Biological nanostructures and applications of nanostructures in biology : electrical, mechanical, and optical properties

Kohanpour, and Salvador Rufo 1. 2. 3. 4. 5. 6. 7. INTRODUCTION FABRICATING QUANTUM DOT SYSTEMS AND THEIR APPLICATIONS AS BIOTAGS RELEVANT PHYSICAL PROPERTIES OF SEMICONDUCTOR QUANTUM DOTS CONCEPTS AND TOOLS UNDERLYING THE INTEGRATION OF QUANTUM DOTS WITH BIOLOGICAL SYSTEMS CONCLUSION ACKNOWLEDGMENT REFERENCES 1 3 13 17 28 28 29 2. BIOMEDICAL APPLICATIONS OF SEMICONDUCTOR QUANTUM DOTS 37 Anupam Singhal, Hans C. Fischer, Johnson Wong, and Warren C. W. Chan 1. 2. 3. INTRODUCTION OPTICAL AND ELECTRONIC PROPERTIES OF SEMICONDUCTOR QUANTUM DOTS SYNTHESIS AND CHARACTERIZATION 3.1. Synthesis Techniques 41 ixCONTENTS xi 2. PHYSIOLOGICAL ASPECTS 2.1. 2.2. 2.3. 2.4. Human Bone Marrow Stromal Cells Cytoskeleton Mechanobiology Fluid Flow 3. BASICS FOR STUDYING CONTRIBUTION OF CYTOSKELETON TO DIFFERENTIATION 3.1. 3.2. 3.3. Differentiating Factors Pharmacological Cytoskeleton Disrupting Agents Mechanical Stimulation of Cells 4. ATOMIC FORCE MICROCOPY (AFM) 4.1. 4.2. 4.3. 4.4. 4.5. Operation Principles Preparation of Cells for AFM Imaging Imaging Conditions AFM Probe Selection Scanning Modes 5. TOPOGRAPHIC IMAGING OF LIVING CELLS WITH AFM 6. FORCE IMAGING OF LIVING CELLS WITH AFM 6.1. AFM in Cytoskeleton Imaging 7. CELL NANOSTRUCTURAL CHANGES INDUCED BY DIFFERENTIATION OR MECHANICAL FORCES 7.1. 7.2. Cell Differentiation Fluid Flow Forces 7.2.1. 7.2.2. Parallel-Plate Flow Chamber Methodology Examples of Cytoskeletal Importance During Fluid Flow 8. CHARACTERIZATION OF LIVING CELLS AND SURROUNDING ENVIRONMENT WITH AFM 8.1. Determination of Surface Roughness and Nanomechanical Properties of Bone Marrow-Derived Mesenchymal Stem Cells 8.2. 8.3. Imaging of of MSCs with AFM Results and Analysis 9. CONCLUDING REMARKS 10. REFERENCES 5. HAIRPIN FORMATION IN POLYNUCLEOTIDES: A SIMPLE FOLDING PROBLEM? Anjum Ansari and Serguei V. Kuznetsovxii CONTENTS 1. 2. INTRODUCTION KINETIC DESCRIPTION OF HAIRPIN FOLDING TRANSITION 2.1. 2.2. 2.3. 2.4. Two-State Description Arrhenius Plots Three-State Description (Nucleation and Zipping) Zipper Model (with Misfolded States) 3. REVIEW OF EXPERIMENTAL RESULTS AND PUZZLES 3.1. 3.2. 3.3. 3.4. 3.5. Why is hairpin formation so slow? What is the activation enthalpy for the hairpin closing step? Is a semiflexible polymer description of ss-polynucleotides valid? What is the viscosity dependence of the opening and closing rates? Does transient trapping in misfolded states slow down hairpin formation? 4. 5. 6. CONCLUSION ACKNOWLEDGMENTS REFERENCES 6. BIOINSPIRED APPROACHES TO BUILDING NANOSCALE DEVICES. Sawitri Mardyani, Weu Jiang, Jonathan Lai, Jane Zhang, and Warren C. W. Chan 1. 2. 3. 4. 5. 6. 7. 8. INTRODUCTION NANOSTRUCTURES AS CORE COMPONENTS FOR BUILDING DEVICES BIOLOGY AS MODEL SYSTEM FOR BUILDING NANOSCALE DEVICES MICROBIAL SYSTEMS FOR ASSEMBLING NANOSTRUCTURES .. CURRENT STATE AND HIGHLIGHTS OF BIOAPPLICATIONS OF NANOSTRUCTURES CONCLUSIONS ACKNOWLEDGMENTS REFERENCES 7. BRIDGING NATURAL NANOTUBES WITH DESIGNED NANOTUBES. Duan P. Chan 1. 2. INTRODUCTION ION CHANNELS: WHAT THEY ARE AND HOW THEY ARE STUDIED 99 101 101 104 105 105 106 111 117 120 127 131 138 140 140 149 149 151 152 155 157 158 158 159 161