d’Alembert–Schrödinger hybrid simulation for laser-induced multiquantum state transitions in a three-dimensional artificial atom

2019 ◽  
Vol 44 (17) ◽  
pp. 4399
Author(s):  
Aiqiang Cheng ◽  
Hui Zeng ◽  
Shitao Chen ◽  
Rushan Chen
Keyword(s):  
Three Dimensional ◽  
Hybrid Simulation ◽  
State Transitions ◽  
Artificial Atom

Macroorganisation and flexibility of thylakoid membranes

2019 ◽  
Vol 476 (20) ◽  
pp. 2981-3018 ◽  
Author(s):  
Petar H. Lambrev ◽  
Parveen Akhtar
Keyword(s):  
Light Harvesting ◽  
Current Knowledge ◽  
Three Dimensional ◽  
Photosynthetic Apparatus ◽  
Dynamic Responses ◽  
State Transitions ◽  
Photochemical Quenching ◽  
Light Harvesting Complex ◽  
Complex Ii ◽  
Light Harvesting Complex Ii

Abstract The light reactions of photosynthesis are hosted and regulated by the chloroplast thylakoid membrane (TM) — the central structural component of the photosynthetic apparatus of plants and algae. The two-dimensional and three-dimensional arrangement of the lipid–protein assemblies, aka macroorganisation, and its dynamic responses to the fluctuating physiological environment, aka flexibility, are the subject of this review. An emphasis is given on the information obtainable by spectroscopic approaches, especially circular dichroism (CD). We briefly summarise the current knowledge of the composition and three-dimensional architecture of the granal TMs in plants and the supramolecular organisation of Photosystem II and light-harvesting complex II therein. We next acquaint the non-specialist reader with the fundamentals of CD spectroscopy, recent advances such as anisotropic CD, and applications for studying the structure and macroorganisation of photosynthetic complexes and membranes. Special attention is given to the structural and functional flexibility of light-harvesting complex II in vitro as revealed by CD and fluorescence spectroscopy. We give an account of the dynamic changes in membrane macroorganisation associated with the light-adaptation of the photosynthetic apparatus and the regulation of the excitation energy flow by state transitions and non-photochemical quenching.

scholarly journals Three-dimensional multispecies hybrid simulation of Titan's highly variable plasma environment

2007 ◽  
Vol 25 (1) ◽  
pp. 117-144 ◽  
Author(s):  
S. Simon ◽  
A. Boesswetter ◽  
T. Bagdonat ◽  
U. Motschmann ◽  
J. Schuele
Keyword(s):  
Plasma Flow ◽  
Flow Direction ◽  
Three Dimensional ◽  
Hybrid Simulation ◽  
Slight Modification ◽  
Magnetospheric Plasma ◽  
Particle Model ◽  
Tail Region ◽  
Simulation Code ◽  
Ion Species

Abstract. The interaction between Titan's ionosphere and the Saturnian magnetospheric plasma flow has been studied by means of a three-dimensional (3-D) hybrid simulation code. In the hybrid model, the electrons form a mass-less, charge-neutralizing fluid, whereas a completely kinetic approach is retained to describe ion dynamics. The model includes up to three ionospheric and two magnetospheric ion species. The interaction gives rise to a pronounced magnetic draping pattern and an ionospheric tail that is highly asymmetric with respect to the direction of the convective electric field. Due to the dependence of the ion gyroradii on the ion mass, ions of different masses become spatially dispersed in the tail region. Therefore, Titan's ionospheric tail may be considered a mass-spectrometer, allowing to distinguish between ion species of different masses. The kinetic nature of this effect is emphasized by comparing the simulation with the results obtained from a simple analytical test-particle model of the pick-up process. Besides, the results clearly illustrate the necessity of taking into account the multi-species nature of the magnetospheric plasma flow in the vicinity of Titan. On the one hand, heavy magnetospheric particles, such as atomic Nitrogen or Oxygen, experience only a slight modification of their flow pattern. On the other hand, light ionospheric ions, e.g. atomic Hydrogen, are clearly deflected around the obstacle, yielding a widening of the magnetic draping pattern perpendicular to the flow direction. The simulation results clearly indicate that the nature of this interaction process, especially the formation of sharply pronounced plasma boundaries in the vicinity of Titan, is extremely sensitive to both the temperature of the magnetospheric ions and the orientation of Titan's dayside ionosphere with respect to the corotating magnetospheric plasma flow.

scholarly journals Plasma environment of magnetized asteroids: a 3-D hybrid simulation study

2006 ◽  
Vol 24 (1) ◽  
pp. 407-414 ◽  
Author(s):  
S. Simon ◽  
T. Bagdonat ◽  
U. Motschmann ◽  
K.-H. Glassmeier
Keyword(s):  
Solar Wind ◽  
Three Dimensional ◽  
Hybrid Simulation ◽  
Interaction Region ◽  
Bow Shock ◽  
The Other ◽  
Simulation Code ◽  
Kinetic Effects ◽  
Intrinsic Magnetic Moment ◽  
The One

Abstract. The interaction of a magnetized asteroid with the solar wind is studied by using a three-dimensional hybrid simulation code (fluid electrons, kinetic ions). When the obstacle's intrinsic magnetic moment is sufficiently strong, the interaction region develops signs of magnetospheric structures. On the one hand, an area from which the solar wind is excluded forms downstream of the obstacle. On the other hand, the interaction region is surrounded by a boundary layer which indicates the presence of a bow shock. By analyzing the trajectories of individual ions, it is demonstrated that kinetic effects have global consequences for the structure of the interaction region.

Hall effect control of magnetotail dawn-dusk asymmetry: A three-dimensional global hybrid simulation

2016 ◽  
Vol 121 (12) ◽  
pp. 11,882-11,895 ◽  
Author(s):  
San Lu ◽  
Y. Lin ◽  
V. Angelopoulos ◽  
A. V. Artemyev ◽  
P. L. Pritchett ◽  
...  
Keyword(s):  
Hall Effect ◽  
Three Dimensional ◽  
Hybrid Simulation

scholarly journals Modeling and Visualizing Cell Type Switching

2014 ◽  
Vol 2014 ◽  
pp. 1-10 ◽  
Author(s):  
Ahmadreza Ghaffarizadeh ◽  
Gregory J. Podgorski ◽  
Nicholas S. Flann
Keyword(s):  
Expression Profiles ◽  
Control Cell ◽  
Three Dimensional ◽  
Myeloid Cell ◽  
Cell Types ◽  
State Transitions ◽  
Cell Type ◽  
New Approach ◽  
Gene Expression Noise ◽  
Lineage Trees

Understanding cellular differentiation is critical in explaining development and for taming diseases such as cancer. Differentiation is conventionally represented using bifurcating lineage trees. However, these lineage trees cannot readily capture or quantify all the types of transitions now known to occur between cell types, including transdifferentiation or differentiation off standard paths. This work introduces a new analysis and visualization technique that is capable of representing all possible transitions between cell states compactly, quantitatively, and intuitively. This method considers the regulatory network of transcription factors that control cell type determination and then performs an analysis of network dynamics to identify stable expression profiles and the potential cell types that they represent. A visualization tool calledCellDiff3Dcreates an intuitive three-dimensional graph that shows the overall direction and probability of transitions between all pairs of cell types within a lineage. In this study, the influence of gene expression noise and mutational changes during myeloid cell differentiation are presented as a demonstration of theCellDiff3Dtechnique, a new approach to quantify and envision all possible cell state transitions in any lineage network.

scholarly journals Geometric Analysis of Regime Shifts in Coral Reef Communities

2020 ◽  
Author(s):  
Edward W. Tekwa ◽  
Lisa C. McManus ◽  
Ariel Greiner ◽  
Madhavi A. Colton ◽  
Michael S. Webster ◽  
...  
Keyword(s):  
Spatial Clustering ◽  
Alternative Stable States ◽  
Geometric Analysis ◽  
Three Dimensional ◽  
Single Species ◽  
Regime Shifts ◽  
State Transitions ◽  
Stable States ◽  
Species Dominance ◽  
Community Grazing

AbstractCoral reefs are among the many communities believed to exhibit regime shifts between alternative stable states, single-species dominance, and coexistence. Proposed drivers of regime shifts include changes in grazing, spatial clustering, and ocean temperature. Here we distill the dynamic regimes of coral-macroalgal interaction into a three-dimensional geometry, akin to thermodynamic phase diagrams of state transitions, to facilitate analysis. Specific regime-shifting forces can be understood as bifurcation vectors through the cubic regime geometry. This geometric perspective allows us to understand multiple forces simultaneously in terms of the stability and persistence of interacting species. For example, in a coral-macroalgae community, grazing on macroalgae can lead to alternative stable states when there is no spatial clustering (e.g., high habitat connectivity). However, with spatial clustering, grazing can lead to coexistence because of elevated local intraspecific competition. The geometrical analysis of regime shifts is applicable to any two-species communities and can help conservation efforts navigate complexity and abrupt changes.

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