The properties of sodium dodecyl sulfate (SDS) aggregates were studied through extensive molecular dynamics simulations with explicit solvent. First, we provide a parametrization of the model within Gromacs. Then, we probe the kinetics of aggregation by starting from a random solution of SDS molecules and letting the system explore its kinetic pathway during the aggregation of multiple units. We observe a structural transition for the surfactant aggregates brought upon by a change in temperature. Specifically, at low temperatures, the surfactants form crystalline aggregates, whereas at elevated temperatures, they form micelles. We also investigate the dependence of aggregation kinetics on surfactant concentration and report on the molecular level structural changes involved in the transition.

Water plays a central role in the assembly and the dynamics of charged systems such as proteins, enzymes, DNA, and surfactants. Yet it remains a challenge to resolve how water affects relaxation at a molecular level, particularly for assemblies of oppositely charged macromolecules. Here, the molecular origin of water’s influence on the glass transition is quantified for several charged macromolecular systems. It is revealed that the glass transition temperature (Tg) is controlled by the number of water molecules surrounding an oppositely charged polyelectrolyte–polyelectrolyte intrinsic ion pair as 1/Tg ∼ ln(nH2O/nintrinsic ion pair). This relationship is found to be “general”, as it holds for two completely different types of charged systems (pH- and salt-sensitive) and for both polyelectrolyte complexes and polyelectrolyte multilayers, which are made by different paths. This suggests that water facilitates the relaxation of charged assemblies by reducing attractions between oppositely charged intrinsic ion pairs. This finding impacts current interpretations of relaxation dynamics in charged assemblies and points to water’s important contribution at the molecular level.

Intrinsically disordered proteins (IDPs) are increasingly recognized for their important roles in a range of biological contexts, both in normal physiological function and in a variety of devastating human diseases. However, their structural characterization by traditional biophysical methods, for the purposes of understanding their function and dysfunction, has proved challenging. Here, we investigate the model IDPs α-Synuclein (αS) and tau, that are involved in major neurodegenerative conditions including Parkinson's and Alzheimer's diseases, using excluded volume Monte Carlo simulations constrained by pairwise distance distributions from single-molecule fluorescence measurements. Using this, to our knowledge, novel approach we find that a relatively small number of intermolecular distance constraints are sufficient to accurately determine the dimensions and polymer conformational statistics of αS and tau in solution. Moreover, this method can detect local changes in αS and tau conformations that correlate with enhanced aggregation. Constrained Monte Carlo simulations produce ensembles that are in excellent agreement both with experimental measurements on αS and tau and with all-atom, explicit solvent molecular dynamics simulations of αS, with much lower configurational sampling requirements and computational expense.