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The interactions of DNA with force are central to manifold fields of inquiry, including the de novo design of DNA nanostructures, the use of DNA to probe the principles of biological self-assembly, and the operation of cellular nanomachines. This work presents a survey of three distinct ways coarse-grained simulations can help characterize these interactions. A non-equilibrium energy landscape reconstruction technique is validated for use with the oxDNA model and a practical framework to guide future applications is established. A novel method for calculating entropic forces in DNA molecules is outlined and contrasted with existing, flawed approaches. Finally, a joint experimental-simulation study of large DNA origami nanostructures under force sheds light on design principles and, through vivid illustrations, their unfolding process. This text provides an accessible and exciting launching point for any student interested in the computational study of DNA mechanics and force interactions.

Chemistry. --- Nanoscale Science and Technology. --- Mathematical and Computational Biology. --- Theoretical and Computational Chemistry. --- Atomic/Molecular Structure and Spectra. --- Physical sciences --- DNA --- Analysis. --- Nanoscale science. --- Nanoscience. --- Nanostructures. --- Biomathematics. --- Chemistry, Physical and theoretical. --- Atomic structure  . --- Molecular structure . --- Structure, Molecular --- Chemical structure --- Structural bioinformatics --- Structure, Atomic --- Atomic theory --- Chemistry, Theoretical --- Physical chemistry --- Theoretical chemistry --- Chemistry --- Biology --- Mathematics --- Nanoscience --- Physics --- Nano science --- Nanoscale science --- Nanosciences --- Science

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This handbook presents structural data on free polyatomic molecules. Since the structure of molecules defines the chemical, physical and biological properties of matter, this information is crucial for understanding, explaining and predicting chemical reactions and biochemical processes, developing new drugs and materials as well as studying interstellar media. Covering the structural data published between 2009 and 2017, this book supplements the previous Landolt–Börnstein volumes “Structure Data of Free Polyatomic Molecules” (eds. K. Kuchitsu, N. Vogt, M. Tanimoto), which included data from the literature published up to 2008. It systematizes and describes peculiarities of molecular structures for about 1000 compounds studied mainly by gas-phase electron diffraction and rotational spectroscopy. All structures are given in three-dimensional representations.

Atomic structure  . --- Molecular structure . --- Physical chemistry. --- Carbohydrates. --- Atomic/Molecular Structure and Spectra. --- Physical Chemistry. --- Carbohydrate Chemistry. --- Carbs (Carbohydrates) --- Biomolecules --- Organic compounds --- Glycomics --- Chemistry, Theoretical --- Physical chemistry --- Theoretical chemistry --- Chemistry --- Structure, Molecular --- Chemical structure --- Structural bioinformatics --- Structure, Atomic --- Atomic theory --- Molecular structure.

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This book describes advanced research on the structures and photochemical properties of polyatomic molecules and molecular clusters having various functionalities under cold gas-phase conditions. Target molecules are crown ethers, polypeptides, large size protonated clusters, metal clusters, and other complex polyatomic molecules of special interest. A variety of advanced frequency and time-domain laser spectroscopic methods are applied. The book begins with the principle of an experimental setup for cold gas-phase molecules and various laser spectroscopic methods, followed by chapters on investigation of specific molecular systems. Through a molecular-level approach and analysis by quantum chemical calculation, it is possible to learn how atomic and molecular-level interactions (van der Waals, hydrogen-bonding, and others) control the specific properties of molecules and clusters. Those properties include molecular recognition, induced fitting, chirality, proton and hydrogen transfer, isomerization, and catalytic reaction. The information will be applicable to the design of new types of functional molecules and nanoparticles in the broad area that includes applied chemistry, drug delivery systems, and catalysts.

Chemistry, Physical organic. --- Spectroscopy. --- Nanochemistry. --- Physical Chemistry. --- Spectroscopy/Spectrometry. --- Atomic/Molecular Structure and Spectra. --- Analysis, Spectrum --- Spectra --- Spectrochemical analysis --- Spectrochemistry --- Spectroscopy --- Chemistry, Analytic --- Interferometry --- Optics --- Radiation --- Wave-motion, Theory of --- Absorption spectra --- Light --- Spectroscope --- Chemistry, Physical organic --- Chemistry, Organic --- Chemistry, Physical and theoretical --- Nanoscale chemistry --- Nanoscience --- Qualitative --- Spectrometry --- Analytical chemistry --- Physical chemistry. --- Atomic structure  . --- Molecular structure . --- Structure, Molecular --- Chemical structure --- Structural bioinformatics --- Structure, Atomic --- Atomic theory --- Chemistry, Theoretical --- Physical chemistry --- Theoretical chemistry --- Chemistry

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This book describes the state of the art across the broad range of spectroscopic techniques used in the study of biological systems. It reviews some of the latest advances achieved in the application of these techniques in the analysis and characterization of small and large biological compounds, covering topics such as VUV/UV and UV-visible spectroscopies, fluorescence spectroscopy, IR and Raman techniques, dynamic light scattering (DLS), circular dichroism (CD/SR-CD), pulsed electron paramagnetic resonance techniques, Mössbauer spectroscopy, nuclear magnetic resonance, X-ray methods and electron and ion impact spectroscopies. The second part of the book focuses on modelling methods and illustrates how these tools have been used and integrated with other experimental and theoretical techniques including also electron transfer processes and fast kinetics methods. The book will benefit students, researchers and professionals working with these techniques to understand the fundamental mechanisms of biological systems.

Spectroscopy. --- Medical physics. --- Cytology --- Spectroscopy and Microscopy. --- Spectroscopy/Spectrometry. --- Medical and Radiation Physics. --- Biological Techniques. --- Atomic/Molecular Structure and Spectra. --- Research --- Methodology. --- Cell biology --- Cellular biology --- Biology --- Cells --- Cytologists --- Health physics --- Health radiation physics --- Medical radiation physics --- Radiotherapy physics --- Radiation therapy physics --- Biophysics --- Physics --- Analysis, Spectrum --- Spectra --- Spectrochemical analysis --- Spectrochemistry --- Spectroscopy --- Chemistry, Analytic --- Interferometry --- Optics --- Radiation --- Wave-motion, Theory of --- Absorption spectra --- Light --- Spectroscope --- Qualitative --- Radioisotopes in biology. --- Radiobiology --- Spectrometry --- Microscopy. --- Radiation. --- Biology—Technique. --- Atomic structure  . --- Molecular structure . --- Structure, Molecular --- Chemical structure --- Structural bioinformatics --- Structure, Atomic --- Atomic theory --- Radiology --- Analysis, Microscopic --- Light microscopy --- Micrographic analysis --- Microscope and microscopy --- Microscopic analysis --- Optical microscopy --- Analytical chemistry

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This book focuses on the study of the interfacial water using molecular dynamics simulation and experimental sum frequency generation spectroscopy. It proposes a new definition of the free O-H groups at water-air interface and presents research on the structure and dynamics of these groups. Furthermore, it discusses the exponential decay nature of the orientation distribution of the free O-H groups of interfacial water and ascribes the origin of the down pointing free O-H groups to the presence of capillary waves on the surface. It also describes how, based on this new definition, a maximum surface H-bond density of around 200 K at ice surface was found, as the maximum results from two competing effects. Lastly, the book discusses the absorption of water molecules at the water–TiO2 interface. Providing insights into the combination of molecular dynamics simulation and experimental sum frequency generation spectroscopy, it is a valuable resource for researchers in the field.

Atomic/Molecular Structure and Spectra. --- Soft and Granular Matter, Complex Fluids and Microfluidics. --- Numerical and Computational Physics, Simulation. --- Spectroscopy and Microscopy. --- Surface and Interface Science, Thin Films. --- Atomic structure  . --- Molecular structure . --- Amorphous substances. --- Complex fluids. --- Physics. --- Spectroscopy. --- Microscopy. --- Surfaces (Physics). --- Interfaces (Physical sciences). --- Thin films. --- Complex liquids --- Fluids, Complex --- Amorphous substances --- Liquids --- Soft condensed matter --- Structure, Molecular --- Chemical structure --- Structural bioinformatics --- Structure, Atomic --- Atomic theory --- Physics --- Surface chemistry --- Surfaces (Technology) --- Analysis, Microscopic --- Light microscopy --- Micrographic analysis --- Microscope and microscopy --- Microscopic analysis --- Optical microscopy --- Optics --- Analysis, Spectrum --- Spectra --- Spectrochemical analysis --- Spectrochemistry --- Spectrometry --- Spectroscopy --- Chemistry, Analytic --- Interferometry --- Radiation --- Wave-motion, Theory of --- Absorption spectra --- Light --- Spectroscope --- Natural philosophy --- Philosophy, Natural --- Physical sciences --- Dynamics --- Films, Thin --- Solid film --- Solid state electronics --- Solids --- Coatings --- Thick films --- Surfaces (Physics) --- Qualitative --- Analytical chemistry