Multiscale simulation of fluid flow interaction with biological macromoleculesPapež, Petra (Avtor) Praprotnik, Matej (Mentor) Merzel, Franci (Komentor) biological macromoleculesdissipative particle dynamicsopen-boundary molecular dynamicssound waveprincipal component analysisshear flowEckart frame formalismvibration and rotationProteins are natural polymers that play an essential role both in living organisms and in biotechnological applications. While most of the protein's function evolves in the thermodynamic equilibrium, proteins can also be exposed to non-equilibrium states generated by mechanical stress that can impair their structure. As the structure of protein molecules is critically related to their function, any excessive structural change can lead to a reduced activity or a complete loss of it. For this reason, it is necessary to understand and determine the susceptibility of these biomolecules to mechanical stress, and the key to this knowledge is usually hidden in their dynamic response. In this thesis, we establish a methodology and an analytical framework that allow us to study the effects of acoustic excitations and hydrodynamic shear flow on the internal, rotational, and conformational dynamics of biological macromolecules. To capture the details of this interaction, we need to allow the molecular system to exchange mass and momentum with its surroundings. This is possible with the open-boundary molecular dynamics (OBMD) method, which enables grand-canonical simulations in and out of equilibrium. In OBMD simulations, the external boundary conditions are imposed on the system by an additional external force without modifying Newton's equations of motion in the bulk. We extend the OBMD method to simulate the propagation of acoustic waves in liquid water described by the mesoscopic dissipative particle dynamics (DPD) and simple point-charge (SPC) water models. Evaluating density variation for sound waves of different frequencies in the terahertz (THz) range, we show that our particle-based methodology can recover the fluctuating hydrodynamic description of acoustic waves in the continuum limit. Furthermore, we apply the developed methodology to excite low-frequency vibrational motions in the protein. To this end, we show that the sub-THz acoustic excitations enhance the protein's internal dynamics. On the other hand, by subjecting the protein to a shear flow of various strengths, we demonstrate that extraordinarily high shear rates must be applied to observe unfolding, the extent of which depends on the applied shear rate. Furthermore, we show that the protein gains vibrational angular momentum at higher shear rates, which is reflected in higher angular velocity and confirmed by analyzing the contributions to the total kinetic energy of the biomolecule.20242024-06-19 08:15:17Doktorsko delo/naloga158660VisID: 139834COBISS_ID: 199420675sl