In just three years, the green fluorescent protein (GFP) from the jellyfish Aequorea victoria has vaulted from obscurity to become one of the most widely studied and exploited proteins in biochemistry and cell biology. Its amazing ability to generate a highly visible, efficiently emitting internal fluorophore is both intrinsically fascinating and tremendously valuable. High-resolution crystal structures of GFP offer unprecedented opportunities to understand and manipulate the relation between protein structure and spectroscopic function. GFP has become well established as a marker of gene expression and protein targeting in intact cells and organisms. Mutagenesis and engineering of GFP into chimeric proteins are opening new vistas in physiological indicators, biosensors, and photochemical memories.

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The green fluorescent protein

Nano-optics of surface plasmon polaritons

Acknowledgements 1. Introduction 2. Electromagnetic wave propagation 3. The absorption of light 4. Specular reflection 5. Single particle scattering: perfect spheres 6. Single particle scattering: irregular particles 7. Propagation in a nonuniform medium: the equation of radiative transfer 8. The bidirectional reflectance of a semi-infinite medium 9. The opposition effect 10. A miscellany of bidirectional reflectances and related quantities 11. Integrated reflectances and planetary photometry 12. Photometric effects of large scale roughness 13. Polarization 14. Reflectance spectroscopy 15. Thermal emission and emittance spectroscopy 16. Simultaneous transport of energy by radiation and conduction Appendix A. A brief review of vector calculus Appendix B. Functions of a complex variable Appendix C. The wave equation in spherical coordinates Appendix D. Fraunhoffer diffraction by a circular hole Appendix E. Table of symbols Bibliography Index.

Theory of Reflectance and Emittance Spectroscopy

Fluorescent probes are one of the cornerstones of real-time imaging of live cells and a powerful tool for cell biologists. They provide high sensitivity and great versatility while minimally perturbing the cell under investigation. Genetically-encoded reporter constructs that are derived from fluorescent proteins are leading a revolution in the real-time visualization and tracking of various cellular events. Recent advances include the continued development of 'passive' markers for the measurement of biomolecule expression and localization in live cells, and 'active' indicators for monitoring more complex cellular processes such as small-molecule-messenger dynamics, enzyme activation and protein-protein interactions.

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Creating new fluorescent probes for cell biology.

Modern cryptography relies on algorithmic one-way functions—numerical functions which are easy to compute but very difficult to invert. This dissertation introduces physical one-way functions and physical one-way hash functions as primitives for physical analogs of cryptosystems. 
Physical one-way functions are defined with respect to a physical probe and physical system in some unknown state. A function is called a physical one-way function if (a) there exists a deterministic physical interaction between the probe and the system which produces an output in constant time; (b) inverting the function using either computational or physical means is difficult; (c) simulating the physical interaction is computationally demanding and (d) the physical system is easy to make but difficult to clone. 
Physical one-way hash functions produce fixed-length output regardless of the size of the input. These hash functions can be obtained by sampling the output of physical one-way functions. For the system described below, it is shown that there is a strong correspondence between the properties of physical one-way hash functions and their algorithmic counterparts. In particular, it is demonstrated that they are collision-resistant and that they exhibit the avalanche effect, i.e., a small change in the physical system causes a large change in the hash value. 
An inexpensive prototype authentication system based on physical one-way hash functions is designed, implemented, and analyzed. The prototype uses a disordered three-dimensional microstructure as the underlying physical system and coherent radiation as the probe. It is shown that the output of the interaction between the physical system and the probe can be used to robustly derive a unique tamper-resistant identifier at a very low cost per bit. The explicit use of three-dimensional structures marks a departure from prior efforts. Two protocols, including a one-time pad protocol, that illustrate the utility of these hash functions are presented and potential attacks on the authentication system are considered. 
Finally, the concept of fabrication complexity is introduced as a way of quantifying the difficulty of materially cloning physical systems with arbitrary internal states. Fabrication complexity is discussed in the context of an idealized machine—a Universal Turing Machine augmented with a fabrication head—which transforms algorithmically minimal descriptions of physical systems into the systems themselves. (Copies available exclusively from MIT Libraries, Rm. 14-0551, Cambridge, MA 02139-4307. Ph. 617-253-5668; Fax 617-253-1690.)

/pdf/physical-one-way-functions-3b8omsfwkl.pdf

Physical one-way functions

On trouve que l'intensite diffusee est augmentee jusqu'a 75% a l'interieur d'un cone etroit centre sur la direction de retrodiffusion

Weak localization and coherent backscattering of photons in disordered media.

We have measured the time autocorrelation function of the light intensity multiply scattered from turbid aqueous suspensions of submicron size polystyrene spheres in directions near backscattering. It is found strongly non-exponential at short times revealing the very fast decay of coherence in extended scattering loops due to the thermal motion of the many spheres involved; the longest living decay time is found remarkably close to the single particle backscattering relaxation time even under conditions of interparticle interactions. These features are only weakly affected by the particular interference effect between time-reversed pairs of loops giving rise to the coherent backscattering enhancement. A simple argument is presented which accounts for these observations.

Multiple Light Scattering from Disordered Media. The Effect of Brownian Motion of Scatterers

Recent experiments have confirmed that coherent effects in the multiple scattering of light affect the angular dependence of the intensity reflected by disordered media. By considering the constructive interferences between time-reversed paths of light in a semi-infinite medium, we analyze the experimental line shape of the albedo within the diffusion approximation and explain the observed effects of polarization.

Coherent backscattering of light by disordered media: Analysis of the peak line shape.

A theoretical study of the coherent backscattering effect of light from disordered semi-inifinite media is presented for various situations including time-dependent effects as well as absorption and amplitude modulation. Particular attention is devoted to the case of anisotropic scattering and to polarization in order to explain quantitatively experimental results. A microscopic derivation of the coherent albedo is given which strongly supports the heuristic formula previously established. In addition the coherent albedo of a fractal system is predicted. The validity of the different approximations used are discussed and some further theoretical developments are presented On inclut les effets dependant du temps, les milieux absorbants et les effets lies a la modulation d'amplitude de la lumiere

Theoretical study of the coherent backscattering of light by disordered media

A detailed experimental study of coherent backscattering of light from aqueous suspensions of polystyrene microspheres is presented. Emphasis is on the effects of particle size, of absorption due to added dye and of light polarization on the shape and height of the backscattering cone. For parallel polarization of incident and scattered beams, the scalar diffusion theory, parametrized by the transport mean free path l*, agrees well with our data up to surprizingly large scattering angles (ql * ~ 1) and quantitatively accounts for the rounding of the cones due to absorption. No deviations from the usual Gaussian statistics of scattered fields is observed up to λ/l* ∼ 0.1.

https://hal.archives-ouvertes.fr/jpa-00210675/document

Pierre-Etienne Wolf

Papers

Weak localization and coherent backscattering of photons in disordered media.

Multiple Light Scattering from Disordered Media. The Effect of Brownian Motion of Scatterers

Coherent backscattering of light by disordered media: Analysis of the peak line shape.

Theoretical study of the coherent backscattering of light by disordered media

Optical coherent backscattering by random media : an experimental study