Search results for " dynamics"
showing 8 items of 4108 documents
Structure and dynamics in liquid bismuth and Bin clusters: A density functional study
2014
Density functional/molecular dynamics simulations with more than 500 atoms have been performed on liquid bismuth at 573, 773, 923, and 1023 K and on neutral Bi clusters with up to 14 atoms. There are similar structural patterns (coordination numbers, bond angles, and ring patterns) in the liquid and the clusters, with significant differences from the rhombohedral crystalline form. We study the details of the structure (structure factor, pair, and cavity distribution functions) and dynamical properties (vibration frequencies, diffusion constants, power spectra), and compare with experimental results where available. While the three short covalent bonds typical to pnictogens are characteristi…
High-Reynolds-number turbulent cavity flow using the lattice Boltzmann method
2018
We present a boundary condition scheme for the lattice Boltzmann method that has significantly improved stability for modeling turbulent flows while maintaining excellent parallel scalability. Simulations of a three-dimensional lid-driven cavity flow are found to be stable up to the unprecedented Reynolds number $\mathrm{Re}=5\ifmmode\times\else\texttimes\fi{}{10}^{4}$ for this setup. Excellent agreement with energy balance equations, computational and experimental results are shown. We quantify rises in the production of turbulence and turbulent drag, and determine peak locations of turbulent production.
Microstructural evaluation and recommendations for face masks in community use to reduce the transmission of respiratory infectious diseases
2022
Funding Information: A.K., H.Y. and R.J. also acknowledges the funding through Academy of Finland BESIMAL (Decision No. 334197) and Aalto University, Department of Communications and Networking. This work has also received funding in part from the EPSRC UK (grant number EP/R012091/1). A.K. would also like to thank Mr. Volkan Kaplan for the fruitful discussions in the early concept generation. Publisher Copyright: © 2022 The Author(s) Background and Objective: Recommendations for the use of face masks to prevent and protect against the aerosols (≤5µm) and respiratory droplet particles (≥5µm), which can carry and transmit respiratory infections including severe acute respiratory syndrome coro…
Designing a graphics processing unit accelerated petaflop capable lattice Boltzmann solver: Read aligned data layouts and asynchronous communication
2016
The lattice Boltzmann method is a well-established numerical approach for complex fluid flow simulations. Recently, general-purpose graphics processing units (GPUs) have become available as high-performance computing resources at large scale. We report on designing and implementing a lattice Boltzmann solver for multi-GPU systems that achieves 1.79 PFLOPS performance on 16,384 GPUs. To achieve this performance, we introduce a GPU compatible version of the so-called bundle data layout and eliminate the halo sites in order to improve data access alignment. Furthermore, we make use of the possibility to overlap data transfer between the host central processing unit and the device GPU with com…
Molecular Basis of SARS-CoV-2 Nsp1-Induced Immune Translational Shutdown as Revealed by All-Atom Simulations.
2021
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic represents the most severe global health crisis in modern human history. One of the major SARS-CoV-2 virulence factors is nonstructural protein 1 (Nsp1), which, outcompeting with the binding of host mRNA to the human ribosome, triggers a translation shutdown of the host immune system. Here, microsecond-long all-atom simulations of the C-terminal portion of the SARS-CoV-2/SARS-CoV Nsp1 in complex with the 40S ribosome disclose that SARS-CoV-2 Nsp1 has evolved from its SARS-CoV ortholog to more effectively hijack the ribosome by undergoing a critical switch of Q/E158 and E/Q159 residues that perfects Nsp1's interactions…
Mechanisms of irreversible aquaporin-10 inhibition by organogold compounds studied by combined biophysical methods and atomistic simulations
2021
Abstract The inhibition of glycerol permeation via human aquaporin-10 (hAQP10) by organometallic gold complexes has been studied by stopped-flow fluorescence spectroscopy, and its mechanism has been described using molecular modelling and atomistic simulations. The most effective hAQP10 inhibitors are cyclometalated Au(III) C^N compounds known to efficiently react with cysteine residues leading to the formation of irreversible C–S bonds. Functional assays also demonstrate the irreversibility of the binding to hAQP10 by the organometallic complexes. The obtained computational results by metadynamics show that the local arylation of Cys209 in hAQP10 by one of the gold inhibitors is mapped int…
Lagrangian matches between observations from aircraft, lidar and radar in a warm conveyor belt crossing orography
2021
Warm conveyor belts (WCBs) are important airstreams in extratropical cyclones, often leading to the formation of intense precipitation and the amplification of upper-level ridges. This study presents a case study that involves aircraft, lidar and radar observations in a WCB ascending from western Europe towards the Baltic Sea during the Hydrological Cycle in the Mediterranean Experiment (HyMeX) and T-NAWDEX-Falcon in October 2012, a preparatory campaign for the THORPEX North Atlantic Waveguide and Downstream Impact Experiment (TNAWDEX). Trajectories were used to link different observations along the WCB, that is, to establish so-called Lagrangian matches between observations. To this aim, a…
Strain hardening in liquid-particle suspensions
2005
The behavior of a liquid-particle suspension induced to sheared motion was analyzed by numerical simulations. When the velocity (strain) of the suspension began to increase, its viscosity first stayed almost constant, but increased then rapidly to a clearly higher level. This increase in viscosity is shown to be related to formation of clusters of suspended particles. Clusters are shown to increase the viscosity by enhanced momentum transfer though clustered particles. This is the mechanism behind the strain-hardening phenomenon observed in small-strain experiments on liquid-particle suspensions.