From quantum-mechanical models of bimolecular systems to causality analysis of structural changes

Mechanisms of structural changes in (bio)molecular systems can either be determined from experimental probability distributions or from physics-based multiscale simulations, including microscopic theories, e.g. Molecular Mechanics/Molecular Dynamics (MM/MD), Quantum Dynamics (QD), Quantum-Classical Molecular Dynamics (QCMD), or mezoscopic models such as Lagrangian and Quaternion Molecular Dynamics (LQMD) or Brownian Dynamics (BD).  Symplectic algorithms conserving the total energy are preferable in molecular dynamics simulations. Relationships between experimental data and theoretical ones become quite complex when accounting for time-dependent processes, and when asking what are causal relations between structural transitions.  Typical problem refers to simulations of mutations which influence the dynamics and function. In general, detecting causal relations in structural changes of (bio)molecular systems from simulation data is of crucial importance for the description of molecular mechanisms and understanding the logic of their functioning. Time-dependent atomic positions, momenta, forces or their functions can be treated as signals. Quantum degrees of freedom can also be incorporated in the analyses. Applications of the mentioned above experimental and theoretical methodologies to selected (bio)molecular systems will be discussed, and future developments will be indicated.

M.Kowal, W.Piechocki, L.Roszkowski, J.Skalski