Extensive coarse-grained molecular dynamics simulations of soft matter: From RNA to hydrogels

Coarse-grained molecular dynamics (CG-MD) simulations are indispensable for investigating the dynamical response of macromolecular structures to external probes. The purpose of this thesis is to utilize CG-MD in order to determine (a) the response of a hydrogel to a time-varying external electric field, (b) the melting time of an RNA hairpin structure as a function of the temperature and the molecule size. Controlling the mechanical response of polyelectrolyte hydrogels to external electric fields is of great importance for hydrogel-based soft actuation systems. The first part of the thesis work involves the study of a semi-infinite polyelectrolyte hydrogel slab to a transient and spatially nonuniform half-sinusoidal electric field by means of both implicit and explicit solvent models. Results with an implicit solvent model demonstrated that an electric field confined to a small volumetric section of the hydrogel slab induces a reversible contraction of the entire slab in the direction perpendicular to the field. The hydrogel initially contracts by almost half of its field-free length and then retracts to its original size, with repeating contraction/retraction cycles exponentially decaying in magnitude akin to an underdamped oscillator. In contrast, almost no contraction occurs when the field is applied uniformly on the whole hydrogel slab. Analyses of contraction times and efficiencies for varying backbone charge fractions, dielectric constants, and salt concentrations confirm the robustness of the phenomenon. Further, by tuning the electric-field frequency and amplitude, both the contraction time and the efficiency can be controlled. Also, this phenomenon is demonstrated by using the explicit solvent model. Results showed that in realistic water concentrations (0.7 M), the contraction of the hydrogel decreases up to 35\%. Although this contraction is observed when an electric field is applied to the hydrogel slab partially like in the implicit solvent model, the field area increased to half of its initial size instead of 10\% for the implicit model. Concluded that our results of the mechanical behavior of the PE hydrogel slab are unconstrained by the solvent model, hydrogel's chemical properties, and electric field parameters. In the second part of the thesis, the melting behavior of an RNA hairpin, another macromolecular system distinguished by its palindromic sequence, investigated again by means of CG-MD simulations. Determination of the structure and dynamical behavior of nucleic acids as a function of temperature is a fundamental problem in polymer physics and is relevant for understanding the intracellular processes in thermophilic bacteria. The characteristic helical structure of these macromolecules is known to play an important role in their folding and melting dynamics. The main focus is on the melting dynamics upon an increase in the ambient temperature. Our results suggest the presence of two distinct dynamical regimes. The "critical regime" close to the equilibrium melting temperature displays an unexpected, non-monotonous dependence of the melting time on the temperature. The second, high-temperature regime is characterized by the entropic competition of the two denatured ends of the linear duplex structure. The scaling behavior of the melting time in both regimes investigated and identified the crossover boundary separating the two as a function of temperature and molecule size.