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Relevant bibliographies by topics / Single-molecule Thermodynamics

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Academic literature on the topic 'Single-molecule Thermodynamics'

Author: Grafiati

Published: 4 June 2021

Last updated: 6 September 2023

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Journal articles on the topic "Single-molecule Thermodynamics"

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Rubi, J. M., D. Bedeaux, and S. Kjelstrup. "Thermodynamics for Single-Molecule Stretching Experiments." Journal of Physical Chemistry B 110, no. 25 (2006): 12733–37. http://dx.doi.org/10.1021/jp061840o.

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Keller, David, David Swigon, and Carlos Bustamante. "Relating Single-Molecule Measurements to Thermodynamics." Biophysical Journal 84, no. 2 (2003): 733–38. http://dx.doi.org/10.1016/s0006-3495(03)74892-9.

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Taniguchi, Yuichi, Peter Karagiannis, Masayoshi Nishiyama, Yoshiharu Ishii, and Toshio Yanagida. "Single molecule thermodynamics in biological motors." Biosystems 88, no. 3 (2007): 283–92. http://dx.doi.org/10.1016/j.biosystems.2006.08.016.

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Toyabe, Shoichi, and Eiro Muneyuki. "Single molecule thermodynamics of ATP synthesis by F1-ATPase." New Journal of Physics 17, no. 1 (2015): 015008. http://dx.doi.org/10.1088/1367-2630/17/1/015008.

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Williams, Mark C., Ioulia Rouzina, and Victor A. Bloomfield. "Thermodynamics of DNA Interactions from Single Molecule Stretching Experiments." Accounts of Chemical Research 35, no. 3 (2002): 159–66. http://dx.doi.org/10.1021/ar010045k.

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Fang, Xiaona, and Jin Wang. "Nonequilibrium Thermodynamics in Cell Biology: Extending Equilibrium Formalism to Cover Living Systems." Annual Review of Biophysics 49, no. 1 (2020): 227–46. http://dx.doi.org/10.1146/annurev-biophys-121219-081656.

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We discuss new developments in the nonequilibrium dynamics and thermodynamics of living systems, giving a few examples to demonstrate the importance of nonequilibrium thermodynamics for understanding biological dynamics and functions. We study single-molecule enzyme dynamics, in which the nonequilibrium thermodynamic and dynamic driving forces of chemical potential and flux are crucial for the emergence of non-Michaelis-Menten kinetics. We explore single-gene expression dynamics, in which nonequilibrium dissipation can suppress fluctuations. We investigate the cell cycle and identify the nutri

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Yi, Fang. "Single Molecule Thermodynamics Hypothesis of Protein Folding and Drug Design." Journal of Biosciences and Medicines 07, no. 11 (2019): 164–72. http://dx.doi.org/10.4236/jbm.2019.711015.

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van Mameren, Joost, Anna Wozniak, and Sid Ragona. "Single-Molecule DNA Stretching Using Optical Tweezers." Microscopy Today 17, no. 1 (2009): 42–43. http://dx.doi.org/10.1017/s1551929500055012.

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The advent of techniques to mechanically manipulate single (bio)molecules has sparked large efforts to precisely study the mechanical and elastic properties of proteins, protein fibers, DNA, RNA, etc. Two widely used techniques in this area are atomic force microscopy (AFM) and optical tweezers. Optical tweezers complement AFM at the lower end of the force regime: forces of typically a few hundred picoNewtons down to fractions of a picoNewton can be assessed using optical tweezers. This has allowed for, among other things, the precise measurement of forces and displacements exerted by individu

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Zhang, X., H. Chen, H. Fu, P. S. Doyle, and J. Yan. "Two distinct overstretched DNA structures revealed by single-molecule thermodynamics measurements." Proceedings of the National Academy of Sciences 109, no. 21 (2012): 8103–8. http://dx.doi.org/10.1073/pnas.1109824109.

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Williams, Mark C., Ioulia Rouzina, and Victor A. Bloomfield. "ChemInform Abstract: Thermodynamics of DNA Interactions from Single Molecule Stretching Experiments." ChemInform 33, no. 24 (2010): no. http://dx.doi.org/10.1002/chin.200224293.

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Dissertations / Theses on the topic "Single-molecule Thermodynamics"

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Lorenzo, Ros Sara de. "Single molecule studies in a temperature-jump optical trap." Doctoral thesis, Universitat de Barcelona, 2015. http://hdl.handle.net/10803/286174.

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In the field of biophysics, the study of the thermodynamic characteristics of biomolecules, such as DNA, RNA or proteins, allows us to understand more about the building blocks of life. The thermodynamic characterization of the biomolecule gives us clues as to their functions and capabilities inside every living organism. The thermodynamic characterization of nucleic acids describes how temperature affects the stability and the structure of double stranded DNA. The melting temperature of DNA (T(M)) is defined as the temperature at which half of the DNA strands in a bulk solution experiment

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Chatterjee, Debarati. "Theoretical Studies Of The Thermodynamics And Kinetics Of Selected Single-Molecule Systems." Thesis, 2011. https://etd.iisc.ac.in/handle/2005/1937.

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This thesis is a report of the work I have done over the last five years to study thermodynamic and kinetic aspects of single-molecule behavior in the condensed phase. It is concerned specifically with the development of analytically tractable models of various phenomena that have been observed in experiments on such single-molecule systems as colloids, double-stranded DNA, multi-unit proteins, and enzymes. In fluid environments, the energetics, spatial conformations, and chemical reactivity of these systems undergo fluctuations that can be characterized experimentally in terms of time cor

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Chatterjee, Debarati. "Theoretical Studies Of The Thermodynamics And Kinetics Of Selected Single-Molecule Systems." Thesis, 2011. http://hdl.handle.net/2005/1937.

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This thesis is a report of the work I have done over the last five years to study thermodynamic and kinetic aspects of single-molecule behavior in the condensed phase. It is concerned specifically with the development of analytically tractable models of various phenomena that have been observed in experiments on such single-molecule systems as colloids, double-stranded DNA, multi-unit proteins, and enzymes. In fluid environments, the energetics, spatial conformations, and chemical reactivity of these systems undergo fluctuations that can be characterized experimentally in terms of time cor

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Nostheide, Sandra. "Kinetics and thermodynamics of unfolding processes in DNA molecules with several conformational states: theory and experiments." Doctoral thesis, 2014. https://repositorium.ub.uni-osnabrueck.de/handle/urn:nbn:de:gbv:700-2014101512898.

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The modelling of single-molecule experiments is of vital interest to gain new insights into processes which were hitherto not accessible by measurements performed on bulk systems. In the first part of this thesis, the kinetics of a triple-branch DNA molecule with four conformational states is investigated by employing pulling experiments with optical tweezers and theoretical modelling. Probability distributions of first rupture forces, which are calculated by applying transition rate theory to a free energy model, show good agreement with experimental findings. Permanently frayed molecules cou

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Books on the topic "Single-molecule Thermodynamics"

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Strasberg, Philipp. Quantum Stochastic Thermodynamics. Oxford University PressOxford, 2022. http://dx.doi.org/10.1093/oso/9780192895585.001.0001.

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Abstract Processes at the nanoscale happen far away from the thermodynamic limit, far from equilibrium and are dominated by fluctuations and, perhaps, even quantum effects. This book establishes a consistent thermodynamic framework for such processes by combining tools from non-equilibrium statistical mechanics and the theory of open quantum systems. The book is accessible for graduate students and of interest to all researchers striving for a deeper understanding of the laws of thermodynamics beyond their traditional realm of applicability. It puts most emphasis on the microscopic derivation

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Sekimoto, Ken. Stochastic Energetics. Springer, 2012.

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Stochastic Energetics. Springer, 2010.

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Sekimoto, Ken. Stochastic Energetics. Springer, 2010.

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Sekimoto, Ken. Stochastic Energetics. Springer, 2010.

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Book chapters on the topic "Single-molecule Thermodynamics"

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Fiorin, Vittorio, David Borthwick, and David A. King. "Surface Thermodynamics: Small Molecule Adsorption Calorimetry on Metal Single Crystals." In Model Systems in Catalysis. Springer New York, 2009. http://dx.doi.org/10.1007/978-0-387-98049-2_9.

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"Nonequilibrium Thermodynamics Of Single Molecules: The Jarzynski And Crooks Identities." In Single Molecule Science. CRC Press, 2015. http://dx.doi.org/10.1201/b18541-11.

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Hummer, Gerhard, and Attila Szabo. "Thermodynamics and Kinetics from Single-Molecule Force Spectroscopy." In Theory and Evaluation of Single-Molecule Signals. WORLD SCIENTIFIC, 2008. http://dx.doi.org/10.1142/9789812793492_0005.

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Strasberg, Philipp. "Classical Stochastic Thermodynamics." In Quantum Stochastic Thermodynamics. Oxford University PressOxford, 2022. http://dx.doi.org/10.1093/oso/9780192895585.003.0002.

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Abstract After an introduction to the phenomenological theory of non-equilibrium thermodynamics, this theory is derived and extended forsmall systems described by a classical Markov process obeying local detailed balance. Thermodynamic definitions for internal energy, heat, work, entropy and entropy production are provided along a single stochastic trajectory. It is shown that the fluctuations in work and entropy production satisfy universal constraints, known as fluctuation theorems. By providing an independent derivation of them starting from microscopically reversible Hamiltonian dynamics in the full system-bath phase space, it is demonstrated that fluctuation theorems also hold in the non-Markovian regime. The theoretical framework established here is called (classical) stochastic thermodynamics. It has found widespread applications in biology and biochemistry, soft condensed matter physics as well as various artificial nanostructures down to the quantum regime. The chapter finishes with a discussion of the particularly relevant setting of single-molecule pulling experiments.

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"Single Molecule Nanocatalysis Reveals Catalytic Kinetics and Thermodynamics of Individual Nanocatalysts." In Single Particle Nanocatalysis. Wiley-VCH Verlag GmbH & Co. KGaA, 2019. http://dx.doi.org/10.1002/9783527809721.ch2.

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Kinz-Thompson, Colin D., Ajeet K. Sharma, Joachim Frank, Ruben L. Gonzalez, and Debashish Chowdhury. "Quantitative Connection between Ensemble Thermodynamics and Single-Molecule Kinetics: A Case Study Using Cryogenic Electron Microscopy and Single-Molecule Fluorescence Resonance Energy Transfer Investigations of the Ribosome." In Series in Structural Biology. World Scientific, 2018. http://dx.doi.org/10.1142/9789813234864_0049.

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McHugh, Mark A. "Solubility of Polymers in Supercritical Carbon Dioxide." In Green Chemistry Using Liquid and Supercritical Carbon Dioxide. Oxford University Press, 2004. http://dx.doi.org/10.1093/oso/9780195154832.003.0012.

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A great deal of information is known about the solvent character of CO2 with a wide range of polymers and copolymers based on well-characterized and systematic solubility studies that are available in the literature (Kirby and McHugh, 1999). Nevertheless, the prediction of polymer solubility in CO2, or any solvent for that matter, presents a formidable challenge since contemporary equations of state are still not facile enough to describe the unique characteristics of a long-chain polymer in solution. The difficulty resides in accounting for the intra- and intersegmental interactions of the many segments of the polymer connected to a single backbone relative to the small number of segments in a solvent molecule. An additional challenge exists to describe the density dependence of the intermolecular potential functions used in the calculations since SCF–polymer solutions (SCF, supercritical fluid) can be highly compressible mixtures. In this brief review, the solvent character of CO2 is described using the principles of molecular thermodynamics and also using a select number of phase behavior studies to reveal the impact of polymer architecture on solubility. To form a stable polymer–SCF solvent solution at a given temperature and pressure, the Gibbs energy, shown in eq. 7.1, must be negative and at a minimum. . . . ΔGmix = ΔHmix − T ΔSmix (7:1) . . . where ΔHmix and ΔSmix are the change of enthalpy and entropy, respectively, on mixing (Prausnitz et al., 1986). Enthalpic interactions depend predominantly on solution density and on polymer segment–segment, solvent–solvent, and polymer segment–solvent interaction energies. The value of ΔSmix depends on both the combinatorial entropy of mixing and the noncombinatorial contribution associated with the volume change on mixing, a so-called equation-of-state effect (Patterson, 1982). The combinatorial entropy always promotes the mixing of a polymer with a solvent. However, the noncombinatorial contribution can have a negative impact on mixing as a result of monomer–monomer interactions that arise due to the connectivity of the segments in the backbone of the polymer chain.

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Conference papers on the topic "Single-molecule Thermodynamics"

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Bennetzen, Martin V., Martin Andersson, and Kristian Mogensen. "Predicting Interfacial Tension Of Multiphase Systems Based On Computational Single-Molecule Quantum Mechanics And Thermodynamics Applying Four Different Physical Models And COSMO-Theory." In SPE EOR Conference at Oil and Gas West Asia. Society of Petroleum Engineers, 2014. http://dx.doi.org/10.2118/169663-ms.

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Kulkarni, Sukrut Shridhar. "Agile Response Aimed at Unprecedented Situation of Truncated Gas Demand Via Holistic Network Modelling of Complex Integrated Facilities for Value Maximization." In International Petroleum Technology Conference. IPTC, 2021. http://dx.doi.org/10.2523/iptc-21470-ms.

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Abstract This paper highlights the efforts to mitigate the unprecedented situation of truncated gas demand via network modeling development and harmoniously harvesting value generation by its implementation. Global Pandemic in year 2020 resulted into unique situation of steep truncated gas demand due to economic slowdown worldwide. Hence as a prudent operator its deemed necessary to pursue strategic ideas and innovative concepts to manage offshore complex gas network to handle reduced supply demand balance, whilst protecting fulfill technical and contractual obligations also by optimizing valu

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Groll, Rodion, and Hans J. Rath. "On Eulerian Modeling of Microchannel Gas Flows Closing Higher Statistical Moments of Molecule Velocity." In ASME 2010 8th International Conference on Nanochannels, Microchannels, and Minichannels collocated with 3rd Joint US-European Fluids Engineering Summer Meeting. ASMEDC, 2010. http://dx.doi.org/10.1115/fedsm-icnmm2010-30212.

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High pressure gradient driven micro-channel flow modelling with very the high ratios of absolute pressure and temperature (see Agrawal et al. 2005 [1]) define the difference between physical and computational results using continuum approaches (see Maurer et al. 2003, Durst et al. 2006, Dongari et al. 2008 [3, 4, 8]). In the present paper this deviation of the computational results is explained by the statistical correlation of the molecular number density and the single molecule velocity inside a compressible gas flow. Classical solutions of Navier-Stokes equations do not satisfy the physical

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Gutman, Ivan. "TOPOLOGICAL INDICES – WHY AND HOW." In 1st INTERNATIONAL Conference on Chemo and BioInformatics. Institute for Information Technologies, University of Kragujevac,, 2021. http://dx.doi.org/10.46793/iccbi21.039g.

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By means of presently available high-level computational methods, based on quantum theory, it is possible to determine (predict) the main structural, electronic, energetic, geometric, and thermodynamic properties of a particular chemical species (usually a molecule), as well as the ways in which it changes in chemical reactions. When one needs to estimate such properties of thousands or millions of chemical species, such high-level calculations are no more feasible. Then simpler, but less accurate, approaches are necessary. One such approach utilized so-called “topological indices”. According

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Escamilla, Antonio, David Sánchez, and Lourdes García-Rodríguez. "Exergy Analysis of Green Power-to-Hydrogen Chemical Energy Storage." In ASME Turbo Expo 2022: Turbomachinery Technical Conference and Exposition. American Society of Mechanical Engineers, 2022. http://dx.doi.org/10.1115/gt2022-82107.

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Abstract Power-to-Hydrogen-to-Power are chemical energy storage systems that store surplus renewable energy in the form of hydrogen, through water electrolysis, for its later use as power when power demand rises again. Due to the very low energy and mass density of H2 at standard conditions, 0.083 kg/m3, compression of hydrogen to pressures as high as 900 bar is usually performed for storage. This is why variations in the operating conditions of the electrolyzers lead to significantly different operating conditions of the hydrogen compression system. Accordingly, a detailed thermodynamic analy

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Saputra, I. Wayan Rakananda, and David S. Schechter. "A Temperature Operating Window Concept for Application of Nonionic Surfactants for EOR in Unconventional Shale Reservoirs." In SPE Annual Technical Conference and Exhibition. SPE, 2021. http://dx.doi.org/10.2118/206346-ms.

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Abstract Surfactant performance is a function of its hydrophobic tail, and hydrophilic head in combination with crude oil composition, brine salinity, rock composition, and reservoir temperature. Specifically, for nonionic surfactants, temperature is a dominant variable due to the nature of the ethylene oxide (EO) groups in the hydrophilic head known as the cloud point temperature. This study aims to highlight the existence of temperature operating window for nonionic surfactants to optimize oil recovery during EOR applications in unconventional reservoirs. Two nonylphenol (NP) ethoxylated non

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