Quasi-Parallel Shock Reformation Seen by Magnetospheric Multiscale and Ion-Kinetic Simulations.
Ontology highlight
ABSTRACT:
SUBMITTER: Johlander A
PROVIDER: S-EPMC9285775 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:We present in-depth analysis of three southward-moving meso-scale (ion-to magnetohydrodynamic-scale) flux transfer events (FTEs) and subsequent crossing of a reconnecting magnetopause current sheet (MPCS), which were observed on 8 December 2015 by the Magnetospheric Multiscale spacecraft in the subsolar region under southward and duskward magnetosheath magnetic field conditions. We aim to understand the generation mechanism of ion-scale magnetic flux ropes (ISFRs) and to reveal causal relationship among magnetic field structures, electromagnetic energy conversion, and kinetic processes in magnetic reconnection layers. Results from magnetic field reconstruction methods are consistent with a flux rope with a length of about one ion inertial length growing from an electron-scale current sheet (ECS) in the MPCS, supporting the idea that ISFRs can be generated through secondary reconnection in an ECS. Grad-Shafranov reconstruction applied to the three FTEs shows that the FTEs had axial orientations similar to that of the ISFR. This suggests that these FTEs also formed through the same secondary reconnection process, rather than multiple X-line reconnection at spatially separated locations. Four-spacecraft observations of electron pitch-angle distributions and energy conversion rate j·E'=j·E+ve×B suggest that the ISFR had three-dimensional magnetic topology and secondary reconnection was patchy or bursty. Previously reported positive and negative values of j·E', with magnitudes much larger than expected for typical MP reconnection, were seen in both magnetosheath and magnetospheric separatrix regions of the ISFR. Many of them coexisted with bi-directional electron beams and intense electric field fluctuations around the electron gyrofrequency, consistent with their origin in separatrix activities.
| S-EPMC10909477 | biostudies-literature
Project description:Plasma shocks are the primary means of accelerating electrons in planetary and astrophysical settings throughout the universe. Which category of shocks, quasi-perpendicular or quasi-parallel, accelerates electrons more efficiently is debated. Although quasi-perpendicular shocks are thought to be more efficient electron accelerators, relativistic electron energies recently observed at quasi-parallel shocks exceed theoretical expectations. Using in situ observations at Earth's bow shock, we show that such relativistic electrons are generated by the interaction between the quasi-parallel shock and a related nonlinear structure, a foreshock transient, through two betatron accelerations. Our observations show that foreshock transients, overlooked previously, can increase electron acceleration efficiency at a quasi-parallel shock by an order of magnitude. Thus, quasi-parallel shocks could be more important in generating relativistic electrons, such as cosmic ray electrons, than previously thought.
| S-EPMC6609210 | biostudies-literature
Project description:Mars lacks a global magnetic field, and instead possesses small-scale crustal magnetic fields, making its magnetic environment fundamentally different from intrinsic magnetospheres like those of Earth or Saturn. Here we report the discovery of magnetospheric ion drift patterns, typical of intrinsic magnetospheres, at Mars using measurements from Mars Atmosphere and Volatile EvolutioN mission. Specifically, we observe wedge-like dispersion structures of hydrogen ions exhibiting butterfly-shaped distributions (pitch angle peaks at 22.5°-45° and 135°-157.5°) within the Martian crustal fields, a feature previously observed only in planetary-scale intrinsic magnetospheres. These dispersed structures are the results of drift motions that fundamentally resemble those observed in intrinsic magnetospheres. Our findings indicate that the Martian magnetosphere embodies an intermediate case where both the unmagnetized and magnetized ion behaviors could be observed because of the wide range of strengths and spatial scales of the crustal magnetic fields around Mars.
| S-EPMC10611764 | biostudies-literature
Project description:In this article we review the key modeling tools available for simulating biomolecular systems. We consider recent developments and representative applications of mixed quantum mechanics/molecular mechanics (QM/MM), elastic network models (ENMs), coarse-grained molecular dynamics, and grid-based tools for calculating interactions between essentially rigid protein assemblies. We consider how the different length scales can be coupled, both in a sequential fashion (e.g. a coarse-grained or grid model using parameterization from MD simulations), and via concurrent approaches, where the calculations are performed together and together control the progression of the simulation. We suggest how the concurrent coupling approach familiar in the context of QM/MM calculations can be generalized, and describe how this has been done in the CHARMM macromolecular simulation package.
| S-EPMC6407689 | biostudies-literature
Project description:Multiscale simulations model phenomena across natural scales using monolithic or component-based code, running on local or distributed resources. In this work, we investigate the performance of distributed multiscale computing of component-based models, guided by six multiscale applications with different characteristics and from several disciplines. Three modes of distributed multiscale computing are identified: supplementing local dependencies with large-scale resources, load distribution over multiple resources, and load balancing of small- and large-scale resources. We find that the first mode has the apparent benefit of increasing simulation speed, and the second mode can increase simulation speed if local resources are limited. Depending on resource reservation and model coupling topology, the third mode may result in a reduction of resource consumption.
| S-EPMC4084531 | biostudies-literature
Project description:In this study, the ion composition of flux transfer events (FTEs) observed within the magnetosheath proper is examined. These FTEs were observed just upstream of the Earth's postnoon magnetopause by the National Aeronautics and Space Administration (NASA) Magnetospheric Multiscale (MMS) spacecraft constellation. The minor ion characteristics are described using energy spectrograms, flux distributions, and ion moments as the constellation encountered each FTE. In conjunction with electron data and magnetic field observations, such observations provide important contextual information on the formation, topologies, and evolution of FTEs. In particular, minor ions, when combined with the field-aligned streaming of electrons, are reliable indicators of FTE topology. The observations are also placed (i) in context of the solar wind magnetic field configuration, (ii) the connection of the sampled flux tube to the ionosphere, and (iii) the location relative to the modeled reconnection line at the magnetopause. While protons and alpha particles were often depleted within the FTEs relative to the surrounding magnetosheath plasma, the He+ and O+ populations showed clear enhancements either near the center or near the edges of the FTE, and the bulk plasma flow directions are consistent with magnetic reconnection northward of the spacecraft and convection from the dayside toward the flank magnetopause.
| S-EPMC7507212 | biostudies-literature
Project description:Smoldyn is a software package for stochastic modelling of spatial biochemical networks and intracellular systems. It was originally developed with an accurate off-lattice particle-based model at its core. This has recently been enhanced with the addition of a computationally efficient on-lattice model, which can be run stand-alone or coupled together for multiscale simulations using both models in regions where they are most required, increasing the applicability of Smoldyn to larger molecule numbers and spatial domains. Simulations can switch between models with only small additions to their configuration file, enabling users with existing Smoldyn configuration files to run the new on-lattice model with any reaction, species or surface descriptions they might already have.Source code and binaries freely available for download at www.smoldyn.org, implemented in C/C++ and supported on Linux, Mac OSX and MS Windows.
| S-EPMC4495299 | biostudies-other
Project description:We present Tinker-HP, a massively MPI parallel package dedicated to classical molecular dynamics (MD) and to multiscale simulations, using advanced polarizable force fields (PFF) encompassing distributed multipoles electrostatics. Tinker-HP is an evolution of the popular Tinker package code that conserves its simplicity of use and its reference double precision implementation for CPUs. Grounded on interdisciplinary efforts with applied mathematics, Tinker-HP allows for long polarizable MD simulations on large systems up to millions of atoms. We detail in the paper the newly developed extension of massively parallel 3D spatial decomposition to point dipole polarizable models as well as their coupling to efficient Krylov iterative and non-iterative polarization solvers. The design of the code allows the use of various computer systems ranging from laboratory workstations to modern petascale supercomputers with thousands of cores. Tinker-HP proposes therefore the first high-performance scalable CPU computing environment for the development of next generation point dipole PFFs and for production simulations. Strategies linking Tinker-HP to Quantum Mechanics (QM) in the framework of multiscale polarizable self-consistent QM/MD simulations are also provided. The possibilities, performances and scalability of the software are demonstrated via benchmarks calculations using the polarizable AMOEBA force field on systems ranging from large water boxes of increasing size and ionic liquids to (very) large biosystems encompassing several proteins as well as the complete satellite tobacco mosaic virus and ribosome structures. For small systems, Tinker-HP appears to be competitive with the Tinker-OpenMM GPU implementation of Tinker. As the system size grows, Tinker-HP remains operational thanks to its access to distributed memory and takes advantage of its new algorithmic enabling for stable long timescale polarizable simulations. Overall, a several thousand-fold acceleration over a single-core computation is observed for the largest systems. The extension of the present CPU implementation of Tinker-HP to other computational platforms is discussed.
| S-EPMC5909332 | biostudies-literature
Project description:Protein functions require specific structures frequently coupled with conformational changes. The scale of the structural dynamics of proteins spans from the atomic to the molecular level. Theoretically, all-atom molecular dynamics (MD) simulation is a powerful tool to investigate protein dynamics because the MD simulation is capable of capturing conformational changes obeying the intrinsically structural features. However, to study long-timescale dynamics, efficient sampling techniques and coarse-grained (CG) approaches coupled with all-atom MD simulations, termed multiscale MD simulations, are required to overcome the timescale limitation in all-atom MD simulations. Here, we review two examples of rotary motor proteins examined using free energy landscape (FEL) analysis and CG-MD simulations. In the FEL analysis, FEL is calculated as a function of reaction coordinates, and the long-timescale dynamics corresponding to conformational changes is described as transitions on the FEL surface. Another approach is the utilization of the CG model, in which the CG parameters are tuned using the fluctuation matching methodology with all-atom MD simulations. The long-timespan dynamics is then elucidated straightforwardly by using CG-MD simulations.
| S-EPMC5899732 | biostudies-literature
Project description:The catalytic promiscuity and fidelity of cytochrome P450 enzymes are widespread in the skeletal modification of terpenoid natural products and have attracted much attention. CYP76AH1 is involved in key modification reactions in the biosynthetic pathway of tanshinone, a well-known medicinal norditerpenoid. In this work, classical molecular dynamic simulations, metadynamics, and DFT calculations were performed to investigate the protein conformational dynamics, ligand binding poses, and catalytic reaction mechanism in wide-type and mutant CYP76AH1. Our results not only reveal a plausible enzymatic mechanism for mutant CYP76AH1 leading to various products but also provide valuable guidance for rational protein engineering of the CYP76 family.
| S-EPMC8207200 | biostudies-literature