Large permeabilities of hourglass nanopores: From hydrodynamics to single file transport

In fluid transport across nanopores, there is a fundamental dissipation that arises from the connection between the pore and the macroscopic reservoirs. This entrance effect can hinder the whole transport in certain situations, for short pores and/or highly slipping channels. In this paper, we explore the hydrodynamic permeability of hourglass shape nanopores using molecular dynamics (MD) simulations, with the central pore size ranging from several nanometers down to a few Angstr{\"o}ms. Surprisingly, we find a very good agreement between MD results and continuum hydrodynamic predictions, even for the smallest systems undergoing single file transport of water. An optimum of permeability is found for an opening angle around 5 degree, in agreement with continuum predictions, yielding a permeability five times larger than for a straight nanotube. Moreover, we find that the permeability of hourglass shape nanopores is even larger than single nanopores pierced in a molecular thin graphene sheet. This suggests that designing the geometry of nanopores may help considerably increasing the macroscopic permeability of membranes

Reconstituting the cyanobacterial circadian clock in vitro

Cyanobacteria are photosynthetic organisms that are known to be responsible for oxygenating Earth’s early atmosphere. Having evolved to ensure optimal survival in the periodic light/dark cycle on this planet, their genetic codes are packed with various tools, including a sophisticated biological timekeeping system. Among the cyanobacteria is Synechococcus elongatus PCC 7942, the simplest clock-harboring organism with a powerful genetic tool that enabled the identification of its intricate timekeeping mechanism. The three central oscillator proteins—KaiA, KaiB, and KaiC—drive the 24 h cyclic gene expression rhythm of cyanobacteria, and the ticking of the oscillator can be reconstituted inside a test tube just by mixing the three recombinant proteins with ATP and Mg2+. Along with its biochemical resilience, the post-translational rhythm of the oscillation can be reset through sensing oxidized quinone, a metabolite that becomes abundant at the onset of darkness. In addition, the output components pick up the information from the central oscillator, tuning the physiological and behavioral patterns and enabling the organism to better cope with the cyclic environmental conditions. In this research, how the cyanobacterial circadian clock functions as a molecular chronometer that readies the host for predictable changes in its surroundings is highlighted and discussed. Since the bottleneck of performing any in vitro experiments is the laborious task of purifying proteins with enough purity, the most efficient method to extract KaiC is introduced, so that other impurities cannot hinder the highly sensitive post-translational activities. Next, CikA, an input component that synchronizes the oscillator to the environmental cues by using a metabolite called “quinone” as a proxy for darkness, is introduced. Finally, KaiC’s C-terminal linear chain undergoes conformational changes that determine the rising or falling phase of the clock. By creating site mutations that constitutively maintain the loop’s exposed conformation, a potentially additional role of another oscillator component, KaiB, is elucidated. Thus, by using the in vitro techniques that are compatible with this bacterial clock, the functional details that lie behind the biochemical workings of the circadian clock are disclosed