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Abstract: Proteins have been empirically linked to memory. If memory relates to proteinstructure, then each conformation would functionally code only one bit, makingit difficult to explain large memories. Nor is there a simple way to relatememory to protein dynamics on current molecular dynamics MD, which ismemoryless. Here we point out that MD may be modified to involve memory abinitio without any new hypothesis: simply replace the electrostatic Coulombforce by the electrodynamic force-which is more accurate. We now need to solvefunctional differential equations FDEs, instead of the ordinary differentialequations ODEs currently solved in MD. Unlike ODEs, retarded FDEs arehistory-dependent: so memory is already present even at the level ofinteracting sites within molecules. The resulting increase in computationalcomplexity is within the reach of current computers. While Amdahl-s law doespose a challenge to parallelised time-stepping with this model, thecompute-intensive part-the force calculation-may still be carried out inparallel. Thus, reformulating MD to use FDEs is feasible, and this could helpto understand the possible dynamical basis of memory.



Autor: C. K. Raju

Fuente: https://arxiv.org/







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