scholarly journals Sweep-tracing algorithm: in silico slip crystallography and tension-compression asymmetry in BCC metals

2022 ◽  
Vol 6 (1) ◽  
Author(s):  
Nicolas Bertin ◽  
L.A. Zepeda-Ruiz ◽  
V.V. Bulatov

AbstractDirect Molecular Dynamics (MD) simulations are being increasingly employed to model dislocation-mediated crystal plasticity with atomic resolution. Thanks to the dislocation extraction algorithm (DXA), dislocation lines can be now accurately detected and positioned in space and their Burgers vector unambiguously identified in silico, while the simulation is being performed. However, DXA extracts static snapshots of dislocation configurations that by themselves present no information on dislocation motion. Referred to as a sweep-tracing algorithm (STA), here we introduce a practical computational method to observe dislocation motion and to accurately quantify its important characteristics such as preferential slip planes (slip crystallography). STA reconnects pairs of successive snapshots extracted by DXA and computes elementary slip facets thus precisely tracing the motion of dislocation segments from one snapshot to the next. As a testbed for our new method, we apply STA to the analysis of dislocation motion in large-scale MD simulations of single crystal plasticity in BCC metals. We observe that, when the crystal is subjected to uniaxial deformation along its [001] axis, dislocation slip predominantly occurs on the {112} maximum resolved shear stress plane under tension, while in compression slip is non-crystallographic (pencil) resulting in asymmetric mechanical response. The marked contrast in the observed slip crystallography is attributed to the twinning/anti-twinning asymmetry of shears in the {112} planes relatively favoring dislocation motion in the twinning sense while hindering dislocations from moving in the anti-twinning directions.

2015 ◽  
Vol 1 (1) ◽  
Author(s):  
Sagar Chandra ◽  
M. K. Samal ◽  
V. M. Chavan ◽  
R. J. Patel

AbstractA hierarchical multiscale modeling approach is presented to predict the mechanical response of dynamically deformed (1100 s−1−4500 s−1) copper single crystal in two different crystallographic orientations.Anattempt has been made to bridge the gap between nano-, micro- and meso- scales. In view of this, Molecular Dynamics (MD) simulations at nanoscale are performed to quantify the drag coefficient for dislocations which has been exploited in Dislocation Dynamics (DD) regime at the microscale. Discrete dislocation dynamics simulations are then performed to calculate the hardening parameters required by the physics based Crystal Plasticity (CP) model at the mesoscale. The crystal plasticity model employed is based on thermally activated theory for plastic flow. Crystal plasticity simulations are performed to quantify the mechanical response of the copper single crystal in terms of stressstrain curves and shape changes under dynamic loading. The deformation response obtained from CP simulations is in good agreement with the experimental data.


Author(s):  
Smriti Sharma ◽  
Vinayak Bhatia

: Pyrazole and its derivatives are a pharmacologically significant active scaffold that have innumerable physiological and pharmacological activities. They can be very good targets for the discovery of novel anti-bacterial, anticancer, anti-inflammatory, anti-fungal, anti-tubercular, antiviral, antioxidant, antidepressant, anti-convulsant and neuroprotective drugs. This review focuses on the importance of in silico manipulations of pyrazole and its derivatives for medicinal chemistry. The authors have discussed currently available information on the use of computational techniques like molecular docking, structure-based virtual screening (SBVS), molecular dynamics (MD) simulations, quantitative structure activity relationship (QSAR), comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) to drug design using pyrazole moieties. Pyrazole based drug design is mainly dependent on the integration of experimental and computational approaches. The authors feel that more studies need to be done to fully explore the pharmacological potential of the pyrazole moiety and in silico method can be of great help.


2019 ◽  
Vol 16 (4) ◽  
pp. 307-313 ◽  
Author(s):  
Nasrin Zarkar ◽  
Mohammad Ali Nasiri Khalili ◽  
Fathollah Ahmadpour ◽  
Sirus Khodadadi ◽  
Mehdi Zeinoddini

Background: DAB389IL-2 (Denileukin diftitox) as an immunotoxin is a targeted pharmaceutical protein and is the first immunotoxin approved by FDA. It is used for the treatment of various kinds of cancer such as CTCL lymphoma, melanoma, and Leukemia but among all of these, treatment of CTCL has special importance. DAB389IL-2 consists of two distinct parts; the catalytic domain of Diphtheria Toxin (DT) that genetically fused to the whole IL-2. Deamidation is the most important reaction for chemical instability of proteins occurs during manufacture and storage. Deamidation of asparagine residues occurs at a higher rate than glutamine residues. The structure of proteins, temperature and pH are the most important factors that influence the rate of deamidation. Methods: Since there is not any information about deamidation of DAB389IL-2, we studied in silico deamidation by Molecular Dynamic (MD) simulations using GROMACS software. The 3D model of fusion protein DAB389IL-2 was used as a template for deamidation. Then, the stability of deamidated and native form of the drug was calculated. Results: The results of MD simulations were showed that the deamidated form of DAB389IL-2 is more unstable than the normal form. Also, deamidation was carried by incubating DAB389IL-2, 0.3 mg/ml in ammonium hydrogen carbonate for 24 h at 37o C in order to in vitro experiment. Conclusion: The results of in vitro experiment were confirmed outcomes of in silico study. In silico and in vitro experiments were demonstrated that DAB389IL-2 is unstable in deamidated form.


RSC Advances ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 7059-7069
Author(s):  
M. Khatouri ◽  
R. Ahfir ◽  
M. Lemaalam ◽  
S. El Khaoui ◽  
A. Derouiche ◽  
...  

In this work, we study the effect of grafted PEO-dodecyl co-polymers on the decane/water microemulsions properties. For this purpose, we combined the MD simulations, the OZ integral equations resolved using the HNC closure, and SANS experiments.


Soft Matter ◽  
2020 ◽  
Vol 16 (26) ◽  
pp. 6191-6205 ◽  
Author(s):  
Fabio Guglietta ◽  
Marek Behr ◽  
Luca Biferale ◽  
Giacomo Falcucci ◽  
Mauro Sbragaglia

Computational Fluid Dynamics is currently used to design and improve the hydraulic properties of biomedical devices, wherein the large scale blood circulation needs to be simulated by accounting for the mechanical response of RBCs at the mesoscale.


Author(s):  
Aaron M. Swedberg ◽  
Shawn P. Reese ◽  
Steve A. Maas ◽  
Benjamin J. Ellis ◽  
Jeffrey A. Weiss

Ligament volumetric behavior controls fluid and thus nutrient movement as well as the mechanical response of the tissue to applied loads. The reported Poisson’s ratios for tendon and ligament subjected to tensile deformation loading along the fiber direction are large, ranging from 0.8 ± 0.3 in rat tail tendon fascicles [1] to 2.98 ± 2.59 in bovine flexor tendon [2]. These Poisson’s ratios are indicative of volume loss and thus fluid exudation [3,4]. We have developed micromechanical finite element models that can reproduce both the characteristic nonlinear stress-strain behavior and large, strain-dependent Poisson’s ratios seen in tendons and ligaments [5], but these models are computationally expensive and unfeasible for large scale, whole joint models. The objectives of this research were to develop an anisotropic, continuum based constitutive model for ligaments and tendons that can describe strain-dependent Poisson’s ratios much larger than the isotropic limit of 0.5. Further, we sought to demonstrate the ability of the model to describe experimental data, and to show that the model can be combined with biphasic theory to describe the rate- and time-dependent behavior of ligament and tendon.


2008 ◽  
Vol 9 (S1) ◽  
Author(s):  
Upinder S Bhalla ◽  
Radhika Madhavan ◽  
Ashesh Dhawale ◽  
Mehrab Modi ◽  
Raamesh Deshpande ◽  
...  
Keyword(s):  

2014 ◽  
Vol 1700 ◽  
pp. 61-66
Author(s):  
Guttormur Arnar Ingvason ◽  
Virginie Rollin

ABSTRACTAdding single walled carbon nanotubes (SWCNT) to a polymer matrix can improve the delamination properties of the composite. Due to the complexity of polymer molecules and the curing process, few 3-D Molecular Dynamics (MD) simulations of a polymer-SWCNT composite have been run. Our model runs on the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS), with a COMPASS (Condensed phase Optimized Molecular Potential for Atomistic Simulations Studies) potential. This potential includes non-bonded interactions, as well as bonds, angles and dihedrals to create a MD model for a SWCNT and EPON 862/DETDA (Diethyltoluenediamine) polymer matrix. Two simulations were performed in order to test the implementation of the COMPASS parameters. The first one was a tensile test on a SWCNT, leading to a Young’s modulus of 1.4 TPa at 300K. The second one was a pull-out test of a SWCNT from an originally uncured EPON 862/DETDA matrix.


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