SearcharxivSearch

arXiv subjects

Daniel J. Sharpe

Publications and source records attributed to Daniel J. Sharpe.

2 recordsLinked to original sources

Stochastic paths controlling speed and dissipation

Near equilibrium, thermodynamic intuition suggests that fast, irreversible processes will dissipate more energy and entropy than slow, quasistatic processes connecting the same initial and final states. Here, we test the hypothesis that this relationship between speed and dissipation holds for stochastic processes far from equilibrium. To analyze these processes on finite timescales, we derive an exact expression for the path probabilities of continuous-time Markov chains from the path summation solution of the master equation. Applying this formula to a model for nonequilibrium self-assembly, we show that more speed can lead to less dissipation when there are strong nonequilibrium currents. In the model, the relative energies of the initial and target states control the speed, and the nonequilibrium currents of a cycle situated between these states control the path-level dissipation. This model serves as a minimal prototype for designing kinetics to sculpt the nonequilibrium path space, so that faster structure-forming paths dissipate less.

cond-mat.stat-mech

Energy landscapes and dynamics of xylo-nucleic acids

Artificial analogues of the natural nucleic acids have attracted recent interest as a diverse class of information storage molecules capable of self-replication. In the present study, we use the computational potential energy landscape framework to investigate the structural and dynamical properties of xylo- and deoxyxylo-nucleic acids (XyNA and dXyNA), which are derived from their respective RNA and DNA analogues by an inversion of configuration at a single chiral center in the sugar moiety of the nucleotide unit. The free energy landscapes of an octameric XyNA sequence and its dXyNA analogue demonstrate the existence of a facile conformational transition between a left-handed helix that is the global free energy minimum, and a closely competing ladder-type structure with approximately zero helicity. The separation of the competing conformational ensembles is better-defined for the dXyNA system, whereas the XyNA analogue is inherently more flexible. The former therefore appear more suitable candidates for a molecular switch. The landscapes differ qualitatively from those reported in previous studies for evolved biomolecules: they are significantly more frustrated, so that XyNAs provide an example of an unnatural system for which the conditions constituting the principle of minimal frustration are, as may be expected, violated.

physics.bio-ph