under brine condition. Specifically the ion pair formations of Na+ and Ca2+ metal cations with sulfonate and carboxylate functional groups were considered. In our simulations, sulfonate and carboxylate functional groups in polyelectrolytes were modeled by mesylate and acetate anions, respectively. The simulations show that the binding strengths of Na+ and Ca2+ with sulfonate group are relatively weak with correlation times for the contact ion pairs being around 300-400 ps. In the case of acetate, the binding strength with Na+ was found to be comparable to the case of sulfonate group, while the binding of acetate with Ca2+ was found to be much stronger with a correlation time of the order of hundreds of nanoseconds. The binding free energies of Na+ and Ca2+ with sulfonate as well as that of Na+ with acetate have been calculated directly from the radial distribution functions. For the case of binding between Ca2+ and acetate constrained MD simulations with umbrella sampling were carried out to improve the sampling of the phase space and the potential of mean force was obtained by the weighted histogram analysis method. The binding free energy of a 2:1 binding event between one Ca2+ ion and two acetates was also calculated. Finally the binding free energies between Ca2+ and acetate were compared for different force field parameters and water models, and also with experimental and calculated values reported in the literature.

physics.chem-ph↗

arXiv2001

Ordering at two length scales in comb-coil diblock copolymers consisting of only two different monomers

The microphase separated morphology of a melt of a specific class of comb-coil diblock copolymers, consisting of an AB comb block and a linear homopolymer A block, is analyzed in the weak segregation limit. On increasing the length of the homopolymer A block, the systems go through a characteristic series of structural transitions. Starting from the pure comb copolymer the first series of structures involve the short length scale followed by structures involving the large length scale. A maximum of two critical points exists. Furthermore, in the two parameter space, characterizing the comb-coil diblock copolymer molecules considered, a non-trivial bifurcation point exists beyond which the structure factor can have two maxima (two correlation hole peaks).

cond-mat.soft↗