Structure and Dynamics of Solvated Polymers near a Silica Surface: On the Different Roles Played by Solvent

Whereas it is experimentally known that the inclusion of nanoparticles in hydrogels can lead to a mechanical reinforcement, a detailed molecular understanding of the adhesion mechanism is still lacking. Here we use coarse-grained molecular dynamics simulations to investigate the nature of the interface between silica surfaces and solvated polymers. We show how differences in the nature of the polymer and the polymer--solvent interactions can lead to drastically different behavior of the polymer--surface adhesion. Comparing explicit and implicit solvent models, we conclude that this effect cannot be fully described in an implicit solvent. We highlight the crucial role of polymer solvation for the adsorption of the polymer chain on the silica surface, the significant dynamics of polymer chains on the surface, and details of the modifications in the structure solvated polymer close to the interface

Recent advances in the modelling and simulation of electrokinetic effects: bridging the gap between atomistic and macroscopic descriptions

Perspective ArticleInternational audienceElectrokinetic phenomena are of great practical importance in fields as diverse as micro-fluidics, colloid science and oil exploration. However, the quantitative prediction of electrokinetic effects was until recently limited to relatively simple geometries that allowed the use of analytical theories. In the past decade, there has been a rapid development in the use of numerical methods that can be used to model electrokinetic phenomena in complex geometries or, more generally, under conditions where the existing analytical approaches fail. The present paper discusses these recent developments, with special emphasis on the advent of coarse-grained models that make it possible to bridge the gap between a purely atomistic and macroscopic descriptions

Realistische Modellierung von Elektrophorese in freier Lösung : eine Studie über geladene Makromoleküle

Im Rahmen der vorliegenden Doktorarbeit aus dem Forschungsgebiet der sogenannten "Weichen Materie" (soft matter) wird im Besonderen der Einfluss hydrodynamischer Wechselwirkungen auf die Elektrophorese linearer Polyelektrolyte in freier Lösung, d. h. in Abwesenheit eines trennenden Gels, untersucht. Hierzu wird eine vergröberte Molekulardynamiksimulation verwendet, die die vollständigen elektrostatischen und hydrodynamischen Wechselwirkungen zwischen allen Komponenten des Systems berücksichtigt. Ein besonderes Gewicht liegt auf der Analyse der Rolle der Hydrodynamik für das elektrophoretische Verhalten geladener Makromoleküle. Diese Arbeit untersucht die Längenabhängigkeit der hydrodynamischen Wechselwirkungen, den Einfluss der Kettenflexibilität und der das Polyelektrolyt umgebenden Gegenionen, sowie ihre gemeinsame Wirkung auf die dynamischen Transportkoeffizienten, die Diffusion und die elektrophoretische Mobilität. Diese Problemstellung wird mit Hilfe umfangreicher Computersimulationen bearbeitet, deren Ergebnisse quantitativ mit experimentellen Resultaten verglichen werden können. Dabei werden bestehende Theorien sorgfältig analysiert und durch die in dieser Arbeit ermittelten Erkenntnisse erweitert.This thesis contributes to the field of soft matter research and studies the importance of hydrodynamic interactions during free-solution electrophoresis of linear polyelectrolytes by means of coarse-grained molecular dynamics simulations including full electro-hydrodynamic interactions. The center of attention is the specific role of hydrodynamic interactions on the electrophoretic behaviour of charged macromolecules. Points of interest are the dependence of hydrodynamic interactions on the chain length, the chain flexibility and the surrounding counterions, and their combined influence on important observables such as the static chain conformations and the dynamic transport coefficients, i.e., the diffusion and the electrophoretic mobility. These problems are addressed by extensive computer simulations that are quantitatively matched with experimental results. Existing theoretical predictions are carefully examined and are augmented by the observations in this thesis

Multiscale modeling for complex macromolecular systems: Methodologies and applications

The objective of this dissertation is to understand the binding mechanism between flexible macromolecules and guest species in solution using multiscale molecular modeling strategies, including: ab initio electronic structure theory, all-atom classical molecular dynamics simulations, coarse-grained molecular dynamics simulations, and statistical eld theory. A brief summary of the subsequent chapters in this thesis is provided. Chapters 2 - 7 and Appendix A are self-contained units complete with literature review and bibliography

Molecular Dynamics Study of Supercoiled DNA Minicircles Tightly Bent and Supercoiled DNA in Atomistic Resolution

Towards the complete understanding of the DNA response to superhelical stress, sequence dependence structural disruptions on the ~100 base pairs supercoiled DNA minicircles were examined through a series of atomistic MD simulations. The results showed the effects from some subtle structural characteristics of DNA on defect formation, including flexibility at base pair step level and anisotropy, whose dynamic information are available only from atomistic MD simulations. For longer supercoiled DNA minicircles (240-340 bp), the molecules adapt into their writhed conformations. Writhe can be calculated by a Gauss’ integral performed along the DNA central axis path. A new mathematical definition for the DNA central axis path was developed for the more exact writhe calculation. Finally, atomistic representation of supercoiled 336 base pairs minicircles was provided by fitting the DNA structure obtained by explicitly solvated MD simulations into the density maps from electron cryo-tomography. Structural data were analysed and provided a decent explanation for the mechanism of the sequence specific binding of the enzyme topoisomerase 1B onto the negatively supercoiled DNA