Macroscopic transport by synthetic molecular machines

Nature uses molecular motors and machines in virtually every significant biological process, but demonstrating that simpler artificial structures operating through the same gross mechanisms can be interfaced with—and perform physical tasks in—the macroscopic world represents a significant hurdle for molecular nanotechnology. Here we describe a wholly synthetic molecular system that converts an external energy source (light) into biased brownian motion to transport a macroscopic cargo and do measurable work. The millimetre-scale directional transport of a liquid on a surface is achieved by using the biased brownian motion of stimuli-responsive rotaxanes (‘molecular shuttles’) to expose or conceal fluoroalkane residues and thereby modify surface tension. The collective operation of a monolayer of the molecular shuttles is sufficient to power the movement of a microlitre droplet of diiodomethane up a twelve-degree incline.

Information processing in biological molecular machines

Biological molecular machines are bi-functional enzymes that simultaneously catalyze two processes: one providing free energy and second accepting it. Recent studies show that most protein enzymes have a rich dynamics of stochastic transitions between the multitude of conformational substates that make up their native state. It often manifests in fluctuating rates of the catalyzed processes and the presence of short-term memory resulting from the preference of selected conformations. For any stochastic protein machine dynamics we proved a generalized fluctuation theorem that leads to the extension of the second law of thermodynamics. Using them to interpret the results of random walk on a complex model network, we showed the possibility of reducing free energy dissipation at the expense of creating some information stored in memory. The subject of our analysis is the time course of the catalyzed processes expressed by sequences of jumps at random moments of time. Since similar signals can be registered in the observation of real systems, all theses of the paper are open to experimental verification. From a broader physical point of view, the division of free energy into the operation and organization energies is worth emphasizing. Information can be assigned a physical meaning of a change in the value of both these functions of state.Comment: The manuscript contains 14 pages, 7 figure

Architecture of viral genome-delivery molecular machines.

From the abyss of the ocean to the human gut, bacterial viruses (or bacteriophages) have colonized all ecosystems of the planet earth and evolved in sync with their bacterial hosts. Over 95% of bacteriophages have a tail that varies greatly in length and complexity. The tail complex interrupts the icosahedral capsid symmetry and provides both an entry for viral genome-packaging during replication and an exit for genome-ejection during infection. Here, we review recent progress in deciphering the structure, assembly and conformational dynamics of viral genome-delivery tail machines. We focus on the bacteriophages P22 and T7, two well-studied members of the Podoviridae family that use short, non-contractile tails to infect Gram-negative bacteria. The structure of specialized tail fibers and their putative role in host anchoring, cell-surface penetration and genome-ejection is discussed

Efficiency of molecular machines with continuous phase space

We consider a molecular machine described as a Brownian particle diffusing in a tilted periodic potential. We evaluate the absorbed and released power of the machine as a function of the applied molecular and chemical forces, by using the fact that the times for completing a cycle in the forward and the backward direction have the same distribution, and that the ratio of the corresponding splitting probabilities can be simply expressed as a function of the applied force. We explicitly evaluate the efficiency at maximum power for a simple sawtooth potential. We also obtain the efficiency at maximum power for a broad class of 2-D models of a Brownian machine and find that loosely coupled machines operate with a smaller efficiency at maximum power than their strongly coupled counterparts.Comment: To appear in EP

Efficiency at maximum power of interacting molecular machines

We investigate the efficiency of systems of molecular motors operating at maximum power. We consider two models of kinesin motors on a microtubule: for both the simplified and the detailed model, we find that the many-body exclusion effect enhances the efficiency at maximum power of the many-motor system, with respect to the single motor case. Remarkably, we find that this effect occurs in a limited region of the system parameters, compatible with the biologically relevant range.Comment: To appear in Phys. Rev. Let