arXiv subjects

David J. Earl

Publications and source records attributed to David J. Earl.

7 recordsLinked to original sources

arXiv2007

Modeling microscopic swimmers at low Reynolds number

We employ three numerical methods to explore the motion of low Reynolds number swimmers, modeling the hydrodynamic interactions by means of the Oseen tensor approximation, lattice Boltzmann simulations and multiparticle collision dynamics. By applying the methods to a three bead linear swimmer, for which exact results are known, we are able to compare and assess the effectiveness of the different approaches. We then propose a new class of low Reynolds number swimmers, generalized three bead swimmers that can change both the length of their arms and the angle between them. Hence we suggest a design for a microstructure capable of moving in three dimensions. We discuss multiple bead, linear microstructures and show that they are highly efficient swimmers. We then turn to consider the swimming motion of elastic filaments. Using multiparticle collision dynamics we show that a driven filament behaves in a qualitatively similar way to the micron-scale swimming device recently demonstrated by Dreyfus et al.

cond-mat.soft↗

arXiv2005

Parallel Tempering: Theory, Applications, and New Perspectives

We review the history of the parallel tempering simulation method. From its origins in data analysis, the parallel tempering method has become a standard workhorse of physiochemical simulations. We discuss the theory behind the method and its various generalizations. We mention a selected set of the many applications that have become possible with the introduction of parallel tempering and we suggest several promising avenues for future research.

physics.comp-ph↗

arXiv2005

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 a balance has evolved between binding affinity and specificity in the mechanism for searching the amino acid sequence space of antibodies.

q-bio.PE↗

arXiv2005

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 analyzes 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.

q-bio.BM↗

arXiv2004

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.

physics.comp-ph↗

arXiv2004

Evolvability is a Selectable Trait

Concomitant with the evolution of biological diversity must have been the evolution of mechanisms that facilitate evolution, due to 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.

q-bio.PE↗

arXiv2004

Optimal Allocation of Replicas to Processors in Parallel Tempering Simulations

The optimal allocation of replicas to a homogeneous or heterogenous set of processors is derived for parallel tempering simulations on multi-processor machines. In the general case, it is possible without substantially increasing wall clock time to achieve nearly perfect utilization of CPU time. Random fluctuations in the execution times of each of the replicas do not significantly degrade the performance of the scheduler.

physics.comp-ph↗