25 papers · ranked by Valyu relevance
K. Hayashi, J. T. Hoeksema, Y. Liu, M. G. Bobra + 2 more
Time-dependent three-dimensional magnetohydrodynamics (MHD) simulation modules are implemented at the Joint Science Operation Center (JSOC) of the Solar Dynamics Observatory (SDO). The modules regularly produce three-dimensional data of the time-relaxed minimum-energy state of the solar corona using global…
Ze Zhong, Yang Guo, M. D. Ding
Whether a solar eruption is successful or failed depends on the competition between different components of the Lorentz force exerting on the flux rope that drives the eruption. The present models only consider the strapping force generated by the background magnetic field perpendicular to the flux rope and the tension…
Michael Shay, Subash Adhikari, Naoki Beesho, Joachim Birn + 21 more
'Jörg Büchner' 'Paul Cassak' 'Li-Jen Chen' 'Yuxi Chen' 'Giulia Cozzani' 'James Drake' 'Fan Guo' 'Michael Hesse' 'Neeraj Jain' 'Yann Pfau-Kempf' 'Yu Lin' 'Yi-Hsin Liu' 'Mitsuo Oka' 'Yuri Omelchenko' 'Minna Palmroth' 'Oreste Pezzi' 'Patricia H. Reiff' 'Marc Swisdak' 'Frank Toffoletto' 'Gabor Toth' 'Richard A. Wolf']…
Philippe-A. Bourdin
Many applications in Solar physics need a 1D atmospheric model as initial condition or as reference for inversions of observational data. The VAL atmospheric models are based on observations and are widely used since decades. Complementary to that, the FAL models implement radiative hydrodynamics and showed the…
Andrew N. Guarendi, Abhilash J. Chandy
Numerical simulations of magnetohydrodynamic (MHD) hypersonic flow over a cylinder are presented for axial- and transverse-oriented dipoles with different strengths. ANSYS CFX is used to carry out calculations for steady, laminar flows at a Mach number of 6.1, with a model for electrical conductivity as a function of…
A. Popovas
Context. With advance of supercomputers we can now afford simulations with very large range of scales. In astrophysical applications, e.g. simulating Solar, stellar and planetary atmospheres, physical quantities, like gas pressure, density, temperature and plasma β can vary by orders of magnitude. This requires a…
Luo, Hongyang, Fan, Yuhong
We describe the numerical algorithms of a global magnetohydrodynamic (MHD) code utilizing the Yin-Yang grid, called the Yin-Yang Magnetic Flux Eruption (Yin-Yang-MFE) code, suitable for modeling the large-scale dynamical processes of the solar corona and the solar wind. It is a single-fluid MHD code taking into account…
Xiao Xiao, Jonghyun Lee, Robert W. Hyers, Douglas M. Matson
Electromagnetic levitation techniques are used in a microgravity environment to allow materials research under containerless conditions while limiting the influence of gravity. The induced advective flow inside a levitated molten alloy droplet is a key factor affecting solidification phenomena while potentially…
M. A. Shay, Subash Adhikari, Naoki Beesho, J. Birn + 21 more
'P. A. Cassak' 'Li‐Jen Chen' 'Yuxi Chen' 'Giulia Cozzani' 'J. Drake' 'Fan Guo' 'M. Hesse' 'Neeraj Jain' 'Yann Pfau‐Kempf' 'Y. Lin' 'Yi‐Hsin Liu' 'M. Oka' 'Y. A. Omelchenko' 'Minna Palmroth' 'Oreste Pezzi' 'P. H. Reiff' 'M. Swisdak' 'F. Toffoletto' 'Gábor Tóth' 'R. A. Wolf'] Physics Department, Auburn University…
I. Krebs, F. J. Artola, C. R. Sovinec, S.C. Jardin + 3 more
'M. Hoelzl' 'N.M. Ferraro'] Abstract. A benchmark exercise for the modeling of vertical displacement events (VDEs) is presented and applied to the 3D nonlinear magneto-hydrodynamic codes M3D-C1 , JOREK and NIMROD. The simulations are based on a vertically unstable NSTX equilibrium enclosed by an axisymmetric resistive…
T. F. Flint, M. C. Smith, P. Shanthraj
The complex interplay between thermal, hydrodynamic, and electromagnetic, forces governs the evolution of multi-phase systems in high technology applications, such as advanced manufacturing and fusion power plant operation. In this work, a new formulation of the time dependent magnetic induction equation is fully…
Satoshi Inoue, Keiji Hayashi, Takahiro Miyoshi
We present a newly developed data-driven magnetohydrodynamics (MHD) simulation code under a zero-β approximation based on a method proposed by Hayashi et al. 2018 and 2019. Although many data-driven MHD simulations have been developed and conducted, there are not many studies on how accurately those simulations can…
Tuan Anh Dao, Murtazo Nazarov
We present a high order, robust, and stable shock-capturing technique for finite element approximations of ideal MHD. The method uses continuous Lagrange polynomials in space and explicit Runge-Kutta schemes in time. The shock-capturing term is based on the residual of MHD which tracks the shock and discontinuity…
N. Nikulsin, R. Ramasamy, M. Hoelzl, Florian Hindenlang + 3 more
'E. Strumberger' 'K. Lackner' 'S. Günter'] Although the basic concept of a stellarator was known since the early days of fusion research, advances in computational technology have enabled the modelling of increasingly complicated devices, leading up to the construction of Wendelstein 7-X, which has recently shown…
Joseph Dwyer, M. Desmond Ramirez, Paul S. Katz, Rolf O. Karlstrom + 1 more
Here we report a strategy to efficiently render opaque biological tissues transparent and demonstrate that this approach can be modified to rapidly label intact samples with antibodies for large volume fluorescence microscopy. This strategy applies a magnetohydrodynamic (MHD) force to accelerate the removal of lipids…
Lin Chen, Yuhan Chen, Ziqi Cheng, Jing Guo + 20 more
MHPC512 is a massively parallel, special-purpose supercomputer designed primarily for atomic-level molecular dynamics (MD) simulations of biomolecular systems. It comprises 512 processor units interconnected by a high-speed three-dimensional torus network and employs a custom chip architecture that uses 35-bit…
Nicolas Castel, François-Xavier Coudert
Mechanical properties of amorphous phases of metal-organic frameworks (MOF), such as MOF glasses, are difficult to determine experimentally. Moreover, computational characterization is limited by the level of theory chosen for the description of interatomic interactions and is often computationally expensive. In this…
Lorién López-Villellas, Carl Christian Kjelgaard Mikkelsen, Juan José Galano-Frutos, Santiago Marco-Sola + 5 more
In molecular dynamics simulations we can often increase the time step by imposing constraints on internal degrees of freedom, such as bond lengths and bond angles. This allows us to extend the length of the time interval and therefore the range of physical phenomena that we can afford to simulate. In this article we…
Arshad Mohammed, James Lincoff, Andrew Natale, Colin Ophus + 3 more
Cryo-electron microscopy (cryoEM) is a powerful tool for atomic- and molecular-resolution structure determination, while molecular dynamics (MD) simulations are similarly powerful tools for predicting molecular trajectories. Given the challenges in estimating biomolecule dynamics with cryoEM alone, MD simulations are…
Authors not listed
A multi-fidelity Monte Carlo framework for molecular dynamics simulations of the diffusion coefficient of liquid water is presented. The model hierarchy is constructed based on the size of the simulation box, taking advantage of the well-known size effects that simulations of the diffusion coefficient suffer from.…
Samuel C. Gill, David Mobley
Sampling multiple binding modes of a ligand in a single molecular dynamics simulation is difficult. A given ligand may have many internal degrees of freedom, along with many different ways it might orient itself a binding site or across several binding sites, all of which might be separated by large energy barriers. We…
Koki Ide, Tetsuro Tsuji, Takayuki Suzuki, Kenji Setoura
Microscale thermophoresis (MST) has garnered significant attention as a manipulation method for chemical species ranging from nanometers to micrometers in liquids. Despite the substantial increase in experimental reports on MST, a comprehensive theoretical model remains elusive due to its intricate mechanism.…
Authors not listed
Machine learning interatomic potentials (MLIPs) have revolutionized molecular simulations, but as they evolve, so does the demand for advanced computing architectures, particularly graphics processing units (GPUs). However, the high cost of GPUs limits accessibility, making it crucial to compare GPU and central…
Claudine Mayer, Arthur Vogt, Tuba Uslu, Nicolas Scalzitti + 2 more
Transcription factors (TF) regulate gene activity in eukaryotic cells by binding specific regions of genomic DNA. In fungi, the most abundant TF class contains a fungal-specific ‘GAL4-like’ Zn2C6 DNA binding domain (DBD), while the second class contains another fungal-specific domain, known as ‘fungal_trans’ or Middle…
Richard Mandle
The cylindrical distribution function (CDF) is a convenient anisotropic analogue of the radial distribution function, the difference being the use of cylindrical shells for binning. As such, CDF analysis can be a powerful tool for the analysis of positional correlations within anisotropic systems, such as liquid…