Related papers: Group theory of icosahedral virus capsids: a dynam…
We investigate the dynamics of microcapsules in linear shear flow within a reduced model with two degrees of freedom. In previous work for steady shear flow, the dynamic phases of this model, i.e. swinging, tumbling and intermittent…
Pairwise models are used widely to model epidemic spread on networks. These include the modelling of susceptible-infected-removed (SIR) epidemics on regular networks and extensions to SIS dynamics and contact tracing on more exotic networks…
The behavior of a colloidal suspension of rod-like {\it fd} viruses in the nematic phase, subjected to steady state and transient shear flows is studied. The monodisperse nature of these rods combined with relatively small textural…
We model the spontaneous assembly of a capsid (a virus's closed outer shell) from many copies of identical units, using entirely irreversible steps and only information local to the growing edge. Our model is formulated in terms of (i) an…
In a seminal paper Caspar and Klug established a theory that provides a family of polyhedra as blueprints for the structural organisation of viral capsids. In particular, they encode the locations of the proteins in the shells that…
Top-down causation has been suggested to occur at all scales of biological organization as a mechanism for explaining the hierarchy of structure and causation in living systems. Here we propose that a transition from bottom-up to top-down…
We present a generalized Landau-Brazovskii free energy for the solidification of chiral molecules on a spherical surface in the context of the assembly of viral shells. We encounter two types of icosahedral solidification transitions. The…
We study the quasi-periodicity phenomena occurring at the transition between tonic spiking and bursting activities in exemplary biologically plausible Hodgkin-Huxley type models of individual cells and reduced phenomenological models with…
There is growing recognition in both the experimental and modelling literature of the importance of spatial structure to the dynamics of viral infections in tissues. Aided by the evolution of computing power and motivated by recent…
We use the nudged elastic band method from computational chemistry to analyze high-dimensional data. Our approach is inspired by Morse theory, and as output we produce an increasing sequence of small cell complexes modeling the dense…
A computer model is described which is used to assess the dynamical complexity of a class of networks of spiking neurons with small-world properties. Networks are constructed by forming an initially segregated set of highly intra-connected…
The cowpea chlorotic mottle virus (CCMV) has emerged as an exemplary model system to assess the balance between electrostatic and topological features of ssRNA viruses, specifically in the context of the viral self-assembly process. Yet, in…
We present a new method, called SISYPHUS (Stochastic Iterations to Strengthen Yield of Path Hopping over Upper States), for extending accessible time-scales in atomistic simulations. The method proceeds by separating phase space into…
The variational method employing the amplitude and width as collective coordinates of the Klein-Gordon oscillon leads to a dynamical system with unstable periodic orbits that blow up when perturbed. We propose a multiscale variational…
A semiclassical model based on the solution of the Vlasov equation for finite systems with a sharp moving surface has been used to study the isoscalar quadrupole and octupole collective modes in heavy spherical nuclei. Within this model, a…
During the lifecycle of a virus, viral proteins and other components self-assemble to form a symmetric protein shell called a capsid. This assembly process is subject to multiple competing constraints, including the need to form a…
This paper develops a formal theory of musical scales and their harmonic coverings and introduces orbit covers: coverings obtained by translating a fixed subset across a scale via a group action. Orbit covers generalize familiar…
We investigate spinodal decomposition kinetics of an initially nematic dispersion of rod-like viruses (fd virus). Quench experiments are performed from a flow-stabilized homogeneous nematic state at high shear rate into the two-phase…
Torus canards are solutions of slow/fast systems that alternate between attracting and repelling manifolds of limit cycles of the fast subsystem. A relatively new dynamic phenomenon, torus canards have been found in neural applications to…
A method for studying the qualitative dynamical properties of abstract computing machines based on the approximation of their program-size complexity using a general lossless compression algorithm is presented. It is shown that the…