bluuebunny/crossref_metadata_2025_split huggingface dataset:
Electron Cryomicroscopy of Molecular Nanomachines and Cells
Authors: Baker Matthew L. , Marsh Michael P. , Chiu Wah 
Published: June 2010

AbstractElectron cryomicroscopy (cryo‐EM) is an emerging biophysical tool that can be used to determine the structures of molecular nanomachines in fully solvated conformations at subnanometer resolutions (<1 nm). Such cryo‐EM maps can reveal long α‐helices and large β‐sheets. In the highest resolution cryo‐EM density maps, it is possible to see bulky side chains and trace the Cα backbone of molecular subunits within a multicomponent nanomachine. Electron cryotomography (cryo‐ET) is equally powerful because of the unique cellular context in which it can capture and reveal cellular nanomachines. Despite reaching only 4–10 nm resolution, cryo‐ET reconstructions are capable of imaging whole cells and distinguishing their molecular components. Both of these methods are complementary to conventional methods of structure determination, including X‐ray crystallography and NMR spectroscopy. Hybrid methods that combine these structural techniques with cryo‐EM and cryo‐ET result in a complete view of nanomachines from atomic detail to their spatial and temporal location within a cell. This chapter will describe the experimental and computational pipeline in cryo‐EM and cryo‐ET and illustrate their effectiveness with examples from an ion channel, spherical virus, cellular motor and the survey of a complete cell.
Pushing Optical Microscopy to the Limit: From Single‐Molecule Fluorescence Microscopy to Label‐Free Detection and Tracking of Biological Nano‐Objects
Authors: Kukura Philipp , Renn Alois , Sandoghdar Vahid 
Published: June 2010

AbstractThe promise and success of current biomedical research is highly dependent on understanding the mechanisms of fundamental biological processes such as protein folding, the function of molecular machines, or the interaction of proteins with molecular complexes. In particular, on the cellular level the heterogeneous and fluctuating environment as well as the intrinsic asynchronicity of protein function requires observation of individual copies rather than ensembles if a detailed understanding of their function is to be obtained. As a consequence, real‐timein vivoimaging is one of the most desirable tools for investigating biological systems at microscopic and nanoscopic levels. In this chapter, we summarize some of the recent advances in optical microscopy with a particular focus on the capabilities and limitations of studies at the single‐molecule and nanoparticle level. We present a detailed account of the intricate interplay between single‐molecule photophysical properties and the attainable signal‐to‐noise ratio in the ability to see, localize and trace single molecules. Furthermore, we discuss the possibility of single‐molecule labels being replaced by tiny light scatterers, such as gold nanoparticles, which offer an inherent photostability and lack of saturation. In particular, we introduce a novel interferometric technique for detecting nanoscopic objects and demonstrate its potential use both for the study of gold nanoparticle labels in scattering media and the label‐free detection of single biological nanoparticles in the absence of additional scatterers.
High‐Content Analysis of Cytoskeleton Functions by Fluorescent Speckle Microscopy
Authors: Applegate Kathryn T. , Yang Ge , Danuser Gaudenz 
Published: June 2010

AbstractThe development of nanomedical strategies requires precise mechanistic models of cellular pathways. At center stage of many of these pathways is the cytoskeleton, which dynamically organizes cellular architecture and mediates cell morphological functions. In this chapter we review the principles and selected applications of quantitative fluorescent speckle microscopy (qFSM), a combined imaging modality and statistical toolset that delivers high‐resolution measurements of cytoskeleton structure and dynamics in living cells. qFSM has emerged as an invaluable tool in studies aimed at delineating the mechanisms of cytoskeleton regulation by the systematic perturbation of molecular signals upstream of cytoskeleton outputs. Additionally, qFSM can be used as a precise readout of cytoskeleton responses in the search for new drugs and nanomedical strategies that alter cellular behavior by intervening with specific cytoskeleton functions.
Mechanical Forces Matter in Health and Disease: From Cancer to Tissue Engineering
Authors: Vogel Viola , Sheetz Michael P. 
Published: June 2010

AbstractCellular microenvironments control many aspects of cell behavior, differentiation and wound healing. When cells are in an inappropriate environment, they often stop growth or enter an apoptotic pathway. Environment is defined by the biological or engineered matrix, soluble molecules, adjacent cells and physical factors of force and geometry that all act at the nanometer (protein) level. The development of nanotechnology tools has provided new ways to measure the forces and control the geometry spatial in which ligands are presented. In this chapter, we focus on reviewing the effects of mechanical force on cellular functions because it is a critical intensive parameter that dynamically affects cell functions in health and disease. For force transmission, cell adhesion sites must be linked mechanically to the cell cytoskeleton and force‐generating machinery within the cell, as well as to the extracellular matrix (ECM). Forces are processed by specialized adhesive structures that are dynamic as the cells actively bind, stretch and remodel their surroundings. Once formed, the early contacts either mature rapidly or break. We will discuss how forces upregulate the maturation of early cell–matrix junctions and regulate the dynamic interplay between the assembly and disassembly of adhesion sites. Once sufficiently stabilized through recruitment of additional focal adhesion proteins, intracellular traction can generate large forces on the adhesive junctions – forces which are easily visualized as strain applied by cells to flexible substrates. Protein stretching and unfolding plays a central role in the recruitment of proteins to an adhesion site, and in regulating intracellular signaling events, including stretch‐dependent tyrosine phosphorylation. The nanoscale machinery of an adhesion site enables the cell to sense and respond to the spatial patterns of its environment, as well as to its rigidity. In response, cells change their protein expression pattern and assemble and remodel the ECM. This in turn regulates cell motility and many other cellular functions. We will then discuss that many diseases have a mechanical origin or show abnormalities in cellular mechanoresponses, from cancer to cardiovascular disorders, from osteoporosis to other aging‐related diseases. Ultimately, mechanotransduction processes regulate tissue formation, remodeling and healing in native wound sites of tissue engineered scaffolds, as well as how stem cells differentiate and whether cells derail and evolve into cancer cells or other disease conditions.
Stem Cells and Nanomedicine: Nanomechanics of the Microenvironment
Authors: Rehfeldt Florian , Engler Adam J. , Discher Dennis E. 
Published: June 2010

AbstractThe various cells in our body interact with different micro/nano‐environments that depend on the tissue as well as the niche within the tissue. Although for many – if not most – cells the environment is maintained throughout the cell's lifetime, there are certainly some events that perturb both the physical and biochemical properties of the cell's surrounding; these events include wounding, regeneration, inflammation and cancer. There are also some cells – particularly adult stem cells – that migrate to and thus probe very different tissues within the body. In this chapter we discuss micro/nano‐elasticity measurements of tissue, and provide a summary of results obtained with adult human mesenchymal stem cells that most likely encounter a range of very differentmechanochemicalmicroenvironments. The interactions of cells with their surroundings reveal complex feedback loops coupled to soluble growth factor pathways, with implications for important new approaches to regenerative medicine.
Bone Nanostructure and its Relevance for Mechanical Performance, Disease and Treatment
Authors: Fratzl Peter , Gupta Himadri S. , Roschger Paul , Klaushofer Klaus 
Published: June 2010

AbstractThe remarkable mechanical properties of bone are due to its hierarchical structure which is optimized at all levels of hierarchy. At the lowest level, bone is a nanocomposite of collagen and mineral particles. The quality of this material is crucial for the mechanical performance of bone as a whole. In this chapter we review the structure and composition of bone material at the nanoscale, and report several examples on how bone material may be affected by disease or treatment strategies.
Nanoengineered Systems for Tissue Engineering and Regeneration
Authors: Khademhosseini Ali , Rajalingam Bimal , Jinno Satoshi , Langer Robert 
Published: June 2010

AbstractThe ability to generate and transplant functional tissue constructs, through the artificial engineering of biological tissues, may provide a solution for a number of biomedical challenges. However, several clinically viable tissue engineering products having been created, limitations such as the lack of a suitable cell source and the inability to generate three‐dimensional (3‐D) tissues with sufficient complexity and functional properties, greatly hinders us from realizing the full potential of tissue engineering. Recently, nanotechnology has been used for tissue engineering by generating materials and devices that can mimic the organization and structure of native tissues or direct cell function. In this chapter we will discuss the use of nanoengineered systems and nanomaterials for generating 3‐D tissues, for controlling stem cell differentiation, as well as analyzing the resultant constructsin vitroandin vivo. The application of nanotechnology for biological studies, as well as drug screening and diagnostics, will also be discussed.
Self‐Assembling Peptide‐Based Nanostructures for Regenerative Medicine
Authors: Capito Ramille M. , Mata Alvaro , Stupp Samuel I. 
Published: June 2010

AbstractBiomaterials designed at the molecular and supramolecular levels to interact with cells, biomolecules such as growth factors and biopolymers, and pharmaceuticals will all have a profound impact on technologies targeted towards the regeneration of damaged tissues as a result of trauma, disease or genetic defects. Advances in materials science, chemistry, genomics and stem cell biology will all contribute towards the development of therapies leading to the successful regeneration of specific tissues. Regenerative medicine therapies should be minimally invasive, and thus the notion of cell scaffolds that self‐assemble from injected liquids is highly attractive for clinical translation. In this regard, self‐assembling materials will play a key role in future regenerative medicine technologies. In this chapter we focus on the current development of injectable, self‐assembling scaffolds that can be designed to provide a biomimetic and bioactive environment to stimulate cell‐signaling pathways that are critical in the regenerative process. We also describe the use of self‐assembling coatings to render traditional inert materials more bioactive and biocompatible, especially in orthopedic applications.
Spin‐Polarized Scanning Tunneling Microscopy
Authors: Getzlaff Mathias 
Published: June 2010

Abstract
This chapter describes the enormous experimental progress in spin‐polarized scanning tunneling microscopy (SP‐STM), which allows magnetically sensitive imaging with ultra‐high resolution down to the atomic scale. The fundamentals of SP‐STM are introduced on the basis of planar tunnel junctions for different electrode materials being superconductors, optically excited GaAs and ferromagnets. It is shown that both ferromagnets and antiferromagnets are suitable tip materials for SP‐STM. Appropriate tip designs and modes of operations are discussed for both types of material. The results of recent laterally resolved measurements performed with different magnetic probe tips and different modes of operation are reviewed. In addition, the limits of this ultimate lateral resolution and the influence of an external magnetic field on the imaging process are discussed. The examples discussed range from bulk material to 2‐D systems such as surfaces, thin films and nanoparticles, and to 1‐D systems such as nanowires. The magnetic properties of individual atoms are also presented.
Nanoscale Imaging and Force Analysis with Atomic Force Microscopy
Authors: Hölscher Hendrik , Schirmeisen André , Fuchs Harald 
Published: June 2010

AbstractThe atomic force microscope – sometimes also referred to as the scanning force microscope – has developed into the most widespread tool used in nanotechnology. The instrument and technique were invented by Binniget al. in 1986, and are today used not only in physical, chemical, biological and medical research laboratories, but also in many companies for tasks such as product development and routine quality control. The success of the technique is based on its high‐resolution imaging capabilities in combination with its versatility, making it possible to image surfaces down to the atomic scale. Due to its universality, atomic force microscopy can be applied to a large variety of samples, and adapted to many different environments (gaseous, liquid, or vacuum). The atomic force microscope can be operated in different modes, which can be categorized as static and dynamic. Here, an introduction is provided of the basic concepts of the two modes, and details applications under different environmental conditions are presented. Some practical issues for the experimentalist are highlighted, while special care is taken to explain the quantitative relationship between experimental parameters and physical magnitudes.
Probing Hydrodynamic Fluctuations with a Brownian Particle
Authors: Jeney Sylvia , Lukic Branimir , Guzman Camilo , Fórró László 
Published: June 2010

AbstractIn this chapter we demonstrate the use of optical trapping interferometry to track and study the motion of a Brownian particle down to hydrodynamic timescales, where the response of the surrounding viscous fluid becomes dominant. A Brownian particle rapidly explores its surrounding medium that in turn alters its trajectory, and hence functions as a probe of its local environment. After an introduction to fundamental aspects of the theory of Brownian motion, which are very often ignored by experimentalists, we describe our instrument with a particular emphasis on position detection, data acquisition and analysis. Comparing the suitable theory with our data allows calibration of our instrument and quantification of the influence of experimentally relevant parameters, such as the trapping force constant, the fluid properties and the Brownian particle itself. The presented approach should ultimately open up the possibility of using a Brownian probe as a direct reporter of even more complex viscoelastic and/or heterogeneous media.
Nanoscale Thermal and Mechanical Interactions Studies using Heatable Probes
Authors: Gotsmann Bernd , Lantz Mark A. , Knoll Armin , Dürig Urs 
Published: June 2010

AbstractThe use of heatable probes in scanning probe microscopy allows the effect of temperature to be studied in combination with the mechanical interaction of the probe tip with a sample surface. Using nanometer‐scale sharp tips, the thermal and thermomechanical properties of solids can be determined locally down to nanometer scale. In this chapter we present a review of heatable probe types, and discuss some of the most prominent applications of these devices. Scanning thermal imaging is described first, followed by a detailed analysis of local heat flow through heated tips in contact with a surface. Nanoindentation of polymers with heated tips is used to uncover fundamentals of thermomechanical interaction with polymers on a small scale. This is described in terms of yielding and deformation kinetics. Finally, patterning applications are discussed, such as thermomechanical probe‐storage using nanoindentation, nanotribology and nanolithography utilizing heated‐tip‐assisted deposition and removal of material.
Materials Integration by Dip‐Pen Nanolithography
Authors: Lenhert Steven , Fuchs Harald , Mirkin Chad A. 
Published: June 2010

Abstract
Dip‐pen nanolithography (DPN) is a versatile tool for nanotechnology that enables the resolution of electron‐beam lithography, integration capabilities typical of inkjet printing, and a high throughput comparable to microcontact printing. By using the tip of an atomic force microscope as an ultra‐sharp pen, DPN represents a constructive method of scanning probe lithography that can be carried out in a massively parallel fashion. This chapter introduces the fundamental concepts in DPN technology, with a focus on aspects that enable materials integration. Theoretical models of ink transport are discussed, and a variety of experimental methods presented. The concept of a driving force is explained, along with various methods for controlling that driving force, both by ink–substrate combinations, humidity and the application of external fields. Various approaches to tip coating are explained and suitable characterization methods presented. Finally, examples of unique applications of materials integration by DPN will be described that cannot be achieved by any other method, including templates, combinatorial chemistry and biological arrays.
Cryoelectron Tomography: Visualizing the Molecular Architecture of Cells
Authors: Thomas Dennis R. , Baumeister Wolfgang 
Published: June 2010

AbstractElectron tomography can generate three‐dimensional reconstructions of the macromolecular machinery of the cellin situwith nanoscale resolution. The principles of electron tomography are the same as those applied to the analysis of isolated single complexes. In recent years technological advances have made it possible to apply tomography to ice‐embedded biological material (‘cryotomography’), thereby ensuring a close‐to‐life preservation of the sample. Tomographic reconstruction of biological samples embedded in vitreous ice, combined with advanced computational methods for their interpretation, provides the possibility of comprehensively mapping the macromolecular architecture inside organelles and cells. Thus we can begin to visualize macromolecular machines at work in their natural enviroment.
Nanoplasmonics
Authors: Steiner Gerald 
Published: June 2010

Abstract
Metallic nanostructures are able to manipulate light on a wide scale of and far below the diffraction limit of the classical optic. The overall process is the excitation of surface plasmons localized in and around metallic nanostructures, recently termed as ‘nanoplasmonic’. Localized surface plasmons are collective charge oscillations in metal clusters of few nanometers in size. Their unique optical properties enable many applications, ranging from the enhancement of scattering processes and light absorption to biosensing on the single molecular level or high‐resolution imaging. This chapter describes briefly the fundamentals of the excitation of localized surface plasmons in single clusters, as well as the interaction between clusters. Some exciting new applications in biosensing, together with the well‐established methods of surface‐enhanced spectroscopy, are described.
Impedance Analysis of Cell Junctions
Authors: Wegener Joachim 
Published: June 2010

AbstractThe term ‘cell junctions’ comprises not only molecular contacts between neighboring cells within a cell assembly but also contacts between cells and the extracellular matrix. Cell junctions are pivotal for many fundamental physiological processes. Structural studies of cell junctions have traditionally been performed using light or electron microscopy, after appropriate labeling. This chapter describes the use of impedance analysis for a more functional and label‐free analysis of cell junctions. The basics of electrical impedance measurements are introduced before examples are described that demonstrate the potency of the approach in monitoring cell junctions.
Catalysis Involving Fluorous Phases: Fundamentals and Directions for Greener Methodologies
Authors: Gladysz John A. 
Published: June 2010

AbstractThis article briefly reviews the fundamentals of fluorous chemistry, with an emphasis on aspects most relevant to catalysis. The development of “greener” fluorous solvents and ponytails (phase tags) is described. Protocols that minimize the use of fluorous solvents are emphasized. Some of these exploit the highly temperature dependent solubilites of fluorous compounds in organic solvents, which can be fine‐tuned by varying the length and number of the (CF2)nsegments in the ponytails. Suitably designed fluorous catalysts can thus be employed under homogeneous conditions at elevated temperatures, and recovered by solid/liquid phase separation at lower temperatures. Fluorous solid supports such as fluoropolymers and fluorous silica gel can be used to aid the recovery of small catalyst quantities, and render phase separation more efficient. The use of CO2pressure as a non‐thermal solubility trigger, and catalyst recovery by solid phase extraction using non‐fluorous solvents, are also detailed.
Chemistry and Applications of Iron–TAMLCatalysts in Green Oxidation Processes Based on Hydrogen Peroxide
Authors: Collins Terrence J. , Khetan Sushil K. , Ryabov Alexander D. 
Published: June 2010

AbstractIron–tetraamido macrocyclic ligand (TAML) activators have been designed and developed to provide small‐molecule mimics, the peroxidase enzymes. Fe–TAML activators are proving to be highly active catalysts that function effectively at very low concentrations from nanomolar to low micromolar. Notably, they are capable of performing many thousands of turnovers per minute under ambient conditions, of functioning over a broad pH range from acidic and most notably for iron catalyst to basic and even to highly basic, of presenting a broad range of selectivities and oxidative aggression determined by the conditions of use and the choice of catalyst over the 14 catalysts presented. The catalysts have fulfilled the design criteria and now provide the basis of platform technology for myriad applications. Published kinetics and mechanistic interpretations are reviewed to illustrate the success of the design protocol. Published applications are briefly described. A highly developed field of use involves the use of Fe–TAML–peroxide for the purification of water of persistent pollutants and hardy pathogens.
Immobilization and Compartmentalization of Homogeneous Catalysts
Authors: Müller Christian , Vogt Dieter 
Published: June 2010

AbstractThe sections in this article areIntroductionSoluble Dendrimer‐bound Homogeneous CatalystsCovalently Linked Dendrimer‐bound CatalystsCarbosilane Dendrimers as Soluble SupportsPoly(Benzyl Ether) Dendrimers as Soluble SupportsDABDendrimers as Soluble SupportsPAMAMDendrimers as Soluble SupportsPPIDendrimers as Soluble SupportsNon‐covalently Linked Dendrimer‐bound CatalystsPolymer‐bound Homogeneous CatalystsCovalently Linked Polymer‐bound CatalystsMolecular Weight Enlargement for Continuous Homogeneous CatalysisSoluble Polymer‐supported Catalysts for Liquid–Liquid Recovery of CatalystsElectrostatically Bound CatalystsConclusion and Outlook