10,244 research outputs found
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
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 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
- …