scholarly journals Characterization of polystyrene under shear deformation using Molecular Dynamics

2021 ◽  
Author(s):  
Maximilian Ries ◽  
Paul Steinmann ◽  
Sebastian Pfaller
Keyword(s):  
Molecular Dynamics ◽  
Shear Deformation ◽  
Pure Shear ◽  
Material Model ◽  
Md Simulations ◽  
Constitutive Law ◽  
Coupling Scheme ◽  
Suitable Material ◽  
Continuum Description ◽  
The Continuum

Nano-filled polymers are becoming more and more important to meet the continuously growing requirements of modern engineering problems. The investigation of these composite materials at the molecular level, however, is either prohibitively expensive or just impossible. Multiscale approaches offer an elegant way to analyze such nanocomposites by significantly reducing computational costs compared to fully molecular simulations.When coupling different time and length scales, however, it is in particular important to ensure that the same material description is applied at each level of resolution.The Capriccio method, for instance, couples a particle domain modeled with molecular dynamics (MD) with a finite element based continuum description and has been used i.a. to investigate the effects of nano-sized silica additives embedded in atactic polystyrene (PS). However, a simple hyperelastic constitutive law is used so far for the continuum description which is not capable to fully match the behavior of the particle domain. To overcome this issue and to enable further optimization of the coupling scheme, the material model used for the continuum should be derived directly from pure MD simulations under thermodynamic conditions identical to those used by the Capriccio method.To this end, we analyze the material response of pure PS under uniaxial deformation using strain-controlled MD simulations. Analogously, we perform simulations under pure shear deformation to obtain a comprehensive understanding of the material behavior.As a result, the present PS shows viscoelastic characteristics for small strains, whereas viscoplasticity is observed for larger deformations. The insights gained and data generated are used to select a suitable material model whose parameters have to be identified in a subsequent parameter optimization.

The Effect of Temperature on Defect Production by Displacement Cascades in alpha;-IRON

1996 ◽  
Vol 439 ◽  
Author(s):  
F. Gao ◽  
D. J. Bacon ◽  
P. E. J. Flewitt ◽  
T. A. Lewis
Keyword(s):  
Molecular Dynamics ◽  
Md Simulations ◽  
Irradiation Temperature ◽  
Effect Of Temperature ◽  
Cascade Process ◽  
Thermal Spike ◽  
Defect Production ◽  
Alpha Iron ◽  
Displacement Cascades ◽  
The Continuum

AbstractMolecular dynamics (MD) simulations have been used to study the number and arrangement of defects produced by displacement cascades as functions of irradiation temperature, Tirr, in α-iron. The continuum treatment of heat conduction was used to adjust the temperature of the MD boundary atoms throughout the cascade process. This new hybrid model has been applied to cascades of either 2 or 5 keV at 100K, 400K, 600K and 900K. The number of Frenkel pairs decreases by about 20–30% as Tir increases from 100K to 900K, due to the increase in the lifetime of the thermal-spike phase. The same effect also brings about an increase in the proportion of selfinterstitial atoms that form clusters.

Validity of Molecular Dynamics by Quantum Mechanics

2013 ◽  
Author(s):  
Thomas Prevenslik
Keyword(s):  
Molecular Dynamics ◽  
Heat Capacity ◽  
Quantum Mechanics ◽  
Statistical Mechanics ◽  
Quantum Electrodynamics ◽  
Md Simulations ◽  
Tensile Tests ◽  
Electron Pairs ◽  
Linear Motors ◽  
The Continuum

MD is commonly used in computational physics to determine the atomic response of nanostructures. MD stands for molecular dynamics. With theoretical basis in statistical mechanics, MD relates the thermal energy of the atom to its momentum by the equipartition theorem. Momenta of atoms in an ensemble are determined by solving Newton’s equations with inter-atomic forces derived from Lennard-Jones potentials. MD therefore assumes the atom always has heat capacity as otherwise the momenta of the atoms cannot be related to their temperature. In bulk materials, the continuum is simulated in MD by imposing PBC on an ensemble of atoms, the atoms always having heat capacity. PBC stands for periodic boundary conditions. MD simulations of the bulk are valid because atoms in the bulk do indeed have heat capacity. Nanostructures differ from the bulk. Unlike the continuum, the atom confined in discrete submicron geometries is precluded by QM from having the heat capacity necessary to conserve absorbed EM energy by an increase in temperature. QM stands for quantum mechanics and EM for electromagnetic. Quantum corrections of MD solutions that would show the heat capacity of nanostructures vanishes are not performed. What this means is the MD simulations of discrete nanostructures in the literature not only have no physical meaning, but are knowingly invalid by QM. In the alternative, conservation of absorbed EM energy is proposed to proceed by the creation of QED induced non-thermal EM radiation at the TIR frequency of the nanostructure. QED stands for quantum electrodynamics and TIR for total internal reflection. The QED radiation creates excitons (holon and electron pairs) that upon recombination produce EM radiation that charges the nanostructure or is emitted to the surroundings — a consequence only possible by QM as charge is not created in statistical mechanics. Invalid discrete MD simulations are illustrated with nanofluids, nanocars, linear motors, and sputtering. Finally, a valid MD simulation by QM is presented for the stiffening of NWs in tensile tests. NW stands for nanowire.

General Elasticity Theory for Graphene Membranes Based on Molecular Dynamics

2007 ◽  
Vol 1057 ◽  
Author(s):  
Kaveh Samadikhah ◽  
Juan Atalaya ◽  
Caroline Huldt ◽  
Andreas Isacsson ◽  
Jari Kinaret
Keyword(s):  
Molecular Dynamics ◽  
Elasticity Theory ◽  
Elastic Energy ◽  
Poisson Ratio ◽  
Md Simulations ◽  
Energy Functional ◽  
Linear Description ◽  
Continuum Description ◽  
External Forces ◽  
Graphene Membranes

ABSTRACTWe have studied the mechanical properties of suspended graphene membranes using molecular dynamics (MD) and generalized continuum elasticity theory (GE) in order to develop and assess a continuum description for graphene. The MD simulations are based on a valence force field model which is used to determine the deformation and the elastic energy of the membrane (EMD) as a function of external forces. For the continuum description, we use the expression Econt = Estretching + Ebending for the elastic energy functional. The elastic parameters (tensile rigidity and Poisson ratio) entering Econt are determined by requiring that Econt = EMD for a set of deformations.Comparisons with the MD results show excellent agreement. We find that the elastic energy of a supported graphene sheets is typically dominated by the nonlinear stretching terms whereas a linear description is valid only for very small deflections. This implies that in some applications, i.e. NEMS, a linear description is of limited applicability.

scholarly journals Multiscale Friction Simulation of Dry Polymer Contacts: Reaching Experimental Length Scales by Coupling Molecular Dynamics and Contact Mechanics

2021 ◽  
Author(s):  
Daniele Savio ◽  
Jannik Hamann ◽  
Pedro A. Romero ◽  
Christoph Klingshirn ◽  
Ravindrakumar Bactavatchalou ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Contact Mechanics ◽  
Adsorbed Water ◽  
Multiscale Model ◽  
Md Simulations ◽  
Constitutive Law ◽  
Multiscale Approach ◽  
Friction Coefficients ◽  
Ether Ether Ketone ◽  
Poly Ether Ether Ketone

Abstract This work elucidates friction in Poly-Ether-Ether-Ketone (PEEK) sliding contacts through multiscale simulations. At the nanoscale, non-reactive classical molecular dynamics (MD) simulations of dry and water-lubricated amorphous PEEK-PEEK interfaces are performed. During a short running-in phase, we observe structural transformations at the sliding interface that result in flattening of the initial nanotopographies accompanied by strong polymer chain alignment in the shearing direction. Our MD simulations reveal a linear pressure-dependence of the shear stress τMD (P,σH2o) [MPa]=0.18P + 50.5 - 1.25σH2o, where σH2o [nm-2] is the surface number density of adsorbed water molecules. This constitutive law is of central importance for our multiscale approach, since it forms a link between MD and elastoplastic contact mechanics calculations. An integration of τMD (P,σH2o) over the real area of contact yields a macroscopic friction coefficient μmacro (σH2o) that allows for a meaningful comparison with friction coefficients μexp≈0.5-0.7 which are in good agreement with the calculated dry friction coefficients μmacro(σH2o=0).For milder experimental loads, our multiscale model suggests that the lower friction states with μexp≈0.2 originate in the presence of physisorbed molecules (e.g. water), which significantly reduce interfacial adhesion.

scholarly journals Characterization of Interfacial Properties of Graphene-Reinforced Polymer Nanocomposites by Molecular Dynamics-Shear Deformation Model

2018 ◽  
Vol 85 (9) ◽  
Author(s):  
Chanwook Park ◽  
Gun Jin Yun
Keyword(s):  
Mechanical Properties ◽  
Molecular Dynamics ◽  
Shear Modulus ◽  
Shear Deformation ◽  
Md Simulations ◽  
Diglycidyl Ether ◽  
Interfacial Shear ◽  
Interfacial Region ◽  
Deformation Model ◽  
Pull Out

In this paper, we present an approach for characterizing the interfacial region using the molecular dynamics (MD) simulations and the shear deformation model (SDM). The bulk-level mechanical properties of graphene-reinforced nanocomposites strongly depend on the interfacial region between the graphene and epoxy matrix, whose thickness is about 6.8–10.0 Å. Because it is a challenge to experimentally investigate mechanical properties of this thin region, computational MD simulations have been widely employed. By pulling out graphene from the graphene/epoxy system, pull-out force and atomic displacement of the interfacial region are calculated to characterize the interfacial shear modulus. The same processes are applied to 3% grafted hydroxyl and carboxyl functionalized graphene (OH-FG and COOH-FG)/epoxy (diglycidyl ether of bisphenol F (DGEBF)/triethylenetetramine (TETA)) systems, and influences of the functionalization on the mechanical properties of the interfacial region are studied. Our key finding is that, by functionalizing graphene, the pull-out force moderately increases and the interfacial shear modulus considerably decreases. We demonstrate our results by comparing them with literature values and findings from experimental papers.

Validity of Molecular Dynamics Heat Transfer by Quantum Mechanics

2013 ◽  
Vol 829 ◽  
pp. 803-807
Author(s):  
Thomas Prevenslik
Keyword(s):  
Molecular Dynamics ◽  
Heat Capacity ◽  
Quantum Mechanics ◽  
Statistical Mechanics ◽  
Quantum Electrodynamics ◽  
Md Simulations ◽  
Tensile Tests ◽  
Electron Pairs ◽  
Submicron Structures ◽  
The Continuum

MD is commonly used in computational physics to determine the atomic response of nanostructures. MD stands for molecular dynamics. With theoretical basis in statistical mechanics, MD relates the thermal energy of the atom to its momentum by the equipartition theorem. Momenta of atoms are derived by solving Newtons equations with inter-atomic forces derived by Lennard-Jones or L-J potentials. MD implicitly assumes the atom always has heat capacity as otherwise the momenta of the atoms cannot be related to their temperature. In bulk materials, the continuum is simulated by imposing PBC on an ensemble of atoms, the atoms always having heat capacity. PBC stands for periodic boundary conditions. MD simulations of the bulk are therefore valid because atoms in the bulk do indeed have heat capacity. Nanostructures differ. Unlike the continuum, the atom confined in discrete submicron structures is precluded by QM from having the heat capacity necessary to conserve absorbed EM energy by an increase in temperature. QM stands for quantum mechanics and EM for electromagnetic. Quantum corrections of MD solutions that would show the heat capacity of nanostructures vanishes are not performed. What this means is the MD simulations of discrete nanostructures published in the literature not only have no physical meaning, but are knowingly invalid by QM. In the alternative, conservation of absorbed EM energy is proposed to proceed by the creation of QED induced non-thermal EM radiation at the TIR frequency of the nanostructure. QED stands for quantum electrodynamics and TIR for total internal reflection. QED radiation creates excitons (holon and electron pairs) that upon recombination produce EM radiation that charges the nanostructure or is lost to the surroundings a consequence only possible by QM as charge is not created in statistical mechanics. Valid and invalid MD simulations from the literature are illustrated with nanofluids and nanocars, respectively. Finally, valid and invalid MD solutions for the stiffening of NWs in tensile tests are presented to illustrate the unphysical findings if QM is ignored at the nanoscale. NW stands for nanowire.

scholarly journals An Estimation Method of a Constitutive-Law for the Rod Model of DNA Using Discrete-Structure Simulations

2009 ◽  
Author(s):  
Adam R. Hinkle ◽  
Sachin Goyal ◽  
Harish J. Palanthandalam-Madapusi
Keyword(s):  
Lattice Structure ◽  
Estimation Method ◽  
Md Simulations ◽  
Interatomic Bond ◽  
Constitutive Law ◽  
Discrete Structure ◽  
Efficient Tool ◽  
Rod Model ◽  
Structural Deformations ◽  
The Continuum

The continuum-rod model has emerged as an efficient tool to describe the long-length-scale structural-deformations of DNA which are critical to understanding the nature of many biological processes such as gene expression. However, a significant challenge in continuum-mechanics-based modeling of DNA is to estimate its constitutive law, which follows from its interatomic bond-stiffness. Experiments and all-atom molecular dynamics (MD) simulations have suggested that the constitutive law is nonlinear and non-homogeneous (sequence-dependent) along the length of DNA. In this paper, we present an estimation method and a validation study using discrete-structure simulations. We consider a simple cantilever-rod with an artificially constructed, discrete lattice-structure which gives rise to a constitutive law. Large deformations are then simulated. An effective constitutive-law is estimated from these deformations using inverse methods. Finally, we test the estimated law by employing it in the continuum rod-model and comparing the simulation results with those of discrete-structure simulations under a different cantilever loading-conditions.

Efficient Treatment of Fixed and Induced Dipolar Interactions

2000 ◽  
Vol 653 ◽  
Author(s):  
Celeste Sagui ◽  
Thoma Darden
Keyword(s):  
Molecular Dynamics ◽  
Md Simulations ◽  
Lagrangian Formalism ◽  
Dipolar Interactions ◽  
Time Step ◽  
Efficient Treatment ◽  
Particle Mesh Ewald ◽  
Fixed Charges ◽  
Self Consistency ◽  
Induced Dipoles

AbstractFixed and induced point dipoles have been implemented in the Ewald and Particle-Mesh Ewald (PME) formalisms. During molecular dynamics (MD) the induced dipoles can be propagated along with the atomic positions either by interation to self-consistency at each time step, or by a Car-Parrinello (CP) technique using an extended Lagrangian formalism. The use of PME for electrostatics of fixed charges and induced dipoles together with a CP treatment of dipole propagation in MD simulations leads to a cost overhead of only 33% above that of MD simulations using standard PME with fixed charges, allowing the study of polarizability in largemacromolecular systems.

Split the Charge Difference in Two! a Rule of Thumb for Adding Proper Amounts of Ions in MD Simulations

2020 ◽  
Author(s):  
Matías R. Machado ◽  
Sergio Pantano
Keyword(s):  
Molecular Dynamics ◽  
Ionic Strength ◽  
Molecular Simulations ◽  
Md Simulations ◽  
Good Practices ◽  
Rule Of Thumb ◽  
Ionic Concentrations

<p> Despite the relevance of properly setting ionic concentrations in Molecular Dynamics (MD) simulations, methods or practical rules to set ionic strength are scarce and rarely documented. Based on a recently proposed thermodynamics method we provide an accurate rule of thumb to define the electrolytic content in simulation boxes. Extending the use of good practices in setting up MD systems is promptly needed to ensure reproducibility and consistency in molecular simulations.</p>

Assessing the Antimalarial Potentials of Phytochemicals: Virtual Screening, Molecular Dynamics and In-Vitro Investigations

2019 ◽  
Vol 16 (3) ◽  
pp. 291-300
Author(s):  
Saumya K. Patel ◽  
Mohd Athar ◽  
Prakash C. Jha ◽  
Vijay M. Khedkar ◽  
Yogesh Jasrai ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Structural Integrity ◽  
Md Simulations ◽  
Tylophora Indica ◽  
Multidrug Resistance Protein 1 ◽  
Receptor Complexes ◽  
Resistance Protein ◽  
Dynamics Simulations ◽  
Stable Trajectory

Background: Combined in-silico and in-vitro approaches were adopted to investigate the antiplasmodial activity of Catharanthus roseus and Tylophora indica plant extracts as well as their isolated components (vinblastine, vincristine and tylophorine). </P><P> Methods: We employed molecular docking to prioritize phytochemicals from a library of 26 compounds against Plasmodium falciparum multidrug-resistance protein 1 (PfMDR1). Furthermore, Molecular Dynamics (MD) simulations were performed for a duration of 10 ns to estimate the dynamical structural integrity of ligand-receptor complexes. </P><P> Results: The retrieved bioactive compounds viz. tylophorine, vinblastin and vincristine were found to exhibit significant interacting behaviour; as validated by in-vitro studies on chloroquine sensitive (3D7) as well as chloroquine resistant (RKL9) strain. Moreover, they also displayed stable trajectory (RMSD, RMSF) and molecular properties with consistent interaction profile in molecular dynamics simulations. </P><P> Conclusion: We anticipate that the retrieved phytochemicals can serve as the potential hits and presented findings would be helpful for the designing of malarial therapeutics.

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