---
title: "Dielectric Continuum Modeling of de novo Calcium Channel CalC6.3: Structure Prep and Ion Selectivi"
id: "biorxiv-0-dielectric-continuum-modeling-for-the-de-novo-designed-calcium-channel-calc6-3"
canonical_url: "https://medichelpline.com/clinical-feed/biorxiv-0-dielectric-continuum-modeling-for-the-de-novo-designed-calcium-channel-calc6-3"
content_type: "clinical_feed_article"
specialty: "Pharmacology"
source_name: "bioRxiv (Biomedical Preprints)"
source_url: "https://www.biorxiv.org/content/10.64898/2026.10.20.760449v1?rss=1"
published_at: "2026-10-23T12:00:00.000Z"
evidence_level: "Verified Feed"
license: "CC-BY-NC-4.0 / Informational Use"
---
# Dielectric Continuum Modeling of de novo Calcium Channel CalC6.3: Structure Prep and Ion Selectivi
## Provenance & Clinical Metadata
- **Canonical URL:** https://medichelpline.com/clinical-feed/biorxiv-0-dielectric-continuum-modeling-for-the-de-novo-designed-calcium-channel-calc6-3
- **Specialty:** [Pharmacology](https://medichelpline.com/clinical-feed/pharmacology.md)
- **Primary Source:** bioRxiv (Biomedical Preprints)
- **Source URL:** [Original Journal Publication](https://www.biorxiv.org/content/10.64898/2026.10.20.760449v1?rss=1)
- **Published At:** 2026-10-23T12:00:00.000Z
- **Evidence Rating:** Verified Feed
## Executive GIST (TL;DR)
- The authors created an integrated software workflow for continuum dielectric modeling of the de novo calcium channel **CalC6.3**. - The source PDB structure (PDB ID: 9DZW) was cleaned and repaired with Python scripts; the paper reported use of **PDB2PQR** to produce a PQR with atomic coordinates, partial charges, and radii. - A Gaussian Ion Channel Molecular Surface Generation package was used to build high-quality triangular molecular surface meshes that preserve the pore geometry while enabling tetrahedral mesh generation for simulation domains including protein, membrane, and solvent. - The integrated pipeline couples structure preparation, mesh generation, and a finite-element solver to compute electrostatic potentials and ionic concentrations from structure to numerical solution. - Numerical simulations included an ionic solution with **Ca2+**, Na+, and Cl−; data indicated preferential accumulation of **Ca2+** within a narrow selectivity filter formed by six Glu residues. - The authors observed that a smoother molecular surface mesh can improve solver convergence and performance; mesh quality therefore affects numeric stability and solution behavior. - The manuscript is a preprint; it has not been peer reviewed. The authors declared no competing interests and acknowledged partial support from the National Science Foundation and the Simons Foundation. - The paper focused on software and numerical modeling methods; the source did not report experimental electrophysiology, specific simulation parameters (such as ion concentrations, boundary conditions, or solver settings), nor did it provide quantitative metrics for selectivity beyond preferential accumulation statements.
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Robert S Eisenberg 1 Rush University; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Robert%2BS%2BEisenberg%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Eisenberg%20RS&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3ARobert%2BS%2BEisenberg%2B) * [ORCID record for Robert S Eisenberg](http://orcid.org/0000-0002-4860-5434 "Open in new tab") * For correspondence: bob.eisenberg@gmail.com Dexuan Xie 2 University of Wisconsin-Milwaukee * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Dexuan%2BXie%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Xie%20D&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3ADexuan%2BXie%2B) * [ORCID record for Dexuan Xie](http://orcid.org/0000-0002-7072-6275 "Open in new tab") * [Abstract](https://www.biorxiv.org/content/10.64898/2026.10.20.760449v1)[](https://www.biorxiv.org/panels_ajax_tab/biorxiv_tab_art/node:5898226/1) * [Info/History](https://www.biorxiv.org/content/10.64898/2026.10.20.760449v1.article-info)[](https://www.biorxiv.org/panels_ajax_tab/biorxiv_tab_info/node:5898226/1) * [Metrics](https://www.biorxiv.org/content/10.64898/2026.10.20.760449v1.article-metrics)[](https://www.biorxiv.org/panels_ajax_tab/article_tab_metrics/node:5898226/1) * [ Preview PDF](https://www.biorxiv.org/content/10.64898/2026.10.20.760449v1.full.pdf+html)[](https://www.biorxiv.org/panels_ajax_tab/biorxiv_tab_pdf/node:5898226/1) ![Loading](https://www.biorxiv.org/sites/all/modules/contrib/panels_ajax_tab/images/loading.gif) ## Abstract This paper presents an integrated software package for continuum dielectric studies of the de novo designed calcium channel CalC6.3. The package combines Python scripts for cleaning and repairing the original PDB structure (PDB ID: 9DZW) with PDB2PQR to generate a corre–sponding PQR file containing atomic coordinates, partial charges, and radii. It incorporates the Gaussian Ion Channel Molecular Surface Generation package to construct high–quality triangular molecular surface meshes that preserve the complex channel pore geometry while maintaining suffi–nterface-fitted tetrahedral meshes of a simulation box consisting of protein, membrane, and solvent regions. The integrated software package further integrates the structure–preparation and mesh– size–nite element solver to compute electrostatic potentials and ionic concentrations, streamlining the complete workflow from structure preparation to numerical solution. Numerical experiments for an ionic solution containing Ca2+, Na+ , and Cl−ions show preferential Ca2+ accumulation in the narrow selectivity filter formed by six Glu residues, supporting the experimentally observed calcium selectivity of CalC6.3. They also suggest that a smoother molecular surface mesh can improve the convergence and performance of the finite element solver. ### Competing Interest Statement The authors have declared no competing interest. ## Funder Information Declared This work was partially supported by the National Science Foundation, USA Simons Foundation, USA Copyright The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a [CC-BY 4.0 International license](http://creativecommons.org/licenses/by/4.0/). bioRxiv and medRxiv thank the following for their generous financial support: > The Chan Zuckerberg Initiative, Cold Spring Harbor Laboratory, the Sergey Brin Family Foundation, California Institute of Technology, Centre National de la Recherche Scientifique, Fred Hutchinson Cancer Center, Imperial College London, Massachusetts Institute of Technology, Stanford University, The University of Edinburgh, University of Washington, and Vrije Universiteit Amsterdam. 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