Article
ENHANCING NUCLEIC ACID SIMULATIONS USING ASYMMETRIC PERIODIC BOUNDARY CONDITIONS
Molecular dynamics and coarse-grained simulations are essential tools for understanding the structural dynamics and functional behavior of nucleic acids at multiple length and time scales. However, conventional symmetric periodic boundary conditions (PBCs) often introduce artificial constraints that can affect accuracy, especially in elongated or directionally biased biomolecular systems such as DNA and RNA. This study presents an advanced simulation framework based on asymmetric periodic boundary conditions (APBCs) to enhance the realism and efficiency of nucleic acid simulations. The proposed approach allows differential periodicity along selected spatial dimensions, enabling more faithful representation of nucleic acid conformational flexibility while reducing finite-size and boundary artifacts. APBCs are implemented and evaluated in both all-atom molecular dynamics and coarse-grained models, demonstrating improved stability, reduced computational overhead, and better agreement with known structural and dynamical properties. The results highlight the effectiveness of asymmetric boundary treatments in multiscale nucleic acid modeling, offering a robust alternative to traditional PBC methods for high-accuracy biomolecular simulations.
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