Pictures from LAMMPS Simulations

The images on this page are from LAMMPS simulations (or its predecessor codes), that have been rendered with various visualization packages. This page has additional pictures with accompanying animations.

All of these images are shown in small size. Click on the image to view a larger version.

Stress field around dislocations

This is work by Ed Webb (ebwebb at sandia.gov), Jon Zimmerman, and Steve Seel at Sandia to compare thermomechanical properties like stress computed in atomistic simulations to their continuum counterparts. Traditional elasticity theory would produce a singularity in stress at the core of a dislocation like that shown below, whereas atomic scale calculations and non-local elasticity theories avoid this shortcoming.

The figures show stress fields (sigma_xx) surrounding the core of an edge dislocation in EAM Al calculated using the discrete (top) and Hardy (bottom) expressions for sigma. The color contour maps represent peak tension in red at 5 GPa and peak compression in blue at -5 GPa. The Burgers vector direction (x) is horizontal in the figure.

This paper has further details:

Reconsideration of Continuum Thermomechanical Quantities in Atomic Scale Simulations, E. B. Webb III, J. A. Zimmerman, S. C. Seel, Mathematics and Mechanics of Solids, 13, 221-266 (2008). (abstract)

Water interacting with self-assembled monolayers

This is work by Matt Lane, Gary Grest, Mike Chandross, and Mark Stevens (all at Sandia) and Chris Lorenz (King's College, London). They studied the interaction of water with self-assembled monolayers (SAMs). Investigations included water penetration of damaged SAMs and water diffusion properties in nanoconfinement. The first snapshot shows the effects of water on SAM coatings with various sized regions of damage. The second shows only the water during penetration. The third snapshot shows water in nanoconfinement between two planar SAMs.

These papers have further details:

Water in Nanoconfinement between Hydrophilic Self-Assembled Monolayers, J. M. D. Lane, M. Chandross, M. J. Stevens, G. S. Grest, Langmuir, 24, 5209-5212 (2008). (abstract)

Water Penetration of Damaged Self-Assembled Monolayers, J. M. D. Lane, M. Chandross, C. D. Lorenz, M. J. Stevens, G. S. Grest, Langmuir, 24, 5734-5739 (2008). (abstract)

Coarse-grained self-assembly of lipids and PEG surfactants

This is work by Wataru Shinoda (AIST Tsukuba, Japan) in collaboration with Russell DeVane (U Penn) and Michael L. Klein (U Penn) to study self-assembly of organic molecules and their long timescale behavior using a novel coarse-grained parametrization scheme.

Both systems in these images have about 1 million particles. The image on the left is of a vesicle interacting with a lipid bilayer. The system on the right represents an aqueous surfactant solution run for 100 nanosecs before it undergoes a phase transition to the final ordered state.

These papers have further details:

Large-Scale Molecular Dynamics Simulations of Self-Assembling Systems, M. L. Klein and W. Shinoda, Science, 321, 798-800 (2008). (abstract)

Coarse-grained molecular modeling of non-ionic surfactant self-assembly, W. Shinoda, R. H. DeVane, M. L. Klein, Soft Matter, 4, 2453-2462 (2008). (abstract)

Spherical polyelectrolyte brushes

This is work by Ran Ni, Dapeng Cao and Wenchuan Wang in the Lab of Molecular and Materials Simulation at Beijing University of Chemical Technology and Arben Jusufi in Princeton University.

They studied the conformational behavior of a coarse-grained model of spherical polyelectrolyte brushes (SPB) in aqueous solutions containing oppositely charged linear polyelectrolytes (LPs). The snapshots show that with increasing concentration of LPs, the SPB undergoes swelling (left) -> collapse (middle) -> re-swelling (right).

This paper has further details:

Conformation of a Spherical Polyelectrolyte Brush in the Presence of Oppositely Charged Linear Polyelectrolytes, R. Ni, D. Cao, W. Wang, and A. Jusufi, Macromolecules, 41, 5477-5484 (2008). (abstract)

Coarse-grained block copolymer generation

This is work by Michel Perez, Olivier Lame, Fabien Leonforte, and Jean-Louis Barrat.

They use a versatile method, largely inspired by chemical "radical polymerization", to generate configurations of coarse-grained models for polymer melts. The two figures show snapshots of lamellar diblocks and triblocks. Equilibrium lamellar spacing depends on the incompatibility between the two (or three) polymers forming the block copolymer.

This paper has further details:

Polymer chain generation for coarse-grained models using radical-like polymerization, M. Perez, O. Lame, F. Leonforte and J.-L. Barrat, J Chem Phys, 128, 234904:1-11 (2008). (abstract)

Polyelectrolytes adsorption and brushes

This is work by Jan-Michael Carrillo (janmikel at gmail.com) and Andrey Dobrynin at the University of Connecticut.

The first picture shows snapshots of an adsorbed layer of hydrophobic polyelectrolytes on a hydrophilic substrate at different surface charge densities (increasing surface charge density from left to right).

The second plot is from the 2nd paper and is a diagram of states of spherical polyelectrolyte brushes : collapsed brushes (circles), bundle brushes (squares), star-like brushes (tilted squares), and micelle-like brushes (triangles). The dotted lines separating different conformational regimes are not actual phase transition lines, lB is the Bjerrum length of the system and Epsilon LJ is the strength of the monomer-monomer interaction.

These papers have further details:

Molecular Dynamics Simulations of Polyelectrolyte Adsorption, J.-M. Y. Carrillo and A. V. Dobrynin, Langmuir, 23, 2472-2482, (2007). (abstract)

Molecular Dynamics Simulations of Polyelectrolyte Brushes: From Single Chains to Bundles of Chains, D. J. Sandberg, J.-M. Y. Carrillo and A. V. Dobrynin, Langmuir, 23, 12716-12728 (2007). (abstract)

Stress in metal nanowires with twin boundaries

This is work by A-Jing Cao (chaoajing at lnm.imech.ac.cn) and Yue-Guang Wei (ywei at lnm.imech.ac.cn) at the Laboratory of Nonlinear Mechanics (LNM), Institute of Mechanics, Chinese Academy of Sciences.

The picture on the left is the equilibrium structure of a nanowire constructed with a fivefold twinned grain boundary running down the axis of the wire. Tensile stress is applied. The picture in the middle shows the resulting dislocation pile-up. The picture on the right shows a different geometry where twin boundaries are oriented perpendicular to the axis of the nanowire. Atoms are colored according to the configuration of their neighbors; the visualization was done with the AtomEye program.

These papers have further details:

Formation of Fivefold Deformation Twins in Nanocrystalline Face-Centered-Cubic Copper Based on Molecular Dynamics Simulations, A. J. Cao and Y. G. Wei, Applied Physics Lett, 89, 041919 (2006). (abstract)

Atomistic simulations of the mechanical behavior of fivefold twinned nanowires, A. J. Cao and Y. G. Wei, Phys Rev B, 74, 214108 (2006). (abstract)

Deformation mechanisms of face-centered-cubic metal nanowires with twin boundaries, A. J. Cao, Y. G. Wei, and S. X. Mao, Applied Physics Letters, 90, 151909 (2007). (abstract)

Nanotip indentation of a coated surface

This is work by Mike Chandross (mechand at sandia.gov), Chris Lorenz, Mark Stevens, and Gary Grest at Sandia.

A 100A radius silica tip makes contact with a silica substrate, coated with a self-assembled monolayer of alkyl silanes for a study of friction and wear. The snapshots were made with VMD, and show deformation and damage to the coating layer due to the tip.

In the rightmost journal cover, the tip image is in the lower center.

These papers have further details:

Nanotribology of Anti-Friction Coatings in MEMS, M. Chandross, C. D. Lorenz, G. S. Grest, M. J. Stevens, and E. B. Webb III, J Minerals, Metals, and Materials (JOM), 57, 55 (2005). (abstract)

Systematic study of the effect of disorder on nanotribology of self-assembled monolayers, M. Chandross, E. B. Webb III, M. J. Stevens, G. S. Grest, and S. H. Garofalini, Phys Rev Lett, 93, 166103/1-4 (2004). (abstract)

Simulations of Nanotribology with Realistic Probe Tip Models, M. Chandross, C. D. Lorenz, M. J. Stevens, G. S. Grest, Langmuir, 24, 1240 (2008). (abstract)

Surface Wetting by Polymer Nanodroplet

This is work by Dave Heine (heinedr at corning.com), Gary Grest (gsgrest at sandia.gov), and Ed Webb (ebwebb at sandia.gov) at Sandia.

Bead-spring polymer chains are placed on a surface in a droplet form. The degree of wetting that results depends on various parameters, including the surface interaction strength and chain length.

These images show cuts through the droplet for different simulation conditions. The blue surface allows for more wetting than the green.

These papers have further details:

Diverse Spreading Behavior of Binary Polymer Nanodroplets, D. R. Heine, G. S. Grest, and E. B. Webb III, Langmuir, 21, 7959 (2005). (abstract)

Liquid nanodroplets spreading on chemically patterned surfaces, G. S. Grest, D. R. Heine, and E. B. Webb III, Langmuir, 22, 4745-4749 (2006). (abstract)

Surface Wetting of Liquid Nanodroplets: Droplet Size Effects, D. R. Heine, G. S. Grest, and E. B. Webb III, Phys Rev Lett, 95, 107801 (2005). (abstract)

Shear of Cu bicrystal

This is work with Doug Spearot (gte432r at prism.gatech.edu) in David McDowell's group at Georgia Tech. A tilt bicrystal interface is formed by joining two Cu crystals and sheared via different deformation paths to study the defect formation and material response.

These images show the resulting strained system after deformation via 3 different paths. The top images color the atoms in each crystal in 2 shades of gray; the bottom images color atoms by the distance they moved from their initial positions.

This paper has further details:

Effect of Deformation Path Sequence on the Behavior of Nanoscale Copper Bicrystal Interfaces, D. E. Spearot, K. I. Jacob, D. L. McDowell, S. J. Plimpton, J Engr Materials and Technology, 127, 374-382 (2005). (abstract)

Solvated dendritic polymer structure

This is work by Seung Soon Jang (jsshys at wag.caltech.edu) in Bill Goddard's group at Cal Tech.

The 1st picture/paper are for a model they've developed of a dendrion diblock copolymer consisting of a dendritic polymer with a hydrophobic backbone. Such materials have interesting nanoscale structural and phase behavior.

The 2nd picture/paper are for simulations of amphiphilic bistable (2)rotaxane molecules which have controllable switching properties as their conformation changes.

The 3rd picture/paper are studies of the structure and surface concentrations of different surfactants in thin Newton black films.

The 1st picture shows the molecular structures of a diblock copolymer system at two different levels of water content. The 2nd picture illustrates conformational changes in a Langmuir monolayer of the rotaxane molecules. The 3rd picture shows film structure at varying surface concentrations (top) and film thicknesses (bottom).

These papers have further details:

Nanophase-segregation and water dynamics in the dendrion diblock copolymer formed from polyaryl ethereal dendrimer and linear PTFE, S. S. Jang, S.-T. Lin, T. Cagin, V. Molinero and W. A. Goddard III, J Phys Chem B, 109, 10154-10167 (2005). (abstract)

Molecular dynamics simulation of amphiphilic bistable (2)rotaxane Langmuir monolayer at air/water interface, S. S. Jang, Y. H. Jang, Y.-H. Kim, W. A. Goddard III, J. W. Choi, J. R. Heath, A. H. Flood, B. W. Laursen, and J. F. Stoddart, J Amer Chem Soc, 127, 14804 (2005). (abstract)

Structures and Properties of Newton Black Films Characterized Using Molecular Dynamics Simulations, S. S. Jang and W. A. Goddard III, J Phys Chem B, 110, 7992-8001 (2006). (abstract)

Metal solidification

This is work by Mark Asta's group at Northwestern and Jeff Hoyt (jjhoyt at sandia.gov) at Sandia. They've developed a simulation strategy for solidifying metals and metal alloys where the temperature of the system is carefully thermostatted so that the velocity of the interface can be accurately measured.

This snapshot is a liquid/solid interface in NiAl. See a movie of solidification on this page.

This paper and related ones on this page have further details:

Calculation of alloy solid-liquid interfacial free energies from atomic-scale simulations, M. Asta, J. J. Hoyt, A. Karma, Phys Rev B, 66, 100101 (2002). (abstract)

Lipid membrane self-assembly and fusion

This is work by Mark Stevens (msteve at sandia.gov) at Sandia on the self-assembly of lipid bilayers and membrane fusion using an idealized bead-spring model for a 2-tail lipid molecule.

Head-head and head-solvent interactions are set to give hydrophilic behavior. Head-tail and tail-solvent interactions are hydrophobic. A 3d random ensemble of lipid molecules in a background solvent will spontaneously self-assemble into bilayers and vesicles as shown by these 2d slice views. When 2 vesicles are gently pushed together they can fuse as tails of individual lipid molecules straddle both membranes. The detailed fusion images were made with VMD.

This paper has further details:

Insights into the molecular mechanism of membrane fusion from simulation: Evidence for the association of splayed tails, M. J. Stevens, J. H. Hoh, T. B. Woolf, Phys Rev Lett, 91, 188102 (2003). (abstract)

Tensile pull on adhesive polymer chains

This is work by Scott Sides (swsides at mrl.ucsb.edu), Gary Grest (gsgrest at sandia.gov), and Mark Stevens (msteve at sandia.gov), all at Sandia, on adhesive properties of polymers.

The simulations are of melts of 500- and 1000-mer bead-spring chains. The systems range from 100-500K total monomers and are run for 10-20 million timesteps. In these snapshots of models with different parameters, the blue chains are the melt, red are tethered and unbroken chains, green are tethered and broken.

These papers have further details:

Large-scale simulation of adhesion dynamics for end-grafted polymers, S. W. Sides, G. S. Grest, M. J. Stevens, Macromolecules, 35, 566-573 (2002). (abstract)

Effect of end-tethered polymers on surface adhesion of glassy polymers, S. W. Sides, G. S. Grest, M. J. Stevens, S. J. Plimpton, Journal of Polymer Science, Part B (Polymer Physics), 42, 199-208 (2004). (abstract)

Crazing of entangled polymer chains

This is work by Joerg Rottler (now at Princeton) and Mark Robbins at JHU. The image shows a polymer glass that has been deformed into a craze at large strains. In the craze, polymers (~0.5 nm diameter) are bundled into an intricate load-bearing network of ~10 nm diameter fibrils. Crazing is largely responsible for the high fracture energy of glassy polymers.

These papers have further details:

Growth, microstructure, and failure of crazes in glassy polymers, J. Rottler and M. O. Robbins, Phys Rev E, 68, 011801 (2003). (abstract)

Jamming under tension in polymer crazes, J. Rottler and M. O. Robbins, Phys Rev Lett, 89, 195501 (2002). (abstract)

Cracks and crazes: On calculating the macroscopic fracture energy of glassy polymers from molecular simulations, J. Rottler, S. Barsky, M. O. Robbins, Phys Rev Lett, 89, 148304 (2002). (abstract)

Stress in metal nanowires

This is work by Min Zhou's group at Georgia Tech on modeling the effect of tensile stress at varying strain rates on single-crystal Cu nanowires of varying dimensions. In the image, atoms are colored to highlight defects and the transverse dimensions are drawn at an exaggerated scale.

This GaTech WWW site has further details.

Shear of large single-crystal metals

This is work with Mark Horstemeyer (mfhorst at me.msstate.edu) at Mississippi State (formerly at Sandia) and Mike Baskes (baskes at lanl.gov) at LANL to study stress/strain effects in large single-crystal metals samples. Simulations with up to 100M atoms were run. This image shows defect formation in a quasi-2d Ni sample undergoing fixed-end shear, where the z-dimension (into the image) is periodic but very thin. The black lines indicate atom displacements as the sample has sheared to the right.

This paper and related ones in the Metals section of this page have further details:

Computational nanoscale plasticity simulations using embedded atom potentials, M. F. Horstemeyer, M. I. Baskes, S. J. Plimpton, Theoretical and Applied Fracture Mechanics, 37, 49-98 (2001). (abstract)