Graph Theory and Networks in Biology

In this paper, we present a survey of the use of graph theoretical techniques in Biology. In particular, we discuss recent work on identifying and modelling the structure of bio-molecular networks, as well as the application of centrality measures to interaction networks and research on the hierarchical structure of such networks and network motifs. Work on the link between structural network properties and dynamics is also described, with emphasis on synchronization and disease propagation.Comment: 52 pages, 5 figures, Survey Pape

Global phase-locking in finite populations of phase-coupled oscillators

We present new necessary and sufficient conditions for the existence of fixed points in a finite system of coupled phase oscillators on a complete graph. We use these conditions to derive bounds on the critical coupling.Comment: 31 pages; to appear in SIAM journal of dynamical systems (SIADS

Fiscal Effects of Aid

Fiscal policy, Aid, Sub-Saharan Africa

The influence of geometry, surface character and flexibility on the permeation of ions and water through biological pores

A hydrophobic constriction site can act as an efficient barrier to ion and water permeation if its diameter is less than the diameter of an ion's first hydration shell. This hydrophobic gating mechanism is thought to operate in a number of ion channels, e.g. the nicotinic receptor, bacterial mechanosensitive channels (MscL and MscS) and perhaps in some potassium channels (e.g. KcsA, MthK, and KvAP). Simplified pore models allow one to investigate the primary characteristics of a conduction pathway, namely its geometry (shape, pore length, and radius), the chemical character of the pore wall surface, and its local flexibility and surface roughness. Our extended (ca. 0.1 \mu s) molecular dynamic simulations show that a short hydrophobic pore is closed to water for radii smaller than 0.45 nm. By increasing the polarity of the pore wall (and thus reducing its hydrophobicity) the transition radius can be decreased until for hydrophilic pores liquid water is stable down to a radius comparable to a water molecule's radius. Ions behave similarly but the transition from conducting to non-conducting pores is even steeper and occurs at a radius of 0.65 nm for hydrophobic pores. The presence of water vapour in a constriction zone indicates a barrier for ion permeation. A thermodynamic model can explain the behaviour of water in nanopores in terms of the surface tensions, which leads to a simple measure of "hydrophobicity" in this context. Furthermore, increased local flexibility decreases the permeability of polar species. An increase in temperature has the same effect, and we hypothesise that both effects can be explained by a decrease in the effective solvent-surface attraction which in turn leads to an increase in the solvent-wall surface free energy.Comment: Peer reviewed article appeared in Physical Biology http://www.iop.org/EJ/abstract/1478-3975/1/1/005

UA Research Summary No. 18

Health-care spending for Alaskans reached about $7.5 billion in 2010. For comparison, that’s close to half the wellhead value of all the oil produced in Alaska that year. It’s also roughly equal to half the wages Alaskans collected in 2010. The state’s health-care spending has been rising fast, tripling since 1990 and jumping 402010—and at current trends it could double by 2020, reaching more than$14 billion. Here we report on who’s paying the bills, what we’re buying, what’s contributing to the growth, and other aspects of health-care spending. We conclude with a discussion of how Alaska could get better value for its health-care dollars

Using minimum tillage to improve the efficiency of ecosystem service delivery on organic farms

Organic farming practices aim to maximise the delivery of ecosystem services in the agricultural landscape. However, in order to maintain optimal crop productivity the mouldboard plough is often used to control weeds and this can have negative effects on a range of soil parameters, thereby jeopardizing delivery of these services. Reduced tillage (RT) can be beneficial to soils and could improve both the efficiency of production and the delivery of ecosystem services on organic farms. However, abandoning the plough on organic farms is challenging due to impaired weed control. Here we report on a two year trial where an RT system with the Ecodyn, with duck feet shares operating at a depth of 7.6 cm in combination with seed drilling, was compared with mouldboard ploughing. Spring oat and spring barley establishment was improved under RT. Weed cover and biomass was greater under RT, but there was no difference in cereal grain yields in either year. The RT system used 71% less fuel and tillage operations took 72% less time that the plough system

Optical Absorption by Dirac Excitons in Single-Layer Transition-Metal Dichalcogenides

We develop an analytically solvable model able to qualitatively explain nonhydrogenic exciton spectra observed recently in two-dimensional (2d) semiconducting transition metal dichalcogenides. Our exciton Hamiltonian explicitly includes additional angular momentum associated with the pseudospin degree of freedom unavoidable in 2d semiconducting materials with honeycomb structure. We claim that this is the key ingredient for understanding the nonhydrogenic exciton spectra that was missing so far.Comment: 4+ pages, 2 figure

Model Prediction of Self-Rotating Excitons in Two-Dimensional Transition-Metal Dichalcogenides

Using the quasiclassical concept of Berry curvature we demonstrate that a Dirac exciton - a pair of Dirac quasiparticles bound by Coulomb interactions - inevitably possesses an intrinsic angular momentum making the exciton effectively self-rotating. The model is applied to excitons in two-dimensional transition metal dichalcogenides, in which the charge carriers are known to be described by a Dirac-like Hamiltonian. We show that the topological self-rotation strongly modifies the exciton spectrum and, as a consequence, resolves the puzzle of the overestimated two-dimensional polarizability employed to fit earlier spectroscopic measurements.Comment: 4+ pages, 2 figures, suppl. mat. added (4 pages), the title changed by PRL editor

Exciton spectrum in two-dimensional transition metal dichalcogenides: The role of Diracness

The physics of excitons, electron-hole pairs that are bound together by their mutual Coulomb attraction, can to great extent be understood in the framework of the quantum-mechanical hydrogen model. This model has recently been challenged by spectroscopic measurements on two-dimensional transition-metal dichalchogenides that unveil strong deviations from a hydrogenic spectrum. Here, we show that this deviation is due to the particular relativistic character of electrons in this class of materials. Indeed, their electrons are no longer described in terms of a Schroedinger but a massive Dirac equation that intimately links electrons to holes. Dirac excitons therefore inherit a relativistic quantum spin-1/2 that contributes to the angular momentum and thus the exciton spectrum. Most saliently, the level spacing is strongly reduced as compared to the hydrogen model, in agreement with spectroscopic measurements and ab-initio calculations.Comment: 3 pages, 1 figure, accepted for publication in the proceedings of ICPS 201