G VENKANNA, K CHAKRAVARTHY, M SWATHI, E SUDHEER 01 01 Molecular dynamics and coarsegrained 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 finitesize and boundary artifacts APBCs are implemented and evaluated in both allatom molecular dynamics and coarsegrained 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 highaccuracy biomolecular simulations Copyright (c) Journal of Science Engineering Technology and Management Science. All rights reserved 2026