Wavelet Monte Carlo dynamics

The Wavelet Monte Carlo dynamics (WMCD) algorithm is developed from scratch to simulate hydrodynamically coupled Brownian particles at low Reynolds numbers. The basic premise is to construct a regularised version of the Oseen tensor out of a distribution of 3-dimensional vector wavelets that displace groups of particles so as to evolve the system in time while correlating the motion of all particles according to their separation. In doing so, the Oseen tensor is made implicit in the simulation code and the computational complexity of WMCD scales with system size N as N lnN (or even linearly in fractal systems), comparing favourably to existing Brownian dynamics algorithms, while the absence of any solvent degrees of freedom also leads to favourable comparisons with explicit-solvent methods. WMCD therefore holds promise to simulate system sizes beyond the reach of the alternatives. Key extensions to the basic algorithm are presented - none of which affect the computational complexity - including additional Fourier moves and smart Monte Carlo biasing to improve the algorithm's dynamical fidelity, as well as schemes to build in polydispersity and hydrodynamic coupling of particle rotations. WMCD is then used in a comprehensive study of the diffusion of isolated polymer chains, using the properties of the centre of mass velocity autocorrelation to identify distinct short and long-time regimes driving the reduction of diffusivity from the Kirkwood value. Using similar methods in a very different context, WMCD is also used to study the enhanced diffusion of passive particles in active suspensions. Here again the velocity autocorrelation proves useful in understanding the underlying physics, with three driving mechanisms identified depending on relative particle sizes. Of particular note is the importance of thermal fluctuations, often neglected in active matter research but central to WMCD

Time reversal of the overdamped Langevin equation and Fixman’s law

We show that the first order Langevin equation for the overdamped dynamics of an interacting system has a natural time reversal of simple but surprising form. This leads to a clear derivation of Fixman’s relation for how interactions modify the time dependent response of the system, and we show the application to the time dependent diffusion of dilute polymer coils. We find the generalized “Fixman Law” for dissipation with a memory kernel, and we also discuss the case of the second order Langevin Equation

Influence of thermal fluctuations on active diffusion at large Péclet numbers

Three-dimensional Wavelet Monte Carlo dynamics simulations are used to study the dynamics of passive particles in the presence of microswimmers—both represented by neutrally buoyant spheres—taking into account the often-omitted thermal motion alongside the hydrodynamic flows generated by the swimmers. Although the Péclet numbers considered are large, we find the thermal motion to have a significant effect on the dynamics of our passive particles and can be included as a decorrelation factor in the velocity autocorrelation with a decay time proportional to the Péclet number. Similar decorrelation factors come from swimmer rotations, e.g., run and tumble motion, and apply to both entrainment and far field loop contributions. These decorrelation factors lead to active diffusivity having a weak apparent power law close to Pe0.2 for small tracer-like particles at Péclet numbers appropriate for E. coli swimmers at room temperature. Meanwhile, the reduced hydrodynamic response of large particles to nearby forces has a corresponding reduction in active diffusivity in that regime. Together, they lead to a non-monotonic dependence of active diffusivity on particle size that can shed light on similar behavior observed in the experiments by Patteson et al. [“Particle diffusion in active fluids is non-monotonic in size,” Soft Matter 12, 2365–2372 (2016)]

Wavelet Monte Carlo dynamics : a new algorithm for simulating the hydrodynamics of interacting Brownian particles

We develop a new algorithm for the Brownian dynamics of soft matter systems that evolves time by spatially correlated Monte Carlo moves. The algorithm uses vector wavelets as its basic moves and produces hydrodynamics in the low Reynolds number regime propagated according to the Oseen tensor. When small moves are removed the correlations closely approximate the Rotne-Prager tensor, itself widely used to correct for deficiencies in Oseen. We also include plane wave moves to provide the longest range correlations, which we detail for both infinite and periodic systems. The computational cost of the algorithm scales competitively with the number of particles simulated, N, scaling as N ln N in homogeneous systems and as N in dilute systems. In comparisons to established lattice Boltzmann and Brownian dynamics algorithms the wavelet method was found to be only a factor of order 1 times more expensive than the cheaper lattice Boltzmann algorithm in marginally semi-dilute simulations, while it is significantly faster than both algorithms at large N in dilute simulations. We also validate the algorithm by checking it reproduces the correct dynamics and equilibrium properties of simple single polymer systems, as well as verifying the effect of periodicity on the mobility tensor

Farmer seed networks make a limited contribution to agriculture? Four common misconceptions

The importance of seed provisioning in food security and nutrition, agricultural development and rural livelihoods, and agrobiodiversity and germplasm conservation is well accepted by policy makers, practitioners and researchers. The role of farmer seed networks is less well understood and yet is central to debates on current issues ranging from seed sovereignty and rights for farmers to GMOs and the conservation of crop germplasm. In this paper we identify four common misconceptions regarding the nature and importance of farmer seed networks today. (1) Farmer seed networks are inefficient for seed dissemination. (2) Farmer seed networks are closed, conservative systems. (3) Farmer seed networks provide ready, egalitarian access to seed. (4) Farmer seed networks are destined to weaken and disappear. We challenge these misconceptions by drawing upon recent research findings and the authors’ collective field experience in studying farmer seed systems in Africa, Europe, Latin America and Oceania. Priorities for future research are suggested that would advance our understanding of seed networks and better inform agricultural and food policy

'To live and die [for] Dixie': Irish civilians and the Confederate States of America

Around 20,000 Irishmen served in the Confederate army in the Civil War. As a result, they left behind, in various Southern towns and cities, large numbers of friends, family, and community leaders. As with native-born Confederates, Irish civilian support was crucial to Irish participation in the Confederate military effort. Also, Irish civilians served in various supporting roles: in factories and hospitals, on railroads and diplomatic missions, and as boosters for the cause. They also, however, suffered in bombardments, sieges, and the blockade. Usually poorer than their native neighbours, they could not afford to become 'refugees' and move away from the centres of conflict. This essay, based on research from manuscript collections, contemporary newspapers, British Consular records, and Federal military records, will examine the role of Irish civilians in the Confederacy, and assess the role this activity had on their integration into Southern communities. It will also look at Irish civilians in the defeat of the Confederacy, particularly when they came under Union occupation. Initial research shows that Irish civilians were not as upset as other whites in the South about Union victory. They welcomed a return to normalcy, and often 'collaborated' with Union authorities. Also, Irish desertion rates in the Confederate army were particularly high, and I will attempt to gauge whether Irish civilians played a role in this. All of the research in this paper will thus be put in the context of the Drew Gilpin Faust/Gary Gallagher debate on the influence of the Confederate homefront on military performance. By studying the Irish civilian experience one can assess how strong the Confederate national experiment was. Was it a nation without a nationalism

Facultative Symbiont Infections Affect Aphid Reproduction

Some bacterial symbionts alter their hosts reproduction through various mechanisms that enhance their transmission in the host population. In addition to its obligatory symbiont Buchnera aphidicola, the pea aphid Acyrthosiphon pisum harbors several facultative symbionts influencing several aspects of host ecology. Aphids reproduce by cyclical parthenogenesis whereby clonal and sexual reproduction alternate within the annual life cycle. Many species, including the pea aphid, also show variation in their reproductive mode at the population level, with some lineages reproducing by cyclical parthenogenesis and others by permanent parthenogenesis. While the role of facultative symbionts has been well studied during the parthenogenetic phase of their aphid hosts, very little is known on their possible influence during the sexual phase. Here we investigated whether facultative symbionts modulate the capacity to produce sexual forms in various genetic backgrounds of the pea aphid with controlled symbiont composition and also in different aphid genotypes from natural populations with previously characterized infection status and reproductive mode. We found that most facultative symbionts exhibited detrimental effects on their hosts fitness under sex-inducing conditions in comparison with the reference lines. We also showed that the loss of sexual phase in permanently parthenogenetic lineages of A. pisum was not explained by facultative symbionts. Finally, we demonstrated that Spiroplasma infection annihilated the production of males in the host progeny by inducing a male-killing phenotype, an unexpected result for organisms such as aphids that reproduce primarily through clonal reproduction

Prox1 Regulates the Notch1-Mediated Inhibition of Neurogenesis

During development of the spinal cord, Prox1 controls the balance between proliferation and differentiation of neural progenitor cells via suppression of Notch1 gene expression

Prox1 Is Required for Granule Cell Maturation and Intermediate Progenitor Maintenance During Brain Neurogenesis

The transcription factor Prox1 plays a crucial role in intermediate progenitor maintenance and hippocampal neuron differentiation during adult neurogenesis in the dentate gyrus region of the hippocampus