Systematic Comparison of Atomistic Force Fields for the Mechanical Properties of Double-Stranded DNA.

The response of double-stranded DNA to external mechanical stress plays a central role in its interactions with the protein machinery in the cell. Modern atomistic force fields have been shown to provide highly accurate predictions for the fine structural features of the duplex. In contrast, and despite their pivotal function, less attention has been devoted to the accuracy of the prediction of the elastic parameters. Several reports have addressed the flexibility of double-stranded DNA via all-atom molecular dynamics, yet the collected information is insufficient to have a clear understanding of the relative performance of the various force fields. In this work, we fill this gap by performing a systematic study in which several systems, characterized by different sequence contexts, are simulated with the most popular force fields within the AMBER family, bcs1 and OL15, as well as with CHARMM36. Analysis of our results, together with their comparison with previous work focused on bsc0, allows us to unveil the differences in the predicted rigidity between the newest force fields and suggests a roadmap to test their performance against experiments. In the case of the stretch modulus, we reconcile these differences, showing that a single mapping between sequence-dependent conformation and elasticity via the crookedness parameter captures simultaneously the results of all force fields, supporting the key role of crookedness in the mechanical response of double-stranded DNA.

Force-dependent elasticity of nucleic acids.

The functioning of double-stranded (ds) nucleic acids (NAs) in cellular processes is strongly mediated by their elastic response. These processes involve proteins that interact with dsDNA or dsRNA and distort their structures. The perturbation of the elasticity of NAs arising from these deformations is not properly considered by most theoretical frameworks. In this work, we introduce a novel method to assess the impact of mechanical stress on the elastic response of dsDNA and dsRNA through the analysis of the fluctuations of the double helix. Application of this approach to atomistic simulations reveals qualitative differences in the force dependence of the mechanical properties of dsDNA with respect to those of dsRNA, which we relate to structural features of these molecules by means of physically-sound minimalistic models.

Intermolecular forces at ice and water interfaces: Premelting, surface freezing, and regelation.

Using Lifshitz theory, we assess the role of van der Waals forces at interfaces of ice and water. The results are combined with measured structural forces from computer simulations to develop a quantitative model of the surface free energy of premelting films. This input is employed within the framework of wetting theory and allows us to predict qualitatively the behavior of quasi-liquid layer thickness as a function of ambient conditions. Our results emphasize the significance of vapor pressure. The ice-vapor interface is shown to exhibit only incomplete premelting, but the situation can shift to a state of complete surface melting above water saturation. The results obtained serve also to assess the role of subsurface freezing at the water-vapor interface, and we show that intermolecular forces favor subsurface ice nucleation only in conditions of water undersaturation. We show that ice regelation at ambient pressure may be explained as a process of capillary freezing, without the need to invoke the action of bulk pressure melting. Our results for van der Waals forces are exploited in order to gauge dispersion interactions in empirical point charge models of water.

Analytical theory for the crossover from retarded to non-retarded interactions between metal plates.

The van der Waals force established between two surfaces plays a central role in many phenomena, such as adhesion or friction. However, the dependence of this forces on the distance of separation between plates is very complex. Two widely different non-retarded and retarded regimes are well known, but these have been traditionally studied separately. Much less is known about the important experimentally accessible cross-over regime. In this study, we provide analytical approximations for the van der Waals forces between two plates that interpolates exactly between the short distance and long distance behavior, and provides new insight into the crossover from London to Casimir forces at finite temperature. At short distance, where the behavior is dominated by non-retarded interactions, we work out a very accurate simplified approximation for the Hamaker constant which adopts analytical form for both the Drude and Lorentz models of dielectric response. We apply our analytical expressions for the study of forces between metallic plates, and observe very good agreement with exact results from numerical calculations. Our results show that contributions of interband transitions remain important in the experimentally accessible regime of decades nm for several metals, including gold.

Lifshitz theory of wetting films at three phase coexistence: The case of ice nucleation on Silver Iodide (AgI).

HYPOTHESIS: As a fluid approaches three phase coexistence, adsorption may take place by the successive formation of two intervening wetting films. The equilibrium thickness of these wetting layers is the result of a delicate balance of intermolecular forces, as dictated by an underlying interface potential. The van der Waals forces for the two variable adsorption layers may be formulated exactly from Dzyaloshinskii-Lifshitz-Pitaevskii theory, and analytical approximations may be derived that extent well beyond the validity of conventional Hamaker theory. CALCULATIONS: We consider the adsorption equilibrium of water vapor on Silver Iodide where both ice and a water layers can form simultaneously and compete for the vapor as the triple point is approached. We perform numerical calculations of Lifshitz theory for this complex system and work out analytical approximations which provide quantitative agreement with the numerical results. FINDINGS: At the three phase contact line between AgI/water/air, surface forces promote growth of ice both on the AgI/air and the water/vapor interfaces, lending support to a contact nucleation mode of AgI in the atmosphere. Our approach provides a framework for the description of adsorption at three phase coexistence, and allows for the study of ice nucleation efficiency on atmospheric aerosols.