Graphical Classification in Multi-Centrality-Index Diagrams for Complex Chemical Networks

AUTOGRAPH: Chemical Reaction Networks in 3D

Understanding and analyzing large-scale reaction networks is a fundamental challenge due to their complexity and size, often beyond human comprehension. In this paper, we introduce AUTOGRAPH, the first web-based tool designed for the interactive three-dimensional (3D) visualization and construction of reaction networks. AUTOGRAPH emphasizes ease of use, allowing users to intuitively build, modify, and explore individual reaction networks in real time. The platform supports a wide range of formats, including CHEMKIN, ensuring compatibility and seamless integration with existing data. Key features of AUTOGRAPH include advanced 3D visualization techniques combined with a fast force-directed algorithm, shortest-path searching, and filtering, facilitating the in-depth exploration of reaction networks. By providing detailed and interactive visualizations, our tool enhances users' ability to comprehend, analyze, and present complex reaction networks, making it a valuable resource for researchers dealing with intricate chemical systems.

In-vacuum active colour sensor and wireless communication across a vacuum-air interface

In situ sensing with wireless digital-data transfer is a potential processing scheme that works very closely to the location of an event monitored by a sensor and converts the sensor’s raw output into digitized and informative small-volume bits, as suggested by recent proposals for edge computing and the Internet of Things (IoT). Colour perception may be a target of in situ sensor data acquisition; however, in contrast to from other sensing devices, colour sensors that detect visible light signals are usually located away from light-emitting sources, collecting light transmitting through the space and attenuating it in some manner. For example, in a vacuum chamber whose gas pressure is much less than the ambient atmosphere in which the sensors usually work, there are many veiled light sources, such as discharge plasma, for various industrial purposes including nanoscale manufacturing. In this study, we designed an in-vacuum colour sensor that can work with analogue-to-digital conversion and transfer data by wireless communication; this sensor is active in a low-pressure plasma chamber, detecting light signals and transferring them to a personal computer located outside the vacuum chamber. In addition to detecting lights with controlled spectra from outside successfully, we achieved complete operation of our in-vacuum active sensor for plasma emissions generated at 100 Pa. Comparing the signals with data from simultaneous monitoring by a monochromator, we established that the recorded signals arose from the plasma, confirming successful direct detection of low-pressure plasma emissions without any filtering effects between the sensor and the target object.

Numerical modelling of the effects of cold atmospheric plasma on mitochondrial redox homeostasis and energy metabolism

A biochemical reaction model clarifies for the first time how cold atmospheric plasmas (CAPs) affect mitochondrial redox homeostasis and energy metabolism. Fundamental mitochondrial functions in pyruvic acid oxidation, the tricarboxylic acid (TCA) cycle and oxidative phosphorylation involving the respiratory chain (RC), adenosine triphosphate/adenosine diphosphate (ATP/ADP) synthesis machinery and reactive oxygen species/reactive nitrogen species (ROS/RNS)-mediated mechanisms are numerically simulated. The effects of CAP irradiation are modelled as 1) the influx of hydrogen peroxide (H[Formula: see text]O[Formula: see text]) to an ROS regulation system and 2) the change in mitochondrial transmembrane potential induced by RNS on membrane permeability. The CAP-induced stress modifies the dynamics of intramitochondrial H[Formula: see text]O[Formula: see text] and superoxide anions, i.e., the rhythm and shape of ROS oscillation are disturbed by H[Formula: see text]O[Formula: see text] infusion. Furthermore, CAPs control the ROS oscillatory behaviour, nicotinamide adenine dinucleotide redox state and ATP/ADP conversion through the reaction mixture over the RC, the TCA cycle and ROS regulation system. CAPs even induce a homeostatic or irreversible state transition in cell metabolism. The present computational model demonstrates that CAPs crucially affect essential mitochondrial functions, which in turn affect redox signalling, metabolic cooporation and cell fate decision of survival or death.