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Diseases caused by pathogenic agents such as bacteria and viruses result in devastating costs on personal and societal levels. However, it is not just the emergence of new diseases that is problematic. Antibiotic resistance among bacteria makes uncomplicated infections difficult and lethal. Resilient disease-causing spores spread in hospitals, the food industry, and water supplies requiring effective detection and disinfection methods. Further, we face complex neurological diseases where no effective treatment or diagnostic methods exist. Thus, we must increase our fundamental understanding of these diseases to develop effective diagnostic, detection, disinfection, and treatment methods.

Classically, the methods used for detecting and studying the underlying mechanics of pathogenic agents work on a large scale, measuring the average macroscopic behavior and properties of these pathogens. However, just as with humans, the average behavior is not always representative of individual behavior. Therefore, it is also essential to investigate the characteristics of these pathogens on a single cell or particle level. 

This thesis develops and applies optical techniques to characterize pathogenic biomaterial on a single cell or particle level. At the heart of all these studies is our Optical Tweezers (OT) instrument. OT are a tool that allows us to reach into the microscopic world and interact with it. Finally, by combining OT with other experimental techniques, we can chemically characterize biomaterials and develop assays that mimic different biological settings. Using these tools, we investigate bacterial adhesion, disinfection, and detection of pathogenic spores and proteins.

Hopefully, the insights of these studies can lessen the burden on society caused by diseases by helping others develop effective treatment, diagnostic, detection, and disinfection methods in the future. 

Harmful chemical and biological agents are a significant threat to health and prosperity worldwide. Recent years have seen an increase in wars and conflicts around the globe, raising concerns about the potential deployment of chemical and biological warfare agents. On a less speculative level, harmful chemicals such as narcotic substances cause immense humanitarian and economic damage through overdoses and associated healthcare costs, while microbes such as pathogenic bacteria and parasites cause hospital-acquired infections and food spoilage at a cost of approximately 1 trillion euros every year. To combat the threat of these harmful agents, we must thus develop rapid and effective detection and diagnostic methods for harmful agents, allowing us to effectively deploy specific treatments and preventative measures.

Classically, while there exist numerous methods for the detection of both harmful chemical and biological agents, they often come with limitations that inhibit their effectiveness. These inhibitions often take the form of bulky equipment that is difficult to apply in the field or time-consuming preparation and measurement processes.

In this thesis we will explore an alternative category of assays for detecting and characterizing harmful materials – optical spectroscopy. Optical spectroscopy is a category of material characterization methods that use light to probe a material. While probing the material, we receive a signal characteristic of the molecules, chemical, and biological structure of our material. These optical spectroscopic methods, such as Raman spectroscopy and fluorescence spectroscopy, can be used to characterize a material within the span of minutes or even seconds, making them ideal for detection applications. Furthermore, they can often be made portable or even handheld, making them a great tool for initial field indication of harmful materials, ahead of thorough lab analysis.

I sincerely hope the studies presented herein can serve as a stepping stone to future technologies and detection assays, capable of saving both money and lives.