To function as gene regulatory elements in response to environmental signals, riboswitches must adopt specific secondary structures on appropriate time scales. We employ kinetic Monte Carlo simulation to model the time-dependent folding during transc
ription of TPP riboswitch expression platforms. According to our simulations, riboswitch transcriptional terminators, which must adopt a specific hairpin configuration by the time they have been transcribed, fold with higher efficiency than Shine-Dalgarno sequesterers, whose proper structure is required only at the time of ribosomal binding. Our findings suggest both that riboswitch transcriptional terminator sequences have been naturally selected for high folding efficiency, and that sequesterers can maintain their function even in the presence of significant misfolding.
We investigate generalized potentials for a mean-field density functional theory of a three-phase contact line. Compared to the symmetrical potential introduced in our previous article [1], the three minima of these potentials form a small triangle l
ocated arbitrarily within the Gibbs triangle, which is more realistic for ternary fluid systems. We multiply linear functions that vanish at edges and vertices of the small triangle, yielding potentials in the form of quartic polynomials. We find that a subset of such potentials has simple analytic far-field solutions, and is a linear transformation of our original potential. By scaling, we can relate their solutions to those of our original potential. For special cases, the lengths of the sides of the small triangle are proportional to the corresponding interfacial tensions. For the case of equal interfacial tensions, we calculate a line tension that is proportional to the area of the small triangle.
A three-phase contact line in a three-phase fluid system is modeled by a mean-field density functional theory. We use a variational approach to find the Euler-Lagrange equations. Analytic solutions are obtained in the two-phase regions at large dista
nces from the contact line. We employ a triangular grid and use a successive over-relaxation method to find numerical solutions in the entire domain for the special case of equal interfacial tensions for the two-phase interfaces. We use the Kerins-Boiteux formula to obtain a line tension associated with the contact line. This line tension turns out to be negative. We associate line adsorption with the change of line tension as the governing potentials change.
