scholarly journals Fully Atomistic Molecular Dynamics Computation of Physico-Mechanical Properties of PB, PS, and SBS

Nanomaterials ◽  
2019 ◽  
Vol 9 (8) ◽  
pp. 1088 ◽  
Author(s):  
Yang Kang ◽  
Dunhong Zhou ◽  
Qiang Wu ◽  
Fuyan Duan ◽  
Rufang Yao ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Strain Rate ◽  
Strain Hardening ◽  
Md Simulation ◽  
Md Simulations ◽  
Strain Rates ◽  
Young’S Moduli ◽  
Plastic Modulus ◽  
Styrene Butadiene ◽  
Butadiene Styrene

The physical properties—including density, glass transition temperature (Tg), and tensile properties—of polybutadiene (PB), polystyrene (PS) and poly (styrene-butadiene-styrene: SBS) block copolymer were predicted by using atomistic molecular dynamics (MD) simulation. At 100 K, for PB and SBS under uniaxial tension with strain rate ε ˙ = 1010 s−1 and 109 s−1, their stress–strain curves had four features, i.e., elastic, yield, softening, and strain hardening. At 300 K, the tensile curves of the three polymers with strain rates between 108 s−1 and 1010 s−1 exhibited strain hardening following elastic regime. The values of Young’s moduli of the copolymers were independent of strain rate. The plastic modulus of PS was independent of strain rate, but the Young’s moduli of PB and SBS depended on strain rate under the same conditions. After extrapolating the Young’s moduli of PB and SBS at strain rates of 0.01–1 s−1 by the linearized Eyring-like model, the predicted results by MD simulations were in accordance well with experimental results, which demonstrate that MD results are feasible for design of new materials.

Morphology and Mechanical Properties of Foamed Polyethylene Blends

2003 ◽  
Vol 22 (4) ◽  
pp. 211-236 ◽  
Author(s):  
Yaolin Zhang ◽  
Denis Rodrigue ◽  
Abdellatif Aït-Kadi
Keyword(s):  
Strain Rate ◽  
Diameter Distribution ◽  
Cell Diameter ◽  
Strain Rates ◽  
Truncated Normal Distribution ◽  
Polyethylene Blends ◽  
Young’S Moduli ◽  
Definite Effect ◽  
Truncated Normal ◽  
Morphology And Mechanical Properties

Blends of polyethylene were foamed (593–782 kg/m3) by compression molding. Their morphology was investigated to understand the effect of polymer molecular structure. It was found that the cell diameter distribution can be approximated by a truncated normal distribution. Torsion, flexural and tensile properties were also measured at different strain rates. It was found that the shear, flexural and Young's moduli of blends and their foams increase with increasing strain rate, while their normalized moduli are almost unchanged. We also confirm that thin skins have a definite effect on shear and flexural moduli, but are negligible on tensile moduli. Finally, normalized yield strength and strain are almost independent on strain rate while break strain and toughness increase with increasing molecular weight and decreasing strain rate.

A boosted unbiased molecular dynamics method for predicting ligands binding mechanisms: probing the binding pathway of dasatinib to Src-kinase

2020 ◽  
Vol 36 (18) ◽  
pp. 4714-4720
Author(s):  
Farzin Sohraby ◽  
Mostafa Javaheri Moghadam ◽  
Masoud Aliyar ◽  
Hassan Aryapour
Keyword(s):  
Molecular Dynamics ◽  
Ligand Binding ◽  
Md Simulation ◽  
Src Kinase ◽  
Deep Understanding ◽  
Md Simulations ◽  
Binding Mode ◽  
Supplementary Information ◽  
Computational Resources ◽  
Binding Mechanisms

Abstract Summary Small molecules such as metabolites and drugs play essential roles in biological processes and pharmaceutical industry. Knowing their interactions with biomacromolecular targets demands a deep understanding of binding mechanisms. Dozens of papers have suggested that discovering of the binding event by means of conventional unbiased molecular dynamics (MD) simulation urges considerable amount of computational resources, therefore, only one who holds a cluster or a supercomputer can afford such extensive simulations. Thus, many researchers who do not own such resources are reluctant to take the benefits of running unbiased MD simulation, in full atomistic details, when studying a ligand binding pathway. Many researchers are impelled to be content with biased MD simulations which seek its validation due to its intrinsic preconceived framework. In this work, we have presented a workable stratagem to encourage everyone to perform unbiased (unguided) MD simulations, in this case a protein–ligand binding process, by typical desktop computers and so achieve valuable results in nanosecond time scale. Here, we have described a dynamical binding’s process of an anticancer drug, the dasatinib, to the c-Src kinase in full atomistic details for the first time, without applying any biasing force or potential which may lead the drug to artificial interactions with the protein. We have attained multiple independent binding events which occurred in the nanosecond time scales, surprisingly as little as ∼30 ns. Both the protonated and deprotonated forms of the dasatinib reached the crystallographic binding mode without having any major intermediate state during induction. Availability and implementation The links of the tutorial and technical documents are accessible in the article. Supplementary information Supplementary data are available at Bioinformatics online.

Tensile Behavior of Ti-5Al-2.5Sn Alloy at Low Temperatures and High Strain Rates

2019 ◽  
Vol 794 ◽  
pp. 135-141
Author(s):  
Bin Zhang ◽  
Yang Wang
Keyword(s):  
Strain Rate ◽  
Strain Hardening ◽  
Low Temperatures ◽  
High Strain ◽  
Testing Temperature ◽  
Tensile Behavior ◽  
Experimental Results ◽  
Strain Rates ◽  
Increasing Temperature ◽  
Strain Hardening Rate

The mechanical responses of Ti-5Al-2.5Sn alloy at low temperatures were investigated under quasi-static and dynamic tensile loads using MTS system and SHTB system, respectively. Tensile stress-strain curves were obtained over the temperature range of 153 to 298K and the rate range of 0.001 to 1050 s-1. Experimental results indicate that the tensile behavior of Ti-5Al-2.5Sn alloy is dependent on strain rate and temperature. Yield stress and flow stress increase with increasing strain rate and decrease with increasing temperature. Results also indicate that strain hardening rate of Ti-5Al-2.5Sn alloy is lower at high strain rate, while strain hardening rate varies little with testing temperature. The Khan-Huang-Liang constitutive model was chosen to characterize the tensile responses of Ti-5Al-2.5Sn alloy at low temperatures and different strain rates. The model results coincide well with the experimental results within the tested temperature and rate ranges.

Strain rate sensitivity of a mild steel at room temperature and strain rates of up to 105s−1

1980 ◽  
Vol 15 (4) ◽  
pp. 201-207 ◽  
Author(s):  
M S J Hashmi
Keyword(s):  
Finite Difference ◽  
Mild Steel ◽  
Strain Rate ◽  
Strain Hardening ◽  
Strain Rate Sensitivity ◽  
Elastic Strain ◽  
Room Temperature ◽  
Numerical Technique ◽  
Rate Sensitivity ◽  
Strain Rates

Experimental results on a mild steel are reported from ballistics tests which gave rise to strain rates of up to 105 s−1. A finite-difference numerical technique which incorporates material inertia, elastic-strain hardening and strain-rate sensitivity is used to establish the strain-rate sensitivity constants p and D in the equation, σ4 = σ1 (1+(∊/D)1/ p). The rate sensitivity established in this study is compared with those reported by other researchers.

Surface Tension Evaluation Via Thermodynamic Analysis of Statistical Data From Molecular Dynamics Simulations

Volume 4 ◽  
2004 ◽  
Author(s):  
Aaron P. Wemhoff ◽  
Van P. Carey
Keyword(s):  
Molecular Dynamics ◽  
Surface Tension ◽  
Density Profile ◽  
Md Simulation ◽  
Md Simulations ◽  
Bulk Liquid ◽  
Interfacial Region ◽  
Lennard Jones Potential ◽  
Jones Potential ◽  
Lennard Jones

Surface tension determination of liquid-vapor interfaces of polyatomic fluids using traditional methods has shown to be difficult due to the requirement of evaluating complex intermolecular potentials. However, analytical techniques have recently been developed that determine surface tension solely by means of the characteristics of the interfacial region between the bulk liquid and vapor regions. A post-simulation application of the excess free energy density integration (EFEDI) method was used for analysis of the resultant density profile of molecular dynamics (MD) simulations of argon using a simple Lennard-Jones potential and diatomic nitrogen using a two-center Lennard-Jones potential. MD simulations were also run for an approximation of nitrogen using the simple Lennard-Jones potential. In each MD simulation, a liquid film was initialized between vapor regions and NVE-type simulations were run to equilibrium. The simulation domain was divided into bins across the interfacial region for fluid density collection, and the resultant interfacial region density profile was used for surface tension evaluation. Application of the EFEDI method to these MD simulation results exhibited good approximations to surface tension as a function of temperature for both a simple and complex potential.

Molecular dynamics study on the tensile properties of graphene/Cu nanocomposite

2017 ◽  
Vol 06 (03) ◽  
pp. 1750021 ◽  
Author(s):  
Jun Hua ◽  
Zhirong Duan ◽  
Chen Song ◽  
Qinlong Liu
Keyword(s):  
Mechanical Properties ◽  
Molecular Dynamics ◽  
Tensile Strength ◽  
Elastic Modulus ◽  
Comparative Analysis ◽  
Strain Rate ◽  
Ultimate Strength ◽  
Strain Rates ◽  
Single Crystal Copper ◽  
Single Slice

In this paper, the mechanical properties, including elastic properties, deformation mechanism, dislocation formation and crack propagation of graphene/Cu (G/Cu) nanocomposite under uniaxial tension are studied by molecular dynamics (MD) method and the strain rate dependence is also investigated. Firstly, through the comparative analysis of tensile results of single crystal copper (Cu), single slice graphene/Cu (SSG/Cu) nanocomposite and double slice graphene/Cu (DSG/Cu) nanocomposite, it is found that the G/Cu nanocomposites have larger initial equivalent elastic modulus and tensile ultimate strength comparing with Cu and the more content of graphene, the greater the tensile strength of composites. Afterwards, by analyzing the tensile results of SSG/Cu nanocomposite under different strain rates, we find that the tensile ultimate strength of SSG/Cu nanocomposite increases with the increasing of strain rate gradually, but the initial equivalent elastic modulus basically remains unchanged.

Constitutive Modeling of a Thermoplastic Olefin Over a Broad Range of Strain Rates

2006 ◽  
Vol 128 (4) ◽  
pp. 551-558 ◽  
Author(s):  
Yan Wang ◽  
Ellen M. Arruda
Keyword(s):  
Strain Rate ◽  
Strain Hardening ◽  
Three Dimensional ◽  
Elastic Response ◽  
Strain Rates ◽  
Strain Behavior ◽  
Rate Dependent ◽  
State Dependent ◽  
Deformation State ◽  
Ann Arbor

A microstructually motivated, three-dimensional, large deformation, strain rate dependent constitutive model has been developed for a semi-crystalline, blended, thermoplastic olefin (TPO) (Wang, Y., 2002, Ph.D. thesis, The University of Michigan, Ann Arbor, MI). Various experiments have been conducted to characterize the TPO and to verify the modeling approach (Wang, Y., 2002, Ph.D. thesis, The University of Michigan, Ann Arbor, MI). The model includes a quantitative rate-dependent Young’s modulus, a nonlinear viscoelastic response between initial linear elastic response and yield due to inherent microstructural irregularity, rate and temperature dependent yield with two distinctive yield mechanisms for low and high strain rates, temperature-dependent strain hardening, plastic deformation of crystalline regions, and adiabatic heating. It has been shown to accurately capture the observed TPO stress-strain behavior including the rate-dependent initial linear elastic response; temperature, strain rate, and deformation state-dependent yield; temperature and deformation state-dependent strain hardening; and pronounced thermal softening effects at high (impact) strain rates. The model has also been examined for its ability to predict the response in plane strain compression based on material parameters chosen to capture the uniaxial compression response. The model is predictive of the initial strain rate dependent stiffness, yield, and strain hardening responses in plane strain. Such predictive capability demonstrates the versatility with which this model captures the three-dimensional anisotropic nature of TPO stress-strain behavior.

scholarly journals Nanoindentation simulations for large atomic systems : an analysis of molecular dynamics and bridged finite element - molecular dynamics methodologies

2021 ◽  
Author(s):  
Jonathan Vandersluis
Keyword(s):  
Molecular Dynamics ◽  
Finite Element ◽  
Md Simulation ◽  
Computational Simulation ◽  
Md Simulations ◽  
Single Step ◽  
Depth Interval ◽  
Simulation Tool ◽  
Custom Made ◽  
Computational Resources

This thesis develops a molecular dynamics (MD) custom made computational tool to perform nanoindentation simulations on copper nanomaterials, a Face Centred Cubic (FCC) metal. The Embedding Atom Method (EAM) is used to model the interatomic forces with the substrate. Further, a bridged finite element - molecular dynamics (FE-MD) simulation tool is also adapted to perform nanoindentation experimentation. Using this bridged FE-MD simulation tool, nanoindentations are performed much more effectively than the MD simulations while saving substantial computational simulation time. While the MD simulation experienced difficulties capturing the behaviour of the system during indentation especially at faster indentation speeds, the bridged FE-MD method is capable of reaching a state of equilibrium within a single step for each indentation depth interval analyzed throughout the nanoindentation. Although the hardness values for these simulations cannot be obtained without larger scale simulations using more powerful computational resources, the simulations provide insight into the behaviour of the copper nanomaterial during nanoindentation. As a result, it is clear that the bridged FE-MD nanoindentation tool is much more effective for executing nanoindentation simulations than the traditional MD methodologies.

scholarly journals Neural relational inference to learn allosteric long-range interactions in proteins from molecular dynamics simulations

2021 ◽  
Author(s):  
Jingxuan Zhu ◽  
Juexin Wang ◽  
Weiwei Han ◽  
Dong Xu
Keyword(s):  
Molecular Dynamics ◽  
Long Range ◽  
Md Simulation ◽  
Biological Process ◽  
Dynamic Networks ◽  
Md Simulations ◽  
Amino Acid Mutation ◽  
Long Range Interactions ◽  
Decoder Architecture ◽  
Dynamics Simulations

Abstract Protein allostery is a biological process facilitated by spatially long-range intra-protein communication, whereby ligand binding or amino acid mutation at a distant site affects the active site remotely. Molecular dynamics (MD) simulation provides a powerful computational approach to probe the allosteric effect. However, current MD simulations cannot reach the time scales of whole allosteric processes. The advent of deep learning made it possible to evaluate both spatially short and long-range communications for understanding allostery. For this purpose, we applied a neural relational inference (NRI) model based on a graph neural network (GNN), which adopts an encoder-decoder architecture to simultaneously infer latent interactions to probe protein allosteric processes as dynamic networks of interacting residues. From the MD trajectories, this model successfully learned the long-range interactions and pathways that can mediate the allosteric communications between the two distant sites in the Pin1, SOD1, and MEK1 systems.

scholarly journals Strain-Rate-Dependent Tensile Response of Ti–5Al–2.5Sn Alloy

Materials ◽  
2019 ◽  
Vol 12 (4) ◽  
pp. 659 ◽  
Author(s):  
Bin Zhang ◽  
Jin Wang ◽  
Yang Wang ◽  
Yu Wang ◽  
Ziran Li
Keyword(s):  
Strain Rate ◽  
Strain Hardening ◽  
Uniaxial Tension ◽  
Temperature Rise ◽  
High Strain ◽  
Adiabatic Temperature ◽  
High Rate ◽  
Strain Rates ◽  
High Strain Rates ◽  
Adiabatic Temperature Rise

This study is an experimental investigation on the tensile responses of Ti–5Al–2.5Sn alloy over a wide range of strain rates. Uniaxial tension tests within the rate range of 10−3–101 s−1 are performed using a hydraulic driven MTS810 machine and a moderate strain-rate testing system. The high-rate uniaxial tension and tension recovery tests are conducted using a split-Hopkinson tension bar to obtain the adiabatic and isothermal stress–strain responses of the alloy under dynamic loading conditions. The experimental results show that the value of the initial yield stress increases with the increasing strain rate, while the strain rate sensitivity is greater at high strain rates. The isothermal strain-hardening behavior changes little with the strain rate, and the adiabatic temperature rise is the main reason for the reduction of the strain-hardening rate during high strain-rate tension. The electron backscatter diffraction (EBSD) analysis of the post-deformed samples indicates that there are deformation twins under quasi-static and high-rate tensile loadings. Scanning electron microscope (SEM) micrographs of the fracture surfaces of the post-deformed samples show dimple-like features. The Zerilli–Armstrong model is modified to incorporate the thermal-softening effect of the adiabatic temperature rise at high strain rates and describe the tension responses of Ti–5Al–2.5Sn alloy over strain rates from quasi-static to 1050 s−1.

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