Large-Scale Molecular Dynamics Simulations Reveal New Insights Into the Phase Transition Mechanisms in MIL-53(Al)

Soft porous crystals have the ability to undergo large structural transformations upon exposure to external stimuli while maintaining their long-range structural order, and the size of the crystal plays an important role in this flexible behavior. Computational modeling has the potential to unravel mechanistic details of these phase transitions, provided that the models are representative for experimental crystal sizes and allow for spatially disordered phenomena to occur. Here, we take a major step forward and enable simulations of metal-organic frameworks containing more than a million atoms. This is achieved by exploiting the massive parallelism of state-of-the-art GPUs using the OpenMM software package, for which we developed a new pressure control algorithm that allows for fully anisotropic unit cell fluctuations. As a proof of concept, we study the transition mechanism in MIL-53(Al) under various external pressures. In the lower pressure regime, a layer-by-layer mechanism is observed, while at higher pressures, the transition is initiated at discrete nucleation points and temporarily induces various domains in both the open and closed pore phases. The presented workflow opens the possibility to deduce transition mechanism diagrams for soft porous crystals in terms of the crystal size and the strength of the external stimulus.

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Atomistic simulation of PDADMAC/PSS oligoelectrolyte multilayers: overall comparison of tri- and tetra-layer systems

Soft Matter ◽

10.1039/c9sm02010a ◽

2019 ◽

Vol 15 (46) ◽

pp. 9437-9451 ◽

Cited By ~ 2

Author(s):

Pedro A. Sánchez ◽

Martin Vögele ◽

Jens Smiatek ◽

Baofu Qiao ◽

Marcello Sega ◽

...

Keyword(s):

Molecular Dynamics ◽

Aqueous Solutions ◽

Molecular Dynamics Simulations ◽

Atomistic Simulation ◽

Large Scale ◽

Layer By Layer ◽

Layer Deposition ◽

Dynamics Simulations

By employing large-scale molecular dynamics simulations of atomistically resolved oligoelectrolytes in aqueous solutions, we study in detail the first four layer-by-layer deposition cycles of a PDADMAC/PSS oligoelectrolyte multilayer.

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Evolution of Metastable Structures in Bimetallic Catalysts from Microscopy and Machine-Learning Molecular Dynamics

10.26434/chemrxiv.11811660.v1 ◽

2020 ◽

Author(s):

Jin Soo Lim ◽

Jonathan Vandermause ◽

Matthijs A. van Spronsen ◽

Albert Musaelian ◽

Christopher R. O’Connor ◽

...

Keyword(s):

Machine Learning ◽

Molecular Dynamics ◽

Large Scale ◽

Materials Science ◽

Complete Characterization ◽

Layer By Layer ◽

Surface Restructuring ◽

Metastable Structures ◽

Mechanistic Investigation ◽

Underlying Mechanisms

Restructuring of interface plays a crucial role in materials science and heterogeneous catalysis. Bimetallic systems, in particular, often adopt very different composition and morphology at surfaces compared to the bulk. For the first time, we reveal a detailed atomistic picture of the long-timescale restructuring of Pd deposited on Ag, using microscopy, spectroscopy, and novel simulation methods. Encapsulation of Pd by Ag always precedes layer-by-layer dissolution of Pd, resulting in significant Ag migration out of the surface and extensive vacancy pits. These metastable structures are of vital catalytic importance, as Ag-encapsulated Pd remains much more accessible to reactants than bulk-dissolved Pd. The underlying mechanisms are uncovered by performing fast and large-scale machine-learning molecular dynamics, followed by our newly developed method for complete characterization of atomic surface restructuring events. Our approach is broadly applicable to other multimetallic systems of interest and enables the previously impractical mechanistic investigation of restructuring dynamics.

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Control of humping phenomenon and analyzing mechanical properties of Al–Si wire-arc additive manufacturing fabricated samples using cold metal transfer process

Proceedings of the Institution of Mechanical Engineers Part C Journal of Mechanical Engineering Science ◽

10.1177/0954406221998402 ◽

2021 ◽

pp. 095440622199840

Author(s):

Yashwant Koli ◽

N Yuvaraj ◽

Aravindan Sivanandam ◽

Vipin

Keyword(s):

Mechanical Properties ◽

Additive Manufacturing ◽

Heat Input ◽

Large Scale ◽

High Deposition Rate ◽

Bead Geometry ◽

Layer By Layer ◽

Cold Metal Transfer ◽

Geometrical Shapes ◽

Wire Arc Additive Manufacturing

Nowadays, rapid prototyping is an emerging trend that is followed by industries and auto sector on a large scale which produces intricate geometrical shapes for industrial applications. The wire arc additive manufacturing (WAAM) technique produces large scale industrial products which having intricate geometrical shapes, which is fabricated by layer by layer metal deposition. In this paper, the CMT technique is used to fabricate single-walled WAAM samples. CMT has a high deposition rate, lower thermal heat input and high cladding efficiency characteristics. Humping is a common defect encountered in the WAAM method which not only deteriorates the bead geometry/weld aesthetics but also limits the positional capability in the process. Humping defect also plays a vital role in the reduction of hardness and tensile strength of the fabricated WAAM sample. The humping defect can be controlled by using low heat input parameters which ultimately improves the mechanical properties of WAAM samples. Two types of path planning directions namely uni-directional and bi-directional are adopted in this paper. Results show that the optimum WAAM sample can be achieved by adopting a bi-directional strategy and operating with lower heat input process parameters. This avoids both material wastage and humping defect of the fabricated samples.

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Elucidating the Onset of Plasticity in Sliding Contacts Using Differential Computational Orientation Tomography

Tribology Letters ◽

10.1007/s11249-021-01451-9 ◽

2021 ◽

Vol 69 (3) ◽

Author(s):

S. J. Eder ◽

P. G. Grützmacher ◽

M. Rodríguez Ripoll ◽

J. F. Belak

Keyword(s):

Grain Boundary ◽

Large Scale ◽

Surface Deformation ◽

Boundary Migration ◽

Material Design ◽

Lattice Rotation ◽

Time Resolved ◽

Near Surface ◽

Color Saturation ◽

Dynamics Simulations

Abstract Depending on the mechanical and thermal energy introduced to a dry sliding interface, the near-surface regions of the mated bodies may undergo plastic deformation. In this work, we use large-scale molecular dynamics simulations to generate “differential computational orientation tomographs” (dCOT) and thus highlight changes to the microstructure near tribological FCC alloy surfaces, allowing us to detect subtle differences in lattice orientation and small distances in grain boundary migration. The analysis approach compares computationally generated orientation tomographs with their undeformed counterparts via a simple image analysis filter. We use our visualization method to discuss the acting microstructural mechanisms in a load- and time-resolved fashion, focusing on sliding conditions that lead to twinning, partial lattice rotation, and grain boundary-dominated processes. Extracting and laterally averaging the color saturation value of the generated tomographs allows us to produce quantitative time- and depth-resolved maps that give a good overview of the progress and severity of near-surface deformation. Corresponding maps of the lateral standard deviation in the color saturation show evidence of homogenization processes occurring in the tribologically loaded microstructure, frequently leading to the formation of a well-defined separation between deformed and undeformed regions. When integrated into a computational materials engineering framework, our approach could help optimize material design for tribological and other deformation problems. Graphic Abstract .

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Large-Scale Membrane Permeability Prediction of Cyclic Peptides Crossing a Lipid Bilayer Based on Enhanced Sampling Molecular Dynamics Simulations

Journal of Chemical Information and Modeling ◽

10.1021/acs.jcim.1c00380 ◽

2021 ◽

Author(s):

Masatake Sugita ◽

Satoshi Sugiyama ◽

Takuya Fujie ◽

Yasushi Yoshikawa ◽

Keisuke Yanagisawa ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Membrane Permeability ◽

Lipid Bilayer ◽

Cyclic Peptides ◽

Large Scale ◽

Enhanced Sampling ◽

Permeability Prediction ◽

Dynamics Simulations

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A numerical study of the transition of jet diffusion flames

Proceedings of the Royal Society of London. Series A: Mathematical and Physical Sciences ◽

10.1098/rspa.1990.0132 ◽

1990 ◽

Vol 431 (1882) ◽

pp. 301-314 ◽

Cited By ~ 29

Keyword(s):

Reynolds Number ◽

Diffusion Coefficient ◽

Large Scale ◽

Numerical Study ◽

Small Scale ◽

Surface Model ◽

Flame Surface ◽

Transition Mechanism ◽

Air Stream ◽

Scale Fluctuation

A numerical study on the transition from laminar to turbulent of two-dimensional fuel jet flames developed in a co-flowing air stream was made by adopting the flame surface model of infinite chemical reaction rate and unit Lewis number. The time dependent compressible Navier–Stokes equation was solved numerically with the equation for coupling function by using a finite difference method. The temperature-dependence of viscosity and diffusion coefficient were taken into account so as to study effects of increases of these coefficients on the transition. The numerical calculation was done for the case when methane is injected into a co-flowing air stream with variable injection Reynolds number up to 2500. When the Reynolds number was smaller than 1000 the flame, as well as the flow, remained laminar in the calculated domain. As the Reynolds number was increased above this value, a transition point appeared along the flame, downstream of which the flame and flow began to fluctuate. Two kinds of fluctuations were observed, a small scale fluctuation near the jet axis and a large scale fluctuation outside the flame surface, both of the same origin, due to the Kelvin–Helmholtz instability. The radial distributions of density and transport coefficients were found to play dominant roles in this instability, and hence in the transition mechanism. The decreased density in the flame accelerated the instability, while the increase in viscosity had a stabilizing effect. However, the most important effect was the increase in diffusion coefficient. The increase shifted the flame surface, where the large density decrease occurs, outside the shear layer of the jet and produced a thick viscous layer surrounding the jet which effectively suppressed the instability.

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