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To decipher the formation mechanism of nitrogen-free substructures in melanoidins, methylglyoxal or 3-deoxyglucosone was used as a substrate to react by aldol reaction under different pH conditionst. The obtained products were characterised by chromatography, mass spectrometry, and spectroscopic methods. Overall, the molecular weights of the polymers structural units varied mainly within 54–56 and 72–74 Da, respectively, due to the different dehydration extent of β-hydroxy aldehyde or ketones, and uneven reduction by NaBH4. Moreover, the nitrogen-free substructures formed by this reaction can cross-link with gluten and dextran to form melanoidins. Therefore, the nitrogen-free substructures by this reaction to formed with units of 54–56 and 72–74 Da, which are similar as the typical polymers in food melanoidins. It is inferred that the typical polymers in food may also be formed by this pathway and which can be used as a detectable biomarker in melanoidins.

Replicating efficient chemical energy utilization of biological nanomotors is one ultimate goal of nanotechnology and energy technology. Here, we report a rationally designed autonomous bipedal nanowalker made of DNA that achieves a fuel efficiency of less than two fuel molecules decomposed per productive forward step, hence breaking a general threshold for chemically powered machines invented to date. As a genuine enzymatic nanomotor without changing itself nor the track, the walker demonstrates a sustained motion on an extended double-stranded track at a speed comparable to previous burn-bridge motors. Like its biological counterparts, this artificial nanowalker realizes multiple chemomechanical gatings, especially a bias-generating product control unique to chemically powered nanomotors. This study yields rich insights into how pure physical effects facilitate harvest of chemical energy at the single-molecule level and provides a rarely available motor system for future development toward replicating the efficient, repeatable, automatic, and mechanistically sophisticated transportation seen in biomotor-based intracellular transport but beyond the capacity of the current burn-bridge motors.

Experimental development of translational DNA nanomotors recently underwent a paradigm shift from bridge-burning monomers to symmetric dimers capable of truly sustainable motion. The focus of direction rectification is changed from carving the external landscape of a single particle to symmetry breaking from within a dimer. The symmetric dimer construction have the potential to facilitate efficient motors as friction, which is inevitable as a single particle moving in a viscous environment, may vanish for paired systems. However, creating high-performing nanomotors remains an open question from a fundamental physics perspective. Here, we present a realistic physical model for dimeric nanomotors that can be exactly solved to yield motor functions from experimentally accessible non-motor elements by mere physical laws—in a surprisingly rich mechanistic variety covering virtually all advanced dimeric DNA nanomotors invented to date plus major biological counterparts to a certain extent. The model exposes a high-performing regime with a sign of superlubricity for efficient motor operation. Reasonably simple for accurate treatments yet mechanistically telling, the present model has potential to evolve into a generic model to guide experimental optimization of DNA nanomotors toward low-dissipation operation.

A bipedal DNA nanowalker was recently reported to convert chemical energy into directional motion autonomously and efficiently. To elucidate its chemomechanical coupling mechanisms, three-dimensional molecular modeling is used to obtain coarse-grained foot-track binding potentials of the DNA nanowalker via unbiased and biased sampling techniques (for the potentials’ basin and high-energy edges, respectively). The binding state that is protected against fuel-induced dissociation responds asymmetrically to forward versus backward forces, unlike the unprotected state, demonstrating a mechanosensing capability to gate fuel binding. Despite complex DNA mechanics, the foot-track potential exhibits a surprisingly neat three-part profile, offering some general guidelines to rationally design efficient nanowalkers. Subsequent modeling of the bipedal walker attached to the track gives estimates of the free energy for each bipedal state, showing how the mechanosensing foot-track binding breaks the symmetry between the rear and front feet, enabling the rear foot to be selectively dissociated by fuel and generating efficient chemomechanical coupling.

Nature has been developing nanoscale machines far longer than people have, but perhaps we are catching up a bit. To design high-performance nanomotors for our own purposes, mechanistic insight is needed. The authors present a synergistic mechanical-kinetic model for a modular DNA-based bipedal nanowalker, revealing counterintuitive properties. The model resolves the motor's working mechanism and identifies a specific structure in the motor's design that limits its performance, offering guidance for its improvement and for creating other motors from the same modular design principle.

Track-walking nanomotors and larger systems integrating these motors are important for wide real-world applications of nanotechnology. However, inventing these nanomotors remains difficult, a sharp contrast to the widespread success of simpler switch-like nanodevices, even though the latter already encompasses basic elements of the former such as engine-like bistate contraction/extension or leg-like controllable binding. This conspicuous gap reflects an impeding bottleneck for the nanomotor development, namely, lack of a modularized construction by which spatially and functionally separable "engines" and "legs" are flexibly assembled into a self-directed motor. Indeed, all track-walking nanomotors reported to date combine the engine and leg functions in the same molecular part, which largely underpins the device-motor gap. Here we propose a general design principle allowing the modularized nanomotor construction from disentangled engine-like and leg-like motifs, and provide an experimental proof of concept by implementing a bipedal DNA nanomotor up to a best working regime of this versatile design principle. The motor uses a light-powered contraction-extension switch to drive a coordinated hand-over-hand directional walking on a DNA track. Systematic fluorescence experiments confirm the motor's directional motion and suggest that the motor possesses two directional biases, one for rear leg dissociation and one for forward leg binding. This study opens a viable route to develop track-walking nanomotors from numerous molecular switches and binding motifs available from nanodevice research and biology.

Control is a hallmark of machines; effective control over a nanoscale system is necessary to turn it into a nanomachine. Nanomotors from biology often integrate a ratchet-like passive control and a power-stroke-like active control, and this synergic active-plus-passive control is critical to efficient utilization of energy. It remains a challenge to integrate the two differing types of control in rationally designed nanomotor systems. Recently a light-powered track-walking DNA nanomotor was developed from a bioinspired design principle that has the potential to integrate both controls. However, it is difficult to separate experimental signals for either control due to a tight coupling of both controls. Here we present a systematic study of the motor and new derivatives using different fluorescence labeling schemes and light operations. The experimental data suggest that the motor achieves the two controls autonomously through a mechanics-mediated symmetry breaking. This study presents an experimental validation for the bioinspired design principle of mechanical breaking of symmetry for synergic ratchet-plus-power stroke control. Augmented by mechanical and kinetic modeling, this experimental study provides mechanistic insights that may help advance molecular control in future nanotechnological systems.

Synthetic molecular shuttles prove that controllable nanoscale translation is possible in the curious shape of molecular rings encircling a linear track. However, a shuttle ring’s movement is limited between a pair of binding sites. Ring-locking may provide a molecular mechanism for implementing a major requirement for inchworm nanowalkers. Here we propose a nanowalker in the form of track-encircling molecular rings that is capable of directed procession along an unlimited track beyond molecular shuttles. A detailed molecular design for the walker is obtained by properly exploiting molecular mechanisms already realized in shuttle systems. A computer simulation using realistic parameters predicts major walker–track parameters for optimal performance of the walker. Several unique features of the proposed walker are discussed in comparison with previously suggested or realized motor systems.

A mapping is established in connecting density matrices, associated with an evolution of a quantum open system, with vector ray in a complex projective Hilbert space. By using the corresponding vector ray to represent the open two-level system, we may observe the geometric phase for the open two-level system. The geometric phase of the open two-level system depends only on the smooth (open or closed) curve in the complex projective Hilbert space of ray, which is formulated entirely in terms of geometric structures on this space.

The energy exchange between a D 2 molecule and the phonon states of a copper surface has been modelled using quantum wavepackets. For processes where the molecule gains internal energy, we predict a gain in molecular energy near the excitation threshold. This gain decreased with increasing translational energy, and was insensitive to the final state of the molecule. For non-activated processes, with a decrease in molecular internal energy, a net loss of energy to the substrate was found. This loss increased as the change in internal energy of the molecule increased. These results are in good agreement with experimental observation.

The atomic force microscope can be used to forcibly unfold and extend single polypeptide chains. The resulting force versus distance curves have been widely interpreted to arise from the loss of entropy that the unfolded polypeptide chain experiences as it is extended. Here, we have used Monte Carlo simulations of unfolded polypeptide chains to examine the average distance between the ends of a polypeptide chain as a function of the force that pulls these ends apart. We examine two types of experiments: (a) A rigid force-sensor (bead-type) experiment: The chain is subjected to a constant stretching force f and the resulting chain extension is measured. (b) A flexible force-sensor (cantilever-type) experiment: The force is measured by the deflection of a cantilever that is attached to one end of the chain. The total length of the chain plus the displacement of the cantilever is fixed. In case (b), in the limit of a large cantilever force constant, the entropic force f is related to the free energy of the chain F(r) constrained to have the end-to-end distance r by the usual thermodynamic relationship: f=dF/dr. However in case (a) this relationship is invalid. The reason of its failure is that large fluctuations in the end-to-end distance r cannot be neglected at the single molecule level and so macroscopic thermodynamics relationships cannot be used. Thus the two types of experiments measure different force extension curves f(r). We compute the force extension curves for a model of a polypeptide chain in each case and find that they are significantly different. We further discuss implications of our findings with regard to the results of cantilever-type unfolding experiments.

The ability of classical mechanics to provide acceptable dissociation probabilities and reflectivities for the reaction of H2 at a single surface site is examined. We find that the initial vibrational state dependence of the dissociation probability at high incident energies is well-reproduced, allowing us to develop an explanation of the results using classical trajectories. The precise details of the motion in the PES elbow are found to be crucial. Extending our analysis to reflectivities, we find reasonable agreement between classical and quantum vibrational state-resolved results, permitting again an analysis in terms of the classical trajectories.

The origin of the forward-backward enhancement of K{sup +} emission observed in symmetric nucleus-nucleus collisions at 1GeV/nucleon has been explored. The nonisotropic pion-baryon reaction leading to K{sup +} production has been found to play a substantial role in creating the forward-backward peak of the kaon angular distribution. By an analysis including also the effects from relevant final-state interactions on kaons, we can reproduce the experimental kaon angular distribution. We argue that the observed nonisotropic kaon emission may provide a support to the pion-induced channel for subthreshold kaon production in heavy ion reactions. {copyright} {ital 1997} {ital The American Physical Society}

Artificial nanowalkers are inspired by biomolecular counterparts from living cells, but remain far from comparable to the latter in design principles. The walkers reported to date mostly rely on chemical mechanisms to gain a direction; they all produce chemical wastes. Here we report a light-powered DNA bipedal walker based on a design principle derived from cellular walkers. The walker has two identical feet and the track has equal binding sites; yet the walker gains a direction by pure physical mechanisms that autonomously amplify an intra-site asymmetry into a ratchet effect. The nanowalker is free of any chemical waste. It has a distinct thermodynamic feature that it possesses the same equilibrium before and after operation, but generates a truly non-equilibrium distribution during operation. The demonstrated design principle exploits mechanical effects and is adaptable for use in other nanomachines., Comment: 17 pages, 4 figures

We use Monte Carlo simulations to estimate the rate of formation of a contact between the ends of a peptide chain as a function of its length N. We find that this rate decreases monotonically with N, in accord with the experimental data of Lapidus, Eaton, and Hofrichter [Proc. Natl. Acad. Sci. U.S.A. 97, 7220 (2000)] and of Bieri et al. [Proc. Natl. Acad. Sci. U.S.A. 96, 9597 (1999)] but in contrast to previous theoretical work predicting a maximum of the rate for N∼10. By comparing our results with those data we estimate the diffusion coefficient for the relative diffusion of the chain ends to be D∼6×10−6 cm2/s, which is close to that found for monomer diffusion.

Track-walking molecular motors are widely used in living cells for transport purposes, and artificial mimics are being vigorously pursued in engineered molecular systems. The defining character for a motor is its intrinsic capability to utilize energy input to rectify a sustained directional motion out of stochastic thermal motion. The energy injection can be coupled to a motor's mechanical steps in different ways, leading to different motor mechanisms. We derive here a formulation for maximum motor performance in terms of a new quantity called directionality based on a general representation of the track-walking motors. Compared to performance measures like velocity and processivity, directionality is a cleaner and more robust indicator of the rectification mechanism that amounts to a motor's inner design/working principles. Meaningful and distinctly different upper limits of directionality were found to exist for a wide variety of experimentally demonstrated and theoretically proposed motors and their biological counterparts. The maximum directionality provides a conceptual framework by which all of these different motors were quantitatively compared and systematically classified according to their mechanistic advancement. The results yield a series of guidelines for artificial motor development, and expose important evolutionary traits of biomotors.

Nonadiabatic dynamical simulations were carried out to study cis-to-trans isomerization of azobenzene under laser irradiation and/or external mechanical loads. We used a semiclassical electron-radiation-ion dynamics method that is able to describe the coevolution of the structural dynamics and the underlying electronic dynamics in a real-time manner. It is found that azobenzene photoisomerization occurs predominantly by an out-of-plane rotation mechanism even under a nontrivial resisting force of several tens of piconewtons. We have repeated the simulations systematically for a broad range of parameters for laser pulses, but could not find any photoisomerization event by a previously suggested in-plane inversion mechanism. The simulations found that the photoisomerization process can be held back by an external resisting force of 90 - 200 pN depending on the frequency and intensity of the lasers. This study also found that a pure mechanical isomerization is possible from the cis state if the azobenzene molecule is stretched by an external force of 1250 -1650 pN. Remarkably, the mechanical isomerization first proceeds through a mechanically activated inversion, and then is diverted to an ultrafast downhill rotation that accomplishes the isomerization. Implications of these findings to azobenzene-based nanomechanical devices are discussed., Comment: 9 printed pages

High-dimensional, wave packet calculations have been carried out to model the surface temperature dependence of rovibrationally inelastic scattering and dissociation of hydrogen molecules from the Cu(111) surface. Both the molecule and the vibrating surface are treated fully quantum-mechanically. It is found, in agreement with experimental data, that the surface temperature dependence of a variety of dynamical processes has an Arrhenius form with an activation energy dependent on molecular translational energy and on the initial and final molecular states. The activation energy increases linearly with decreasing translational energy below the threshold energy. Above threshold the behavior is more complex. A quasianalytical model is proposed that faithfully reproduces the Arrhenius law and the translational energy dependence of the activation energy. In this model, it is essential to include quantized energy transfer between the surface and the molecule. It further predicts that for any process characterized by a large energy barrier and multiphonon excitation, the linear change in activation energy up to threshold has slope-1. This explains successfully the universal nature of the unit slope found experimentally for H2 and D2 dissociation on Cu.

The surface temperature dependence of activated inelastic scattering and dissociation of D2 from the Cu(111) surface has been computed using quantum wave-packet methods. It is found, in agreement with experimental data, that the surface temperature dependence generally has an Arrhenius form with an activation energy dependent on molecular translational energy and on the initial and final internal molecular states. The translational energy dependence of the activation energy is linear up to the threshold energy, with an abrupt change thereafter. On the basis of the wave-packet calculations, a model has been developed to explain these findings and highlight their general nature.

Directional motion of nanoscale motors and driven particles in an isothermal environment costs a finite amount of energy despite zero work as decreed by the 2nd law, but quantifying this general limit remains difficult. Here we derive a universal equality linking directional fidelity of an arbitrary nanoscale object to the least possible energy driving it. The fidelity-energy equality depends on the environmental temperature alone; any lower energy would violate the 2nd law in a thought experiment. Real experimental proof for the equality comes from force-induced motion of biological nanomotors by three independent groups - for translational as well as rotational motion. Interestingly, the natural self-propelled motion of a biological nanomotor (F1-ATPase) known to have nearly 100% energy efficiency evidently pays the 2nd law decreed least energy cost for direction production.

Molecular motors capable of directional track-walking or rotation are abundant in living cells, and inspire the emerging field of artificial nanomotors. Some biomotors can convert 90% of free energy from chemical fuels into usable mechanical work, and the same motors still maintain a speed sufficient for cellular functions. This study exposed a new regime of universal optimization that amounts to a thermodynamically best working regime for molecular motors but is unfamiliar in macroscopic engines. For the ideal case of zero energy dissipation, the universally optimized working cycle for molecular motors is infinitely slow like Carnot cycle for heat engines. But when a small amount of energy dissipation reduces energy efficiency linearly from 100%, the speed is recovered exponentially due to Boltzmann's law. Experimental data on a major biomotor (kinesin) suggest that the regime of universal optimization has been largely approached in living cells, underpinning the extreme efficiency-speed trade-off in biomotors. The universal optimization and its practical approachability are unique thermodynamic advantages of molecular systems over macroscopic engines in facilitating motor functions. The findings have important implications for the natural evolution of biomotors as well as the development of artificial counterparts.

Two-headed biomotor myosin V autonomously coordinates its two identical heads in fuel consumption and mechanical stepping, so that the dimerized motor as a whole gains the capability of processive, unidirectional movement along cytoskeletal filament. How the dimer-level functions like sustained direction rectification and autonomous coordination emerge out of physical principles poses an outstanding question pertinent to motor protein biology as well as the nascent field of bioinspired nanomotors. Here the comprehensive physical mechanism for myosin V motor is identified by a dimer-level free-energy analysis that is methodologically calibrated against experimental data. A hallmark of the identified mechanism is a mechanically mediated symmetry breaking that occurs at the dimer level and prevails against ubiquitous thermal fluctuations. Another character is the onset of substantial free-energy gaps between major dimer-track binding configurations. The symmetry breaking is the basis for myosin V's directional rectification, and the energy gaps facilitate autonomous head-head coordination. The mechanism explains the experimental finding that myosin V makes ATP-independent consecutive steps under high opposing loads but not under pushing loads. Interestingly, myosin V and another major biomotor kinesin 1 are found to share essentially the same core mechanism but for distinctly different working regimes.

Nanomotors capable of directed transportation along an unlimited linear track are being vigorously pursued both theoretically and experimentally. This study generalizes a previously proposed mechanism for nanoscale track walkers by explicitly treating key molecular details of the walker-track systems. An energy-diagram analysis identifies pathways of energy flow through the walker's movement cycle, and thereby enables us to develop an analytical theory for the track-walking mechanism. Realistic simulations of the walker's movement cycles are also conducted. The results show that the walker's directionality, run length, and speed depend critically on several key dimensional parameters of the walker-track systems. Most notably, the walker's performance as a function of the binding site interval of the track exhibits an oscillating pattern, which is accurately reproduced by the analytical theory. The wealth of nanocontrol mechanisms identified in the proposed track-walker systems not only provides a framework for optimizing performance of the walker, but also clarifies major requirements for future experimental implementation.

We argue that the average scalar extension of a molecule 〈|r|〉 is not what is measured in a typical single protein stretching experiment, contrary to Neumann’s belief. We further show that Neumann’s “disagreement” with our results is based on his misinterpretation of our work.

Within the framework of Bohm’s reformulation of quantum physics we revisit the activated dissociation of hydrogen molecules at metal surfaces. The quantum-mechanical force, which accounts for most of quantum effects in the method, and is caused by nonlocal, topographical properties of the wave function, is computed using time-dependent wave packets obtained using conventional, spectral methods. Driven by a combination of the classical force together with the quantum force, trajectories carrying probability density either succeed in overcoming the barrier for dissociation or are scattered back into the gas phase. The Bohmian picture for the dissociation process has enabled us to develop a novel mechanism to account for vibrationally enhanced molecular dissociation. This is relevant to the recently observed promotion of dissociation of very highly vibrationally excited NO molecules at Cu surfaces.

The emerging field of artificial track-walking molecular motors is reviewed. The author attempted to clarify the scientific and technological challenges that face the field. A comprehensive mechanistic diagram for molecular walkers was introduced, thereby the directions and possible routes for future development were suggested.