Applications of Top Hat Output Laser Beams in Bioinformatics

A top hat output laser beam displays a uniform intensity profile that looks like a mountain top or the hat of a magician. The top hat distribution pattern has an area of constant radiance surrounded by hard edges that separate the high-intensity core area from the low-intensity region. This distribution pattern ensures consistent energy delivery across the cross-section of the laser beam which is critical for various industrial applications. Most naturally occurring light beams exhibit a Gaussian-like beam profile with a central maximum intensity point surrounded by gradually decaying edges. As a result of these slowly decaying edges, light extends beyond the desired area of operation, resulting in a noteworthy energy loss. Unlike Gaussian beams, which have an uneven intensity distribution, a top-hat laser beam displays a well-defined energy profile, reducing energy loss and improving efficiency.

How to Generate a Top Hat Distribution in Laser Beams?

To eliminate the unevenness of Gaussian beams, we need to shape or modify the intensity profile or phase of the input beam. There are a variety of beam-shaping methods that can be used to convert a laser beam profile into a top hat distribution pattern. Some common laser beam shapers are diffractive optical elements, microlens arrays, and flat-top diffusers. While diffractive optical elements are useful to modify the phase of a single-mode Gaussian laser beam, a flat-top diffuser can transform a multi-mode Gaussian beam.

Applications of Top Hat Output Beams in Bioinformatics

Top hat laser beams have a long list of industrial and medical applications. In recent times, the concept of a top hat output beam has been used in bioinformatics, especially in RNA sequencing (RNA-seq) and genomic research. RNA-seq or sequencing RNA transcripts is one of the powerful methods to study gene expression. The Top Hat distribution pattern acts as a crucial tool for genome analysis. The Top Hat program is designed to map RNA sequences to a reference genome. Original TopHat uses the Bowtie algorithm to align short-read sequences and detect exon-exon splice junctions efficiently. As a top hat output laser beam offers even energy distribution for precision applications, the TopHat algorithm ensures accurate RNA alignment and reduces errors in genome-wide studies.

Within bioinformatics workflows, a structured directory is essential for organizing sequencing data, alignment results, and processed files. The uniformity of top hat output is useful for streamlining genome analysis and obtaining more efficient results.

Other Major Applications of Top Hat Laser Beams

The consistent irradiance profile of a tophat output beam is used in several industrial applications that require coherent laser beams to be focused with precision into specific shapes and sizes. A well-designed DOE can modify the intensity distributions of the Top Hat laser beam into different shapes, including lines, circles, squares, rectangles, or even more complex geometrical shapes.

Some notable applications of top hat output beams are laser cutting, laser-scribing- electrodes, dias, etc., laser micromachining- micro-drilling, ablation, and kerf removal, lithography, microscopy & light-sheet cytometry, annealing and surface treatments, metrology of semiconductor wafers and many other.

Typical Setup for a Top Hat Beam Shaper

A typical setup for a top hat beam shaper includes diffractive optical elements placed between an input laser beam and a focusing lens. The focusing lens can positioned at any place after the DOEs. The focal plane of the lens reproduces the DOE’s far-field pattern.

To get the optimal performance from the top hat beam shaper, the length of the aperture and other optics across the beam path should be at least twice the diameter of the input laser beam. The lens and additional optics, such as folding mirrors, must ensure diffraction-limited and field-corrected performance. Despite these requirements, one can easily integrate top hat beam shapers into very small laser systems