Pictures from LAMMPS Simulations

The images on this page, submitted by users, are from LAMMPS simulations. They have been rendered with various visualization packages. This page has additional images with accompanying animations.

thermal degradation of polyethylene nanowire surface dislocation reflection
dislocation dynamics acid-containing polymer dynamics
density-functional tight-binding rigid polymer nanoparticle coatings
BOP potential for carbon nanoprojectile impacts
jamming of extremely polydisperse granular materials polymeric fullerene film coating
ELBA coarse-grained water electrochemical adsorption of OH
nanoparticle assembly and aggregation liquid crystal film rupture
polymer shear thinning ionomer morphologies
amorphous carbon film growth electro-catalytically active gold nanoparticles
bilayer phases thermal conductivity of CNTs
free energies via LAMMPS and PLUMED capillary filling in CNTs
shock loading of polymer foam carbon nanotube fiber design
shock loading of inhomogeneous PBX single-point diamond turning
nanoparticle coating structure in the presence of solvent two-temperature model for electronic heat conduction
atom-to-continuum coupling with the ATC package stress field around dislocations
water interacting with self-assembled monolayers coarse-grained self-assembly of lipids and PEG surfactants
spherical polyelectrolyte brushes coarse-grained block copolymer generation
polyelectrolyte adsorption and brushes stress in metal nanowires with twin boundaries
nanotip indentation of a coated surface surface wetting by polymer nanodroplet
shear of Cu bicrystal solvated dendritic polymer phase behavior
metal solidification lipid membrane self-assembly and fusion
tensile pull on adhesive polymer chains crazing of entangled polymer chains
stress in metal nanowires shear of large single-crystal metals

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

High-rate thermal degradation of polyethylene

This work by Matt Lane and Nathan Moore (Sandia), aims to understand the high-rate thermal decomposition of organics by simulation of conditions comparable to recent Z machine X-ray ablation experiments. They determined the rate-dependent chemical processes were important to understanding the physics of polymer degradation. They also developed a kinetic model of these processes for polyethylene which is being incorporated into future continuum-scale calculations.

The images show the molecular states of polyethylene at 300, 2100 and ~3000 K before/during/after an extremely high-rate temperature ramp from 10^10 to 10^14 K/s, such as expected in laser-driven and X-ray ablation experiments. Carbon atoms are color-coded by the number of C–C bonds they share. Orange, for one bond, indicates a terminal carbon. Blue, for two bonds, indicates a backbone or cyclic carbon. Green, for three or more C–C bonds, indicates a branch point, or a condensed carbon phase. Hydrogen atoms are white or, if they form molecular hydrogen H2, yellow.

Order of 3 images: 2100K, 300K, 3000K

This paper has further details:

Molecular and Kinetic Models for High-Rate Thermal Degradation of Polyethylene, J. M. D. Lane and N. W. Moore, The Journal of Physical Chemistry A, 122, 3962-3970 (2018). (abstract), (

Nanowire surface dislocation reflection

This is work by G. Sainath and collaborators (Indira Gandhi Centre for Atomic Research, HBNI, Kalpakkam, India).

MD was used to model the multiple reflections of partial dislocations from nanowire surfaces. The continuous repetition of this process along the length of nanowire results in the formation of stacking faults with triangular wave shape. This reflection of dislocations has been observed in Cu nanowires with size less than 2.17 nm.

This paper has further details:

Size dependent deformation behaviour and dislocation mechanisms in <100> Cu nanowires, G. Sainath , P. Rohith and B. K. Choudhary, Philosophical Magazine, 97, 2632-2657 (2017). (abstract),

Dislocation dynamics

This is work by Luis Zepeda-Ruiz, Tomas Oppelstrup, and Vasily Bulatov at LLNL, and Alex Stukowski (Technische Universitat Darmstadt), to model dislocation dynamics in bcc tantalum.

The cover image is from Alex Stukowski, with the accompanying text from the journal. The stress-strain curves are also a figure from the paper.

The cover shows an intricate network of lattice defects — dislocation lines — whose motion makes metal tantalum flow under compression. Fully dynamic atomistic simulations of plastic deformation in metals are extremely demanding computationally and usually involve mesoscale approximations. In this issue, Vasily Bulatov and his colleagues present fully dynamic atomic-level simulations of metal plasticity that feature up to 268 million atoms, each such simulation generating around 2 exabytes (1 exabyte = 1018 bytes) of data. Using their model, the authors probe how body-centred-cubic metal tantalum responds to ultrahigh-strain-rate deformation. They find that on reaching certain limiting conditions, dislocations can no longer relieve mechanical loads and twinning — the sudden reorientation of the crystal lattice — takes over. They also find that below such critical conditions, flow stress and dislocation density achieve a steady state in which the metal can be kneaded indefinitely like a piece of dough.

This paper has further details:

Probing the limits of metal plasticity with molecular dynamics simulations, L. A. Zepeda-Ruiz, A. Stukowski, T. Oppelstrup, and V. V. Bulatov, Nature, 550, 492 (2017). (abstract), doi:10.1038/nature23472.

Acid-containing polymer chain dynamics

This is work by Amalie Frischknecht (Sandia), Karen Winey (U Penn), and coworkers to understand chain dynamics in precise acid-containing polymers.

The journal cover page shows the comparison of quasi-elastic neutron scattering (QENS) and atomistic molecular dynamics simulations for poly(ethylene-co-acrylic acid) polymers that have acid groups spaced every 21 carbons along the polyethylene backbone. The simulation snapshots show the movement of acid groups from one aggregate to another over approximately 1 ns.

This paper has further details:

Heterogeneous Chain Dynamics and Aggregate Lifetimes in Precise Acid-Containing Polyethylenes: Experiments and Simulations, L. R. Middleton, J. D. Tarver, J. Cordaro, M. Tyagi, C. L. Soles, A. L. Frischknecht, and K. I. Winey, Macromolecules 49, 9176-9185 (2016). (abstract),

Density-functional tight-binding models

This is work by Nir Goldman (LLNL) and collaborators using a modified version of the DFTB+ code which can be hooked to LAMMPS through its library interface to perform quantum MD simulations. DFTB+ computes quantum density-functional forces via the semi-empirical tight-binding approximation; LAMMPS does the timestepping.

They have used this coupled framework to study a variety of interesting systems, as shown in these journal cover images. The first is synthesis of carbon fibers from graphite which has been liquified and evaporates due to a laser pulse. The second is a model of a laser pulse inducing a shock which triggers exothermic chemistry in hydrogen peroxide. The final example models the creation of prebiotic organic molecules via shock compression of icy materials, analogous to what may occur when a comet strikes the surface of the Earth.

Thes papers have further details:

Carbyne fiber synthesis in evaporating metallic liquid carbon, C. Cannella and N. Goldman, J Phys Chem C, 21605, 119 (2015). (abstract)

Control of reactivity via ultrafast compression rates, M. R. Armstrong, J. M. Zaug, N. Goldman, I-F. W. Kuo, J. C. Crowhurst, W. M. Howard, J. A. Carter, M. Kashgarian, J. M. Chesser, T. W. Barbee, and S. Bastea, J Phys Chem A, 117, 13051 (2013). (abstract)

Prebiotic Chemistry Within a Simple Impacting Icy Mixture, N. Goldman and I. Tamblyn, J Phys Chem A, 117, 5124 (2013). (abstract)

Rigid polymer nanoparticle coatings

This is work by Sabina Maskey & Dvora Perahia of Clemson University and Matt Lane (jlane at & Gary Grest at Sandia, which describes the unique morphologies possible when nanoparticles are grafted with rigid luminescent polymers like dialkyl poly(p-phenylene ethynylene)s (PPEs) and placed in poor solvents. The macromolecules assemble into bundles, exhibiting a distinctively different interfacial structure than that formed by grafted flexible and semiflexible polymers.

The images show the rigid nanoparticle (yellow) and grafted polymers (green) in different morphologies from compact to extended.

This paper has further details:

Structure of Rigid Polymers Confined to Nanoparticles: Molecular Dynamics Simulations Insight, S. Maskey, J. M. D. Lane, D. Perahia, and G. S. Grest, Langmuir, 32, 2102–2109 (2016). ( (abstract)

BOP potential for carbon

This is work by Xiaowang Zhou (xzhou at, Don Ward, and Michael Foster at Sandia to develop and test a new bond-order potential (BOP) suitable for carbon in many of its forms (diamond, graphite, graphene, nanotubes). The potential is available in LAMMPS via the pair_style bop command.

This paper has further details:

An Analytical Bond-Order Potential for Carbon, X. W. Zhou, D. K. Ward, and M. E. Foster, J Comp Chem, 36, 1719-1786 (2015). (abstract)

Nanoprojectile impacts

This is work by Eduardo Bringa (ebringa at at Universidad Nacional de Cuyo (Argentina) and collaborators to model the impact of nanoparticles up to 55 nm in diameter hitting substrate targets with up to 10 billion particles. The difference in cratering mechanisms was found to change for small vs large particles with the latter transitioning to plastic flow mechanisms characterisitic of microparticle experiments. The large simulations were performed with LAMMPS.

This paper has further details:

Why Nanoprojectiles Work Differently than Macroimpactors: The Role of Plastic Flow, C. Anders, E. M. Bringa, G. Ziegenhain, G. A. Graham, J. F. Hansen, N. Park, N. E. Teslich, and H. M. Urbassek, Phys Rev Lett 108, 027601 (2012). (abstract)

Jamming and deformation of extremely polydisperse granular materials

This is work by Agnieszka Herman (oceagah at at the Institute of Oceanography, University of Gdansk (Poland) to model the response of two-dimensional, extremely poly-disperse granular materials (with power law grain size distribution) to various types of deformation (convergence, shear, etc.). The work concentrates on the role of polydispersity in shaping the behavior and properties of the modeled system. The model is applied to analyze the deformation of sea ice composed of individual, interacting ice floes in response to wind and/or ocean currents.

The first two figures show snapshots of contact networks in the modeled system subject to shear deformation. The last two show the correlation coefficient between velocity anomalies of a selected grain (dark brown) and all other grains. In the first and third figures, an unjammed state are shown; in the second and fourth a jammed state is shown, for comparison.

These papers have further details:

Shear-jamming in two-dimensional granular materials with power-law grain-size distribution, A. Herman, Entropy, 15, 4802-4821 (2013). (abstract)

Numerical modeling of force and contact networks in fragmented sea ice, A. Herman, Annals Glaciology, 54, 114-120 (2013). (abstract)

Polymeric fullerene film coated on Si

This is work by Minwoong Joe (mjoe122 at, Young-Kyu Han, Kwang-Ryeol Lee, Hiroshi Mizuseki, and Seungchul Kim (sckim at at KIST to model polymeric fullerene coatings on Si electrodes in Lithium ion batteries, which leads to durability of the battery performance, using the Tersoff potential with parameters suggested by Erhart and Albe.

The first figure shows a graphical representation of the polymerized fullerene film grown at E = 180 eV. Each C60 molecule is a different color, but the same color is used when they are connected by carbon atoms for which the coordination number CN = 3. Black balls are carbon atoms with CN = 2 and 4.

The second figure shows the superior mechanical flexibility of the polymerized fullerene coating on Si. Even under conditions of substrate Si rupture by huge compressive (b) and tensile strain (c), the polymeric fullerene film does not undergo mechanical failure, implying superior flexibility to adapt to the volume change of the Si anode. The atoms color is encoded using the CN: burly wood for 2; forest green for 3; gray for 4; and red for 5.

This paper has further details:

An ideal polymeric C60 coating on a Si electrode for durable Li-ion batteries, M. Joe, Y.-K. Han, K.-R. Lee, H. Mizuseki, S. Kim, Carbon, 77, 1140 (2014). (abstract)

Mixing of atomistic solutes and coarse-grained water

This is work by Mario Orsi (m.orsi at and coworkers at QMUL. The ELBA coarse-grained water is a single-site "Lennard-Jones plus point dipole model" which can capture many fundamental properties of bulk liquid water and the water-vapor interface. The model can also be used to hydrate atomistic solutes, including small organic molecules and proteins; importantly, the ELBA water force field is shown to be directly compatible with common atomistic force fields.

The images below show a sketch of the coarse-graining strategy (left), a vapor-liquid phase diagram (left-center), and two snapshots of simulations of atomistic proteins hydrated by ELBA water (right-center and right).

These papers have further details:

Direct Mixing of Atomistic Solutes and Coarse-Grained Water, M. Orsi, W. Ding, M. Palaiokostas, Journal of Chemical Theory and Computation, 10, 4684-4693 (2014); (abstract)

Comparative assessment of the ELBA coarse-grained model for water, M. Orsi, Molecular Physics,112, 1566-1576 (2014); (abstract)

Electrochemical Adsorption of OH

This is work by Wolfgang Schmickler (wolfgang.schmickler at at the University of Ulm and coworkers to investigate the adsorption of the hydroxyl ion on a Pt(111) surface. To perform this study a combination of DFT with molecular dynamics was used and the results suggest that OH can be adsorbed either as a metastable, physisorbed ion or as a chemisorbed radical.

The picture on the left shows a snapshot from a molecular dynamics simulation; the OH can be seen on the left with a blue oxygen and a green hydrogen atom. The middle picture presents the Volumetric charge density difference for the OH adsorption on a Pt(111) surface; blue indicates electron depletion and red stands for electron excess.

This paper has further details:

Electrochemical Adsorption of OH on Pt(111) in Alkaline Solutions: Combining DFT and Molecular Dynamics, L. M. C. Pinto, P. Quaino, M. D. Arce, E. Santos, and W. Schmickler, Chem Phys Chem, 15, 2003-2009 (2014); (abstract)

Nanoparticle assembly and aggregation

This is work by Matt Lane (jlane at and Gary Grest at Sandia to model the self-assembly and aggregation of coated nanoparticles at a water-vapor interface. The terminal groups of a nanoparticle coating can dramatically alter the coating shape at the interface, producing very different assembly morphologies

The left and middle images show side and top views of nanoparticles on the surface of a water layer. The yellow spheres are the gold nanoparticles, the alkane chains (coatings) are in blue/white, and the water in red/white. Some chains are terminated with COOH (polar), others with CH3 (non-polar), which determines their affinity for the surrounding water.

This paper has further details:

Assembly of responsive-shape coated nanoparticles at water surfaces, J. M. D. Lane and G. S. Grest, Nanoscale, 6, 5132-5137 (2014). (abstract)

Liquid crystal film rupture

This is work by Trung Dac Nguyen (nguyentd at, Jan-Michael Carrillo, and Mike Brown at ORNL to model liquid crystal thin films and investigate their stability. These were large-scale simulations of up to 26 million ellipsoidal particles, each representing a LC mesogen, run using the GPU-accelerated GayBerne potential developed by Mike Brown, on the Titan machine at ORNL.

The left image shows a hole formed in a nematic film where the LC mesogens are colored by their distance to the substrate. The image in the middle shows the top-view of a hole in a nematic film where the LC mesogens are colored by their alignment with their neighbors. The right image shows surface undulations in a nematic film where pink corresponds to thick regions and green to thinner regions.

This paper has further details:

Rupture mechanism of liquid crystal thin films realized by large-scale molecular simulations, T. D. Nguyen, J-M Y. Carrillo, M. A. Matheson, and W. M. Brown, Nanoscale, 6, 3083 (2014). (abstract)

Polymer shear thinning

"This is work by KR Prathyusha (prathyushakr at and collaborators at the Indian Institute of Technology Madras (India) and the University of Memphis to model short polymer segemnts which bind together to form networks, as a model for "living" polymers. When sheared, the systems self-assemble into various morphologies.

The cover page shows a columnar phase, formed when the system is sheared. The right figure shows various shear-induced phases which appear as the interaction parameters are varied.

This paper has further details:

Shear-thinning and isotropic-lamellar-columnar transition in a model for living polymers, K. R. Prathyusha, A. P. Deshpande, M. Laradji, and P. B. S. Kumar, Soft Matter, 9, 9983 (2013). (abstract)

Ionomer morphologies

This is work by Dan Bolinteneau, Mark Stevens, and Amalie Frischknecht (alfrisc at at Sandia to model the structure of ionic aggregates in ionomers, which are polymers with both neutral and ionized segments.

The left figure shows representative snapshots of ionic aggregates in simulations of poly(ethylene-co-acrylic acid) ionomer melts with 10%, 43% and 100% Li neutralization (left to right). Only H, Li and O atoms are shown and all atoms in the same aggregate have the same color. The lower right image is a zoom of the 43% Li system showing the interaggregate spacing that yields the ionomer peak in scattering data. The individual aggregate shows an alternating Li (yellow) and O (red) motif, with some hydrogen bonding (H in white). In contrast to the traditional view of spherical ionic aggregates, the schematic in the lower right depicts the string-like aggregates observed in simulations. The right figure gives more details of the structures as a function of neutralization percentage.

This paper has further details:

Atomistic Simulations Predict a Surprising Variety of Morphologies in Precise Ionomers, D. S. Bolintineanu, M. J. Stevens, and A. L. Frischknecht, ACS Macro Letters, 2, 206-210 (2013). (abstract) (paper)

Amorphous carbon film growth

This is work by Minwoong Joe (mjoe122 at, Myoung-Woon Moon, Jungsoo Oh, Kyu-Hwan Lee, and Kwang-Ryeol Lee (krlee at at KIST to model impact-induced surface instabilities in amorphous carbon (a-C) film growth, which leads to surface roughening under grazing impacts of energetic C atoms, using the reactive empirical bond order (REBO) potential.

The first figure shows cross-sectional snapshots of the growing film, depending on incidence angles.

The second figure shows a flying view of the surface after 36,000 C impacts on a larger substrate (approximately 9x larger).

The third figure shows a comparison of the cross-sections of a-C film under normal (a) and grazing incidence (b). The color of the deposited atoms encodes the order of atom entry; the later atoms range from blue to red, and the original substrate is grey. This indicates a shadowing effect at work even under 0.2 nm rms surface roughness.

This paper has further details:

Molecular dynamics simulation study of the growth of a rough amorphous carbon film by the grazing incidence of energetic carbon atoms, M. Joe, M.-W. Moon, J. Oh, K.-H. Lee, K.-R. Lee, Carbon, 50, 404 (2012). (abstract)

Electro-catalytically active gold nanoparticles

This is work by Yang-Hee Lee, Ji-Hoon Jang, Juyeong Kim, and Young-Uk Kwon (ywkwon at at Sungkyunkwan University, Gunn Kim (kimgunn at, for DFT calculation) at Sejong University, and Minwoong Joe and Kwang-Ryeol Lee (mjoe122 at, for MD simulation) at KIST to model enhancement of electrocatalytic activity of gold nanoparticles, produced by sonochemical treatment, using the embedded atom potential.

The cover page schematically shows supercooled molten gold nanoparticles by sonochemical treatment, which can have enhanced electrocatalytic activity for hydrogen oxidation reaction.

The 2nd figure shows coordination numbers of gold atoms of calculated structures of gold NPs equilibrated at 0 K (a), 300 K (b), 500 K (c), 700 K (d), 900 K (e), and 1100 K (f).

This paper has further details:

Enhancement of Electrocatalytic Activity of Gold Nanoparticles by Sonochemical Treatment, Y.-H. Lee, G. Kim, M. Joe, J.-H. Jang, J. Kim, K.-R. Lee, Y.-U. Kwon, Chem Comm, 46, 5656 (2010). (abstract)

Bilayer phases

This is work by Mario Orsi (orsimario at at U Southampton. LAMMPS was used together with the ELBA-LAMMPS toolkit to simulate simple models of biological membranes. Notably, depth-dependent lateral pressure and electrical potential profiles were computed for mixed PC/PE bilayers at different relative compositions.

The images below show a sketch of the molecular models (left), a series of snapshots from a self-assembly simulation of a lamellar structure (center), and a series of snapshots from a simulation of spontaneous phase transition from lamellar to inverse hexagonal (right).

This paper has further details:

Physical properties of mixed bilayers containing lamellar and nonlamellar lipids: insights from coarse-grain molecular dynamics simulations, M. Orsi and J. W. Essex, Faraday Discussions, DOI: 10.1039/C2FD20110K. (abstract) Link to paper

Thermal conductivity of CNTs

This is work by Ajing Cao (a-cao at and Jianmin Qu at Northwestern University to use LAMMPS to model the thermal conductivity of single-walled carbon nanotubes. Specifically, they found that the size-dependent thermal conductivity of single-walled carbon nanotubes can be described by κ(L,d) ~ κg(L)(1−e−0.185d/a0), where L is the tube length, d is the diameter, a0 = 2.46 Å is the graphene lattice constant, and κg(L) proportional to Lα is the thermal conductivity of a graphene of length L.

The plots on the cover show the spectral energy density (SED) of single-walled CNTs. The top three figures are for the (5, 5) tube, and the bottom three are for the (40, 40) tube. Both tubes are 100 nm-long SWCNT at T = 300 K. The color indicates the magnitude of the SED at a given point (k,w). From the left to the right are the longitudinal modes Ez, twist modes Eu, and radial breathing modes Er, respectively.

This paper has further details:

Size dependent thermal conductivity of single-walled carbon nanotubes, A. Cao and J. Qu, J Appl Phys, 112, 013503 (2012); (abstract)

Free energies via LAMMPS and PLUMED

This is work by Andrew Stack (stackag at at ORNL and collaborators to use LAMMPS in conjunction with the PLUMED free energy package to model growth and dissolution on mineral surfaces via metadynamics. Specifically they looked at barium ions attaching to and detaching from a barite surface. The detachment dynamics and associated free energy diagram are shown in the following figures.

This paper has further details:

Accurate Rates of the Complex Mechanisms for Growth and Dissolution of Minerals Using a Combination of Rare-Event Theories, A. G. Stack, P. Raiteri, and J. D. Gale, JACS, 134, 11–14 (2012). (abstract)

Capillary filling in CNTs

This is work by Laurent Joly (ljoly.ulyon at of U Lyon on studies of capillary filling on nanopores such as CNTs, examining the effects of liquid viscosity, the friction coefficient between the liquid and wall, and viscous dissipation at the pore entrance.

The images show capillary effects in 2.7 nm and 4.1 nm diameter pores.

This paper has further details:

Capillary filling with giant liquid/solid slip: Dynamics of water uptake by carbon nanotubes, L. Joly, THE JOURNAL OF CHEMICAL PHYSICS, 135, 214705 (2011). (abstract)

Laurent has also posted his scripts for performing these kinds of simulations on the User Script page.

Shock loading of polymer foam

This is work by Matt Lane (jlane at and Aidan Thompson (athomps at at Sandia to model the shock compression of all-atom polymer foams, using the ReaxFF potential to allow for dissociation of the polymer bonds. Their model captures the Hugoniot response of the foam in good agreement with experiment and DFT calculations.

The images show a PMP system with 1.44M atoms, with a lattice of spherical voids. The initial sample is at the left; the shocked sample is in the middle, which shows jetting of polymer fragments into the voids. These images were used on the cover of a special issue of the MRS Bulletin (May 2012) devoted to many-body potentials like ReaxFF.

These papers have further details:

Shock compression of dense polymer and foam systems using molecular dynamics and DFT, J. M. D. Lane, G. S. Grest, A. P. Thompson, K. R. Cochrane, M. P. Desjarlais, and T. R. Mattsson, in M. Elert et. al., editor, AIP Conference Proceedings, Shock Compression of Condensed Matter 2011, 1426, 1401 (2011). (abstract)

Computational Aspects of Many-body Potentials", MRS Bulletin, S. J. Plimpton and A. P. Thompson, 37, 513-521 (2012). (abstract)

Carbon nanotube fiber design

This is work by Charles Cornwell (Charles.F.Cornwell at and Charles Welch at the US Army ERDC to model the tensile response of bundles of carbon nanotubes containing 1.2M atoms, with additional cross-linking bonds between individual tubes, using the AIREBO force field. They found the fibers had strengths up to 60 GPa, which is about 30x higher than that of high-strength steel.

The first figure shows the bundle geometry. The second shows the rupture of the bundle at high tensile strain.

This paper has further details:

Very-high-strength (60-GPa) carbon nanotube fiber design based on molecular dynamics simulations, Charles F. Cornwell and Charles R. Welch, J Chem Phys, 134, 204708 (2011). (abstract)

Shock loading of inhomogeneous PBX

This is work by Sergey Zybin (zybin at and collaborators at Caltech to model shock-induced instabilities in explosive materials which have heterogeneous features, such as defects or interfaces, using the ReaxFF force field.

The figure shows shock loading of PBX in a 3.6M atom model with a saw-tooth interface between RDX and its polymer binder. The color represents slip which is highest at the interface.

This paper has further details:

Elucidation of the dynamics for hot-spot initiation at nonuniform interfaces of highly shocked materials, Qi An, Sergey V. Zybin, William A. Goddard III, Andres Jaramillo-Botero, Mario Blanco, and Sheng-Nian Luo, Phys Rev B, 84, 220101 (2011). (abstract)

Single point diamond turning

This is work by Saurav Goel and Xichun Luo (Heriot Watt University) to simulate single point diamond turning (SPDT) of cubic SiC, as an application of ultra-precision machining. This work includes an MD model for quantification of wear of diamond tools involving graphitization.

The figures show the sp3 to sp2 transition and consequent wear of a diamond tool during SPDT of cubic SiC.

This paper has further details:

Molecular dynamics simulation model for the quantitative assessment of tool wear during single point diamond turning of cubic silicon carbide, S. Goel, X. Luo, R. L. Reuben, Comp Matl Sci, 51 402–408 (2011). (abstract)

Nanoparticle coating structure in the presence of solvent

This is work by Matthew Lane and Gary Grest (Sandia) to model the structure of nanoparticle coatings in solution. It demonstrates that small spherical nanoparticles -- coated with a simple polymer -- produce highly asymmetric coating arrangements even when one would expect otherwise. When particles are placed at the solvent surface, the asymmetric coatings are amplified and oriented by the surface.

The first 3 images show nanoparticles 2nm, 4nm, 8nm in diameter in various solvents: decane, implicit, water. The 4th image shows nanoparticles of various sizes at a water/vapor interface.

Spontaneous Asymmetry of Coated Spherical Nanoparticles in Solution and at Liquid-Vapor Interfaces, J. M. D. Lane and G. S. Grest, Phys Rev Lett, 104, 235501 (2010), (abstract)

Two-temperature model for electronic heat conduction

This is work by Carolyn Phillips (U Michigan) and Paul Crozier (Sandia) to add a two-temperature model to LAMMPS so that the effect of electronic heat conduction can be included in a classical MD atomic simulation. Including these effects strongly influences the rate and extent of annealing in LJ crystals. The new fix ttm for LAMMPS was tested on a single-component LJ crystal that easily recrystallizes and on a binary glass-forming LJ crystal that tends to retain permanent damage. Both systems were tested across a range of electron-ion coupling parameter values and electronic thermal conductivity values.

The doc page for the fix ttm command has further details.

The first figure shows a hot damage spot in the center (red spheres) and a cold heat sink at the corners (blue spheres).

The second plot shows the effect of the electronic subsystem parameters on damage annealing.

An energy-conserving two-temperature model of radiation damage in single-component and binary Lennard-Jones crystals, C. L. Phillips and P. S. Crozier, J Chem Phys, 131, 074701:1-11 (2009). (abstract)

Atom-to-continuum coupling with the ATC package

This is work by Reese Jones (rjones at, Jeremy Templeton (jatempl at, and Jon Zimmerman (jzimmer at at Sandia using their ATC package to couple finite element (FE) and molecular dynamics (MD) calculations. The package creates a FE mesh and passes information back and forth between the MD and FE representations of the problem each timestep.

The figures show (left to right):

The doc page for the fix atc command has further details and cites these 2 papers:

An atomistic-to-continuum coupling method for heat transfer in solids, G. J. Wagner, R. E. Jones, J. A. Templeton, and M. L. Parks, Special Issue of Computer Methods and Applied Mechanics, 197, 3351-3365 (2008). (abstract)

Calculation of stress in atomistic simulation, J. A. Zimmerman, E. B. Webb III, J. J. Hoyt, R. E. Jones, P. A. Klein, and D. J. Bammann, Special Issue of Modelling and Simulation in Materials Science and Engineering, 12, S319 (2004). (abstract)

Stress field around dislocations

This is work by Ed Webb (ebwebb at, 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 and Michael Klein (Temple U) 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 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 and Yue-Guang Wei (ywei at 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, 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, Gary Grest (gsgrest at, and Ed Webb (ebwebb at 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 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 in Bill Goddard's group at Caltech.

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 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 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, Gary Grest (gsgrest at, and Mark Stevens (msteve at, 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 at Mississippi State (formerly at Sandia) and Mike Baskes (baskes at 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)