2026-10-13T17:10:00Z https://api.figshare.com/v2/oai

oai:figshare.com:article/33995605 2026-09-25T14:15:44Z category_1 category_4 category_915 category_7 category_21 category_873 category_734 category_931 category_61 category_64 category_133 category_135 portal_63 item_type_3 month_year_09_2026

Improving All-Atom Molecular Dynamics Models for Quantitative Prediction of Nanopore Blockade Current Jingqian Liu (5705123) Crystal Rodriguez (25110487) Min Chen (147733) Aleksei Aksimentiev (1234707) Biophysics Biochemistry Physical Sciences not elsewhere classified Medicine Biotechnology Chemical Sciences not elsewhere classified Biological Sciences not elsewhere classified Information Systems not elsewhere classified Developmental Biology Cancer Plant Biology Computational Biology reproduce experimental data molecular dynamics method ionic current modulations ionic current flowing atom molecular dynamics applied electric field nonbonded interactions within nanopore blockade current experiments designed specifically brute force simulation nanopore sensing simulations typical nanopore experiment simulations show refined interactions nanopore sensors nanopore report surgical corrections relationship directly refined parameterization quantitative prediction protein nanopores often insufficient initially developed indispensable tool favorable agreement desired level computational studies broader applications biological information All-atom molecular dynamics has become an indispensable tool in the development of nanopore sensors of biological information. In a typical nanopore experiment, measurements of ionic current flowing through a nanopore report on the chemical structure of biomolecules that pass through the nanopore. Alone, such experiments are often insufficient to relate the structure of the biomolecules to the ionic current modulations. The molecular dynamics method can establish such a relationship directly through a brute force simulation under an applied electric field. Here, we examine the ability of molecular dynamics force fields to reproduce experimentally measured nanopore blockade currents produced by single-stranded DNA. Our simulations show that none of the “off-the-shelf” force fields (CHARMM36, AMBER Parmbsc1, and DES-AMBER) can reproduce experimental data with the desired level of accuracy. To improve the accuracy, we examined and refined interactions between ions, protein nanopores, and DNA, guided by experiments designed specifically for this purpose. Ultimately, the introduction of surgical corrections to nonbonded interactions within the CHARMM36 force field produced a favorable agreement between simulation and experiment. This refined parameterization, initially developed for nanopore sensing simulations, may have broader applications in computational studies of DNA–protein systems. 2026-09-25T00:00:00Z Dataset Dataset 10.1021/acs.jctc.6c01180.s001 https://figshare.com/articles/dataset/Improving_All-Atom_Molecular_Dynamics_Models_for_Quantitative_Prediction_of_Nanopore_Blockade_Current/33995605 CC BY-NC 4.0