Fibrin fiber deformation mechanisms: insights from phenomenological modeling to molecular details

The deformation mechanism of fibrin fibers has been a long-standing challenge to uncover due to the fiber's complex structure and mechanical behaviors. In this paper, a phenomenological, bilinear, force-strain model is derived to accurately reproduce the fibrin fiber force-strain curve, and then, the phenomenological model is converted to a mechanistic model using empirical relationships developed from particle simulation data. The mechanistic model assumes that the initial linear fibrin fiber force-strain response is due to entropic extension of polypeptide chains, and the final linear response is due to enthalpic extension of protofibrils. This model is the first fibrin fiber tensile force-strain equation to simultaneously (1) reproduce the bilinear force-strain curve of fibrin fibers in tension; (2) explicitly include the number of protofibrils through the fibrin fiber cross section, persistence length of [Formula: see text]-regions, and stiffness of fibrin protofibrils; and (3) make demonstrably reasonable/accurate predictions of fibrin fiber mechanics when tempered against experimental results. The model predicted that the count of protofibrils through the cross section for the analyzed fibrin fibers is between 207 and 421, the persistence length of [Formula: see text]-regions is [Formula: see text], and the stiffness of protofibrils in a deforming fiber is [Formula: see text]. The predicted [Formula: see text]-region persistence length is within the range typical of amino acid residue lengths [Formula: see text] and the predicted protofibril stiffness is shown to correspond to half-staggered protofibrils of unfolded fibrin monomers. Our analysis supports the proposition that entropic extension of [Formula: see text]-regions could be responsible for fibrin fiber's initial force-strain stiffness and suggests a structural change in fibrin protofibrils during fibrin fiber deformation. The results from the model are compared to those from five candidate deformation mechanisms reported in the literature. Our work provides (1) strong quantitative support to a deformation mechanism that was previously supported by anecdote and qualitative argument, and (2) a model for rigorously analyzing fibrin fiber force-strain data and simulating fibrin fibers in tension.

The metaphysical underdetermination of time-reversal invariance

In this paper I argue that the concept of time-reversal invariance in physics suffers from metaphysical underdetermination, that is, that the concept may be understood differently depending on one's metaphysics about time, laws, and a theory's basic properties. This metaphysical under-determinacy also affects subsidiary debates in philosophy of physics that rely on the concept of time-reversal invariance, paradigmatically the problem of the arrow of time. I bring up three cases that, I believe, fairly illustrate my point. I conclude, on the one hand, that any formal representation of time reversal should be explicit about the metaphysical assumptions of the concept that it intends to represent; on the other, that philosophical arguments that rely on time reversal to argue against a direction of time require additional premises.

Drift as constitutive: conclusions from a formal reconstruction of population genetics

This article elaborates on McShea and Brandon's idea that drift is unlike the rest of the evolutionary factors because it is constitutive rather than imposed on the evolutionary process. I show that the way they spelled out this idea renders it inadequate and is the reason why it received some (good) objections. I propose a different way in which their point could be understood, that rests on two general distinctions. The first is a distinction between the underlying mathematical apparatus used to formulate a theory and a concept proposed by that theory. With the aid of a formal reconstruction of a population genetic model, I show that drift belongs to the first category. That is, that drift is constitutive of population genetics in the same sense that multiplication is constitutive in classical mechanics, or that circle is constitutive in Ptolemaic astronomy. The second distinction is between eliminating a concept from a theory and setting its value to zero. I will show that even though drift can be set to zero just like the rest of the evolutionary factors (as others have noted in their criticism of McShea and Brandon), eliminating drift is much harder than eliminating those other factors, since it would require changing the entire mathematical apparatus of standard population genetic theory. I conclude by drawing some other implications from the proposed formal reconstruction.

Lee Pedersen’s work in theoretical and computational chemistry and biochemistry

Nature at the lab level in biology and chemistry can be described by the application of quantum mechanics. In many cases, a reasonable approximation to quantum mechanics is classical mechanics realized through Newton’s equations of motion. Dr. Pedersen began his career using quantum mechanics to describe the properties of small molecular complexes that could serve as models for biochemical systems. To describe large molecular systems required a drop-back to classical means and this led surprisingly to a major improvement in the classical treatment of electrostatics for all molecules, not just biological molecules. Recent work has involved the application of quantum mechanics for the putative active sites of enzymes to gain greater insight into the key steps in enzyme catalysis.