scholarly journals Information-to-free-energy conversion: Utilizing thermal fluctuations

BIOPHYSICS ◽  
2013 ◽  
Vol 9 (0) ◽  
pp. 107-112 ◽  
Author(s):  
Shoichi Toyabe ◽  
Eiro Muneyuki
Keyword(s):  
Free Energy ◽  
Energy Conversion ◽  
Thermal Fluctuations

Fe–N–C Electrocatalysts in the Oxygen and Nitrogen Cycles in Alkaline Media: The Role of Iron Carbide

2021 ◽  
Author(s):  
Tomer Y. Burshtein ◽  
Denial Aias ◽  
Jin Wang ◽  
Matan Sananis ◽  
Eliyahu M. Farber ◽  
...  
Keyword(s):  
Free Energy ◽  
Energy Conversion ◽  
Oxygen Reduction ◽  
Iron Carbide ◽  
Alkaline Media ◽  
Great Promise ◽  
Nitrogen Cycles

Fe–N–C electrocatalysts hold a great promise for Pt-free energy conversion, driving the electrocatalysis of oxygen reduction and evolution, oxidation of nitrogen fuels, and reduction of N2, CO2, and NOx. Nevertheless,...

scholarly journals An Asymmetric Mechanism in a Symmetric Molecular Machine

2020 ◽  
Author(s):  
Florian Blanc ◽  
Marco Cecchini
Keyword(s):  
Free Energy ◽  
Large Scale ◽  
Technological Development ◽  
Thermal Fluctuations ◽  
Free Energy Calculations ◽  
Molecular Machine ◽  
Free Energy Surface ◽  
Promising Area ◽  
Sequential Mechanism ◽  
External Stimuli

The design of molecular architectures exhibiting functional motions is a promising area for disruptive technological development. Towards this goal, rotaxanes and catenanes, which undergo relative motions of their sub-units in response to external stimuli, are prime candidates. Here, we report on the computational analysis of the contraction/extension of a bistable [c2]-daisy chain rotaxane. Using free energy calculations and transition path optimizations, we explore the free energy landscape governing the functional motions of a prototypical molecular machine with atomic resolution.<br>The calculations reveal a sequential mechanism for contraction/extension in which the asynchronous gliding of each ring is preferred over the concerted movement suggested by chemical intuition. Analysis of the underlying free energy surface indicates that dissymmetric gliding is favored because it entails crossings of much smaller barriers.<br>Our findings illustrate an important design principle for molecular machines, namely that efficient exploitation of thermal fluctuations may be realized by breaking down the large-scale functional motions into smaller steps.

scholarly journals On the beneficent thickness of water

2019 ◽  
Vol 9 (6) ◽  
pp. 20190061 ◽  
Author(s):  
E. Branscomb ◽  
M. J. Russell
Keyword(s):  
Free Energy ◽  
Energy Conversion ◽  
Recent Work ◽  
Chemical Reactions ◽  
Driving Forces ◽  
Anomalous Behaviour ◽  
Reciprocal Relations ◽  
Far From Equilibrium

In the 1930s, Lars Onsager published his famous ‘reciprocal relations’ describing free energy conversion processes. Importantly, these relations were derived on the assumption that the fluxes of the processes involved in the conversion were proportional to the forces (free energy gradients) driving them. For chemical reactions, however, this condition holds only for systems operating close to equilibrium—indeed very close; nominally requiring driving forces to be smaller than k B T . Fairly soon thereafter, however, it was quite inexplicably observed that in at least some biological conversions both the reciprocal relations and linear flux–force dependency appeared to be obeyed no matter how far from equilibrium the system was being driven. No successful explanation of how this ‘paradoxical’ behaviour could occur has emerged and it has remained a mystery. We here argue, however, that this anomalous behaviour is simply a gift of water, of its viscosity in particular; a gift, moreover, without which life almost certainly could not have emerged. And a gift whose appreciation we primarily owe to recent work by Prof. R. Dean Astumian who, as providence has kindly seen to it, was led to the relevant insights by the later work of Onsager himself.

scholarly journals A GEOMETRIC APPROACH TO CORRELATIONS AND QUARK NUMBER SUSCEPTIBILITIES

2012 ◽  
Vol 27 (10) ◽  
pp. 1250055 ◽  
Author(s):  
STEFANO BELLUCCI ◽  
VINOD CHANDRA ◽  
BHUPENDRA NATH TIWARI
Keyword(s):  
Free Energy ◽  
Critical Temperature ◽  
Finite Temperature ◽  
Geometric Approach ◽  
Geometric Realization ◽  
Thermal Fluctuations ◽  
Quark Number ◽  
Self Consistent ◽  
Thermodynamic Geometry ◽  
Quark Number Susceptibility

We study the thermodynamic geometry arising from the free energy for the two- and three-flavor finite temperature hot QCD near the critical temperature. We develop a geometric notion for QCD thermodynamics, relating it with the existing microscopic quantities, e.g. quark-number susceptibility, which appears naturally within an approximately self-consistent resummation of perturbative QCD. We further incorporate thermal fluctuations in the free energy, thus yielding the geometric properties of local and global chemical correlations. These investigations are perturbative in nature. Nevertheless, one could apply the same line of thought for the geometric realization of underlying quark susceptibilities, either in the fabric of lattice QCD or in that of nonperturbative QCD.

scholarly journals Energy Conversion in Bull Sperm Flagella

1969 ◽  
Vol 54 (6) ◽  
pp. 782-805 ◽  
Author(s):  
Robert Rikmenspoel ◽  
Sandra Sinton ◽  
John J. Janick
Keyword(s):  
Free Energy ◽  
Energy Conversion ◽  
Conversion Efficiency ◽  
Antimycin A ◽  
Incubation Chamber ◽  
Bull Sperm ◽  
The Absolute ◽  
The Difference ◽  
At Will

With the use of a specially developed incubation chamber the rates of motility, respiration, and fructolysis were measured simultaneously on semen samples. By inhibiting the respiration with antimycin A, and/or the fructolysis with 2-deoxyglucose, the rates of each of the two ATP-producing pathways could be reduced independently. In this way the ratio of the amount of free energy produced by respiration and by fructolysis could be varied at will from 1 to 0. In uninhibited preparations approximately 75% of the free energy derives from respiration, and 25% from fructolysis. By the use of the absolute rates of respiration, fructolysis, and motility, the efficiency of the conversion of free energy into hydrodynamic work was calculated. After correction for the decay of the preparation during the experiment, this conversion efficiency was found to be 30–45% lower for free energy from respiration than for free energy from fructolysis. The difference in distribution of the enzymes for fructolysis and respiration over the flagellum was ruled out as the cause of the efficiency difference. The respiration could be 70% inhibited by oligomycin. It is concluded that approximately one-third of the free energy from respiration is used for maintenance of the mitochondria.

scholarly journals An Asymmetric Mechanism in a Symmetric Molecular Machine

2020 ◽  
Author(s):  
Florian Blanc ◽  
Marco Cecchini
Keyword(s):  
Free Energy ◽  
Large Scale ◽  
Technological Development ◽  
Thermal Fluctuations ◽  
Free Energy Calculations ◽  
Molecular Machine ◽  
Free Energy Surface ◽  
Promising Area ◽  
Sequential Mechanism ◽  
External Stimuli

The design of molecular architectures exhibiting functional motions is a promising area for disruptive technological development. Towards this goal, rotaxanes and catenanes, which undergo relative motions of their sub-units in response to external stimuli, are prime candidates. Here, we report on the computational analysis of the contraction/extension of a bistable [c2]-daisy chain rotaxane. Using free energy calculations and transition path optimizations, we explore the free energy landscape governing the functional motions of a prototypical molecular machine with atomic resolution.<br>The calculations reveal a sequential mechanism for contraction/extension in which the asynchronous gliding of each ring is preferred over the concerted movement suggested by chemical intuition. Analysis of the underlying free energy surface indicates that dissymmetric gliding is favored because it entails crossings of much smaller barriers.<br>Our findings illustrate an important design principle for molecular machines, namely that efficient exploitation of thermal fluctuations may be realized by breaking down the large-scale functional motions into smaller steps.

THERMAL FLUCTUATIONS IN CASIMIR PISTONS

2012 ◽  
Vol 14 ◽  
pp. 425-434
Author(s):  
M. LOMNITZ ◽  
C. VILLARREAL
Keyword(s):  
Free Energy ◽  
Internal Energy ◽  
Thermal Fluctuations ◽  
Energy Entropy

We present analytical and simple expressions to determine the free energy, internal energy, entropy, as well as the pressure acting at the interface of a perfectly conducting rectangular Casimir piston. We show that infrared divergencies linear in temperature become cancelled within the piston configuration, and show a continuous behavior consistent with intuitive expectations.

scholarly journals Stokes Efficiency of Molecular Motor-Cargo Systems

2008 ◽  
Vol 2008 ◽  
pp. 1-13 ◽  
Author(s):  
Hongyun Wang ◽  
Hong Zhou
Keyword(s):  
Free Energy ◽  
Molecular Motor ◽  
Planck Equation ◽  
Viscous Friction ◽  
Thermal Fluctuations ◽  
Viscous Drag ◽  
Langevin Equations ◽  
Stochastic Motion ◽  
Chemical Free Energy ◽  
Surrounding Fluid

A molecular motor utilizes chemical free energy to generate a unidirectional motion through the viscous fluid. In many experimental settings and biological settings, a molecular motor is elastically linked to a cargo. The stochastic motion of a molecular motor-cargo system is governed by a set of Langevin equations, each corresponding to an individual chemical occupancy state. The change of chemical occupancy state is modeled by a continuous time discrete space Markov process. The probability density of a motor-cargo system is governed by a two-dimensional Fokker-Planck equation. The operation of a molecular motor is dominated by high viscous friction and large thermal fluctuations from surrounding fluid. The instantaneous velocity of a molecular motor is highly stochastic: the past velocity is quickly damped by the viscous friction and the new velocity is quickly excited by bombardments of surrounding fluid molecules. Thus, the theory for macroscopic motors should not be applied directly to molecular motors without close examination. In particular, a molecular motor behaves differently working against a viscous drag than working against a conservative force. The Stokes efficiency was introduced to measure how efficiently a motor uses chemical free energy to drive against viscous drag. For a motor without cargo, it was proved that the Stokes efficiency is bounded by 100% [H. Wang and G. Oster, (2002)]. Here, we present a proof for the general motor-cargo system.

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