Edge-Native Molecular Dynamics on Mobile ARM Hardware: NVT Simulation of Dengue Virus NS3 Protease and the Path Toward Decentralized Computational Drug Discovery

ABSTRACT Molecular dynamics (MD) simulation is a cornerstone of structure-based drug discovery; however, its application to neglected tropical diseases remains constrained by the cost of high-performance computing infrastructure. We present a native C++ molecular dynamics engine targeting mobile ARM processors that achieves stable NVT simulation of the Dengue virus NS3 serine protease (PDB: 2FOM; N = 1,718 atoms) at physiological temperature (310 K) on a consumer smartphone. The engine integrates O(N) Cell-Linked List spatial partitioning, 1–2 and 1–3 exclusion lists, per-element atomic masses, an angle-bending potential with crystal-structure equilibrium geometry, and a Langevin BBK thermostat within a four-phase equilibration protocol. Thermal convergence (308–329 K) and structural stability (backbone RMSD 0.032–0.119 Å over 2,000 integration steps) are demonstrated quantitatively, achieving 276.5 integration steps per second—a 3.4× improvement over our prior implementation—without GPU acceleration or cloud-based resources. We discuss the implications for decentralized drug discovery, mobile swarm computing, and scientific sovereignty in the Global South. STATEMENT OF PRIOR ART AND LICENSE TERMS (Aligned with PolyForm Noncommercial License 1.0.0) 1. Permitted Use Academic research, independent study, education, benchmarking, validation, reproducibility studies, and experimental evaluation, is permitted under the terms of the PolyForm Noncommercial License 1.0.0, provided proper attribution is given. 2. Statement of Prior Art This document constitutes a formal public disclosure establishing prior art for the Molecular dynamics (MD). 3. Scope of the License All implementations of the methods described herein—whether in software or hardware—are governed exclusively by the PolyForm Noncommercial License 1.0.0. This includes implementations in any programming language and on any programmable or dedicated hardware platform, including but not limited to CPU, GPU, FPGA, ASIC, or similar architectures. 4. Noncommercial Restriction Any use of this work that falls outside the definition of noncommercial use, as defined by the PolyForm Noncommercial License 1.0.0, is not permitted under this license. 5. Commercial and Operational Use Any commercial, operational, institutional, governmental, regulatory, or production deployment of this work constitutes use outside the scope of the PolyForm Noncommercial License 1.0.0 and therefore requires separate authorization from the authors, in accordance with the terms of that license. For the purposes of this document, authors refers to the original author and any officially recognized co-authors or principal contributors, as reflected in the associated public repository and its contribution records. 6. Derivative Works and Functional Equivalence Reimplementation, translation, refactoring, architectural modification, optimization, or claims of functional equivalence do not remove a work from the scope of the PolyForm Noncommercial License 1.0.0. Any such implementation remains subject to the same license terms. 6.a. Code Size Irrelevance (No Minimum Threshold) For the avoidance of doubt, the applicability of the PolyForm Noncommercial License 1.0.0 is independent of code size, number of lines, percentage of implementation, degree of literal similarity, or partial extraction. There is no minimum threshold of code volume or implementation extent required for a work to fall within the scope of this license. Any use, reproduction, reimplementation, refactoring, selective reuse, architectural translation, or functional incorporation of the disclosed concepts—regardless of size or extent—is subject to the terms of the PolyForm Noncommercial License 1.0.0. 7. Knowledge Contamination and Attribution Exposure to this work constitutes prior knowledge of the disclosed methods. Subsequent implementations making material use of the disclosed concepts remain subject to attribution and license requirements as defined by the PolyForm Noncommercial License 1.0.0. 8. Intellectual Property Ownership Nothing in this document shall be construed as transferring ownership of intellectual property.All intellectual property rights remain with the authors, subject only to the permissions explicitly granted under the PolyForm Noncommercial License 1.0.0. 9. No Additional Rights Granted This document does not grant any rights beyond those expressly provided by the PolyForm Noncommercial License 1.0.0.In the event of any conflict, the terms of the PolyForm Noncommercial License 1.0.0 shall control. 10. Enforcement and Remedies Any use of this work in violation of the PolyForm Noncommercial License 1.0.0 shall be addressed exclusively through the remedies and enforcement mechanisms provided by that license and by applicable law. Correspondence AuthorAndrés Sebastián Pirolo andrespirolo@gmail.com lctrnc1@gmail.com