An experimentally-achieved information-driven Brownian motor shows maximum power at the relaxation time

We present an experimental realization of an information-driven Brownian motor by periodically cooling a Brownian particle trapped in a harmonic potential connected to a single heat bath, where cooling is carried out by the information process consisting of measurement and feedback control. We show that the random motion of the particle is rectified by symmetry-broken feedback cooling where the particle is cooled only when it resides on the specific side of the potential center at the instant of measurement. Studying how the motor thermodynamics depends on cycle period tau relative to the relaxation time tau(B) of the Brownian particle, we find that the ratcheting of thermal noise produces the maximum work extraction when tau >= 5 tau(B) while the extracted power is maximum near tau= tau(B), implying the optimal operating time for the ratcheting process. In addition, we find that the average transport velocity is monotonically decreased as tau increases and present the upper bound for the velocity

Energy consumption in chemical fuel-driven self-assembly

Nature extensively exploits high-energy transient self-assembly structures that are able to perform work through a dissipative process. Often, self-assembly relies on the use of molecules as fuel that is consumed to drive thermodynamically unfavourable reactions away from equilibrium. Implementing this kind of non-equilibrium self-assembly process in synthetic systems is bound to profoundly impact the fields of chemistry, materials science and synthetic biology, leading to innovative dissipative structures able to convert and store chemical energy. Yet, despite increasing efforts, the basic principles underlying chemical fuel-driven dissipative self-assembly are often overlooked, generating confusion around the meaning and definition of scientific terms, which does not favour progress in the field. The scope of this Perspective is to bring closer together current experimental approaches and conceptual frameworks. From our analysis it also emerges that chemically fuelled dissipative processes may have played a crucial role in evolutionary processes

Reducing vortex density in superconductors using the ratchet effect

A serious obstacle that impedes the application of low and high temperature superconductor (SC) devices is the presence of trapped flux. Flux lines or vortices are induced by fields as small as the Earth's magnetic field. Once present, vortices dissipate energy and generate internal noise, limiting the operation of numerous superconducting devices. Methods used to overcome this difficulty include the pinning of vortices by the incorporation of impurities and defects, the construction of flux dams, slots and holes and magnetic shields which block the penetration of new flux lines in the bulk of the SC or reduce the magnetic field in the immediate vicinity of the superconducting device. Naturally, the most desirable would be to remove the vortices from the bulk of the SC. There is no known phenomenon, however, that could form the basis for such a process. Here we show that the application of an ac current to a SC that is patterned with an asymmetric pinning potential can induce vortex motion whose direction is determined only by the asymmetry of the pattern. The mechanism responsible for this phenomenon is the so called ratchet effect, and its working principle applies to both low and high temperature SCs. As a first step here we demonstrate that with an appropriate choice of the pinning potential the ratchet effect can be used to remove vortices from low temperature SCs in the parameter range required for various applications.Comment: 7 pages, 4 figures, Nature (in press

Supramolecularly directed rotary motion in a photoresponsive receptor

Stimuli-controlled motion at the molecular level has fascinated chemists already for several decades. Taking inspiration from the myriad of dynamic and machine-like functions in nature, a number of strategies have been developed to control motion in purely synthetic systems. Unidirectional rotary motion, such as is observed in ATP synthase and other motor proteins, remains highly challenging to achieve. Current artificial molecular motor systems rely on intrinsic asymmetry or a specific sequence of chemical transformations. Here, we present an alternative design in which the rotation is directed by a chiral guest molecule, which is able to bind non-covalently to a light-responsive receptor. It is demonstrated that the rotary direction is governed by the guest chirality and hence, can be selected and changed at will. This feature offers unique control of directional rotation and will prove highly important in the further development of molecular machinery

The Goldbeter-Koshland switch in the first-order region and its response to dynamic disorder

In their classical work (Proc. Natl. Acad. Sci. USA, 1981, 78:6840-6844), Goldbeter and Koshland mathematically analyzed a reversible covalent modification system which is highly sensitive to the concentration of effectors. Its signal-response curve appears sigmoidal, constituting a biochemical switch. However, the switch behavior only emerges in the "zero-order region", i.e. when the signal molecule concentration is much lower than that of the substrate it modifies. In this work we showed that the switching behavior can also occur under comparable concentrations of signals and substrates, provided that the signal molecules catalyze the modification reaction in cooperation. We also studied the effect of dynamic disorders on the proposed biochemical switch, in which the enzymatic reaction rates, instead of constant, appear as stochastic functions of time. We showed that the system is robust to dynamic disorder at bulk concentration. But if the dynamic disorder is quasi-static, large fluctuations of the switch response behavior may be observed at low concentrations. Such fluctuation is relevant to many biological functions. It can be reduced by either increasing the conformation interconversion rate of the protein, or correlating the enzymatic reaction rates in the network.Comment: 23 pages, 4 figures, accepted by PLOS ON

Quantum dynamics in strong fluctuating fields

A large number of multifaceted quantum transport processes in molecular systems and physical nanosystems can be treated in terms of quantum relaxation processes which couple to one or several fluctuating environments. A thermal equilibrium environment can conveniently be modelled by a thermal bath of harmonic oscillators. An archetype situation provides a two-state dissipative quantum dynamics, commonly known under the label of a spin-boson dynamics. An interesting and nontrivial physical situation emerges, however, when the quantum dynamics evolves far away from thermal equilibrium. This occurs, for example, when a charge transferring medium possesses nonequilibrium degrees of freedom, or when a strong time-dependent control field is applied externally. Accordingly, certain parameters of underlying quantum subsystem acquire stochastic character. Herein, we review the general theoretical framework which is based on the method of projector operators, yielding the quantum master equations for systems that are exposed to strong external fields. This allows one to investigate on a common basis the influence of nonequilibrium fluctuations and periodic electrical fields on quantum transport processes. Most importantly, such strong fluctuating fields induce a whole variety of nonlinear and nonequilibrium phenomena. A characteristic feature of such dynamics is the absence of thermal (quantum) detailed balance.Comment: review article, Advances in Physics (2005), in pres

Phenomenological analysis of ATP dependence of motor protein

In this study, through phenomenological comparison of the velocity-force data of processive motor proteins, including conventional kinesin, cytoplasmic dynein and myosin V, we found that, the ratio between motor velocities of two different ATP concentrations is almost invariant for any substall, superstall or negative external loads. Therefore, the velocity of motor can be well approximated by a Michaelis-Menten like formula V=\atp k(F)L/(\atp +K_M), with $L$ the step size, and $k(F)$ the external load $F$ dependent rate of one mechanochemical cycle of motor motion in saturated ATP solution. The difference of Michaelis-Menten constant $K_M$ for substall, superstall and negative external load indicates, the ATP molecule affinity of motor head for these three cases are different, though the expression of $k(F)$ as a function of $F$ might be unchanged for any external load $F$. Verifications of this Michaelis-Menten like formula has also been done by fitting to the recent experimental data

Magnetism, FeS colloids, and Origins of Life

A number of features of living systems: reversible interactions and weak bonds underlying motor-dynamics; gel-sol transitions; cellular connected fractal organization; asymmetry in interactions and organization; quantum coherent phenomena; to name some, can have a natural accounting via $physical$ interactions, which we therefore seek to incorporate by expanding the horizons of `chemistry-only' approaches to the origins of life. It is suggested that the magnetic 'face' of the minerals from the inorganic world, recognized to have played a pivotal role in initiating Life, may throw light on some of these issues. A magnetic environment in the form of rocks in the Hadean Ocean could have enabled the accretion and therefore an ordered confinement of super-paramagnetic colloids within a structured phase. A moderate H-field can help magnetic nano-particles to not only overcome thermal fluctuations but also harness them. Such controlled dynamics brings in the possibility of accessing quantum effects, which together with frustrations in magnetic ordering and hysteresis (a natural mechanism for a primitive memory) could throw light on the birth of biological information which, as Abel argues, requires a combination of order and complexity. This scenario gains strength from observations of scale-free framboidal forms of the greigite mineral, with a magnetic basis of assembly. And greigite's metabolic potential plays a key role in the mound scenario of Russell and coworkers-an expansion of which is suggested for including magnetism.Comment: 42 pages, 5 figures, to be published in A.R. Memorial volume, Ed Krishnaswami Alladi, Springer 201

Modulation of porosity in a solid material enabled by bulk photoisomerization of an overcrowded alkene

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Charging a Capacitor from an External Fluctuating Potential using a Single Conical Nanopore

We explore the electrical rectification of large amplitude fluctuating signals by an asymmetric nanostructure operating in aqueous solution. We show experimentally and theoretically that a load capacitor can be charged to voltages close to 1 V within a few minutes by converting zero time-average potentials of amplitudes in the range 0.5–3 V into average net currents using a single conical nanopore. This process suggests that significant energy conversion and storage from an electrically fluctuating environment is feasible with a nanoscale pore immersed in a liquid electrolyte solution, a system characteristic of bioelectronics interfaces, electrochemical cells, and nanoporous membranes.We acknowledge the support from the Ministry of Economic Affairs and Competitiveness and FEDER (project MAT2012-32084) and the Generalitat Valenciana (project Prometeo/GV/0069).Gómez Lozano, V.; Ramirez Hoyos, P.; Cervera Montesinos, J.; Nasir, S.; Ali, M.; Ensinger, W.; Mafé, S. (2015). Charging a Capacitor from an External Fluctuating Potential using a Single Conical Nanopore. Scientific Reports. 5(9501):1-5. https://doi.org/10.1038/srep09501S1559501Astumian, R. D. Stochastic conformational pumping: A mechanism for free-energy transduction by molecules. Annu. Rev. Biophys. 40, 289–313 (2011).Qian, H. Cooperativity in cellular biochemical processes: Noise-enhanced sensitivity, fluctuating enzyme, bistability with nonlinear feedback and other mechanisms for sigmoidal responses. Annu. Rev. Biophys. 41, 179–204 (2012).Hille, B. Ionic Channels of Excitable Membranes (Sinauer Associates Inc., Sunderland, MA, 1992).Levin, M. Molecular bioelectricity in developmental biology: new tools and recent discoveries: control of cell behavior and pattern formation by transmembrane potential gradients. Bioessays 34, 205–217 (2012).Queralt-Martín, M. et al. Electrical pumping of potassium ions against an external concentration gradient in a biological ion channel. Appl. Phys. Lett. 103, 043707 (2013).Hudspeth, A. J., Choe, Y., Mehta, A. D. & Martin, P. Putting ion channels to work: Mechanoelectrical transduction, adaptation and amplification by hair cells. Proc. Nat. Acad. Sci. U.S.A. 97, 11765–11772 (2000).Siwy, Z. & Fuliński, A. Fabrication of a Synthetic Nanopore Ion Pump. Phys. Rev. Lett. 89, 198103 (2002).Siwy, Z. & Fuliński, A. A nanodevice for rectification and pumping ions. Am. J. Phys. 72, 567–574 (2004).Ramirez, P., Gomez, V., Ali, M., Ensinger, W. & Mafe, S. Net currents obtained from zero-average potentials in single amphoteric nanopores. Electrochem. Commun. 31, 137–140 (2013).Ali, M. et al. Current rectification by nanoparticle blocking in single cylindrical nanopores. Appl. Phys. Lett. 104, 043703 (2014).Misra, N. et al. Bioelectronic silicon nanowire devices using functional membrane proteins. Proc. Natl. Acad. Sci. U.S.A. 106, 13780–13784 (2009).Ramirez, P., Ali, M., Ensinger, W. & Mafe, S. Information processing with a single multifunctional nanofluidic diode. Appl. Phys. Lett. 101, 133108 (2012).Hou, Y., Vidu, R. & Stroeve, P. Solar energy storage methods. Ind. Eng. Chem. Res. 50, 8954–8964 (2011).Guo, W. et al. Energy harvesting with single-ion-selective nanopores: A concentration-gradient-driven nanofluidic power source. Adv. Funct. Mater. 20, 1339–1344 (2010).Cervera, J., Ramirez, P., Mafe, S. & Stroeve, P. Asymmetric nanopore rectification for ion pumping, electrical power generation and information processing applications. Electrochim. Acta, 56, 4504–4511 (2011).Tybrandt, K., Forchheimer, R. & Berggren, M. Logic gates based on ion transistors. Nat. Commun., 3, 871 (2012)Apel, P. Track etching technique in membrane technology. Radiat. Meas. 34, 559–566 (2001).Ali, M., Ramirez, P., Mafe, S., Neumann, R. & Ensinger, W. A pH-tunable nanofluidic diode with a broad range of rectifying properties. ACS Nano 3, 603–608 (2009).Albrecht, T. How to Understand and Interpret Current Flow in Nanopore/Electrode Devices. ACS Nano 5, 6714–6725 (2011).Ali, M. et al. Carbohydrate-Mediated Biomolecular Recognition and Gating of Synthetic Ion Channels. J. Phys. Chem. C 117, 18234–18242 (2013)