Operation Of Molecular Machines Research Articles

Correlated translational motions in pseudo-rotaxane complexes controlled by a single chemical stimulus.

Coordinated motions are essential in the operation of molecular machines. This feature can be achieved by landscaping the energy surface along the movement coordinates. Herein, we present an approach of using a single stimulus to modify the free energy curve describing the threading and shuttling of a ring along a linear molecule. This approach has been realized by locating two identical ring-binding sites near the axle termini.

Mechano-Nanoarchitectonics: Design and Function.

Mechanical stimuli have rather ambiguous and less-specific features among various physical stimuli, but most materials exhibit a certain level of responses upon mechanical inputs. Unexplored sciences remain in mechanical responding systems as one of the frontiers of materials science. Nanoarchitectonics approaches for mechanically responding materials are discussed as mechano-nanoarchitectonics in this review article. Recent approaches on molecular and materials systems with mechanical response capabilities are first exemplified with two viewpoints: i) mechanical control of supramolecular assemblies and materials and ii) mechanical control and evaluation of atom/molecular level structures. In the following sections, special attentions on interfacial environments for mechano-nanoarchitectonics are emphasized. The section entitled iii) Mechanical Control of Molecular System at Dynamic Interface describes coupling of macroscopic mechanical forces and molecular-level phenomena. Delicate mechanical forces can be applied to functional molecules embedded at the air-water interface where operation of molecular machines and tuning of molecular receptors upon macroscopic mechanical actions are discussed. Finally, the important role of the interfacial media are further extended to the control of living cells as described in the section entitled iv) Mechanical Control of Biosystems. Pioneering approaches on cell fate regulations at liquid-liquid interfaces are discussed in addition to well-known mechanobiology.

Emergent Memory and Kinetic Hysteresis in Strongly Driven Networks

Stochastic network-dynamics are typically assumed to be memory-less. Involving prolonged dwells interrupted by instantaneous transitions between nodes such Markov networks stand as a coarse-graining paradigm for chemical reactions, gene expression, molecular machines, spreading of diseases, protein dynamics, diffusion in energy landscapes, epigenetics and many others. However, as soon as transitions cease to be negligibly short, as often observed in experiments, the dynamics develops a memory. That is, state-changes depend not only on the present state but also on the past. Here, we establish the first thermodynamically consistent -- dissipation-preserving -- mapping of continuous dynamics onto a network, which reveals ingrained dynamical symmetries and an unforeseen kinetic hysteresis. These symmetries impose three independent sources of fluctuations in state-to state kinetics that determine the `flavor of memory'. The hysteresis between the forward/backward in time coarse-graining of continuous trajectories implies a new paradigm for the thermodynamics of active molecular processes in the presence of memory, that is, beyond the assumption of local detailed balance. Our results provide a new understanding of fluctuations in the operation of molecular machines as well as catch-bonds involved in cellular adhesion.

Enhanced diffusion, chemotaxis, and pumping by active enzymes: progress toward an organizing principle of molecular machines.

Active enzymes diffuse more rapidly than inactive enzymes. This phenomenon may be due to catalysis-driven conformational changes that result in "swimming" through the aqueous solution. Recent additional work has demonstrated that active enzymes can undergo chemotaxis toward regions of high substrate concentration, whereas inactive enzymes do not, and, further, that active enzymes immobilized at surfaces can directionally pump liquids. In this Perspective, I will discuss these phenomena in light of Purcell's work on directed motion at low Reynold's number and in the context of microscopic reversibility. The conclusions suggest that a deep understanding of catalytically driven enhanced diffusion of enzymes and related phenomena can lead toward a general organizing principle for the design, characterization, and operation of molecular machines.

Evolution of molecular machines: from solution to soft matter interface

In the molecular machine concept, single molecules and/or small molecular assemblies operate as independent machines in the ultimate miniaturization of functional systems. For the development of molecular machines, changing the medium of operation from solution to solid surface satisfies several demands for machine functions including allowing direct observation, enabling connection with devices and facilitation of sequential actions. However, the field of molecular machines on solid surfaces is still immature when compared with the sophisticated molecular mechanical systems observed in Nature. Required further developments of molecular machines include improved dynamic operations so that investigations of molecular machine functionality at dynamic interfacial media have become important. In this paper, the development of research on molecular machines in solution and at solid interfaces is described together with an introduction of recent challenges in the operation of molecular machines at soft matter interfaces.