Experimentally, the solubility of oligoglycines in water decreases as its length increases. Computationally, the free energy of solvation becomes more favorable with chain length for short (n = 1–5) oligoglycines. We present results of large scale simulations with over 600 pentaglycines at varying concentrations in explicit solvent to consider the mechanism of aggregation. The solubility limit of Gly5 for the force field used was calculated and compared with experimental values. We find that intermolecular interactions between pentaglycines are favored over interactions between glycine and water, leading to their aggregation. However, the interaction driving peptide associations, liquid–liquid phase separation, are not predominantly hydrogen bonding. Instead, non-hydrogen bonding interactions between partially charged atoms on the peptide backbone allow the formation of dipole–dipole and charge layering correlations that mechanistically stabilize the formation of large, stable peptide clusters.

Details of the reaction coordinate for DNA melting are fundamental to much of biology and biotechnology. Recently, it has been shown experimentally that there are at least three states involved. To clarify the reaction mechanism of the melting transition of DNA, we perform 100-ns molecular dynamics simulations of a homo-oligomeric, 12-basepair DNA duplex, d(A(12)).d(T(12)), with explicit salt water at 400 K. Analysis of the trajectory reveals the various biochemically important processes that occur on different timescales. Peeling (including fraying from the ends), searching for Watson-Crick complements, and dissociation are recognizable processes. However, we find that basepair searching for Watson-Crick complements along a strand is not mechanistically tied to or directly accessible from the dissociation steps of strand melting. A three-step melting mechanism is proposed where the untwisting of the duplex is determined to be the major component of the reaction coordinate at the barrier. Though the observations are limited to the characteristics of the system being studied, they provide important insight into the mechanism of melting of other more biologically relevant forms of DNA, which will certainly differ in details from those here.

We have investigated the impact of single droplets of various surfactant solutions on a low-surface-energy solid substrate using a high-frequency visualization technique (one picture every 100 μs). Whatever the surfactant, the drop spreads and retracts in about 1 s under the action of inertia and capillarity, respectively. During retraction, the capillary waves can be amplified and, in some cases, even yield droplet bouncing. Then, the droplet may slowly spread again due to gravity and the unbalanced capillary forces at the contact line between the droplet and the substrate. During the fast spreading process (2-3 ms), the droplet surface increases by almost one order of magnitude since its shape changes from a sphere to a flat pancake; this causes a strong deviation from thermodynamic equilibrium. The relevant surface property is therefore the dynamic surface tension which we have evaluated using a maximum bubble pressure apparatus. We have shown that droplet retraction is drastically influenced by the adsorption kinetics of the surfactant which limits the return to equilibrium surface tension.

DNA orientation near surfaces determines many properties related to hybridization efficiency. We performed a 40-ns molecular dynamics simulation to study the structure and orientation of a 12-base-pair DNA duplex tethered to a neutral, epoxide-coated silica surface. Starting with a canonical B-form tethered in an up-right position, normal to the surface, the DNA tilted to over 55 degrees and back. The time scale was a few nanoseconds for tilting events. The linker between the DNA and the surface went from standing upright to tilted, and finally collapsed on the surface. Although the DNA conformation fluctuated, it remained closed to B-form for the entire 40 ns. Calculations of helical parameters of the DNA show that the tethered end of the DNA changed its conformation noticeably when attracted to the surface.

Although detailed atomic models may be applied for a full description of solvation, simpler phenomenological models are particularly useful to interpret the results for scanning many, large, complex systems where a full atomic model is too computationally expensive to use. Among the most costly are solvation free energy evaluations by simulation. Here we develop a fast way to calculate electrostatic solvation free energy while retaining much of the accuracy of explicit solvent free energy simulation. The basis of our method is to treat the solvent not as a structureless dielectric continuum, but as a structured medium by making use of universal proximal radial distribution functions. Using a deca-alanine peptide as a test case, we compare the use of our theory with free energy simulations and traditional continuum estimates of the electrostatic solvation free energy.