Global attractors and extinction dynamics of cyclically competing species

Transitions to absorbing states are of fundamental importance in nonequilibrium physics as well as ecology. In ecology, absorbing states correspond to the extinction of species. We here study the spatial population dynamics of three cyclically interacting species. The interaction scheme comprises both direct competition between species as in the cyclic Lotka-Volterra model, and separated selection and reproduction processes as in the May-Leonard model. We show that the dynamic processes leading to the transient maintenance of biodiversity are closely linked to attractors of the nonlinear dynamics for the overall species' concentrations. The characteristics of these global attractors change qualitatively at certain threshold values of the mobility and depend on the relative strength of the different types of competition between species. They give information about the scaling of extinction times with the system size and thereby the stability of biodiversity. We define an effective free energy as the negative logarithm of the probability to find the system in a specific global state before reaching one of the absorbing states. The global attractors then correspond to minima of this effective energy landscape and determine the most probable values for the species' global concentrations. As in equilibrium thermodynamics, qualitative changes in the effective free energy landscape indicate and characterize the underlying nonequilibrium phase transitions. We provide the complete phase diagrams for the population dynamics and give a comprehensive analysis of the spatio-temporal dynamics and routes to extinction in the respective phases

Depletion of atmospheric nitrate and chloride as a consequence of the Toba Volcanic Eruption

Continuous measurements of SO42− and electrical conductivity (ECM) along the GISP2 ice core record the Toba mega‐eruption at a depth 2590.95 to 2091.25 m (71,000±5000 years ago). Major chemical species were analyzed at a resolution of 1 cm per sample for this section. An ∼6‐year long period with extremely high volcanic SO42− coincident with a 94% depletion of nitrate and 63% depletion of chloride is observed at the depth of the Toba horizon. Such a reduction of chloride in a volcanic layer preserved in an ice core has not been observed in any previous studies. The nearly complete depletion of nitrate (to 5 ppb) encountered at the Toba level is the lowest value in the entire ∼250,000 years of the GISP2 ice core record. We propose possible mechanisms to explain the depletion of nitrate and chloride resulting from this mega‐eruption

Systems biology analysis of drivers underlying hallmarks of cancer cell metabolism.

Malignant transformation is often accompanied by significant metabolic changes. To identify drivers underlying these changes, we calculated metabolic flux states for the NCI60 cell line collection and correlated the variance between metabolic states of these lines with their other properties. The analysis revealed a remarkably consistent structure underlying high flux metabolism. The three primary uptake pathways, glucose, glutamine and serine, are each characterized by three features: (1) metabolite uptake sufficient for the stoichiometric requirement to sustain observed growth, (2) overflow metabolism, which scales with excess nutrient uptake over the basal growth requirement, and (3) redox production, which also scales with nutrient uptake but greatly exceeds the requirement for growth. We discovered that resistance to chemotherapeutic drugs in these lines broadly correlates with the amount of glucose uptake. These results support an interpretation of the Warburg effect and glutamine addiction as features of a growth state that provides resistance to metabolic stress through excess redox and energy production. Furthermore, overflow metabolism observed may indicate that mitochondrial catabolic capacity is a key constraint setting an upper limit on the rate of cofactor production possible. These results provide a greater context within which the metabolic alterations in cancer can be understood

Potential atmospheric impact of the Toba Mega‐Eruption ∼71,000 years ago

An ∼6‐year long period of volcanic sulfate recorded in the GISP2 ice core about 71,100 ± 5000 years ago may provide detailed information on the atmospheric and climatic impact of the Toba mega‐eruption. Deposition of these aerosols occur at the beginning of an ∼1000‐year long stadial event, but not immediately before the longer glacial period beginning ∼67,500 years ago. Total stratospheric loading estimates over this ∼6‐year period range from 2200 to 4400 Mt of H2SO4 aerosols. The range in values is given to compensate for uncertainties in aerosol transport. Magnitude and longevity of the atmospheric loading may have led directly to enhanced cooling during the initial two centuries of this ∼1000‐year cooling event

File compression using typogenetic computation

Typogenetic algorithms are a break from classical approaches to computation. Based on gene expression and intercellular processes, typo-genetic computation can offer a new approach to the algorithmic problems of system security, data compression and encryption. The method has a potential of much higher compression ratios at the limited computational costs i.e. processing time. This paper presents a formal system based on typogenetics for the purposes of compression. Lossless data compression is an important part of computer science. While the ability to reduce consumption of hard disk space or transmission bandwidth through statistical redundancy has served well in the past, the explosive growth in high quality media content (*.mp3, *.mpg) on the internet in the past few years have highlighted the limitations of traditional statistical techniques for compression. © 2008 IEEE

The Raman optical activity of β-D-xylose: where experiment and theory meet

Besides its applications in bioenergy and biosynthesis, β-D-xylose is a very simple monosaccharide that exhibits relatively high rigidity. As such, it provides the best basis to study the impact of different solvation shell radii on the computation of its Raman optical activity (ROA) spectrum. Indeed, this chiroptical spectroscopic technique provides exquisite sensitivity to stereochemistry, and benefits much from theoretical support for interpretation. Our simulation approach combines density functional theory (DFT) and molecular dynamics (MD) in order to efficiently account for the crucial hydration effects in the simulation of carbohydrates and their spectroscopic response predictions. Excellent agreement between the simulated spectrum and the experiment was obtained with a solvation radius of 10 Å. Vibrational bands have been resolved from the computed ROA data, and compared with previous results on different monosaccharides in order to identify specific structure–spectrum relationships and to investigate the effect of the solvation environment on the conformational dynamics of small sugars. From the comparison with ROA analytical results, a shortcoming of the classical force field used for the MD simulations has been identified and overcome, again highlighting the complementary role of experiment and theory in the structural characterisation of complex biomolecules. Indeed, due to unphysical puckering, a spurious ring conformation initially led to erroneous conformer ratios, which are used as weights for the averaging of the spectral average, and only by removing this contribution was near perfect comparison between theory and experiment achieved