Joerg Rottler

A systematically coarse-grained model for DNA and its predictions for persistence length, stacking, twist, and chirality

We introduce a coarse-grained model of DNA with bases modeled as rigid-body ellipsoids to capture their anisotropic stereochemistry. Interaction potentials are all physicochemical and generated from all-atom simulation/parameterization with minimal phenomenology. Persistence length, degree of stacking, and twist are studied by molecular dynamics simulation as functions of temperature, salt concentration, sequence, interaction potential strength, and local position along the chain for both single- and double-stranded DNA where appropriate. The model of DNA shows several phase transitions and crossover regimes in addition to dehybridization, including unstacking, untwisting, and collapse, which affect mechanical properties such as rigidity and persistence length. The model also exhibits chirality with a stable right-handed and metastable left-handed helix.

Identifying Structural Flow Defects in Disordered Solids Using Machine-Learning Methods

We use machine-learning methods on local structure to identify flow defects-or particles susceptible to rearrangement-in jammed and glassy systems. We apply this method successfully to two very different systems: a two-dimensional experimental realization of a granular pillar under compression and a Lennard-Jones glass in both two and three dimensions above and below its glass transition temperature. We also identify characteristics of flow defects that differentiate them from the rest of the sample. Our results show it is possible to discern subtle structural features responsible for heterogeneous dynamics observed across a broad range of disordered materials.

Simulations of aging and plastic deformation in polymer glasses

We study the effect of physical aging on the mechanical properties of a model polymer glass using molecular dynamics simulations. The creep compliance is determined simultaneously with the structural relaxation under a constant uniaxial load below yield at constant temperature. The model successfully captures universal features found experimentally in polymer glasses, including signatures of mechanical rejuvenation. We analyze microscopic relaxation time scales and show that they exhibit the same aging characteristics as the macroscopic creep compliance. In addition, our model indicates that the entire distribution of relaxation times scales identically with age. Despite large changes in mobility, we observe comparatively little structural change except for a weak logarithmic increase in the degree of short-range order that may be correlated with an observed decrease in aging with increasing load.

Microscopic View of Accelerated Dynamics in Deformed Polymer Glasses

A molecular level analysis of segmental trajectories obtained from molecular dynamics simulations is used to obtain the full relaxation time spectrum in aging polymer glasses subject to three different deformation protocols. As in experiments, dynamics can be accelerated by several orders of magnitude, and a narrowing of the distribution of relaxation times during creep is directly observed. Additionally, the acceleration factor describing the transformation of the relaxation time distributions is computed and found to obey a universal dependence on the strain, independent of age and deformation protocol.

Deformation-induced accelerated dynamics in polymer glasses.

Molecular dynamics simulations are used to investigate the effects of deformation on the segmental dynamics in an aging polymer glass. Individual particle trajectories are decomposed into a series of discontinuous hops, from which we obtain the full distribution of relaxation times and displacements under three deformation protocols: step stress (creep), step strain, and constant strain rate deformation. As in experiments, the dynamics can be accelerated by several orders of magnitude during deformation, and the history dependence is entirely erased during yield (mechanical rejuvenation). Aging can be explained as a result of the long tails in the relaxation time distribution of the glass, and similarly, mechanical rejuvenation is understood through the observed narrowing of this distribution during yield. Although the relaxation time distributions under deformation are highly protocol specific, in each case they may be described by a universal acceleration factor that depends only on the strain.

Predictors of Cavitation in Glassy Polymers under Tensile Strain: A Coarse-Grained Molecular Dynamics Investigation

The nucleation of cavities in a homogenous polymer under tensile strain is investigated in a coarse-grained molecular dynamics simulation. In order to establish a causal relation between local microstructure and the onset of cavitation, a detailed analysis of some local properties is presented. In contrast to common assumptions, the nucleation of a cavity is neither correlated to a local loss of density nor, to the stress at the atomic scale and nor to the chain ends density in the undeformed state. Instead, a cavity in glassy polymers nucleates in regions that display a low bulk elastic modulus. This criterion allows one to predict the cavity position before the cavitation occurs. Even if the localization of a cavity is not directly predictable from the initial configuration, the elastically weak zones identified in the initial state emerge as favorite spots for cavity formation.

Predicting plasticity with soft vibrational modes: from dislocations to glasses.

We show that quasilocalized low-frequency modes in the vibrational spectrum can be used to construct soft spots, or regions vulnerable to rearrangement, which serve as a universal tool for the identification of flow defects in solids. We show that soft spots not only encode spatial information, via their location, but also directional information, via directors for particles within each soft spot. Single crystals with isolated dislocations exhibit low-frequency phonon modes that localize at the core, and their polarization pattern predicts the motion of atoms during elementary dislocation glide in two and three dimensions in exquisite detail. Even in polycrystals and disordered solids, we find that the directors associated with particles in soft spots are highly correlated with the direction of particle displacements in rearrangements.

Time dependent elastic response to a local shear transformation in amorphous solids

The elastic response of a two-dimensional amorphous solid to induced local shear transformations, which mimic the elementary plastic events occurring in deformed glasses, is investigated via molecular-dynamics simulations. We show that for different spatial realizations of the transformation, despite relative fluctuations of order one, the long-time equilibrium response averages out to the prediction of the Eshelby inclusion problem for a continuum elastic medium. We characterize the effects of the underlying dynamics on the propagation of the elastic signal. A crossover from a propagative transmission in the case of weakly damped dynamics to a diffusive transmission for strong damping is evidenced. In the latter case, the full time-dependent elastic response is in agreement with the theoretical prediction, obtained by solving the diffusion equation for the displacement field in an elastic medium.

Mechanical rejuvenation and overaging in the soft glassy rheology model

Mechanical rejuvenation and overaging of glasses is investigated through stochastic simulations of the soft glassy rheology (SGR) model. Strain- and stress-controlled deformation cycles for a wide range of loading conditions are analyzed and compared to molecular dynamics simulations of a model polymer glass. Results indicate that deformation causes predominantly rejuvenation, whereas overaging occurs only at very low temperatures, small strains, and for high initial energy states. Although the creep compliance in the SGR model exhibits full aging independent of applied load, large stresses in the nonlinear creep regime cause configurational changes leading to rejuvenation of the relaxation time spectrum probed after a stress cycle. During recovery, however, the rejuvenated state rapidly returns to the original aging trajectory due to collective relaxations of the internal strain.

Atomistic study of diffusion-mediated plasticity and creep using phase field crystal methods

The nonequilibrium dynamics of diffusion-mediated plasticity and creep in materials subjected to constant load at high homologous temperatures is studied atomistically using phase field crystal (PFC) methods. Creep stress and grain size exponents obtained for nanopolycrystalline systems, m similar or equal to 1.02 and p similar or equal to 1.98, respectively, closely match those expected for idealized diffusional Nabarro-Herring creep. These exponents are observed in the presence of significant stress-assisted diffusive grain boundary migration, indicating that Nabarro-Herring creep and stress-assisted boundary migration contribute in the same manner to the macroscopic constitutive relation. When plastic response is dislocation-mediated, power-law stress exponents inferred from dislocation climb rates are found to increase monotonically from m similar or equal to 3, as expected for generic climb-mediated natural creep, to m similar or equal to 5.8 as the dislocation density.d is increased beyond typical experimental values. Stress exponents m greater than or similar to 3 directly measured from simulations that include dislocation nucleation, climb, glide, and annihilation are attributed primarily to these large rho(d) effects. Extrapolation to lower rho(d) suggests that m similar or equal to 4-4.5 should be obtained from our PFC description at typical experimental rho(d) values, which is consistent with expectations for power-law creep via mixed climb and glide. The anomalously large stress exponents observed in our atomistic simulations at large rho(d) may nonetheless be relevant to systems in which comparable densities are obtained locally within heterogeneous defect domains such as dislocation cell walls or tangles.