Mechanical and dielectric properties of pure-silica-zeolite low-k materials.
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Crystallography, X-Ray↗
Biomedical subjects
David J Earl
Publications and source records attributed to David J Earl.
Quantifying influenza vaccine efficacy and antigenic distance.
We introduce a new measure of antigenic distance between influenza A vaccine and circulating strains. The measure correlates well with efficacies of the H3N2 influenza A component of the annual vaccine between 1971 and 2004, as do results of a theory of the immune response to influenza following vaccination. This new measure of antigenic distance is correlated with vaccine efficacy to a greater degree than are current state of the art phylogenetic sequence analyses or ferret antisera inhibition assays. We suggest that this new measure of antigenic distance be used in the design of the annual influenza vaccine and in the interpretation of vaccine efficacy monitoring.
Algorithms↗
Glassy dynamics in the adaptive immune response prevents autoimmune disease.
The immune system normally protects the human host against death by infection. However, when an immune response is mistakenly directed at self-antigens, autoimmune disease can occur. We describe a model of protein evolution to simulate the dynamics of the adaptive immune response to antigens. Computer simulations of the dynamics of antibody evolution show that different evolutionary mechanisms, namely, gene segment swapping and point mutation, lead to different evolved antibody binding affinities. Although a combination of gene segment swapping and point mutation can yield a greater affinity to a specific antigen than point mutation alone, the antibodies so evolved are highly cross reactive and would cause autoimmune disease, and this is not the chosen dynamics of the immune system. We suggest that in the immune system's search for antibodies, a balance has evolved between binding affinity and specificity.
Animals↗
Markov chains of infinite order and asymptotic satisfaction of balance: application to the adaptive integration method.
Adaptive Monte Carlo methods can be viewed as implementations of Markov chains with infinite memory. We derive a general condition for the convergence of a Monte Carlo method whose history dependence is contained within the simulated density distribution. In convergent cases, our result implies that the balance condition need only be satisfied asymptotically. As an example, we show that the adaptive integration method converges.
Algorithms↗
Induced and spontaneous deracemization in bent-core liquid crystal phases and in other phases doped with bent-core molecules.
Recently discovered chiral properties of several bent-core smectic liquid crystal phases are summarized and discussed in detail under the assumption that typical bent-core molecules may exist in chiral conformational states and are achiral only on average. Results of atomistic computer simulations are presented which indicate the existence of strongly chiral conformational states for typical bent-core mesogens. A theory is developed which describes a possible shift of equilibrium between left- and right-handed conformations in a macroscopically chiral phase. The theory describes a chirality induction in the B2 bent-core phase and a reduction of the helical pitch in cholesteric and chiral SmC* phases doped with bent-core molecules. Finally, the possibility of spontaneous deracemization in bent-core smectic phases is discussed in detail.
Journal Article↗
Evolvability is a selectable trait.
Concomitant with the evolution of biological diversity must have been the evolution of mechanisms that facilitate evolution, because of the essentially infinite complexity of protein sequence space. We describe how evolvability can be an object of Darwinian selection, emphasizing the collective nature of the process. We quantify our theory with computer simulations of protein evolution. These simulations demonstrate that rapid or dramatic environmental change leads to selection for greater evolvability. The selective pressure for large-scale genetic moves such as DNA exchange becomes increasingly strong as the environmental conditions become more uncertain. Our results demonstrate that evolvability is a selectable trait and allow for the explanation of a large body of experimental results.
Computer Simulation↗
Calculations of helical twisting powers from intermolecular torques.
We present a Monte Carlo molecular simulation method that calculates the helical twisting power of a chiral molecule by sampling intermolecular torques. The approach is applied to an achiral nematic liquid crystalline system, composed of Gay-Berne particles, that is doped with chiral molecules. Calculations are presented for six chiral dopant molecules and the results show a good correlation with the sign and magnitude of experimentally determined helical twisting powers.
Computer Simulation↗