Molecules off equilibrium

Fluctuation theorems

Jarzynski identity

cond-mat/0511629
C. Bustamante , J. Liphardt , F. Ritort
Journal-ref: Physics Today, vol. 58 (2005) 43-48

Work probability distribution in single molecule experiments
10.1209/epl/i2004-10390-3
Inequivalence of Statistical Ensembles in Single Molecule Measurements
cond-mat/0412504
Supurna Sinha , Joseph Samuel
Mechanical Stretching of Proteins: Calmodulin and Titin
q-bio/0412032
Marek Cieplak
Simultaneous current-, force- and work function measurement with atomic resolution
10.1063/1.1900316
On practical applicability of the Jarzynski relation in statistical mechanics: a pedagogical example
10.1021/jp0455428
An experimental test of the Jarzynski equality in a mechanical experiment
cond-mat/0502395
F. Douarche (Phys-ENS), S. Ciliberto (Phys-ENS), A. Petrosyan (Phys-ENS), I. Rabbiosi (Phys-ENS)
Distribution of work in isothermal non-equilibrium processes
10.1103/PhysRevE.70.066112
Unified Treatment of Quantum Fluctuation Theorem and Jarzynski Equality in Terms of microscopic reversibility
cond-mat/0410623
T.Monnai
Inferring DNA sequences from mechanical unzipping: an ideal-case study
cond-mat/0506221
V. Baldazzi , S. Cocco , E. Marinari , R. Monasson
Estimate of the free energy difference in mechanical systems from work fluctuations: experiments and models
cond-mat/0504465
Frederic Douarche (Phys-ENS), Sergio Ciliberto (Phys-ENS), Artem Petrosyan (Phys-ENS)
Work distribution functions for hysteresis loops in a single-spin system
10.1103/PhysRevE.72.066112
Nonequilibrium Potential Function of Chemically Driven Single Macromolecules via Jarzynski-Type Log-Mean-Exponential Work
10.1021/jp0545391
Equilibrium free energies from fast-switching trajectories with large time steps
cond-mat/0507375
Wolfgang Lechner , Harald Oberhofer , Christoph Dellago , Phillip L. Geissler
Work probability distribution in systems driven out of equilibrium
10.1103/PhysRevE.72.046114
Jarzynski equality for the Jepsen gas
cond-mat/0506289
I. Bena , C. Van den Broeck , R. Kawai
Journal-ref: Europhysics Letters 71, pp. 879-885 (2005).
Validity condition of the Jarzynski relation for a classical mechanical system
cond-mat/0506214
Jaeyoung Sung
Phys. Rev. E 56, 5018 (1997): Jarzynski - Equilibrium free-energy differences from...
Flaw of Jarzynski's equality when applied to systems with several degrees of freedom
cond-mat/0508721
D.H.E.Gross
Reply to comments by D.H.E. Gross
cond-mat/0509344
Christopher Jarzynski
Reply to Jarzynski's comment cond-mat/0509344
cond-mat/0509648
D.H.E.Gross
Force Unfolding Single RNAs: from Equilibrium to Far-from Equilibrium
cond-mat/0504236
Fei Liu , Zhong-can Ou-Yang
Entropy production along a stochastic trajectory and an integral fluctuation theorem
cond-mat/0503686
Udo Seifert
Journal-ref: Phys Rev Lett, 95, 040602, 2005
Work distribution and path integrals in general mean-field systems
10.1209/epl/i2005-10067-5
Breakdown of the Jarzynski relation for an adiabatic stretching of an isotropic spring
cond-mat/0510119
Jaeyoung Sung
Note on cond-mat/0510119: Jarzynski equation for adiabatically stretched rotor
cond-mat/0510270
Markus Bier
Reversible Unfolding of Single RNA Molecules by Mechanical Force -- Liphardt et al. 292 (5517): 733 -- Science
Equilibrium Information from Nonequilibrium Measurements in an Experimental Test of Jarzynski's Equality -- Liphardt et al. 296 (5574): 1832 -- Science
Calculating potentials of mean force and diffusion coefficients from nonequilibirum processes without Jarzynski's equality
10.1063/1.2166379
Non-equilibrium work relations
cond-mat/0511073
Jorge Kurchan
Direct evaluation of large-deviation functions
cond-mat/0511248
Cristian Giardina' , Jorge Kurchan , Luca Peliti
Illustration of the Jarzynski nonequilibrium work relation for an ideal gas
cond-mat/0511302
Rhonald C. Lua
Work-probability distribution in systems driven out of equilibrium
Unified treatment of the quantum fluctuation theorem and the Jarzynski equality in terms of microscopic reversibility
Fluctuations of work from quantum subensembles: The case against quantum work-fluctuation theorems
Fluctuation and dissipation of work in a Joule experiment
10.1103/PhysRevLett.96.050601
Work distribution functions in polymer stretching experiments
A simple proof of the Jarzynski equality?
cond-mat/0512181
Frédéric Douarche (Phys-ENS)
Reply to Note on cond-mat/0510270: Jarzynski equation for adiabatically stretched rotor
cond-mat/0512250
Jaeyoung Sung
Non-equilibrium thermodynamics of small-scale systems
cond-mat/0512268
J.M. Rubi
Verification of the Crooks fluctuation theorem and recovery of RNA folding free energies
cond-mat/0512266
D. Collin , F. Ritort , C. Jarzynski , S. B. Smith , I. Tinoco , C. Bustamante
Journal-ref: Nature, vol. 437 (2005) 231-234
A possible generalized form of Jarzynski equality
cond-mat/0512443
Z. C. Tu , Zicong Zhou
A one-dimensional model for theoretical analysis of single molecule experiments
cond-mat/0601263
Erik Van der Straeten , Jan Naudts
Fluctuation Theorems of Brownian Particles Controlled by a Maxwell's Demon
physics/0601085
Kyung Hyuk Kim , Hong Qian
Time-symmetric fluctuations in nonequilibrium systems
cond-mat/0601299
Christian Maes , Maarten H. van Wieren
Evaluation of free energy landscapes from manipulation experiments
10.1088/1742-5468/2006/03/P03005
Heat Fluctuations in Brownian Transducers
cond-mat/0602144
A. Gomez-Marin , J.M. Sancho
Journal-ref: Phys. Rev. E 73, 045101(R) (2006)
Fluctuation symmetries for work and heat
cond-mat/0602311
Marco Baiesi , Tim Jacobs , Christian Maes , Nikos S. Skantzos
Inequivalence of statistical ensembles in single molecule measurements
Three-dimensional bead position histograms reveal single-molecule nanomechanics
Probability distributions of the work in the 2D-Ising model
cond-mat/0602580
Christophe Chatelain (LPM), Dragi Karevski (LPM)
A proof of Jarzynski's non-equilibrium work theorem for dynamical systems that conserve the canonical distribution
cond-mat/0603856
Elisabeth Scholl-Paschinger , Christoph Dellago
Work fluctuations for a Brownian particle between two thermostats
cond-mat/0605069
Paolo Visco
Path-integral analysis of fluctuation theorems for general Langevin processes
cond-mat/0605471
Vladimir Y. Chernyak (Wayne State), Michael Chertkov (LANL), Christopher Jarzynski (LANL)
Heat fluctuations in Brownian transducers
Rare events and the convergence of exponentially averaged work values
Fluctuation theorems for quantum master equations
[cond-mat/0606361] Thermodynamics for single-molecule stretching experiments
[cond-mat/0607575] Validation of the Jarzynski relation for a system with strong thermal coupling: an isothermal ideal gas model
[cond-mat/0609085] Jarzynski Equality with Maxwell's Demon
[cond-mat/0611078] The distribution function of entropy flow in stochastic systems
[cond-mat/0611516] A charged particle in a magnetic field - Jarzynski Equality
[cond-mat/0612021] Non-equilibrium work fluctuations for oscillators in non-Markovian baths
[cond-mat/0612305] Comparison of far-from-equilibrium work relations
[cond-mat/0612527] Failure of the Jarzynski identity for a simple quantum system
[cond-mat/0612423] Asymmetry of the work probability distribution
[cond-mat/0701003] Comment on "Failure of the Jarzynski identity for a simple quantum system"
[cond-mat/0701303] Work Fluctuations and Stochastic Resonance
[cond-mat/0702044] Temperature-extended Jarzynski relation: Application to the numerical calculation of the surface tension
[cond-mat/0703189] Fluctuation theorems: Work is not an observable
[0705.1945] The Jarzynski equality. Thermodynamic analysis and microscopic foundations
[0706.1994] On the Quantum Jarzynski Identity
[0706.3749] Quantum Operation Time Reversal

Gallavotti-Cohen

Breakdown of Gallavotti-Cohen symmetry for stochastic dynamics
cond-mat/0512159
R. J. Harris , A. Rákos , G. M. Schuetz
Fluctuation theorem for currents and Schnakenberg network theory
cond-mat/0512254
David Andrieux , Pierre Gaspard
Fluctuation theorem for constrained equilibrium systems
cond-mat/0601435
T. Gilbert , J. R. Dorfman
Fluctuation theorem applied to the Nos\'e-Hoover thermostated Lorentz gas
cond-mat/0602458
Thomas Gilbert
Fluctuation theorems for quantum master equations
cond-mat/0602679
Massimiliano Esposito , Shaul Mukamel
Nonequilibrium statistical mechanics and entropy production in a classical infinite system of rotators
[cond-mat/0606477] Entropy, Nonequilibrium, Chaos and Infinitesimals
[cond-mat/0606690] Entropy, Thermostats and Chaotic Hypothesis
[cond-mat/0612019] Is it possible to experimentally verify the fluctuation relation? A review of theoretical motivations and numerical evidence
[cond-mat/0612260] Test of the fluctuation theorem for stochastic entropy production in a nonequilibrium steady state
[cond-mat/0612397] Gallavotti-Cohen theorem, Chaotic Hypothesis and the zero-noise limit
[physics/0612167] Fluctuation theorem for entropy production during effusion of an ideal gas with momentum transfer
[cond-mat/0701124] Quantum Nonequilibrium and Entropy creation
[cond-mat/0702376] Fluctuation theorem for counting-statistics in electron transport through quantum junctions
[cond-mat/0702553] Fluctuation theorems for stochastic dynamics
[cond-mat/0703254] A novel fluctuation relation for a L\'evy particle
[cond-mat/0703347] Quantum fluctuation theorem: Can we go from micro to meso?
[cond-mat/0703798] Fluctuation theorems for harmonic oscillators

Felix

Experimental test of Hatano and Sasa's nonequilibrium steady-state equality
E. H. Trepagnier *, , C. Jarzynski , F. Ritort , G. E. Crooks ¶, C. J. Bustamante *, , ||, ** and J. Liphardt PNAS | October 19, 2004 | vol. 101 | no. 42 | 15038-15041
A two-state kinetic model for the unfolding of single molecules by mechanical force
F. Ritort , C. Bustamante , and I. Tinoco, Jr. PNAS | October 15, 2002 | vol. 99 | no. 21 | 13544-13548
Bias and error in estimates of equilibrium free-energy differences from nonequilibrium measurements
Jeff Gore *, Felix Ritort * and Carlos Bustamante PNAS | October 28, 2003 | vol. 100 | no. 22 | 12564-12569
Single molecule experiments in biophysics: exploring the thermal behavior of nonequilibrium small systems
F. Ritort cond-mat/0509606
Work and heat fluctuations in two-state systems: a trajectory thermodynamics formalism
F Ritort J. Stat. Mech. (2004) P10016 doi:10.1088/1742-5468/2004/10/P10016 URL: http://stacks.iop.org/1742-5468/2004/P10016
Work and heat fluctuations in two-state systems: a trajectory thermodynamics formalism
F. Ritort cond-mat/0405707
Thermodynamic and kinetic aspects of RNA pulling experiments
Maria Manosas, Felix Ritort cond-mat/0405035
The Nonequilibrium Thermodynamics of Small Systems
[cond-mat/0606254] Force dependent fragility in RNA hairpins
[cond-mat/0606254] Force dependent fragility in RNA hairpins
[cond-mat/0609378] Single-molecule experiments in biological physics: methods and applications
[cond-mat/0511629] The Nonequilibrium Thermodynamics of Small Systems
[0705.0455] Nonequilibrium fluctuations in small systems: From physics to biology
[0707.0089] Bayesian estimates of free energies from nonequilibrium work data in the presence of instrument noise

[0704.0761] Failure of the work-Hamiltonian connection for free energy calculations
[0704.2992] Fluctuation theorems and orbital magnetism in nonequilibrium state
[0704.3318] A fluctuation theorem for currents and non-linear response coefficients
[0704.0761] Failure of the work-Hamiltonian connection for free energy calculations
[0705.1252] The Tasaki-Crooks quantum fluctuation theorem
[0705.4248] Fluctuation theorem for black-body radiation
[0706.0559] Measuring thermodynamic length
[0706.1134] Comment on: Failure of the work-Hamiltonian connection for free energy calculations
[0707.0439] Work and heat probability distribution of an optically driven Brownian particle: Theory and experiments
[0707.0962] Entropy fluctuation theorems in driven open systems: application to electron counting statistics

Motors

Brownian motors: noisy transport far from equilibrium
cond-mat/0010237
Peter Reimann (Universitaet Augsburg)
Journal-ref: Phys. Rep. 361, 57 (2002)
Molecular Chemical Engines: Pseudo-Static Processes and the Mechanism of Energy Transduction
cond-mat/0508037
Kazuo Sasaki
Tunable ratchet effects for vortices pinned by periodic magnetic dipole arrays
cond-mat/0508318
Gilson Carneiro
Detecting a true quantum pump effect
cond-mat/0508176
Colin Benjamin
Oscillations in molecular motor assemblies
10.1088/0953-8984/17/47/018
Two-body problem in periodic potentials
cond-mat/0509093
M. Wouters , G. Orso
Inhomogeneous soliton ratchets under two ac forces
cond-mat/0509051
Luis Morales-Molina , Franz G. Mertens , Angel Sanchez
Physics of Transport and Traffic Phenomena in Biology: from molecular motors and cells to organisms
physics/0509025
Debashish Chowdhury , Andreas Schadschneider , Katsuhiro Nishinari
Symmetry and environment effects on rectification mechanisms in quantum pumps
cond-mat/0509129
Liliana Arrachea
Dynamic Phase Transitions in Coupled Motor Proteins
cond-mat/0509457
Evgeny B. Stukalin , Anatoly B. Kolomeisky
Ratchet Effect and Nonlinear Transport for Particles on Random Substrates with Crossed ac Drives
cond-mat/0509311
C. Reichhardt , C.J. Olson Reichhardt
Journal-ref: Phys. Rev. E 73, 011102 (2006)
Phase transitions in systems with two species of molecular motors
10.1209/epl/i2003-10155-6
Feedback control in a collective flashing ratchet
10.1103/PhysRevLett.93.040603
Stability and Dynamics of Crystals and Glasses of Motorized Particles
cond-mat/0403180
Tongye Shen , Peter G. Wolynes
Stability and Dynamics of Crystals and Glasses of Motorized Particles
Ken Sekimoto Journal of the Physical Society of Japan Vol.66 No.5, May, 1997 pp. 1234-1237 URL : http://jpsj.ipap.jp/link?JPSJ/66/1234/ DOI : 10.1143/JPSJ.66.1234
Directed transport of Brownian particles in a double symmetric potential
cond-mat/0404731
Laurent Sanchez-Palencia
Journal-ref: Physical Review E 70 (2004) 011102
A spin-boson thermal rectifier
cond-mat/0405472
Dvira Segal , Abraham Nitzan
Journal-ref: Phys. Rev. Lett. 94, 034301 (2005).
Rectification of thermal fluctuations in ideal gases
cond-mat/0407180
P. Meurs , C. Van den Broeck , A. Garcia
Duality Relation for Quantum Ratchets
10.1103/PhysRevE.71.010101
The charge shuttle as a nanomechanical ratchet
10.1103/PhysRevLett.94.036806
Walks of molecular motors interacting with immobilized filaments
10.1016/j.physa.2004.11.023
Ratchet effect for cold atoms in an optical lattice
cond-mat/0409185
Emil Lundh , Mats Wallin (KTH, Sweden)
Dynamics of Molecular Motors with Finite Processivity on Heterogeneous Tracks
cond-mat/0409198
Yariv Kafri , David K. Lubensky , David R. Nelson
Efficiency of Brownian Motors
cond-mat/9803302
J.M.R. Parrondo , J.M. Blanco , F.J. Cao , R. Brito (Universidad Complutense de Madrid, Spain)
Journal-ref: Europhys. Lett, 43 (3), 248-254 (1998)
Directed Chaotic Transport in Hamiltonian Ratchets
10.1103/PhysRevE.71.026228
Coupled Brownian motors: Anomalous hysteresis and zero-bias negative conductance
Coupled Brownian Motors
Energetics of rocked inhomogeneous ratchets
Ground state, vibrational spectrum, and deterministic transport of a chain of charged particles
S. I. Denisov and E. S. Denisova Phys. Rev. B 68, 064301 (2003) URL: http://link.aps.org/abstract/PRB/v68/e064301 doi:10.1103/PhysRevB.68.064301
Efficiency of Brownian motors
J. M. R. Parrondo 1, J. M. Blanco 2, F. J. Cao 2 and R. Brito Europhys. Lett, 43 (3), pp. 248-254 (1998) DOI: 10.1209/epl/i1998-00348-5 http://www.edpsciences.org/articles/epl/abs/1998/15/43303/43303.html
http://www.eprairie.com/printer/article.asp?newsletterID=4574
Kinesin HomePage
Minimal Brownian Ratchet: An Exactly Solvable Model
Youngki Lee,1,2 Andrew Allison,3 Derek Abbott,3 and H. Eugene Stanley Phys. Rev. Lett. 91, 220601 (2003) URL: http://link.aps.org/abstract/PRL/v91/e220601 doi:10.1103/PhysRevLett.91.220601
Phys. Rev. E 57, 7297 (1998): Parrondo - Reversible ratchets as Brownian...
Phys. Rev. E 61, 6287 (2000): Buceta et al. - Negative resistance and anomalous...
Phys. Rev. Lett. 80, 5251 (1998): Kamegawa et al. - Energetics of a Forced...
pubs.html
reu.pdf (application/pdf Object)
Paradoxical non-linear response of a Brownian particle
cond-mat/0406155
Ralf Eichhorn , Peter Reimann
Spontaneous Ratchet Effect in a Granular Gas
Directed Chaotic Transport in Hamiltonian Ratchets
10.1103/PhysRevE.71.026228
Brownian motors: current fluctuations and rectification efficiency
10.1103/PhysRevE.70.061105
Diffusion accompanying noise induced transport in frictional ratchets
cond-mat/0409287
Raishma Krishnan , Debasis Dan , A. M. Jayannavar
Driven quantum transport on the nanoscale
10.1016/j.physrep.2004.11.002
Driven quantum transport on the nanoscale
doi:10.1103/PhysRevE.70.021102
10.1016/j.physrep.2004.11.002
Transient behavior of particle transport in a Brownian motor
Random walks of molecular motors arising from diffusional encounters with immobilized filaments
Directed transport of Brownian particles in a double symmetric potential
Bioinspired laser-operated molecular locomotive
Paradoxical nonlinear response of a Brownian particle
Rectification in Luttinger liquids
cond-mat/0410089
D. E. Feldman , S. Scheidl , V. M. Vinokur
Journal-ref: Phys. Rev. Lett. 94, 186809 (2005)
Brownian motors
cond-mat/0410033
P. Hänggi , F. Marchesoni , F. Nori
Journal-ref: P. H\"anggi, F. Marchesoni, F. Nori, Annalen der Physik, Vol. 14 (1-3) 2005
Asymmetric pores in a silicon membrane acting as massively parallel brownian ratchets
Phys. Rev. E 61, 312 (2000): Kettner et al. - Drift ratchet
Efficiency of discrete-time ratchets
cond-mat/0410173
P. Amengual , R. Toral , A. Allison , D. Abbott
Fluctuation-response relation in a rocking ratchet
Flashing ratchet model with high efficiency
Diffusion and current of Brownian particles in tilted piecewise linear potentials: Amplification and coherence
Cooperative effects on the kinetics of ATP hydrolysis in collective molecular motors
Chaotic Hamiltonian ratchets for pulsed periodic double-well potentials: Classical correlations and the ratchet current
Stochastic resonance in a biological motor under complex fluctuations
Twirling DNA Rings - Swimming Nanomotors Ready for a Kickstart
cond-mat/0410197
Igor M. Kulic , Rochish Thaokar , Helmut Schiessel
Ratchet behavior in nonlinear Klein-Gordon systems with point-like inhomogeneities
cond-mat/0410320
Luis Morales-Molina , Franz G. Mertens , Angel Sanchez
Nonequilibrium stationary states with ratchet effect
10.1103/PhysRevE.71.036111
Flux reversal in a two-state symmetric optical thermal ratchet
cond-mat/0506285
Sang-Hyuk Lee , David G. Grier
Ratchet, pawl and spring Brownian motor
cond-mat/0506543
A. Gomez-Marin , J.M. Sancho
Journal-ref: Physica D 216 (2006) 214-219
3-junction SQUID rocking ratchet
cond-mat/0507017
A. Sterck , R. Kleiner , D. Koelle
A random walker on a ratchet
cond-mat/0507027
Jose L. Mateos
Journal-ref: Physica A 351 (2005) 79-87
A Multiscale Approach to Brownian Motors
cond-mat/0504403
G.A. Pavliotis
Pattern formation of microtubules and motors: inelastic interaction of polar rods
10.1103/PhysRevE.71.050901
A "Burnt Bridge'' Brownian Ratchet
10.1103/PhysRevE.72.046104
Closed-loop control strategy with improved current for a flashing ratchet
cond-mat/0505125
L. Dinis , F. J. Cao , J. M. R. Parrondo
Vortex Motion Rectification in Josephson Junction Arrays with a Ratchet Potential
Quantum Ratchets in Dissipative Chaotic Systems
Noise-Enhanced Performance of Ratchet Cellular Automata
Optimal strategy for controlling transport in inertial Brownian motors
10.1088/0953-8984/17/47/007
Two approaches toward a high-efficiency flashing ratchet
Renewal processes and fluctuation analysis of molecular motor stepping
10.1088/1478-3975/2/3/008
Thermal Brownian motor
cond-mat/0505753
P. Meurs , C. Van den Broeck
Vectorial Loading of Processive Motor Proteins: Implementing a Landscape Picture
cond-mat/0506185
Young C. Kim , Michael E. Fisher
Rectification in one--dimensional electronic systems
cond-mat/0506095
Bernd Braunecker , D. E. Feldman , J. B. Marston
Journal-ref: Phys. Rev. B 72, 125311 (2005)
Coupling of Two Motor Proteins: a New Motor Can Move Faster
cond-mat/0502474
Evgeny B. Stukalin , Hubert Phillips III , Anatoly B. Kolomeisky
Movements of molecular motors: Ratchets, random walks and traffic phenomena
10.1016/j.physe.2005.05.037
Dynamic Properties of Motor Proteins with Two Subunits
cond-mat/0503169
Anatoly B. Kolomeisky , Hubert Phillips III
Noise enhanced performance of ratchet cellular automata
cond-mat/0503279
Dusan Babic (1 and 2), Clemens Bechinger (1) ((1) 2. Physikalisches Institut, Universitaet Stuttgart, Stuttgart, Germany,(2) Faculty for Mathematics and Physics, University of Ljubljana, Ljubljana, Slovenia)
Energetics of a simple microscopic heat engine
cond-mat/0503578
Mesfin Asfaw , Mulugeta Bekele
Experimental Tunneling Ratchets -- Linke et al. 286 (5448): 2314 -- Science
Universal properties of interacting Brownian motors
Yashar Aghababaie*, Gautam I. Menon, and Michael Plischke Phys. Rev. E 59, 2578–2586 (1999) URL: http://link.aps.org/abstract/PRE/v59/p2578 DOI: 10.1103/PhysRevE.59.2578
Quantum Ratchets at High Temperatures
cond-mat/0412566
D. Zueco , J. L. Garcia-Palacios
Noise induced currents and reliability of transport in frictional ratchets
cond-mat/0501106
Raishma Krishnan , Debasis Dan , A. M. Jayannavar
Molecular Motor Constructed from a Double-Walled Carbon Nanotube Driven by Axially Varying Voltage
10.1103/PhysRevB.72.033404
Optimal number of disperse states in the model of Brownian motors
Pushmepullyou: An efficient micro-swimmer
math-ph/0501049
J.E. Avron , O. Kenneth , D.H. Oaknin
Journal-ref: New J. Phys. 7 234 (2005)
Observation of Flux Reversal in a Symmetric Optical Thermal Ratchet
cond-mat/0411731
Sang-Hyuk Lee , Kosta Ladavac , Marco Polin , David G. Grier
Symmetric Brownian motor
cond-mat/0411604
A. Gomez-Marin , J. M. Sancho
Journal-ref: Phys. Rev. E 71, 021101 (2005)
Enhanced thermodynamic efficiency in time asymmetric ratchets
10.1088/1742-5468/2005/04/P04012
Speeding up a single-molecule DNA motor with a simple catalyst
cond-mat/0412287
Yufang Wang , Y. Zhang , N. P. Ong
Journal-ref: Phys. Rev. E 72, 051918 (2005)
Force generation in small ensembles of Brownian motors
q-bio/0412026
Martin Linden , Tomi Tuohimaa , Ann-Beth Jonsson , Mats Wallin
Pump process of the rotatory molecular motor and its energy efficiency
physics/0411061
Hiroshi Miki , Masatoshi Sato , Mahito Kohmoto
Rectification efficiency of a Brownian motor
Spatiotemporal dynamics of optical molecular motors
Nanomachines: Methods to induce a directed motion at nanoscale
Towards understanding the guessing game: a dynamical systems’ perspective
Stefan Reimann Physica A: Statistical Mechanics and its Applications Volume 339, Issues 3-4 , 15 August 2004, Pages 559-573 doi:10.1016/j.physa.2004.03.012
New aspects on Current enhancement in Brownian motors driven by non Gaussian noises
cond-mat/0410576
S. Bouzat (CAB-Ib) H.S.Wio (IFCA)
Microscopic model of the actin-myosin interaction in muscular contractions
Motor protein with nonequilibrium potential: Its thermodynamics and efficiency
Anomalous transport in unbound and ratchet potentials
Noiseless limit of a ferrofluid ratchet
cond-mat/0411060
Volker Becker , Andreas Engel
Efficiency optimization in a correlation ratchet with asymmetric unbiased fluctuations
Motion of a rotatory molecular motor and the chemical reaction rate
Current reversal with type-I intermittency in deterministic inertia ratchets
Adiabatic rocking ratchets: Optimum-performance regimes
Voltage rectification in two dimensional Josephson junction arrays
cond-mat/0510039
Veronica I. Marconi
Evidence of ratchet effect in nanowires of a conducting polymer
cond-mat/0510188
A. Rahman , M. K. Sanyal , R. Gangopadhayy , A. De , I. Das
Journal-ref: Phys. Rev. B 73, 125313 (2006)
Diffusion in Flashing Periodic Potentials
cond-mat/0510170
Bernardo Spagnolo , Alexander Dubkov
Molecular heat pump
cond-mat/0510262
Dvira Segal , Abraham Nitzan
Journal-ref: Phys. Rev E 73 026109 (2006)
Soliton ratchets in homogeneous nonlinear Klein-Gordon systems
cond-mat/0510704
Luis Morales-Molina , Niurka R. Quintero , Franz G. Mertens , Angel Sanchez
Ratchet Effect in Magnetization Reversal of Stoner Particles
cond-mat/0511135
Z. Z. Sun , X. R. Wang
``Burnt-bridge'' mechanism of molecular motor motion
Transport reversal in a thermal ratchet
Physical analysis of a processive molecular motor: The conventional kinesin
Quantum Brownian motion in ratchet potentials: duality relation and its consequences
10.1016/j.chemphys.2005.07.004
Flux reversal in a two-state symmetric optical thermal ratchet
Elastically coupled two-dimensional Brownian motors
Deterministic directed transport of inertial particles in a flashing ratchet potential
Molecular motor traffic in a half-open tube
10.1088/0953-8984/17/47/014
Traffic of Molecular Motors
cond-mat/0512119
Stefan Klumpp , Melanie J. I. Muller , Reinhard Lipowsky
Active diffusion of motor particles
10.1103/PhysRevLett.95.268102
Cooperative Cargo Transport by Several Molecular Motors
10.1073/pnas.0507363102
Forcing inertial Brownian motors: efficiency and negative differential mobility
cond-mat/0512152
Marcin Kostur , Lukasz Machura , Peter Hänggi , Jurek Luczka , Peter Talkner
Demonstration of a controllable three-dimensional Brownian motor in symmetric potentials
10.1103/PhysRevLett.96.190602
Collective dynamics of molecular motors pulling on fluid membranes
q-bio/0512018
O. Campas , Y. Kafri , K.B. Zeldovich , J. Casademunt , J.-F. Joanny
Cold atom realizations of Brownian motors
cond-mat/0512550
F. Renzoni
Journal-ref: Contemp. Phys. 46, 161 (2005)
Theory of self-assembly of microtubules and motors
cond-mat/0512659
Igor S. Aronson , Lev S. Tsimring
Coherent Spin Ratchets
cond-mat/0601118
Andreas Pfund , Dario Bercioux , Klaus Richter
Discrete soliton ratchets driven by biharmonic fields
nlin/0601044
Yaroslav Zolotaryuk , Mario Salerno
Vibrational ratchets
cond-mat/0601609
M. Borromeo , F. Marchesoni
Mechanical coupling in flashing ratchets
cond-mat/0602097
Erin M. Craig , Martin J. Zuckermann , Heiner Linke
Brownian refrigerator
cond-mat/0602153
C. Van den Broeck , R. Kawai
Optical ratchets with discrete cavity solitons
nlin/0602004
Andrey V. Gorbach , Sergey Denisov , Sergej Flach
Ratchet effect and nonlinear transport for particles on random substrates with crossed ac drives
Single-polymer Brownian motor: A simulation study
Vibrational ratchets
Rotary motor powered by stochastic uncorrelated dipoles
Analytical theory of the stochastic dynamics of the power stroke in nonprocessive motor proteins
Energetics of a simple microscopic heat engine
Two approaches toward a high-efficiency flashing ratchet
Dynamics of molecular motors with finite processivity on heterogeneous tracks
Symmetric Brownian motor
Directed chaotic transport in Hamiltonian ratchets
Overdamped Deterministic Ratchets Driven By Multifrequency Forces
cond-mat/0603128
David Cubero (1), Jesús Casado-Pascual (1), Azucena Alvarez (1), Manuel Morillo (1), Peter Hänggi (2) ((1) Física Teórica, Universidad de Sevilla, Spain, (2) Institut für Physik, Universität Augsburg, Germany)
Stoke's efficiency of temporally rocked ratchets
cond-mat/0603778
Raishma Krishnan , Jim Chacko , Mamata Sahoo , A. M. Jayannavar
Dynamic stability of spindles controlled by molecular motor kinetics
q-bio/0603036
Otger Campas , Jaume Casademunt , Ignacio Pagonabarraga
Collective Effects in Models for Interacting Molecular Motors and Motor-Microtubule Mixtures
cond-mat/0604163
Gautam I. Menon
Brownian molecular motors driven by rotation-translation coupling
cond-mat/0604087
Brian Geislinger , Ryoichi Kawai
Efficiency and Fluctuation in Tight-Coupling Model of Molecular Motor
cond-mat/0605185
Hidetsugu Sakaguchi
Threshold feedback control for a collective flashing ratchet: threshold dependence
cond-mat/0605275
M. Feito , F. J. Cao
Exploring the operation of a tiny heat engine
cond-mat/0605233
Mesfin Asfaw , Mulugeta Bekele
Powering a burnt bridges Brownian ratchet: A model for an extracellular motor driven by proteolysis of collagen
Thermal Rectification in Billiard-like Systems
cond-mat/0605710
Jean-Pierre Eckmann , Carlos Mejia-Monasterio
Quantum ratchet with cold atoms in a pair of pulsed optical lattices
cond-mat/0605695
Gabriel G. Carlo , Giuliano Benenti , Giulio Casati , Sandro Wimberger , Oliver Morsch , Riccardo Mannella , Ennio Arimondo
Weak chaos and fractional dynamics in an optically driven colloidal ring
cond-mat/0605686
Yael Roichman , George Zaslavsky , David G. Grier
Overdamped thermal ratchets in one and more dimensions. Kinesin transport and protein folding
Quantum diffusion in biased washboard potentials: Strong friction limit
Dynamic transitions in coupled motor proteins
Mechanical coupling in flashing ratchets
Brownian motor with time-delayed feedback
Nonlinear dynamics and self-organization of rotary molecular motor ensembles
[cond-mat/0606305] Rectifying effect of RF current in single magnetic nanowire
[cond-mat/0606302] Nanomachines driven by thermal bath
[cond-mat/0606487] One-dimensional nonrelativistic and relativistic Brownian motions: A microscopic collision model
[quant-ph/0606124] Current behavior of a quantum Hamiltonian ratchet in resonance
[cond-mat/0607322] From aggressive driving to molecular motor traffic
[cond-mat/0607380] Zeeman ratchets for ballistic spin currents
[cond-mat/0609069] Tight coupling in thermal Brownian motors
[cond-mat/0609004] Phase synchronization in tilted deterministic ratchets
[cond-mat/0608569] The design of a thermal rectifier
The design of a thermal rectifier
[cond-mat/0610262] Quasiperiodically driven ratchets for cold atoms
[cond-mat/0609608] Two hard spheres in a spherical pore: Exact analytic results in two and three dimensions
[cond-mat/0609546] Role of interactions in ferrofluid thermal ratchets
[cond-mat/0609560] Reversible Vortex Ratchet Effects and Ordering in Superconductors with One-Dimensional Asymmetric Potential Arrays
[cond-mat/0609452] Absolute negative mobility by forcing inertial Brownian particles in periodic potential
[cond-mat/0610369] Symmetries of the ratchet current
[cond-mat/0610360] Generalized Einstein Relation for Brownian Motion in Tilted Periodic Potential
Theory of self-assembly of microtubules and motors
Hsp70 chaperones accelerate protein translocation and the unfolding of stable protein aggregates by entropic pulling -- De Los Rios et al. 103 (16): 6166 -- Proceedings of the National Academy of Sciences
[cond-mat/0610847] Spin current and rectification in one-dimensional electronic systems
[cond-mat/0610757] Fluctuations, Responses and Energetics of Molecular Motors
[q-bio/0610045] Kinesin as an electrostatic machine
[cond-mat/0610651] Exact Solutions of Burnt-Bridge Models for Molecular Motor Transport
[cond-mat/0611140] A Granular Brownian Ratchet Model
[cond-mat/0611283] Granular Brownian Motor
[cond-mat/0611277] Transport of Forced Quantum Motors in the Strong Friction Limit
[cond-mat/0611250] Magnetically Induced Thermal Rectification
[cond-mat/0611247] Transport of a heated granular gas in a washboard potential
[cond-mat/0611508] Current rectification by asymmetric molecules: An ab initio study
[cond-mat/0611436] Rectification effects in coherent transport through single molecules
[cond-mat/0611432] Dynamics of Quantum Dissipative Systems: The Example of Quantum Brownian Motors
[cond-mat/0611630] Universality in ratchets without spatial asymmetry
[cond-mat/0612059] Heat production and energy balance in nanoengines driven by time-dependent fields
[cond-mat/0611771] Two simple models of classical heat pumps
[physics/0611302] Controllable 3D atomic Brownian motor in optical lattices
[q-bio/0612026] Dwell time symmetry in random walks and molecular motors
[cond-mat/0612390] Rocking ratchets in 2D Josephson networks: collective effects and current reversal
[cond-mat/0701076] Colloids in a periodic potential: driven lattice gas in continuous space
[cond-mat/0701169] Propulsion of a molecular machine by asymmetric distribution of reaction--products
[cond-mat/0701168] Designing phoretic micro- and nano-swimmers
[cond-mat/0701445] Dipole-induced vortex ratchets in superconducting films with arrays of micromagnets
[cond-mat/0701522] Heteropolymer translocation through nanopores
[cond-mat/0701505] Analytical Solution to Transport in Brownian Ratchets via Gambler's Ruin Model
[cond-mat/0702668] Dissipationless Directed Transport in Rocked Single-Band Quantum Dynamics
[physics/0702194] Traffic phenomena in biology: from molecular motors to organisms
[quant-ph/0702066] Rectification of the lateral Casimir force in a vibrating non-contact rack and pinion
[cond-mat/0703492] Information and flux in a feedback controlled Brownian ratchet
[cond-mat/0703583] Interaction Between Motor Domains Can Explain the Complex Dynamics of Heterodimeric Kinesins
[physics/0703048] Illusion of Control in a Brownian Game
[cond-mat/0703404] Anomalous Dynamics of Unbiased Polymer Translocation through a Narrow Pore
[0704.1911] Motor driven microtubule shape fluctuations - force from within the lattice
[0704.3692] Analytically solvable model of a driven system with quenched dichotomous disorder
[0704.3794] Non-equilibrium mechanics and dynamics of motor activated gels
[0704.3802] Entropic Studies of Cytoskeletal Motors Jamming
[0704.3817] Trapping mechanism in overdamped ratchets with quenched noise
[0704.3955] Characterisation of a three-dimensional Brownian motor in optical lattices
[0705.0138] Symmetry Relations for Trajectories of a Brownian Motor
[0705.0690] Dynamic Properties of Molecular Motors in Burnt-Bridge Models
[0705.2057] The geometric theory of mesoscopic stochastic pump and reversible ratchet effects
[0705.2594] Molecular Spiders in One Dimension
[0705.2596] Molecular Spiders with Memory
[0705.2669] Motion-reversal in a simple microscopic swimmer
[0705.2905] Brownian ratchets driven by asymmetric nucleation of hydrolysis waves
[0705.3463] Transient rectification of Brownian diffusion with asymmetric initial distribution
[0705.4041] Multidimensional coupling in a controllable three-dimensional Brownian motor in optical lattices
[0706.1496] Time-Delayed Feedback control of a flashing ratchet
[0706.3276] The ratchet effect and the transporting islands in the chaotic sea
[0706.3726] Reversible stochastic pump currents in interacting nanoscale conductors
[0706.4466] Flux enhancement and multistability induced by time delays in a feedback controlled flashing ratchet
[0707.0901] Effect of time delay on feedback control of a flashing ratchet

generalities

Stationary nonequilibrium statistical mechanics

tweezers

[cond-mat/0606022] Quantum-based Mechanical Force Realization in Pico-Newton Range
[physics/0612252] Towards absolute calibration of optical tweezers
[physics/0702044] Collecting single molecules with conventional optical tweezers
[physics/0702047] Nanotrapping and the thermodynamics of optical tweezers
Magnetic Tweezers
Optical Tweezers Introduction
Optical Tweezers
[physics/0607286] Modelling optical micro-machines
[cond-mat/0609276] Colloidal transport through optical tweezer arrays

various

[cond-mat/0611003] A simple model for protein mechanical unfolding
[cond-mat/0612433] Measuring the energy landscape roughness and the transition state location of biomolecules using single molecule mechanical unfolding experiments
[cond-mat/0703040] Isolated Non-Equilibrium Systems in Contact
[cond-mat/0703455] Organic Spintronics
[0706.2818] Protein mechanical unfolding: a model with binary variables

cytoskeleton

[0706.0393] Micro- and Macrorheological Properties of Isotropically Cross-linked Actin Networks
[0706.0388] Cross-linker unbinding and self-similarity in bundled cytoskeletal networks


Created automatically on Wednesday 14 November 2007 11:47:52