Phenomenological Perspectives in Biophysics

At the subcellular scale, physical properties of living matter, such as viscoelasticity, emerge from the collective dynamics of molecular constituents. Inspired by the idea of Laplace’s demon, which presumes perfect predictability given full microscopic information, this thesis addresses the seemingly inherent unpredictability and complexity of biological systems. Heterogeneity and emergent behavior limit reductionist strategies and suggest a phenomenological perspective to understand how macroscopic function arises from microscopic interactions. The central objective of this thesis is to advance the quantitative understanding of biological matter at the mesoscale by developing and applying label-free measurement techniques. I demonstrate that key biophysical parameters can be inferred without exogenous tracers, by exploiting light-matter interactions. In particular, I focus on differential dynamic microscopy (DDM), a technique that provides access to dynamical, structural, and viscoelastic information from living and complex biological specimens, without the need for fluorescent or mechanical labels. The theoretical framework for this work is firmly grounded in statistical mechanics. A major focus of this research is the cytoplasm, studied through experiments on Xenopus laevis egg extract and supported by theoretical modeling and simulations. The results establish that DDM enables quantitative assessment of emergent dynamics, such as subdiffusive viscoelasticity, the role of the cytoskeleton, and the degree of molecular crowding and heterogeneity. These findings show that complex biological dynamics can be reliably measured in their native context, without the need for exogenous probes. In addition to microrheological analysis, I develop and apply label-free optical methods to estimate local mass density from refractive index measurements. This approach provides further insight into the spatial organization and compositional heterogeneity within cells and tissues. By combining microrheological and optical strategies, the thesis establishes a basis for a unified, phenomenological framework that connects the dynamical, structural, and compositional aspects of biological matter. The work concludes by outlining how this integrated, label-free methodology offers a practical path forward for biophysical research. By minimizing perturbation and facilitating physical interpretability, the approach developed here provides a means to investigate the emergence of function and order in living systems, and highlights open questions for future experimental and theoretical work.