Linear and non-linear theory of a parametric instability of hydrodynamic warps in Keplerian discs

We consider the stability of warping modes in Keplerian discs. We find them to be parametrically unstable using two lines of attack, one based on three-mode couplings and the other on Floquet theory. We confirm the existence of the instability, and investigate its nonlinear development in three dimensions, via numerical experiment. The most rapidly growing non-axisymmetric disturbances are the most nearly axisymmetric (low m) ones. Finally, we offer a simple, somewhat speculative model for the interaction of the parametric instability with the warp. We apply this model to the masing disc in NGC 4258 and show that, provided the warp is not forced too strongly, parametric instability can fix the amplitude of the warp.Comment: 14 pages, 6 figures, revised version with appendix added, to be published in MNRA

Towards Automated Benchmarking of Atomistic Forcefields: Neat Liquid Densities and Static Dielectric Constants from the ThermoML Data Archive

Atomistic molecular simulations are a powerful way to make quantitative predictions, but the accuracy of these predictions depends entirely on the quality of the forcefield employed. While experimental measurements of fundamental physical properties offer a straightforward approach for evaluating forcefield quality, the bulk of this information has been tied up in formats that are not machine-readable. Compiling benchmark datasets of physical properties from non-machine-readable sources require substantial human effort and is prone to accumulation of human errors, hindering the development of reproducible benchmarks of forcefield accuracy. Here, we examine the feasibility of benchmarking atomistic forcefields against the NIST ThermoML data archive of physicochemical measurements, which aggregates thousands of experimental measurements in a portable, machine-readable, self-annotating format. As a proof of concept, we present a detailed benchmark of the generalized Amber small molecule forcefield (GAFF) using the AM1-BCC charge model against measurements (specifically bulk liquid densities and static dielectric constants at ambient pressure) automatically extracted from the archive, and discuss the extent of available data. The results of this benchmark highlight a general problem with fixed-charge forcefields in the representation low dielectric environments such as those seen in binding cavities or biological membranes

Advection of vector fields by chaotic flows

We have introduced a new transfer operator for chaotic flows whose leading eigenvalue yields the dynamo rate of the fast kinematic dynamo and applied cycle expansion of the Fredholm determinant of the new operator to evaluation of its spectrum. The theory hs been tested on a normal form model of the vector advecting dynamical flow. If the model is a simple map with constant time between two iterations, the dynamo rate is the same as the escape rate of scalar quantties. However, a spread in Poincar\'e section return times lifts the degeneracy of the vector and scalar advection rates, and leads to dynamo rates that dominate over the scalar advection rates. For sufficiently large time spreads we have even found repellers for which the magnetic field grows exponentially, even though the scalar densities are decaying exponentially.Comment: 12 pages, Latex. Ask for figures from [email protected]

Evidence of strong small-scale population structure in the Antarctic freshwater copepod Boeckella poppei in lakes on Signy Island, South Orkney Islands

Environmental conditions were particularly severe during the Last Glacial Maximum, altering the distribution of the Southern Hemisphere biota, particularly at higher latitudes. The copepod Boeckella poppei is the only macroscopic continental invertebrate species known to be distributed today across the three main biogeographic regions in Antarctica as well as in southern South America. Signy Island (South Orkney Islands) is a unique location for the study of Antarctic freshwater ecosystems due to its location and geographic isolation; it contains 17 lakes in several low altitude catchments. We conducted phylogeographic and demographic analyses using the cox1 gene on 84 individuals of B. poppei from seven lakes across Signy Island. We recorded low levels of genetic diversity and a strong genetic differentiation signal between the eastern and western valleys within the island. Phylogeographic structure and demographic inference analyses suggested at least one asymmetrical dispersal event from west to east. Demographic inference detected a strong signal of population growth during the deglaciation process, which may have followed either (1) a strong genetic bottleneck due to a reduction in population size during the last glacial period, or (2) a founder effect associated with postglacial recolonization of Signy Island from elsewhere. The genetic architecture of this island's populations of B. poppei shows that historical events, rather than continuous dispersal events, likely played a major role in the species' current distribution. Finally, our study considers possible mechanisms for dispersal and colonization success of the most dominant species in the Antarctic freshwater community

Size-Dependent Transition to High-Dimensional Chaotic Dynamics in a Two-Dimensional Excitable Medium

The spatiotemporal dynamics of an excitable medium with multiple spiral defects is shown to vary smoothly with system size from short-lived transients for small systems to extensive chaos for large systems. A comparison of the Lyapunov dimension density with the average spiral defect density suggests an average dimension per spiral defect varying between three and seven. We discuss some implications of these results for experimental studies of excitable media.Comment: 5 pages, Latex, 4 figure

Best practices for constructing, preparing, and evaluating protein-ligand binding affinity benchmarks

Free energy calculations are rapidly becoming indispensable in structure-enabled drug discovery programs. As new methods, force fields, and implementations are developed, assessing their expected accuracy on real-world systems (benchmarking) becomes critical to provide users with an assessment of the accuracy expected when these methods are applied within their domain of applicability, and developers with a way to assess the expected impact of new methodologies. These assessments require construction of a benchmark - a set of well-prepared, high quality systems with corresponding experimental measurements designed to ensure the resulting calculations provide a realistic assessment of expected performance when these methods are deployed within their domains of applicability. To date, the community has not yet adopted a common standardized benchmark, and existing benchmark reports suffer from a myriad of issues, including poor data quality, limited statistical power, and statistically deficient analyses, all of which can conspire to produce benchmarks that are poorly predictive of real-world performance. Here, we address these issues by presenting guidelines for (1) curating experimental data to develop meaningful benchmark sets, (2) preparing benchmark inputs according to best practices to facilitate widespread adoption, and (3) analysis of the resulting predictions to enable statistically meaningful comparisons among methods and force fields

Falling behind and catching up : India’s transition from a colonial economy

India fell behind during colonial rule. The absolute and relative decline of Indian GDP per capita with respect to Britain began before colonization and coincided with the rising textile trade with Europe in the 18th century. The decline of traditional industries was not the main driver Indian decline and stagnation. Inadequate investment in agriculture and consequent decline in yield per acre stalled economic growth. Modern industries emerged and grew relatively fast. The falling behind was reversed after independence. Policies of industrialization and a green revolution in agriculture increased productivity growth in agriculture and industry, but Indian growth has been led by services. A strong focus on higher education under colonial policy had created an advantage for the service sector, which today has a high concentration of human capital. However, the slow expansion in primary education was a disadvantage in comparison with the high growth East Asian economies

Introduction to the special issue: after trust

“Trust” has long been seen as critical to the success and durability of trading networks, and conceptualised as a positive moral sentiment that is embedded in shared kinship, ethnicity or friendship, or in shared frameworks of morality. Other recent studies of business communities suggest that the ability to work in settings characterised by pervasive mistrust is a key factor in the development of commercial acumen and determining success. This Special Issue argues that the focus on trust and mistrust, and the underlying concern with ethics and morality, obscure equally critical aspects that inform the durability of trading networks. It offers ethnographic accounts of different inter-Asian trading networks active in the city of Yiwu. One of China’s most dynamic and diverse ‘international trade cities’, Yiwu is home to the largest wholesale market of small commodities in the world, and attracts traders and merchants from across the planet; over 12,000 foreign traders are also resident in the city. The collected articles analyse the durability of these networks in relation to broader geopolitical processes and contexts, arguing that success often depends on the ability to negotiate geopolitical shifts and the faultlines of political identity. The articles trace traders’ efforts to create institutions that allow them to withstand geopolitical transformations. They also document the ability of trading networks to operate flexibly across different social fields, showing that resilience often depends on the ability to navigate and profit from shifting relations between economic, political and familial domains

The regulatory subunit of PKA-I remains partially structured and undergoes β-aggregation upon thermal denaturation

Background: The regulatory subunit (R) of cAMP-dependent protein kinase (PKA) is a modular flexible protein that responds with large conformational changes to the binding of the effector cAMP. Considering its highly dynamic nature, the protein is rather stable. We studied the thermal denaturation of full-length RIα and a truncated RIα(92-381) that contains the tandem cyclic nucleotide binding (CNB) domains A and B. Methodology/Principal Findings: As revealed by circular dichroism (CD) and differential scanning calorimetry, both RIα proteins contain significant residual structure in the heat-denatured state. As evidenced by CD, the predominantly α-helical spectrum at 25°C with double negative peaks at 209 and 222 nm changes to a spectrum with a single negative peak at 212-216 nm, characteristic of β-structure. A similar α→β transition occurs at higher temperature in the presence of cAMP. Thioflavin T fluorescence and atomic force microscopy studies support the notion that the structural transition is associated with cross-β-intermolecular aggregation and formation of non-fibrillar oligomers. Conclusions/Significance: Thermal denaturation of RIα leads to partial loss of native packing with exposure of aggregation-prone motifs, such as the B' helices in the phosphate-binding cassettes of both CNB domains. The topology of the β-sandwiches in these domains favors inter-molecular β-aggregation, which is suppressed in the ligand-bound states of RIα under physiological conditions. Moreover, our results reveal that the CNB domains persist as structural cores through heat-denaturation. © 2011 Dao et al