Controlled self-aggregation of polymer-based nanoparticles employing shear flow and magnetic fields

Rotational Dynamics of a Protein under Shear Flow Studied by the Eckart Frame Formalism

Proteins are natural polymers that play an essential role in both living organisms and biotechnological applications. During certain bioprocessing steps, they can be exposed to significant mechanical stress induced by, for example, shear flow or sonication, resulting in reduced therapeutic efficacy, aggregation, or even a loss of activity. For this reason, there is a need to understand and determine the susceptibility of the protein activity to the experienced mechanical stress. To acquire this knowledge, it is necessary to study the rotational dynamics of the protein. Commonly, the rotational dynamics of soft molecules is interpreted based on a theoretical analysis performed in an inertial laboratory frame. However, the obtained angular velocity mixes pure rotations and vibrations with angular momentum, consequently lacking a clear dynamical interpretation. On the other hand, the use of the noninertial internal Eckart frame allows the determination of pure angular velocity as it minimizes the coupling between the rotational and vibrational degrees of freedom. In the present work, by conducting open-boundary molecular dynamics simulations and exploiting the Eckart frame formalism, we study the rotational dynamics of a small protein under the shear flow of various strengths. Our results show that the angular velocity increases nonlinearly with increasing shear rate. Furthermore, the protein gains vibrational angular momentum at higher shear rates, which is reflected in the higher angular velocity computed by employing the Eckart frame formalism and confirmed by analysis of the contributions to the total kinetic energy of the biomolecule.

On the yielding of a point-defect-rich model crystal under shear: insights from molecular dynamics simulations

In real crystals and at finite temperatures point defects are inevitable. Under shear their dynamics severely influence the mechanical properties of these crystals, giving rise to non-linear effects, such as ductility. In an effort to elucidate the complex behavior of crystals under plastic deformation it is crucial to explore and to understand the interplay between the timescale related to the equilibrium point-defect diffusion and the shear-induced timescale. Based on extensive non-equilibrium molecular dynamics simulations we present a detailed investigation on the yielding behavior of cluster crystals, an archetypical model for a defect-rich crystal: in such a system clusters of overlapping particles occupy the lattice sites of a regular (FCC) structure. In equilibrium particles diffuse via site-to-site hopping while maintaining the crystalline structure intact. We investigate these cluster crystals at a fixed density and at different temperatures where the system remains in the FCC structure: temperature allows us to vary the diffusion timescale appropriately. We then expose the crystal to shear, thereby choosing shear rates which cover timescales that are both higher and lower than the equilibrium diffusion timescales. We investigate the macroscopic and microscopic response of our cluster crystal to shear and find that the yielding scenario of such a system does not rely on the diffusion of the particles - it is rather related to the plastic deformation of the underlying crystalline structure. The local bond order parameters and the measurement of local angles between neighboring clusters confirm the cooperative movement of the clusters close to the yield point. Performing complementary, related simulations for an FCC crystal formed by harshly repulsive particles reveals similarities in the yielding behavior between both systems. Still we find that the diffusion of particles does influence characteristic features in the cluster crystal, such as a less prominent increase of order parameters close to the yield point. Our simulations provide for the first time an insight into the role of the diffusion of defects in the yielding behavior of a defect-rich crystal under shear. These observations will thus be helpful in the development of theories for the plastic deformation of defect-rich crystals.

Phase Transitions of Oppositely Charged Colloidal Particles Driven by Alternating Current Electric Field

We study systems containing oppositely charged colloidal particles under applied alternating current electric fields (AC fields) using overdamped Langevin dynamics simulations in three dimensions. We obtain jammed bands perpendicular to the field direction under intermediate frequencies and lanes parallel with the field under low frequencies. These structures also depend upon the particle charges. The pathway for generating jammed bands follows a stepwise mechanism, and intermediate bands are observed during lane formation in some systems. We investigate the component of the pressure tensors in the direction parallel to the field and observe that the jammed to lane transition occurs at a critical value for this pressure. We also find that the stable steady states appear to satisfy the principle of maximum entropy production. Our results may help to improve the understand of the underlying mechanisms for these types of dynamic phase transitions and the subsequent cooperative assemblies of colloidal particles under such non-equilibrium conditions.