# Publications

## Biophysics and Non-equilibrium physics

### • P. Rissone, C. V. Bizarro and F. Ritort, *Stem-loop formation drives RNA folding in mechanical unzipping experiments*, PNAS (USA), 119 3 (2022). Understanding how complementary RNA single strands anneal to form the native structure requires accurate knowledge of the energetics of hybridization and the kinetics driving the hairpin fold. The annealing dynamics are highly complex for RNA, where multiple long-lived intermediate states occur along the folding pathway. We mechanically unzip a 2-kbp RNA hairpin with optical tweezers in sodium and magnesium, deriving the 10 RNA nearest-neighbor free energies and modeling the hybridization kinetics in a barrier energy landscape of stem–loop secondary structures. Our study contributes to a better understanding of the RNA folding problem. The paper also includes additional information as supplementary material.

### • M. Rico-Pasto, R. K. Schmitt, M. Ribezzi-Crivellari, J. M. R. Parrondo, H. Linke, J. Johansson and F. Ritort, *Dissipation Reduction and Information-to-Measurement Conversion in DNA Pulling Experiments with Feedback Protocols*, Physical Review X, 11 031052 (2021). The thermodynamics of small systems under feedback control has emerged as a fertile field of research in physics and beyond. To date, feedback protocols have focused on work extraction in equilibrium systems. However, most systems in nature are out of equilibrium and dissipative. Can we use feedback to reduce dissipation in nonequilibrium systems? Can we take advantage of such a reduction to extract equilibrium information (e.g., a system’s free energy)? Here, we combine theory and experiment to investigate how feedback reduces dissipation in small nonequilibrium systems. The paper also includes additional information as supplementary material.

### • X. Viader-Godoy, C. R. Pulido, B. Ibarra, M. Manosas and F. Ritort, *Cooperativity-dependent folding of single-stranded DNA*, Physical Review X, 11 031037 (2021). A new model of how single strands of DNA fold into themselves shows promise in helping enrich understanding of how molecules in cells contort to perform various biological functions. The paper also includes additional information as supplementary material.

### • V. S. Rajan, X. Viader-Godoy, Y. L. Lin, U. Dutta, F. Ritort, F. Westerlund and L. M. Wilhelmsson. *Mechanical characterization of base analogue modified nucleic acids by force spectroscopy*, Physical Chemistry Chemical Physics, 23, 14151 (2021).

### • X. Viader-Godoy, M. Manosas and F. Ritort. *Sugar-Pucker Force-Induced Transition in Single-Stranded DNA*, International Journal of Molecular Sciences, 22, 4745 (2021).

### • I. Di Terlizzi, F. Ritort, and M. Baiesi. *Explicit solution of the generalised Langevin equation*, Journal of Statistical Physics, 181, 1609–1635 (2020).

### • A. L. Thorneywork, J. Gladrow, Y. Qing, M. Rico-Pasto, F. Ritort, H. Bayley and U. F. Keyser. *Direct detection of molecular intermediates from first-passage times*, Science Advances, 6(18), eaaz4642 (2020). The paper also includes additional information as supplementary material.

### • F. Landuzzi, X. Viader-Godoy, F. Cleri, I. Pastor and F. Ritort *Detection of single DNA mismatches by force spectroscopy in short DNA hairpins*, The Journal of Chemical Physics,152.7: 074204 (2020). The paper also includes additional information as supplementary material.

### • A. Severino, A. M. Monge, P. Rissone and F. Ritort *Efficient methods for determining folding free energies in single-molecule pulling experiments*, Journal of Statistical Mechanics: Theory and Experiment 124001 (2019).

### • M. Ribezzi-Crivellari and F. Ritort *Work extraction, information-content and the Landauer bound in the continuous Maxwell Demon*, Journal of Statistical Mechanics: Theory and Experiment 084013 (2019).

### • J. Gladrow, M. Ribezzi-Crivellari, F. Ritort and U.F. Keyser *Experimental evidence of symmetry breaking of transition-path times*, Nature Communications 10:55 (2019). The paper also includes additional information as supplementary material.

### •M. Ribezzi-Crivellari and F.Ritort *Large work extraction and the Landauer limit in a continuous Maxwell demon*, Nature Physics 15, 660–664 (2019) . The paper also includes additional information as supplementary material.

### • T. Naranjo, K. M. Lemishko, S. de Lorenzo, Á. Somoza, F.Ritort, E. M. Pérez and B. Ibarra *Dynamics of individual molecular shuttles under mechanical force*, Nature Communications 9:4512 (2018). The paper also includes additional information as supplementary material.

### • R. Sorkin, G. Bergamaschi, D. Kamsma, G. Brand, E. Dekel, Yifat Ofir-Birin, Ariel Rudik, Marta Gironella, Felix Ritort, Neta Regev-Rudzki, Wouter H. Roos and G. J. L. Wuite *Probing cellular mechanics with acoustic force spectroscopy*, Molecular Biology of the Cell Vol 29, No. 16 (2018). The paper also includes additional information as supplementary material.

### •I. Tadeo, E. Gamero-Sandemetrio, A. P. Berbegall, M. Gironella, F. Ritort, A. Cañete, G. Bueno, S. Navarro, R. Noguera, * Lymph microvascularization as a prognostic indicator in neuroblastoma*, Oncotarget, Vol. 9 (2018) 26157-26170.

### • A. Crisanti, M. Picco and F. Ritort *Derivation of the spin-glass order parameter from stochastic thermodynamics*, Physical Review E 97, 052103 (2018).

### • M. Sanchez-Milla, I. Pastor, M. Maly, M. J. Serramia, R. Gomez, J. Sanchez-Nieves, F. Ritort, M. A. Munoz-Fernandez, F. J. de la Mata *Study of non-covalent interactions on dendriplex formation: Influence of hydrophobic, electrostatic and hydrogen bonds interactions*, Colloids Surf B Biointerfaces 162 (2018) 380-388.

### • A.M. Monge, M. Manosas and F. Ritort *Experimental test of ensemble inequivalence and the fluctuation theorem in the force ensemble in DNA pulling experiments*, Physical Review E 98, 032146 (2018).

### • M. Rico-Pasto, I. Pastor and F. Ritort *Force feedback effects on single molecule hopping and pulling experiments*, The Journal of Chemical Physics 148, 123327 (2018).

### • P.Pietzonka, F. Ritort and Udo Seifert *Finite-time generalization of the thermodynamic uncertainty relation*, Physical Review E 012101 (2017).

### • M. Manosas, J. Camunas-Soler, V. Croquette and F. Ritort, *Single molecule high-throughput footprinting of small and large DNA ligands*, Nature Communications Volume 8, 2041-1723 (2017).

### • J.M. Huguet, M. Ribezzi-Crivellari, C.V. Bizarro and F. Ritort, *Derivation of nearest-neighbor DNA parameters in magnesium from single molecule experiments*, Nucleic Acids research Volume 45, Issue 22, 12921–12931 (2017). The paper also includes additional information as supplementary material.

### • A. Alemany and F. Ritort, *Force-Dependent Folding and Unfolding Kinetics in DNA Hairpins Reveals Transition-State Displacements along a Single Pathway*, The Journal of Physical Chemistry Letters Volume 8, 895–900 (2017).

### • J. Camunas-Soler, A. Alemany and F. Ritort, *Experimental measurement of binding energy, selectivity, and allostery using fluctuation theorems*, Science Volume 355, Issue 6323, 412-415 (2017).

### • E. Dieterich, J. Camunas-Soler, M. Ribezzi-Crivellari, U. Seifert, and F. Ritort, *Control of force through feedback in small driven systems*, Physical Review E Volume 94 July 2016 012107.

### • A. Alemany, B. Rey-Serra, S. Frutos, C. Cecconi, and F. Ritort, *Mechanical Folding and Unfolding of Protein Barnase at the Single-Molecule Level*, Biophysical Journal Volume 110 January 2016 63-74.

### • E. Dieterich, J. Camunas-Soler, M. Ribezzi-Crivellari, U. Seifert, and F. Ritort, *Single-molecule measurement of the effective temperature in non-equilibrium steady states*, Nature Physics, 971–977 (2015).

### • A. Alemany, M. Ribezzi-Crivellari, and F. Ritort, *From free energy measurements to thermodynamic inference in nonequilibrium small systems*, New Journal Physics 17 (2015) 075009.

### • S. de Lorenzo, M. Ribezzi-Crivellari, R. Arias-Gonzalez, S.B. Smith and F. Ritort,* A Temperature-Jump Optical Trap for Single-Molecule Manipulation*, Biophysical Journal, 108 (2015) 2854-2864. The paper also includes additional information as supplementary material.

### • J. Camunas-Soler, M. Manosas, S. Frutos, J. Tulla-Puche, F. Albericio and F. Ritort, *Single-molecule kinetics and footprinting of DNA bis-intercalation: the paradigmatic case of Thiocoraline*, Nucleic Acids Research, 43 (2015) 2767-2779. In this paper we use force spectroscopy to characterize the thermodynamics, kinetics and selectivity of binding of an anticancer peptide bis-intercalating DNA. We find that the kinetics of bis-intercalation are very slow (hours) and strongly force-dependent showing the existence of a mono-intercalated intermediate state that remained elusive until now. Binding selectivity is demonstrated through a novel single-molecule footprinting assay that provides rapid access to the sequence-selectivity of small ligands with one base pair resolution. The paper also includes additional information as supplementary material, as well as a supplementary movie.

### • M. Ribezzi-Crivellari, A. Alemany and F. Ritort, *Universal axial fluctuations in optical tweezers*, Optics Letters, 40 (2015) 800-803.

### • M. Ribezzi-Crivellari and F. Ritort, *Free-energy inference from partial work measurements in small systems*, Proceedings of the National Academy of Sciences, 111 (2014) E3386-E3394. This paper introduces the new concept of thermodynamic inference or the possibility to extract useful and otherwise inaccessible information about irreversible processes in small systems. I foresee this approach will pave the way to characterize a wide range of fundamental biophysical problems. The paper also includes additional information on data analysis, considerations about hydrodynamic effects and theoretical calculations. You can download it at supplementary material.

### • A. Alemany and F. Ritort, *Determination of the elastic properties of short DNA molecules by mechanically folding and unfolding DNA hairpins*, Biopolymers 101 (2014) 1193-1199. The paper also includes additional information as supplementary material.

### • A. Alemany, N. Sanvicens, S. De Lorenzo, P. Marco and F. Ritort, *Bond Elasticity Controls Molecular Recognition Specificity in Antibody-Antigen Binding*, Nano Letters 13 (2013) 5197-5202. The paper also includes additional information as supplementary material.

### • M. Manosas, S. K. Perumal, P. Bianco, F. Ritort, S. J. Benkovic, V. Croquette, *RecG and UvsW catalyse robust DNA rewinding critical for stalled DNA replication fork rescue*, Nature Communications 4 (2013) doi:10.1038/ncomms3368. The paper also includes additional information as supplementary material.

### • A. Bosco, J. Camunas-Soler and F. Ritort, *Elastic properties and secondary structure formation of single-stranded DNA at monovalent and divalent salt conditions*, Nucleic Acids Research 44, (2014) 2064-2074. The paper also includes additional information as supplementary material.

### • J. Camunas-Soler, S. Frutos, C. V. Bizarro, S. de Lorenzo, M. E. Fuentes-Perez, R. Ramsch, S. Vilchez, C. Solans, F. Moreno-Herrero, F. Albericio, R. Eritja, E. Giralt, S. B. Dev, and F. Ritort, *Electrostatic Binding and Hydrophobic Collapse of Peptide-Nucleic Acid Aggregates Quantified Using Force Spectroscopy*, ACS Nano, 7 (2013) 5102-5113. The paper also includes additional information as supplementary material

### • M. Ribezzi and F. Ritort, *Counter-propagating dual-trap optical tweezers based on linear momentum conservation*, Review of Scientific Instruments, 84 (2013) 043104. The paper also includes additional information as supplementary material

### • M. Ribezzi and F. Ritort, *Force Spectroscopy with Dual-Trap Optical Tweezers:Molecular Stiffness Measurements and Coupled Fluctuations Analysis*, Biophysical Journal, 103 (2012) 1919-1928. The paper also includes additional information as supplementary material

### • A. Alemany, A. Mossa, I. Junier and F. Ritort, *Experimental free-energy measurements of kinetic molecular states using fluctuation theorems*, Nature Physics, 8 (2012) 688-694. The paper also includes supplementary material such as additional calculations and animations. A enlightening news and views commentary on the paper has been written by Jan Liphardt, Single molecules: Thermodynamic limits, Nature Physics, 8 (2012) 638-639. You can access the commentary here.

### • K. Hayashi, S. De Lorenzo, M. Manosas, J. M. Huguet and F. Ritort, *Single-molecule stochastic resonance*, Physical Review X, 2 (2012) 031012. The paper is accompanied by a beautifully written editorial popular summary and some supplementary material.

### • C. V. Bizarro, A. Alemany and F. Ritort, *Non-specific binding of Na+ and Mg2+ to RNA determined by force spectroscopy methods*, Nucleic Acids Research (2012) doi: 10.1093/nar/gks289. The paper also includes additional information as supplementary material

### • M. Palassini and F. Ritort, *Improving free-energy estimates from unidirectional work measurements: Theory and Experiment*, Physical Review Letters, 107 (2011) 060601. The paper also includes additional information as supplementary material. This paper was recently highlighted in the number of August 2011 by Nature Physics.

### • M. Ribezzi, M. Wagner and F. Ritort, *Bayesian approach to the determination of the kinetic parameters of DNA hairpins under tension*, Journal of Nonlinear Mathematical Physics, 18 (2011) 397 .

### • N. Forns, S. De Lorenzo, M. Manosas, K. Hayashi, J. M. Huguet and F. Ritort, *Improving Signal/Noise Resolution in Single-Molecule Experiments Using Molecular Constructs with Short Handles*, Biophysical Journal, 100 (2011) 1765-1774. The paper also includes additional information on experiments and data analysis as supplementary material.

### • S. Engel, A. Alemany, N. Forns, P. Maas and F. Ritort, *Folding and unfolding of a triple-branch DNA molecule with four conformational states*, Philosophical Magazine, 91 (2011) 2041-2065.

### • J. M. Huguet, C. V. Bizarro, N. Forns, S. B. Smith, C. Bustamante and F. Ritort, S*ingle-molecule derivation of salt dependent base-pair free energies in DNA*, Proceedings of the National Academy of Sciences, 107 (2010) 15431-15436. The paper also includes additional information on the minitweezers instrument and data analysis as supplementary material.

### • J. M. Huguet, N. Forns and F. Ritort, *Statistical properties of metastable intermediates in DNA unzipping*, Physical Review Letters, 103 (2009) 248106. The paper also includes additional information as supplementary material.

### • A. Mossa, S. De Lorenzo, J. M. Huguet and F. Ritort, *Measurement of work in single-molecule experiments*, Journal of Chemical Physics, 130 (2009) 234116.

### • R. Sunyer, F. Ritort, R. Farre and D. Navajas, *Thermal activation and ATP dependence of the cytoskeleton remodeling dynamics*, Physical Review E, 79 (2009) 051920.

### • M. Manosas, A. Mossa, N. Forns, J. M. Huguet and F. Ritort, *Dynamic force spectroscopy of DNA hairpins (II): Irreversibility and dissipation*, J. Stat. Mech (Theor. and Exp.) (2009) P02061.

### • A. Mossa, M. Manosas, N. Forns, J. M. Huguet and F. Ritort, *Dynamic force spectroscopy of DNA hairpins (I): force kinetics and free energy landscapes*, J. Stat. Mech (Theor. and Exp.) (2009) P02060.

### • I. Junier, A. Mossa, M. Manosas and F. Ritort, *Recovery of free energy branches in single molecule experiments*, Physical Review Letters, 102 (2009) 070602.

### • M. Manosas, I. Junier and F. Ritort, *Force-induced misfolding in RNA secondary structures*, Physical Review E, 78 (2008) 061925.

### • P. Maragakis, F. Ritort, C. Bustamante, M. Karplus and G. E. Crooks, *Bayesian estimates for free energies from nonequilibrium work data in the presence of instrument noise*, Journal of Chemical Physics, 129 (2008) 024102.

### • I. Junier and F. Ritort, *Unstructured intermediate states in single protein force experiments*, Proteins: structure, function and bioinformatics, 71 (2008) 1145-1155.

### • M. Manosas, J. D. Wen, P. T. X. Li, S. B. Smith,C. Bustamante, I. Tinoco Jr and F. Ritort, *Force unfolding kinetics of RNA using optical tweezers. II. Modeling experiments*, Biophysical Journal, 92 (2007) 3010-3021.

### • J. D. Wen, M. Manosas, P. T. X. Li, S. B. Smith,C. Bustamante, F. Ritort and I. Tinoco Jr, *Force unfolding kinetics of RNA using optical tweezers. I. Effects of experimental variables on measured results*, Biophysical Journal, 92 (2007) 2996-3009.

### • M. Manosas, D. Collin and F. Ritort, *Force dependent fragility in RNA hairpins*, Physical Review Letters, 96 (2006) 218301.

### • F. Ritort, S. Mihardja, S. B. Smith and C. Bustamante, *Condensation transition in DNA-Polyaminoamide dendrimer fibers studied using optical tweezers*, Physical Review Letters, 96 (2006) 118301.

### • D. Collin, F. Ritort, C. Jarzynski, S. B. Smith, I. Tinoco Jr and C. Bustamante, *Verification of the Crooks fluctuation theorem and recovery of RNA folding free energies*, Nature, 437 (2005) 231-234. You can access the letter at the Nature web site. The paper also includes supplementary material. A enlightening commentary on that paper has appeared in Nature, Wesley P. Wong & Evan Evans, *Biological physics: Rare returns on lost effort*, Nature 437, 198 – 199 (2005). You can access the commentary here.

### • M. Manosas and F. Ritort, *Thermodynamic and kinetic aspects of RNA pulling experiments*, Biophysical Journal, 88 (2005)3224-3242.

### • F. Ritort, *Work and heat fluctuations in two-state systems*, Journal of Statistical Mechanics (Theory and Experiment), P10016 (2004).

### • E. Trepagnier, C. Jarzynski, F. Ritort, G. Crooks, C. Bustamante and J. Liphardt, *Experimental test of Hatano and Sasa’s nonequilibrium steady-state equality*, Proceedings of the National Academy of Sciences, 101 (2004) 15038-15041

### • J. Gore, F. Ritort and C. Bustamante, *Bias and error in estimates of equilibrium free-energy differences from non-equilibrium measurements*, Proceedings of the National Academy of Sciences, 100 (2003) 12564-12569

### • F. Ritort, C. Bustamante and I. N. Tinoco Jr, *A two-state kinetic model for the unfolding of single molecules by mechanical force*, Proceedings of the National Academy of Sciences, 99 (2002) 13544-13548.

### • A. Crisanti, M. Picco and F. Ritort, *Fluctuation relation for weakly ergodic systems*, Physical Review Letters, 110 (2013) 080601. The paper also includes additional information as supplementary material.

### • A. Garriga, I. Pagonabarraga and F. Ritort, *Negative fluctuation-dissipation ratios in the backgammon model*, Physical Review E, 79 (2009) 041122

### • A. Garriga, P. Sollich, I. Pagonabarraga and F. Ritort, *Universality of fluctuation-dissipation ratios: The ferromagnetic model*, Physical Review E, 72 (2005) 056114

### • A. Garriga and F. Ritort, *Mode-dependent nonequilibrium temperature in aging systems*, Physical Review E, 72 (2005) 031505

### • F. Ritort, *Resonant nonequilibrium temperatures*, Journal of Physical Chemistry B, 109 (2005) 6787-6792

### • F. Ritort, *Spontaneous and stimulated relaxation in generalized oscillator models for glassy dynamics*, Journal of Physical Chemistry B, 108 (2004) 6893-6900

### • A. Crisanti and F. Ritort, *Intermittency of glassy relaxation and the emergence of a non-equilibrium spontaneous measure in the aging regime*, Europhysics Letters, 66 (2004) 253-259.

**Review articles**

### • J. Gieseler, J. R. Gomez-Solano, A. Magazzù, I. Pérez Castillo, L. Pérez García, M. Gironella-Torrent, X. Viader-Godoy, F. Ritort, G. Pesce, A. V. Arzola, K. Volke-Sepúlveda, and G. Volpe *Optical tweezers — from calibration to applications: a tutorial*, Advances in Optics and Photonics, Vol.13, No.1 (2021). In this tutorial, we provide a primer on how to calibrate optical tweezers and how to use them for advanced applications. After a brief general introduction on optical tweezers, we focus on describing and comparing the various available calibration techniques. Then, we discuss some cutting-edge applications of optical tweezers in a liquid medium, namely, to study single-molecule and single-cell mechanics, microrheology, colloidal interactions, statistical physics, and transport phenomena. Finally, we consider optical tweezers in vacuum, where the absence of a viscous medium offers vastly different dynamics and presents new challenges. We conclude with some perspectives for the field and the future applications of optical tweezers. This tutorial provides both a step-by-step guide ideal for non-specialists entering the field and a comprehensive manual of advanced techniques useful for expert practitioners.

### • F. Ritort, *The noisy and marvelous molecular world of biology*, Inventions 4, 24 (2019). At the molecular level biology is intrinsically noisy. The forces regulating the myriad of molecular reactions in a cell are tiny, on the order of piconewtons, yet they proceed in concerted action making life possible. This mini-review describes the role played by energy and physical information in biology from a personal biophysical perspective. The article is written in memoriam of Jorge Wagensberg, physics professor at the University of Barcelona, who passed away on the 3rd March 2018 at the age of 69. Wagensberg was an inspiring scientist and philosopher who saw in science and art the beauty of nature and knowledge. His love for all expressions of intellectual mankind will remain as a source of inspiration and legacy to future generations of scientists.

### • F. Ritort, *Pinzas ópticas y su aplicación a sistemas biológicos*, Revista Española de Física Vol 32, No 4 (2018). The 2018 Nobel Prize for Physics was awarded “for groundbreaking inventions in the field of laser physics” to Arthur Ashkin (1/2 of the prize), Donna Strickland and Gérard Mourou (who together shared the other 1/2). This review (written in spanish) focuses on the work of Arthur Ashkin – the oldest living Nobel laureate! – who got the prize for the invention of Optical Tweezers.The tweezers turned out to a fabulous tool for manipulating small objects and performing quantitative measurements on them. They have been used in particular in the field of biophysics to measure mechanical properties of DNA, RNA and proteins and from these measurements we have learnt a lot how these molecules of life work, but there is a lot yet to be explored!

### • J. Camunas-Soler, M. Ribezzi-Crivellari and F. Ritort, *Elastic properties of nucleic acids by single-molecule force spectroscopy*, Annual Review of Biophysics, vol. 45, 65-84 (2016). We review the current knowledge on the use of single-molecule force spectroscopy techniques to extrapolate the elastic properties of nucleic acids. We emphasize the lesser-known elastic properties of single-stranded DNA. We discuss the importance of accurately determining the elastic response in pulling experiments, and we review the simplest models used to rationalize the experimental data as well as the experimental approaches used to pull single-stranded DNA. Applications used to investigate DNA conformational transitions and secondary structure formation are also highlighted. Finally, we provide an overview of the effects of salt and temperature and briefly discuss the effects of contour length and sequence dependence.

### • F. Ritort, *The physics of small systems: From energy to information*, The focus of this review is the recent developments in the non-equilibrium physics of small systems. Special emphasis is placed on single-molecule experiments and their contribution to expanding our current understanding of fundamental concepts, such as temperature, energy, entropy, and information

### • A. Alemany, M. Ribezzi and F. Ritort, *Recent progress in fluctuation theorems and free energy recovery*, R.Klages, W.Just, C.Jarzynski (Eds.), Nonequilibrium Statistical Physics of Small Systems: Fluctuation Relations and Beyond (Wiley-VCH, Weinheim, 2012; ISBN 978-3-527-41094-1) Here we review applications of fluctuation theorems to recover free energy differences from single molecule pulling experiments. After briefly reminding key concepts about free energy measurements and calculations we discuss issues concerning the correct definition of mechanical work, the non-Galilean invariance of fluctuation theorems and free energy recovery from unidirectional work measurement.

### • A. Alemany and F. Ritort, *Fluctuation theorems in small systems: extending thermodynamics to the nanoscale*, Europhysics News, vol. 41, 27-30 (2010). Single molecule experiments make it possible to resolve energy processes with unprecedented detail at the level of 1 kBT, the typical energy scale of Brownian fluctuations. This is a very concise review about fluctuation theorems and the application to obtain equilibrium information from non-equilibrium experiments.

### • F. Ritort, *Fluctuations in open systems*, Physics, vol. 2, 43 (2009). Small nonequilibrium systems behave quite unexpectedly when in contact with a thermal reservoir. However, all of them, from molecular machines to molecular magnets, are described by a single fluctuation theorem.

### • A. Mossa, J. M Huguet and F. Ritort, *Investigating the thermodynamics of small biosystems with optical tweezers*, Physica E (Low-dimensional Systems and Nanostructures), doi:10.1016/j.physe.2009.06.055. We present two examples of how single-molecule experimental techniques applied to biological systems can give insight into problems within the scope of equilibrium and nonequilibrium mesoscopic thermodynamics. The first example is the mapping of the free energy landscape of a macromolecule, the second the experimental verification of Crooks fluctuation theorem. In both cases the experimental setup comprises optical tweezers and DNA molecules.

### • F. Ritort, *Nonequilibrium fluctuations in small systems: from physics to biology*, Advances in Chemical Physics, vol. 137, 31-123 (2008). Ed. Stuart. A. Rice, Wiley publications. A general review paper on nonequilibrium fluctuations in small systems, fluctuation theorems and applications to examples extracted from physics and biology. It presents a general discussion on path thermodynamics, work/heat fluctuations and large deviation functions. Finally it briefly addresses the topic of glassy dynamics.

### • F. Ritort, *The nonequilibrium thermodynamics of small systems*, Comptes Rendus Physique,8 (2007) 528-539.Nonequilibrium thermodynamics of small systems describes energy exchange processes between a system and its environment in the low energy range of a few kBT where Brownian fluctuations are dominant. In this article I discuss some aspects about fluctuation theorems and path thermodynamics that call for the necessity of a better understanding of large deviations in nonequilibrium statistical physics. I also emphasize how single molecule experiments are a valuable source of knowledge and information that can greatly contribute to the unveiling of the most important and relevant questions in this exciting field of research.

### • F. Ritort, *Single molecule experiments in biological physics: methods and applications*, Journal of Physics C (Condensed Matter),18 (2006) R531-R583. A general review paper on single molecule experiments and their applications in modern biophysics. It covers experimental techniques such as atomic force microscopy and optical tweezers and applications to many topics including nucleic acids, proteins, molecular motors and experimental tests of foundations in statistical mechanics. It has been selected as the top 10 review papers in 2006 by IOP. The IOP commentary.

### • C. Bustamante, J. Liphardt and F. Ritort, *The nonequilibrium thermodynamics of small systems*, Physics Today,58 (2005) 43-48. This is a very introductory review on how single molecule experiments allow us to deepen in the world of tiny objects such as biomolecular machines.

### • J. L. Acebron, L. L. Bonilla, C. Perez-Vicente, F. Ritort and R. Spigler, *The Kuramoto model: A simple paradigm for synchronization phenomena*, Review of Modern Physics,77 (2005) 137-185.

### • F. Ritort, *Work fluctuations and transient violations of the second law: perspectives in theory and experiments*, Seminaire Poincare 2 (2004) 193-226. This is a report article on a contribution to the Poincare seminar held the 6th December 2003 in Paris.

### • A. Crisanti and F. Ritort, *Violation of the fluctuation-dissipation theorem in glassy systems: basic notions and the numerical evidence*, Journal of Physics A (Math. Gen.), 36 (2003) R181-R290.

### • F. Ritort and P. Sollich, *Glassy dynamics of kinetically constraint models*, Advances in Physics, 52 (2003) 219-342.

**Other publications**

## Aging systems

### • F. Ritort, *Universal dependence of the fluctuation-dissipation ratio on the transition rates in trap models*, Journal of Physics A (Math. Gen.), 36 (2003) 10791.

### • A. Garriga, J. Kurchan and F. Ritort, *Strong Soret effect in one dimension, Journal of Statistical Physics*, 106 Nos.1/2, (2002).

### • A. Garriga and F. Ritort, *Heat transfer and Fourier’s law in off-equilibrium systems*, European Journal of Physics B, 21 (2001) 115-120.

### • A. Garriga and F. Ritort, *Validity of the zero-th law in off-equilibrium coupled harmonic oscillators*, European Journal of Physics B, 20 (2001) 105-122.

### • L. L. Bonilla, F. G. Padilla and F. Ritort, *Aging in the linear harmonic oscillator*, Physica A (Amsterdam), 250 (1998) 315-326.

### • F. G. Padilla and F. Ritort, *Langevin dynamics of the Lebowitz-Percus model*, Journal of Physics A (Math. Gen.), 30 (1997) 7089.

### • S. Franz and F. Ritort, *Relaxational processes and entropic traps in the Backgammon model*, Journal of Physics A (Math. Gen.), 30 (1997) L357-L362.

### • L. L. Bonilla, F. G. Padilla, G. Parisi and F. Ritort, *Closure of the Monte Carlo dynamical equations in the spherical Sherrington-Kirkpatrick model*, Physical Review B, 54 (1996) 4170-4182.

### • S. Franz and F. Ritort, *Glassy Mean-Field dynamics of the Backgammon model*, Journal of Statistical Physics, 85 (1996) 131-150.

### • L. L. Bonilla, F. Padilla, G. Parisi and F. Ritort, *Analytical Solution of the Monte Carlo dynamics of a simple spin-glass model*, Europhysics Letters, 34 (1996)

### • S. Franz and F. Ritort, Dynamical solution of a model without energy barriers, Europhysics Letters, 31 (1995) 507-512

### • L. F. Cugliandolo, J. Kurchan and F. Ritort, *Evidence of aging in spin glass mean-field models*, Physical Review B, 49 (1994) 6331-6334.

**Glass transition**

### • F. Rao, A. Crisanti and F. Ritort, *Frequency domain study of relaxation in a spin-glass model for the structural glass transition*, Europhysics Letters, 62 (2003) 869.

### • L. Leuzzi and F. Ritort, *The disordered Backgammon model*, Physical Review E, 65 (2002) 056125.

### • A. Crisanti, B. Coluzzi, E. Marinari, F. Ritort and A. Rocco, *A new method to compute the configurational entropy in spin glasses*, European Journal of Physics B, 32 (2003) 495-502.

### • A. Crisanti and F. Ritort, *A real-space description of the glass transition based on heterogeneities and entropy barriers,* Philosophical Magazine B 82, (2002) 143 – 149.

### • A. Crisanti, A. Rocco , F. Ritort and M. Sellito, *Inherent-structures and non-equilibrium dynamics of 1D constrained kinetic models: A comparison study*, Journal of Chemical Physics, 113 (2000) 10615.

### • A. Crisanti and F. Ritort, *Activated processes and Inherent Structure dynamics of finite-size mean-field models for glasses*, Europhysics Letters, 52 (2000) 640-646.

### • A. Crisanti and F. Ritort, Potential energy landscape of simple p-spin models for glasses, Europhysics Letters, 51 (2000) 147-153.

### • M. Heerema and F. Ritort, *Damage spreading transition in glasses: a probe for the ruggedness of the configurational landscape*, Physical Review E, 69 (1999) 3646.

### • M. Heerema and F. Ritort, *Damage spreading in the mode-coupling theory for glasses*, Journal of Physics A (Math. Gen.), 31 (1998) 8423-8429.

### • D. Alvarez, S. Franz and F. Ritort, *Fragile-glass behavior of a short-range p-spin model*, Physical Review B, 54 (1996) 9756-9764.

### • E. Follana and F. Ritort, *Evidence of a Critical time in Constrained Kinetic Ising models*, Physical Review B, 54 (1996) 930-937.

### • F. Ritort, *Glassiness in a model without energy barriers*, Physical Review Letters, 75 (1995) 1190-1193.

### • E. Marinari, G. Parisi and F. Ritort, *Replica theory and Large D Josephson Junction Hypercubic Models*, Journal of Physics A (Math. Gen.), 28 (1995) 4481-4503.

### • E. Marinari, G. Parisi and F. Ritort, *The Fully Frustrated Hypercubic Model is Glassy and Aging at Large D,* Journal of Physics A (Math. Gen.), 28 (1995) 327-334.

### • L. F. Cugliandolo, J. Kurchan, G. Parisi and F. Ritort, *Matrix Models as Solvable Glass Models*, Physical Review Letters, 74 (1995) 1012-1015.

### • G. Migliorini and F. Ritort, *Dynamical Behaviour of Low Autocorrelation Models*, Journal of Physics A (Math. Gen.), 27 (1994) 7669-7686.

### • E. Marinari, G. Parisi and F. Ritort, *Replica Field Theory for Deterministic Models (II): A non Random Spin Glass with Glassy Behaviour*, Journal of Physics A (Math. Gen.), 27 (1994) 7647-7668. Download it here

### • E. Marinari, G. Parisi and F. Ritort, *Replica Field Theory for Deterministic Models (I): Binary Sequences with Low Autocorrelation*, Journal of Physics A (Math. Gen.), 27 (1994) 7615-7646.

**Spin glasses**

### • M. Picco and F. Ritort, *Dynamical AC study of Heisenberg spin glasses*, Physical Review B, 71 (2005) 100406(R).

### • M. Palassini, M. Sales and F. Ritort, *Order-parameter fluctuations in Ising spin glasses at low temperatures*, Physical Review B, 68 (2003) 224430.

### • M. Picco, F. Ritort and M. Sales, *Statistics of lowest droplets in two-dimensional Gaussian spin glasses*, Physical Review B, 67 (2003) 184221.

### • M. Sales, J. P. Bouchaud and F. Ritort, *Temperature shifts in the Sinai model: static and dynamical effect*s, Journal of Physics A (Math. Gen.), 36 (2003) 665-684.

### • D. S. Dean and F. Ritort, *Squared interaction matrix Sherrington-Kirkpatrick model for a spin glass*, Physical Review B, 65 (2002) 224209.

### • M. Picco, F. Ricci Tersenghi and F. Ritort, *Aging experiments and dynamic scaling in the 3d Edwards-Anderson model: a comparison with experiments*, European Journal of Physics B, 21 (2001) 211-217.

### • F. Ritort and M. Sales, *Scaling approach to order parameter fluctuations in disordered frustrated systems*, Journal of Physics A (Math. Gen.), 34 (2001) L333-L339.

### • M. Picco, F. Ritort and M. Sales, *Order parameter fluctuations (OPF) in spin glasses: Monte Carlo simulations and exact results for small sizes*, European Journal of Physics B, 19 (2001) 565-582.

### • M. Picco, F. Ricci-Tersenghi and F. Ritort, *Chaotic, memory and cooling rate effects in spin glasses: Is the Edwards-Anderson model a good spin glass?*, Physical Review B, 63 (2001) 174412.

### • F. Ritort and M. Sales, *A conjectured scenario for order parameter fluctuations in spin glasses*, Journal of Physics A (Math. Gen.), 33 (2000) 6505-6526.

### • F. Ricci-Tersenghi and F. Ritort, *Absence of aging in the remanent magnetization in Migdal-Kadanoff spin glasses*, Journal of Physics A (Math. Gen.), 33 (2000) 3727-3734.

### • M. Campellone and F. Ritort, *Complexity and line of critical points in a short-range spin-glass model*, Physica A, 286 (2000) 1-9.

### • G. Parisi, M. Picco and F. Ritort, *Continuous phase transition in a model without time reversal symmetry*, Physical Review E, 60 (1999) 58-68.

### • E. Marinari, C. Naitza, F. Zuliani, G. Parisi, M. Picco and F. Ritort, *A general method to determine replica symmetry breaking transitions*, Physical Review Letters, 81 (1998) 1698-1702.

### • M. Picco and F. Ritort, *Tempering simulations in the 4D binary Ising spin glass*, Physica A (Amsterdam), 250 (1998) 46-57.

### • E. Marinari, G. Parisi, F. Ritort and J. J. Ruiz-Lorenzo, *Numerical Evidence for Spontaneously broken replica symmetry in 3D Spin Glasses*, Physical Review Letters, 76 (1996) 843-846.

### • V. Azcoiti, E. Follana and F. Ritort, *Static chaos in spin glasses: the case of quenched disorder perturbations*, Journal of Physics A (Math. Gen.), 28 (1995) 3863-3875.

### • E. De Santis, G. Parisi and F. Ritort, *On the Static and Dynamical Transition in the mean-field Potts Glass*, Journal of Physics A (Math. Gen.), 28 (1995) 3025-3041.

### • F. Ritort, *Replica Symmetry Breaking Effects in spin glasses*, Phililosophical Magazine B, 71 (1995) 515

### • M. Picco and F. Ritort, *Numerical study of the Ising spin glass in a magnetic field*, Journal de Physique I (France), 4 (1994) 1619-1625.

### • E. Marinari, G. Parisi and F. Ritort, *On the 3d Ising spin glass*, Journal of Physics A (Math. Gen.), 27 (1994) 2687-2708.

### • F. Ritort, *Static Chaos and Scaling Behaviour in the spin-glass phase*, Physical Review B, 50 (1994) 6844-6853.

### • J. C. Ciria, G. Parisi, F. Ritort and J. J. Ruiz-Lorenzo, *The de Almeida-Thouless line in the four dimensional Ising spin glass*, Journal de Physique I (France), 3 (1993) 2207-2227.

### • J. C. Ciria, G. Parisi and F. Ritort, *Four dimensional Ising spin glass: scaling within the spin-glass phase*, Journal of Physics A (Math. Gen.), 26 (1993) 6731-6745.

### • G. Parisi and F. Ritort, *Replica symmetry breaking in four dimensional spin glasses*, Journal of Physics A (Math. Gen.), 26 (1993) 6711-6730.

### • G. Parisi and F. Ritort, *The remanent magnetization in spin-glass models*, Journal de Physique I (France), 3 (1993) 969-985.

### • D. Badoni, J. C. Ciria, G. Parisi, J. Pech, F. Ritort and J. J. Ruiz-Lorenzo, *Numerical evidence of a critical line in the 4d Ising spin glass*, Europhysics Letters, 21 (1993) 495-499.

### • G. Parisi, F. Ritort and F. Slanina, *Several results on the finite-size corrections in the Sherrington-Kirkpatrick spin-glass model*, Journal of Physics A (Math. Gen.), 26 (1993) 3775-3789.

### • G. Parisi, F. Ritort and F. Slanina, *Critical finite size corrections in the Sherrington-Kirkpatrick model*, Journal of Physics A (Math. Gen.), 26 (1993) 247-259.

### • R. Brunetti, G. Parisi and F. Ritort, *Asymmetric Little Spin-Glass Model*, Physical Review B, 46 (1992) 5339-5350.

### • R. Brunetti, G. Parisi and F. Ritort, *A study of the Asymmetric Little model*, Physica A (Amsterdam), 185} (1992) 247-253

### • R. Brunetti, G. Parisi and F. Ritort, *On the Replica Symmetry for Random Weighted Matchings*, Journal of Physics A (Math. Gen.), 24 (1991) 5077-5083.

### • G. Parisi, F. Ritort and J. M. RubÃ, *Numerical Results on a Hypercubic Cell Spin-Glass Model*, Journal of Physics A (Math. Gen.), 24 (1991) 5307-5320.

**Synchronization models**

### • L. L. Bonilla, C. Perez-Vicente, F. Ritort and J. Soler, *Exactly solvable phase oscillator models with synchornization dynamics*, Physical Review Letters, 81 (1998) 3643-3646.

### • F. Ritort, *Solvable dynamics in a system of interacting random tops*, Physical Review Letters, 80 (1998) 6-9.

### • C. J. Perez-Vicente and F. Ritort, *A new approach to the dynamical solution of the Kuramoto model*, Journal of Physics A (Math. Gen.), 30 (1997) 8095-8100.

**Quantum phase transitions**

### • Th. M. *Nieuwenhuizen and F. Ritort, Quantum phase transition in p-interaction spin glasses in a transverse field*, Physica A (Amsterdam), 250 (1998) 8-45.

### • F. Ritort, *Quantum critical effects in mean-field glassy systems*, Physical Review B, 55 (1997) 14096-14099.

### • D. Lancaster and F. Ritort, *Solving the Schroedinger equation for the Sherrington-Kirkpatrick model in a transverse field*, Journal of Physics A (Math. Gen.), 30 (1997) L41-L47.

### • J. V. Alvarez and F. Ritort, *Quantum Monte Carlo study of the infinite-range Ising spin glass in a transverse field*, Journal of Physics A (Math. Gen.), 29 (1996) 7355-7366.

**Other subjects**

### • O. Iglesias, A. Labarta, F. Ritort, Monte Carlo *Study of the Finite Size Effects on the Magnetization of Maghemite Small Particles*, Journal of Applied Physics, 89 (2001) 7597.

### • A. Giannelli, C. Giovanella and F. Ritort, *Devil staircase dynamics in arrays of overdamped Josephson junctions*, Europhysics Letters, 29 (1995) 419-424.

**Proceeding articles**

### • I. Junier and F. Ritort, *Single-domain protein folding: a multi-faceted problem*, Invited oral contribution to II Congreso Nacional del BIFI (Zaragoza, Spain) February 2005. Published in AIP Conference Proceedings, vol 851, (2006) 70-95.

### • F. Ritort, S*ingle molecule experiments in biophysics: Exploring the thermal behavior of nonequilibrium small systems*, Invited oral contribution to Statphys 22 Conference (Bangalore, India) July 2005. Published in Pramana Journal of Physics, vol 64, No. 6 (2005) 1135-1147.

### • F. Ritort, *Stimulated and spontaneous relaxation in glassy systems*, Presentation at the Congress “Unifying concepts in granular media and glassy systems” 26-29 June 2003. Eds. A. Coniglio et al. (Springer-Verlag) 2004. Available as Preprint cond-mat/0311370.

### • F. Rao, A. Crisanti and F. Ritort, *Frequency domain study of the $\alpha$-relaxation in the random orthogonal model*, “9th International Workshop on Disordered Systems”, Andalo (Trento), Italy, 12-15 March 2001.

### • A. Crisanti and F. Ritort, *Inherent Structures, Configurational Entropy and Slow Glassy Dynamics*, Proceedings of the SPHINX meeting `Glassy behaviour of kinetically constrained models’ (Barcelona, Marzo 22-25, 2001). J. Phys. C (Cond. Matt.) 14 1381-1395 (2002)

### • A. Crisanti, F. Ritort, A. Rocco and M. Sellitto, *Is the Stillinger and Weber decomposition relevant for coarsening models?*, Proceedings of the SPHINX meeting Glassy behaviour of kinetically constrained models’ (Barcelona, March 22-25, 2001). J. Phys. C (Cond. Matt.) 14 1523-1537 (2002)

### • A. Crisanti and F. Ritort, *A glass transition scenario based on heterogeneities and entropy barriers*, “8th International Workshop on Disordered Systems”, Andalo (Trento), Italy, 12-15 March 2001.

### • O. Iglesias, A. Labarta and F. Ritort, Finite *Size Effects in Small Particle Systems*, Presented at the NATO-ASI Workshop in Rodos (Greece): Magnetic Storage Systems Beyond 2000.

### • A. Crisanti and F. Ritort, *Configurational entropy and the one-step RSB scenario in glasses*, Proceedings of the Conference “Disordered and Complex Systems”, International Conference on Mathematical Physics, 10-14 July 2000, Kings College (London)

### • A. Crisanti and F. Ritort, *Are Mean-Field Spin-Glass Models Relevant for the Structural Glass Transition?*, Proceedings of the “International Conference on Statistical Mechanics and Strongly Correlated System”, 2nd Giovanni Paladin Memorial, Roma 27-29 Septiembre 1999, Physica A, 280 1-2 (2000) pp. 155-160

### • A. Crisanti and F. Ritort, *Equilibrium and Aging Dynamics of Simple Models for Glasses*, Proceedings of the Workshop “Unifying Concepts in Glass Physics”, ICTP Trieste (Italy) (15-18 Septiembre 1999) Preprint cond-mat/9912207 and J. Phys. C (Condensed Matter) 12 (2000) 6413-6422

### • F. Ritort, *Dynamical phase transitions in glasses induced by the ruggedness of the free energy landscape*, Proceedings of the Workshop “Unifying Concepts in Glass Physics”, ICTP Trieste (Italia) (15-18 Septiembre 1999) Preprint cond-mat/9911144 and J. Phys. C (Condensed Matter) 12 (2000) 6453-6461

### • F. Ritort, *Classical and Quantum Behavior in mean-field glassy systems*, Proceedings for the XIV Sitges Conference “Complex Behavior in Glassy systems”, Sitges 1996 (Barcelona) Spain. Springer-Verlag Ed. by M. Rubi

### • E. Marinari, G. Parisi, F. Ritort and J. J. Ruiz-Lorenzo, *3D Spin glasses: Numerical Evidence for a Mean-Field Behavior at low temperature*, Common trends in Condensed Matter and High Energy Physics. Proceedings of the fourth Chia meeting. World Scientific, Singapore 1996. Ed. by A. Devoto

### • S. Franz and F. Ritort, *Dynamical solution of a model without energy barriers*, Journal de Physique I (France) 6 (1996) 21-65 Proceedings for the conference “Recent advances in the theory of disordered systems: Spin glasses, Random fields and Random Polymers” Saclay, Orme des Merisers, (France) 3-7 July 1995.

### • C. Giovannella, F. Ritort, A. Giannelli, *Effect of disorder and frustration on the dynamics of arrays of overdamped Josephson junctions*, Weak Superconductivity, Edited by S. Benacka, P. Seidel and V. Strbik, IEESAS, 1994, p. 174

**Feature articles and other contributions**

### • F. Ritort, *Open questions about DNA melting: Comment on “DNA melting and energetics of the double helix” by Maxim Frank-Kamenetskii et al.*, Physics of Life Reviews Volume 25, August 2018, Pages 34-36.

### • F. Ritort, Book Review: *Defects and Geometry in Condensed Matter Physics (by D. R. Nelson, Cambridge University Press 2002)*, Journal of Statistical Physics, 112 (2002) 883-884.

### • F. Ritort, Book Review: *Introduction to the Replica Theory of Disordered Statistical Systems (by Viktor Dotsenko, Cambridge University Press 2000)*, Journal of Statistical Physics, 105 (2001) 403-404.

### • P. Sollich and F. Ritort, *Proceedings of the Barcelona workshop on “Glassy dynamics in kinetically constrained models”*, Journal of Physics C (Cond. Matt.), 14 (2002) 1381-1696.