Condensed Matter Theory

Abstract:

A minimal design for a molecular swimmer is proposed that is based on a mechanochemical propulsion mechanism. Conformational changes are induced by electrostatic actuation when specific parts of the molecule temporarily acquire net charges through catalyzed chemical reactions involving ionic components. The mechanochemical cycle is designed such that the resulting conformational changes would be sufficient for achieving low Reynolds number propulsion. The system is analyzed within the recently developed framework of stochastic swimmers to take account of the noisy environment at the molecular scale. The swimming velocity of the device is found to depend on the concentration of the fuel molecule according to the Michaelis-Menten rule in enzymatic reactions.

Abstract:

A class of artificial microswimmers with combined translational and rotational self-propulsion is studied experimentally. The chemically fueled microswimmers are made of doublets of Janus colloidal beads with catalytic patches that are positioned at a fixed angle relative to one another. The mean-square displacement and the mean-square angular displacement of the active doublets are analyzed in the context of a simple Langevin description, using which the physical characteristics of the microswimmers such as the spontaneous translational and rotational velocities are extracted. Our work suggests strategies for designing microswimmers that could follow prescribed cycloidal trajectories.

Abstract:

A systematic analysis of B-DNA elasticity cross-terms was performed using molecular dynamics simulations of three different duplexes designed to contain all dinucleotide steps including a 6-mer A-tract. The influence of ionic strength was also evaluated by several trajectories of each molecule with different NaCl concentrations at physiological rank. Simulations show DNA flexibility is independent of salt, in agreement with the Odijk-Skolnick-Fixman model. In addition, our results demonstrate DNA asymmetry at this scale is more complex than predicted by long-scale DNA models, with the cross-terms relating twist, slide, roll, and twist on the one hand and tilt and shift on the other being most essential. We find the rest of the coupling terms can be generally discarded due to their lack of correlation, with the exception of purine-purine's rise-tilt and shift-tilt. More specifically, A-tracts do not present any specific features in terms of their flexibility and chirality properties within those expected for purine-purine steps. Finally, some hints about coupling mechanisms are provided; we suggest cup deformation is mostly responsible for the positive twist-rise correlation at step level, whereas roll-rise and tilt-rise correlations can be understood via changes in stagger.