Jean-Pierre Launay and Michel Verdaguer
- Published in print:
- 2017
- Published Online:
- November 2018
- ISBN:
- 9780198814597
- eISBN:
- 9780191852411
- Item type:
- book
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/oso/9780198814597.001.0001
- Subject:
- Physics, Atomic, Laser, and Optical Physics, Condensed Matter Physics / Materials
The book treats in a unified way electronic properties of molecules (magnetic, electrical, photophysical), culminating with the mastering of electrons, i.e. molecular electronics and spintronics and ...
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The book treats in a unified way electronic properties of molecules (magnetic, electrical, photophysical), culminating with the mastering of electrons, i.e. molecular electronics and spintronics and molecular machines. Chapter 1 recalls basic concepts. Chapter 2 describes the magnetic properties due to localized electrons. This includes phenomena such as spin cross-over, exchange interaction from dihydrogen to extended molecular magnetic systems, and magnetic anisotropy with single-molecule magnets. Chapter 3 is devoted to the electrical properties due to moving electrons. One considers first electron transfer in discrete molecular systems, in particular in mixed valence compounds. Then, extended molecular solids, in particular molecular conductors, are described by band theory. Special attention is paid to structural distortions (Peierls instability) and interelectronic repulsions in narrow-band systems. Chapter 4 treats photophysical properties, mainly electron transfer in the excited state and its applications to photodiodes, organic light emitting diodes, photovoltaic cells and water photolysis. Energy transfer is also treated. Photomagnetism (how a photonic excitation modifies magnetic properties) is introduced. Finally, Chapter 5 combines the previous knowledge for three advanced subjects: first molecular electronics in its hybrid form (molecules connected to electrodes acting as wires, diodes, memory elements, field-effect transistors) or in the quantum computation approach. Then, molecular spintronics, using, besides the charge, the spin of the electron. Finally the theme of molecular machines is presented, with the problem of the directionality control of their motion.Less
The book treats in a unified way electronic properties of molecules (magnetic, electrical, photophysical), culminating with the mastering of electrons, i.e. molecular electronics and spintronics and molecular machines. Chapter 1 recalls basic concepts. Chapter 2 describes the magnetic properties due to localized electrons. This includes phenomena such as spin cross-over, exchange interaction from dihydrogen to extended molecular magnetic systems, and magnetic anisotropy with single-molecule magnets. Chapter 3 is devoted to the electrical properties due to moving electrons. One considers first electron transfer in discrete molecular systems, in particular in mixed valence compounds. Then, extended molecular solids, in particular molecular conductors, are described by band theory. Special attention is paid to structural distortions (Peierls instability) and interelectronic repulsions in narrow-band systems. Chapter 4 treats photophysical properties, mainly electron transfer in the excited state and its applications to photodiodes, organic light emitting diodes, photovoltaic cells and water photolysis. Energy transfer is also treated. Photomagnetism (how a photonic excitation modifies magnetic properties) is introduced. Finally, Chapter 5 combines the previous knowledge for three advanced subjects: first molecular electronics in its hybrid form (molecules connected to electrodes acting as wires, diodes, memory elements, field-effect transistors) or in the quantum computation approach. Then, molecular spintronics, using, besides the charge, the spin of the electron. Finally the theme of molecular machines is presented, with the problem of the directionality control of their motion.
Joachim Frank
- Published in print:
- 2006
- Published Online:
- April 2010
- ISBN:
- 9780195182187
- eISBN:
- 9780199893416
- Item type:
- book
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780195182187.001.0001
- Subject:
- Biology, Biochemistry / Molecular Biology
In this book, the mathematical principles and working methods of single-particle reconstruction are described; a method designed to retrieve three-dimensional structural information from electron ...
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In this book, the mathematical principles and working methods of single-particle reconstruction are described; a method designed to retrieve three-dimensional structural information from electron micrographs showing thousands of “copies” of biological molecules trapped in a thin layer of ice. This technique is uniquely suited to obtain three-dimensional images of molecular machines in different functional states, as it dispenses with the need for crystals. The book starts with an introduction of image formation in the electron microscope, which includes the definition of the contrast transfer function. Next, averaging techniques and tools for image alignment, multivariate data analysis, and classification are described. An introduction into the mathematical principles underlying reconstruction of an object from its projections is followed by detailed accounts on how projection angles are determined, and how reconstruction is done in practice. The book concludes with a chapter on interpretation of density maps reconstructed, including methods for segmentation as well as fitting and docking of atomic coordinates.Less
In this book, the mathematical principles and working methods of single-particle reconstruction are described; a method designed to retrieve three-dimensional structural information from electron micrographs showing thousands of “copies” of biological molecules trapped in a thin layer of ice. This technique is uniquely suited to obtain three-dimensional images of molecular machines in different functional states, as it dispenses with the need for crystals. The book starts with an introduction of image formation in the electron microscope, which includes the definition of the contrast transfer function. Next, averaging techniques and tools for image alignment, multivariate data analysis, and classification are described. An introduction into the mathematical principles underlying reconstruction of an object from its projections is followed by detailed accounts on how projection angles are determined, and how reconstruction is done in practice. The book concludes with a chapter on interpretation of density maps reconstructed, including methods for segmentation as well as fitting and docking of atomic coordinates.
Giovanni Zocchi
- Published in print:
- 2018
- Published Online:
- January 2019
- ISBN:
- 9780691173863
- eISBN:
- 9781400890064
- Item type:
- chapter
- Publisher:
- Princeton University Press
- DOI:
- 10.23943/princeton/9780691173863.003.0003
- Subject:
- Physics, Soft Matter / Biological Physics
Enzymes are catalysts as well as the molecular machines that generate and maintain the nonequilibrium state of the cell. There are roughly two main mechanisms by which enzymes provide the control ...
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Enzymes are catalysts as well as the molecular machines that generate and maintain the nonequilibrium state of the cell. There are roughly two main mechanisms by which enzymes provide the control function for the network of chemical reactions in the cell. One is the presence or absence of the enzyme, controlled by gene expression. The other is allosteric control: the modulation of the activity of an individual enzyme caused by binding of a specific ligand, often a small metabolite, or else caused by so-called post-translational modifications. This chapter addresses what could be variously called the quasi-equilibrium aspects, or steady state, or kinematics, of enzyme operation, and what one learns from time-independent perturbations of this steady state. Topics discussed include Michaelis–Menten kinetics, the method of the DNA springs, force and elastic energy in the enzyme–DNA chimeras, injection of elastic energy vs. activity modulation, and connection to nonlinear dynamics.Less
Enzymes are catalysts as well as the molecular machines that generate and maintain the nonequilibrium state of the cell. There are roughly two main mechanisms by which enzymes provide the control function for the network of chemical reactions in the cell. One is the presence or absence of the enzyme, controlled by gene expression. The other is allosteric control: the modulation of the activity of an individual enzyme caused by binding of a specific ligand, often a small metabolite, or else caused by so-called post-translational modifications. This chapter addresses what could be variously called the quasi-equilibrium aspects, or steady state, or kinematics, of enzyme operation, and what one learns from time-independent perturbations of this steady state. Topics discussed include Michaelis–Menten kinetics, the method of the DNA springs, force and elastic energy in the enzyme–DNA chimeras, injection of elastic energy vs. activity modulation, and connection to nonlinear dynamics.
Franklin M. Harold
- Published in print:
- 2014
- Published Online:
- May 2015
- ISBN:
- 9780226174143
- eISBN:
- 9780226174310
- Item type:
- chapter
- Publisher:
- University of Chicago Press
- DOI:
- 10.7208/chicago/9780226174310.003.0006
- Subject:
- Biology, Biochemistry / Molecular Biology
This chapter tackles the evolution of cellular organization. How did intricate subcellular machines, such as ribosomes, flagella and ion pumps come to exist? How do cells transmit their functional ...
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This chapter tackles the evolution of cellular organization. How did intricate subcellular machines, such as ribosomes, flagella and ion pumps come to exist? How do cells transmit their functional organization to their offspring, and how did that evolve? And where did cellular organization come from in the first place? Contrary to the claims of Intelligent Design, there is ample evidence that random variation of genes winnowed by natural selection played a large role. But conventional views on these matters are too restrictive. Cells transmit structural organization by a hierarchy of mechanisms that includes genes, self-organization, the continuity of membranes and other structures, and a role for the cytoskeleton in helping a growing cell to model new structures upon the existing ones. How cells as we know them originated remains to be discovered, a subject for speculation and wonder but not yet for explication.Less
This chapter tackles the evolution of cellular organization. How did intricate subcellular machines, such as ribosomes, flagella and ion pumps come to exist? How do cells transmit their functional organization to their offspring, and how did that evolve? And where did cellular organization come from in the first place? Contrary to the claims of Intelligent Design, there is ample evidence that random variation of genes winnowed by natural selection played a large role. But conventional views on these matters are too restrictive. Cells transmit structural organization by a hierarchy of mechanisms that includes genes, self-organization, the continuity of membranes and other structures, and a role for the cytoskeleton in helping a growing cell to model new structures upon the existing ones. How cells as we know them originated remains to be discovered, a subject for speculation and wonder but not yet for explication.
Giovanni Zocchi
- Published in print:
- 2018
- Published Online:
- January 2019
- ISBN:
- 9780691173863
- eISBN:
- 9781400890064
- Item type:
- chapter
- Publisher:
- Princeton University Press
- DOI:
- 10.23943/princeton/9780691173863.003.0004
- Subject:
- Physics, Soft Matter / Biological Physics
This chapter discusses the deformability of enzymes. This property allows enzymes to couple a chemical process to a cycle of deformations of the molecule, which can perform a task in the cell. This ...
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This chapter discusses the deformability of enzymes. This property allows enzymes to couple a chemical process to a cycle of deformations of the molecule, which can perform a task in the cell. This is the celebrated “molecular machine” aspect of enzymes. The dynamics of enzyme deformability presents universal features when ensemble-averaged trajectories are examined. The mechanical response is viscoelastic. The remainder of the chapter covers the nonlinearity of the enzyme's mechanics, timescales, enzymatic cycle and viscoelasticity, internal dissipation, origin of the restoring force g, models based on chemical kinetics, different levels of microscopic description, connection to information flow, normal mode analysis, many states of the folded protein, and interesting topics in nonequilibrium thermodynamics relating to enzyme dynamics.Less
This chapter discusses the deformability of enzymes. This property allows enzymes to couple a chemical process to a cycle of deformations of the molecule, which can perform a task in the cell. This is the celebrated “molecular machine” aspect of enzymes. The dynamics of enzyme deformability presents universal features when ensemble-averaged trajectories are examined. The mechanical response is viscoelastic. The remainder of the chapter covers the nonlinearity of the enzyme's mechanics, timescales, enzymatic cycle and viscoelasticity, internal dissipation, origin of the restoring force g, models based on chemical kinetics, different levels of microscopic description, connection to information flow, normal mode analysis, many states of the folded protein, and interesting topics in nonequilibrium thermodynamics relating to enzyme dynamics.