Blog Posts

3 posts in total

All Arch4Chem Blog Cryptography FPGA Molecular Dynamics Parallel Computing Verilog

Can PIM Accelerate Molecular Dynamics?

Molecular Dynamics (MD) is a core simulation method in drug design and biomolecular research. MD involves heavy memory traffic, but on a single GPU only about 10–25% of total runtime is genuinely memory-bound and PIM-suitable; even a 10× speedup on that slice yields only 1.1–1.3× overall. So PIM isn't the best fit for the single-GPU timestep loop—but for trajectory analysis, neighbour-list preprocessing, and ensemble workflows, where data movement dominates, PIM and in-storage processing remain promising.

May 13, 2026 20 min read

Arch4Chem Molecular Dynamics Blog

分子动力学可以用PIM优化的可行性

分子动力学是药物设计和生物分子研究中的关键模拟方法，主要通过计算原子间力并更新位置来模拟原子运动。虽然 MD 过程涉及大量内存读写，但在单 GPU 环境下，仅约 10–25% 的运行时间属于 memory‑bound 且适合 PIM 加速，即使该部分实现 10 倍加速，整体性能提升也仅约 1.1–1.3 倍。因而 PIM 不是单 GPU MD 主循环的最佳加速方案，但在轨迹分析、邻居列表构建等数据密集型环节仍有潜在价值。

May 13, 2026 9 min read

Arch4Chem Molecular Dynamics Blog

Multi-Core RC4 Decoder/Cracker

FPGA-based multi-core RC4 decoder design and implementation using Verilog with parallel processing architecture for efficient cryptanalysis.

March 18, 2022 2 min read

FPGA Verilog Cryptography Parallel Computing