Blood clotting inspired polymer physics

Abstract

The blood clotting process is one of the human body's masterpieces in targeted molecular manipulation, as it requires the activation of the clotting cascade at a specific place and a specific time. Recent research in the biological sciences have discovered that one of the protein molecules involved in the initial stages of the clotting response, von Willebrand Factor (vWF), exhibits counterintuitive and technologically useful properties that are driven in part by the physical environment in the bloodstream at the site of a wound. In this thesis, we take inspiration from initial observations of the vWF in experiments, and aim to describe the behaviors observed in this process within the context of polymer physics. By understanding these physical principles, we hope to harness nature's ability to both direct molecules in both spatial and conformational coordinates. This thesis is presented in three complementary sections. After an initial introduction describing the systems of interest, we first describe the behavior of collapsed Lennard-Jones polymers in the presence of an infinite medium. It has been shown that simple bead-spring homopolymer models describe vWF quite well in vitro. We build upon this previous work to first describe the behavior of a collapsed homopolymer in an elongational fluid flow. Through a nucleation-protrusion mechanism, scaling relationships can be developed to provide a clear picture of a first-order globule-stretch transition and its ramifications in dilute-solution rheology. The implications of this behavior and its relation to the current literature provides qualitative explanations for the physiological process of vasoconstriction. In an effort to generalize these observations, we present an entire theory on the behavior of polymer globules under influence of any local fluid flow. Finally, we investigate the internal dynamics of these globules by probing their pulling response in an analogous fashion to force spectroscopy. We elucidate the presence of both a solid-liquid dynamic globule transition and a contour-based description of internal globule friction. It is possible to incrementally add levels of details to these Lennard-Jones polymer models to more accurately represent biological molecules. In the second section of this thesis, we investigate the consequences of incorporating a Bell-model behavior into single homopolymer interactions to describe a "self-associating" polymer. We first demonstrate how this model is, in equilibrium, essentially the same as a Lennard-Jones polymer, however we demonstrate that the polymer dynamics are indeed both drastically different and tunable. This has ramifications under the presence of dynamic loads, and we investigate single-molecule response to both shear and pulling stimuli. In the former, we find novel and tunable giant non-monotonic stretching responses. In the latter, we use our observations to develop a complete and general theory of pulling these types of molecules that has ramifications in both the study of biological polymers and in the design of soft materials with tunable mechanical response. The final section introduces concepts related to the behavior of collapsed polymers in fluid flows near surfaces. During the blood clotting process, vWF undergoes a counterintuitive adsorption process and here we begin to develop the physical fundamentals required to understand this process. After a brief introduction to the relevant hydrodynamic treatment we use in simulations, we first describe the presence of a hydrodynamic lift force and the formalism we use as we include it in the context of our theory. We reveal the presence of a non-monotonic lift force, and subsequently utilize this theoretical formalism to describe the adsorption and desorption behavior of a collapsed polymer globule near an attractive surface. We investigate the limit of large flows and highly attractive surfaces by providing a description of the conformational and hydrodynamic behavior of a polymer tethered at a surface. We finally discuss the behaviors of a polymer that associates with a surface, and postulate the importance of such processes in vWF function. We finally include an addendum that describes an unrelated project that investigates the possibilities of using superparamagnetic beads as a tool for hydrodynamic propulsion by assembling these beads into "rotors" near a surface to create micro-walkers that have interesting applications in self-assembled microfluidic chips.