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The properties of semiflexible polymers tethered by one end to an impenetrable wall and exposed to oscillatory shear flow are investigated by mesoscale simulations. A polymer, confined in two dimensions, is described by a linear bead-spring…
In this Thesis we first show how the shape of the Peierls barrier and its dependence on the applied loading can be extracted from the data obtained in atomistic studies at 0 K. We consider the Peierls barrier as a two-dimensional periodic…
By means of molecular dynamics simulations, we study the stationary points of the potential energy in a Lennard-Jones liquid, giving a purely geometric characterization of the energy landscape of the system. We find a linear relation…
We investigate the nonequilibrium dynamics of semiflexible polymers driven by motor proteins (MPs) in two-dimensional motility assays under harmonic confinement. Using a coarse-grained agent-based model that incorporates stochastic motor…
We consider the impact of the elastomer network on the structure and fluctuations in the isotropic-genesis nematic elastomer, via a phenomenological model that underscores the role of network compliance. The model contains a…
Molecular dynamics simulations are increasingly being used to investigate the structural evolution of polymers during mechanical deformation, but relatively few studies focus on the influence of boundary conditions on this evolution, in…
The presence of one or more species at some spatial locations but not others is a central matter in ecology. This phenomenon is related to ecological pattern formation. Nonlocal interactions can be considered as one of the mechanisms…
Two ring polymers close to each other in space may be either in a segregated phase if there is a strong repulsion between monomers in the polymers, or intermingle in a mixed phase if there is a strong attractive force between the monomers.…
Low-connectivity polymer networks were recently found to behave auxetically when subjected to small tensions, that is, their Poisson's ratio $\nu$ becomes negative. In addition, for specific state points, numerical simulations revealed that…
We present a numerical Monte Carlo analysis of a continuos spin Ising chain that can describe the statistical proterties of folded proteins. We find that depending on the value of the Metropolis temperature, the model displays the three…
Motivated by results from an earlier Brownian Dynamics (BD) simulation for the collapse of a single, stiff polymer in a poor solvent [B. Schnurr, F. C. MacKintosh, and D. R. M. Williams, Europhys. Lett. 51 (3), 279 (2000)] we calculate the…
We generalize a recently investigated lattice model of semiflexible polymers formed under equilibrium polymerization in a solution and conduct a comprehensive investigation of its melting properties. The model is characterized by six…
The statistical theory of flow stress, including yield strength, for polycrystalline materials under quasi-static plastic deformation suggested in [arxiv:1803.08247[cond-mat.mtr-sci], arxiv:1805.08623[cond-mat.mtr-sci]] is developed in the…
Initially straight slender elastic rods with geometrically constrained ends buckle and form stable two-dimensional shapes when compressed by bringing the ends together. It is also known that beyond a critical value of the pre-stress,…
In granular media, the presence of even small amounts of interparticle cohesion manifests as an increase in the bulk strength and stiffness, effects that are typically associated with an increase in the average number of constraints per…
We introduce a mesoscopic model of dynamic Tetra-PEG hydrogel networks based on a hybrid Dissipative Particle Dynamics/Monte Carlo (DPD/MC) approach. Polymer chains are described by Finite Extensible Nonlinear Elastic (FENE) potential,…
In this study, we consider a linearized compressible flow structure interaction PDE model for which the interaction interface is under the effect of material derivative term. While the linearization takes place around a constant pressure…
Against common sense, auxetic materials expand or contract perpendicularly when stretched or compressed, respectively, by uniaxial strain, being characterized by a negative Poisson's ratio $\nu$. The amount of deformation in response to the…
We present a new apparatus that probes simultaneously the macroscopic mechanical response and the microscopic motion in polymer networks under uni-axial strain. The setup leverages photon correlation imaging, a space- and time-resolved…
Mono- and poly-disperse melts of oligomers (average length 10 monomers) of trans-1,4-polyisoprene are simulated in full atomistic detail. The force-field is developed by means of a mixture of ab initio quantum-chemistry and an automatic…