Biosensor based on Surface Plasmon Resonance

Other most common technology commercially available is Surface Plasmon Resonance (SPR). SPR optical biosensor is often used for binding kinetics stud-ies, measuring antibody affinity and protein concentration. Figure 1.8 illustrates the principal scheme of SPR biosensor. It consists of a glass slide coated with no-ble metal thin film, which works as a sensor surface. On the sensor surface antigen is immobilized, which serves as transducer for antibody detection.

The principle of SPR is based on the interaction of metals with electromagnetic radiation. The surface charge density oscillations associated with surface plasmons at the interface between a metal and a dielectric can give rise to strongly enhanced optical near-fields specially confined near the metal surface. At a certain reso-nant condition under plasmon excitation, it can be used for immune biosensing applications. When a buffer solution with antibody is immobilized on the dielec-tric surface, it cause changes in the local index of refraction that are subsequently monitored .

Though SPR biosensor has the advantage of measuring binding rates in protein-protein interaction studies and in binding strengths, however some of the dominant

Figure 1.8:Principal scheme of SPR biosensor.

techniques suffer from low throughput in processing different samples, compli-cated microfluidics, expensive chips and limited sensitivity. Problem with sensitiv-ity is especially pronounced when working with protein-small-molecules, as well as with low concentrations, weak binders, and low levels of immobilized com-pounds. This type of biosensor is also limited by analytical specificity and non-specific binding, since any substance binding to the surface causes a change in the refractive index.

Other optical methods such as resonant waveguide grating (RWG) and bio-layer interferometry (BLI) are actively used for biosensing applications. The RWG, also named photonic crystal biosensor, relies on the resonant coupling of light into a waveguide. Such biosensor consits of a substrate and a periodic-embedded waveg-uide thin film. Similar to SPR it utilize evanescent wave interaction with the ana-lyte, as a result changes in local refractive index are measured. Contrary to SPR, BLI optical biosensor, is based on analysis of interference pattern in the reflected light intensity form the biosensor surface. White light irradiates two surfaces: a layer of immobilized protein, and a reference layer (usually glass), and reflected intensity as a function of wavelength is monitored.

Basic concepts

2.1 Introduction

Control over chemical reactions is a fascinating theme in physics and chemistry.

With the invention of laser in the 1960s, remarkable theoretical and experimental progress has been achieved in the area of control of molecular processes. Initially monochromatic lasers were proposed for bond-selective control of chemical reac-tions [53, 54]. The idea was simply to use a laser with a frequency tuned, to a specific chemical bond, so it could absorb radiation that would lead to its cleav-ing without damage of others. However, soon it was realized that the energy ab-sorbed at one bond is redistributed amongst other degrees of freedom of the excited molecule. Early attempts using selective laser excitation were thereby thwarted by fast intramolecular energy redistribution [55,56,57,58,59].

In 1980s femtosecond lasers have become available with the development of mode-locking techniques. So the issue of energy redistribution could be over-come using pulses with the duration of the chemical reaction time. Since then the application of femtosecond laser in new field of femtosecond spectroscopy and femtochemistry has developed rapidly. A Nobel laureate in Chemistry in 1999, Ahmed Zewail proposed to use femtosecond laser to study a motion of atoms and molecules during chemical reactions. A significant step forward was made in at-tempting to control microscopic system on the ultrafast time scale by using tailored laser pulses with femtosecond temporal resolution.

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Quantum control uses the properties of the laser to create a coherent super-position of vibrational eigenstates in excited molecules. Control of molecular wavepackets on the excited states became possible by manipulation of quantum in-terference of different pathways within a femtosecond time resolution. Several the-oretical methods were introduced and verified experimentally. In the first scheme, proposed theoretically by Brumer and Sharipo in 1986 [60,61], branching ratios in molecular photodissociation were controlled, and experimentally demonstrated in 1990 [62]. In this scenario two monochromatic lasers with tunable frequencies are simultaneously used to excite a continuum of vibronic states of molecule. It was shown that by adjusting the relative phase between two laser fields induces constructive or destructive interference in the desired and undesired reaction path-ways. A second approach introduced by Tannor, Koslov, and Rice [5,6] in 1985 is based on the sequences of femtosecond laser pulses, where control over molec-ular photodissociation was achieved by varying the time-delay. One of the pulses creates a vibrational wavepacket on the excited potential energy surface, while it travels to reach a particular point the second pulse probes at the time to re-excite the population to the ground surface, thereby promoting the desired reaction pathway.

These two schemes by Brumer-Sharipo and Tanor-Kosloff-Rice were implemented experimentally in 1990s with the development of femtosecond lasers [63,64,65].

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Figure 2.1: Quantum control pump-dump Tannor-Kosloff-Rice scheme. First pump pulse creates a wavepacket on the first excited state potential energy surface. Second laser pulse dumps the wavepacket into the desired product channel [5,6,7,8].

These approaches lead to the idea of designing specific tailored ultrashort laser pulses which can drive a molecule to a particular target state. This idea was relied on the continuous interaction of complex laser field with quantum system during the time of evolution of the molecular wave packet, until a desired outcome is reached [66,67,68,66,69,70]. With the development of pulse shaping techniques to modulate phase and amplitude, considerable progress has been made in fem-tosecond spectroscopy. In 1992, Judson and Rabitz proposed using a pulse shaping device in combination with a searching algorithm [71]. Employing feedback from the molecular system an optimal electric field which optimized a desired outcome can be found. At that time the concept of optimal control was introduced, and opened up numerous research avenues.

In this Chapter we introduce the basic principle of quantum control and show how the manipulation of molecular wave packets on the excited states can be used for the discrimination of molecules that have similar spectroscopic features. Most of the molecular systems that have biological significance, such as proteins, have an important compound Tryptophan (Trp). Trp is an aromatic amino-acid, which is often used as a protein reporter. Hereafter we describe the general properties of this molecule, reported in Section 2.4.