Entropy production and fluctuation theorems on complex networks.

Entropy production (EP) is a fundamental quantity useful for understanding irreversible process. In stochastic thermodynamics, EP is more evident in probability density functions of trajectories of a particle in the state space. Here, inspired by a previous result that complex networks can serve as state spaces, we consider a data packet transport problem on complex networks. EP is generated owing to the complexity of pathways as the packet travels back and forth between two nodes along the same pathway. The total EPs are exactly enumerated along all possible shortest paths between every pair of nodes, and the functional form of the EP distribution is proposed based on our numerical results. We confirm that the EP distribution satisfies the detailed and integral fluctuation theorems. Our results should be pedagogically helpful for understanding trajectory-dependent EP in stochastic processes and exploring nonequilibrium fluctuations associated with the entanglement of dividing and merging among the shortest pathways in complex networks.

AFM study of the differential inhibitory effects of the green tea polyphenol (-)-epigallocatechin-3-gallate (EGCG) against Gram-positive and Gram-negative bacteria.

(-)-Epigallocatechin-3-gallate (EGCG), a main constituent of tea catechins, affects Gram-positive and Gram-negative bacteria differently; however, the underlying mechanisms are not clearly understood. Atomic force microscopy (AFM) was used to compare morphological alterations in Gram-positive and Gram-negative bacteria induced by EGCG and by H(2)O(2) at sub-minimum inhibitory concentrations (MICs). EGCG initially induced aggregates in the cell envelopes of Staphylococcus aureus and eventually caused cell lysis, which was not observed in cells treated with H(2)O(2). It initially induced nanoscale perforations or microscale grooves in the cell envelopes of Escherichia coli O157:H7 which eventually disappeared, similar to E. coli cells treated with H(2)O(2). An E. coli O157:H7 tpx mutant, with a defect in thioredoxin-dependent thiol peroxidase (Tpx), was more severely damaged by EGCG when compared with its wild type. Similar differing effects were observed in other Gram-positive and Gram-negative bacteria when exposed to EGCG; it caused aggregated in Streptococcus mutans, while it caused grooves in Pseudomonas aeruginosa. AFM results suggest that the major morphological changes of Gram-negative bacterial cell walls induced by EGCG depend on H(2)O(2) release. This is not the case for Gram-positive bacteria. Oxidative stress in Gram-negative bacteria induced by EGCG was confirmed by flow cytometry.

Dynamics of prey-flock escaping behavior in response to predator's attack.

The dynamic behavior of prey-flock in response to predator's attack was investigated by using molecular dynamics (MD) simulations in a two-dimensional (2D) continuum model. By locally applying interactive forces between prey individuals (e.g. attraction, repulsion, and alignment), a coherently moving state in the same direction was obtained among individuals in prey-flock. When a single predator was introduced to the prey population, the prey-flock was correspondingly deformed by the predator's continuous attacks towards the prey-flock's center. In response to the predator's attack, three regimes in the flock size (compression (Regime I), expansion (Regime II), compression (Regime III)) were revealed if the predator's attack speed (kappa) was comparatively low to the escape speed of prey-flock. If noise was added to the predator's attacking course, a higher degree of variation was observed in the patterns of compression and expansion in the prey-flock size. However, the scaling behavior in the changes in prey-flock size was present in different levels of noise with the increase in predation risk (R) when kappa takes an appropriately low value. During the procedure of escaping, order breaking in alignment (phi) of prey population was observed, while the degree of alignment was dependent upon the changes in parameters of kappa and R.

Double slit with continuously variable width and center-to-center separation.

Linear polarizers and a half-wave plate are used to make a double slit whose width and center-to-center separation are continuously variable.