Rotation Dynamics of Star Block Copolymers under Shear Flow

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.

Multi-particle collision dynamics for a coarse-grained model of soft colloids

The growing interest in the dynamical properties of colloidal suspensions, both in equilibrium and under an external drive such as shear or pressure flow, requires the development of accurate methods to correctly include hydrodynamic effects due to the suspension in a solvent. In the present work, we generalize Multiparticle Collision Dynamics (MPCD) to be able to deal with soft, polymeric colloids. Our methods build on the knowledge of the monomer density profile that can be obtained from monomer-resolved simulations without hydrodynamics or from theoretical arguments. We hereby propose two different approaches. The first one simply extends the MPCD method by including in the simulations effective monomers with a given density profile, thus neglecting monomer-monomer interactions. The second one considers the macromolecule as a single penetrable soft colloid (PSC), which is permeated by an inhomogeneous distribution of solvent particles. By defining an appropriate set of rules to control the collision events between the solvent and the soft colloid, both linear and angular momenta are exchanged. We apply these methods to the case of linear chains and star polymers for varying monomer lengths and arm number, respectively, and compare the results for the dynamical properties with those obtained within monomer-resolved simulations. We find that the effective monomer method works well for linear chains, while the PSC method provides very good results for stars. These methods pave the way to extend MPCD treatments to complex macromolecular objects such as microgels or dendrimers and to work with soft colloids at finite concentrations.