UC Merced

Active matter systems are those whose individual constituents convert energy to move or perform mechanical work. Physicists have long been fascinated by active matter systems as they are inherently out of thermal equilibrium, making them much more difficult to classify and quantify using the traditional techniques of statistical mechanics. Biology, being comprised of many such systems, has become one of the most sought-after fields for the physics community. In this work, we are predominantly interested in biological machines that consume chemical energy, like ATP, and use this fuel to exert forces on their surroundings. We utilize theoretical and computational techniques to investigate these systems as in silico is a cost effective way to span the parameter space and learn design principles that can both decipher the current generation of in vivo and in vitro experiments and propel the next. Here, we develop minimal mechanical models, conduct computer simulations, and apply quantitative analytics at the cellular level (chapters 2, 3, and 4) and subcellular scale (chapter 5) to both gain insight into relevant design principles and make testable predictions regarding the system constituents and emergent behavior thereof. Specifically, in chapter 2, we ask if cells modeled solely as coarse grained anisotropic contractile force dipoles are sufficient to produce branched multicellular network structures and how the mechanical properties of the substrate and cell response to the substrate affect this tendency. In chapter 3, we ask if cells modeled as contractile dipoles in a discretized elastic medium can give rise to a strong nonlinearity in force production as a function of density suggested by recent experiments of fibroblasts embedded in collagen gels. In chapter 4, motivated by a wide variety of systems like synthetic Janus colloids in an alternating electric field and magnetotactic bacteria, we explore the collective behavior of highly motile contractile anisotropic dipoles. Lastly, in chapter 5, we ask if the geometric helicity of microtubules coupled to motor propulsion is sufficient to produce emergent chiral motion of isolated microtubules, rather than a fundamental chirality given by intrinsic curvature.