Computational Biophysics in Cellular Biological Systems

A special issue of Cells (ISSN 2073-4409). This special issue belongs to the section "Cell Methods".

Deadline for manuscript submissions: 31 December 2025 | Viewed by 3952

Special Issue Editors


E-Mail
Guest Editor Assistant
Department of Physics, University of Texas, 500 West University Ave, El Paso, TX 79968, USA
Interests: computational biology; protein–protein interaction; biochemistry; virus capsid assembly; molecular motors; kinesin
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Computational approaches are revolutionizing our understanding of cellular biological systems, offering profound insights into biomolecular structure, dynamics, and function. Techniques such as cryo-electron microscopy (cryo-EM) and X-ray crystallography provide detailed structural information, while molecular dynamics (MD) simulations and coarse-grained modeling shed light on the dynamic behaviors and interactions within cellular networks. These computational methods complement traditional biophysical techniques—including fluorescence microscopy and atomic force microscopy (AFM)—by enabling the real-time observation of molecular processes in live cells. Furthermore, genetic and biochemical assays integrated with computational tools reveal the regulatory mechanisms underlying cellular functions. This Special Issue explores the latest advancements in the computational biophysics of cellular systems, including how these methods uncover the intricacies of cellular function, disease pathways, and therapeutic potential. We encourage submissions that utilize innovative computational strategies and multidisciplinary approaches to expand our understanding of cellular biophysics. We look forward to your valuable contributions to this pivotal area of research.

Original papers and high-quality review articles are welcome for this Special Issue. Potential topics include, but are not limited to, the following:

  • High-Resolution Computational Modeling of Membrane Protein Complexes;
  • In Silico Approaches to Protein–Protein Interactions in Cellular Signaling Networks;
  • Molecular Dynamics Simulations in Cellular Processes;
  • Virtual Screening and Molecular Docking for Drug Discovery Targeting;
  • Computational Modeling of Post-Translational Modifications in Protein Regulation;
  • Multiscale Computational Modeling of Cellular Metabolic Pathways;
  • Innovative Computational Methods for Single-Cell Biophysical Analysis.     

Dr. Lin Li
Dr. Wenhan Guo
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Cells is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • cellular process
  • protein–protein interactions
  • single-cell analysis
  • drug design
  • molecular dynamics simulations

Benefits of Publishing in a Special Issue

  • Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
  • Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
  • Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
  • External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
  • Reprint: MDPI Books provides the opportunity to republish successful Special Issues in book format, both online and in print.

Further information on MDPI's Special Issue policies can be found here.

Published Papers (2 papers)

Order results
Result details
Select all
Export citation of selected articles as:

Research

Jump to: Review

24 pages, 8095 KB  
Article
Integrated Bioinformatics and Experimental Analysis Revealed Crosstalk Between IL-6, Autophagy, Ubiquitination, and Key miRNAs in Female Infertility: Insights from Ovarian Endometriosis and Polycystic Ovary Syndrome
by Saber Nahdi, Maria Arafah and Abdel Halim Harrath
Cells 2025, 14(21), 1693; https://doi.org/10.3390/cells14211693 - 28 Oct 2025
Viewed by 253
Abstract
Female infertility, affecting millions worldwide, involves complex molecular mechanisms such as chronic inflammation, impaired cellular death, and protein regulation. This study explores how the cytokine IL-6, the autophagy marker LC3, ubiquitination process, and three miRNAs, miR-146a-5p, miR-9-5p, and miR-9-3p, contribute to the control [...] Read more.
Female infertility, affecting millions worldwide, involves complex molecular mechanisms such as chronic inflammation, impaired cellular death, and protein regulation. This study explores how the cytokine IL-6, the autophagy marker LC3, ubiquitination process, and three miRNAs, miR-146a-5p, miR-9-5p, and miR-9-3p, contribute to the control of ovarian function and female infertility. Two expression profile datasets (GSE199225 and GSE146856) were screened and downloaded from GEO. DEGs were screened using the GEO2R and ggVennDiagram tools. The three miRNAs were retrieved from datasets using the multiMiR tool, and IL6-targeted genes were retrieved from MSigDB. IL6 and miRNA interaction networks were constructed. Further, the cross-correlation of LC3 and ubiquitination with the DEGs associated miRNAs was demonstrated. Meanwhile, GO/KEGG pathway enrichment analyses and molecular network interaction analysis were performed. Lastly, immunohistochemistry and quantitative PCR (qPCR) were used to confirm the expression of IL6, LC3, and miRNA in ovarian endometrial tissues compared to control tissues. The results showed that IL-6 drives inflammation in conditions of PCOS and ovarian endometriosis, which then disrupts ovulation and embryo implantation. miR-146a-5p reduced inflammation by targeting the gene TRAF6, while miR-9-5p regulated protein degradation via SQSTM1. In agreement with the bioinformatic approach, experimental analysis revealed reduced IL6 protein expression in ovarian endometriosis tissues while the mRNA IL6 level was increased, suggesting the presence of post-transcriptional regulatory mechanisms that act to limit excessive inflammation, probably through miRNAs. Indeed, the levels of miR-146a-5, which plays a role in immune modulation and inflammatory signaling, were significantly upregulated. Interestingly, an alteration in autophagic markers revealed by elevated LC3 was also observed. Aligned with these experimental data, bioinformatic analysis showed that autophagy genes LC3 and ATG5 and ubiquitination processes were tightly linked to ovarian health, with disruptions accelerating follicle loss and oxidative damage. In conclusion, the results showed that IL-6, miRNAs, and autophagy processes work together to control inflammation and cellular repair in ovarian disorders. This study opens new avenues for targeted treatments to improve fertility outcomes by connecting molecular networks to clinical insights. Full article
(This article belongs to the Special Issue Computational Biophysics in Cellular Biological Systems)
Show Figures

Figure 1

Review

Jump to: Research

22 pages, 2859 KB  
Review
Modeling Viral Capsid Assembly: A Review of Computational Strategies and Applications
by Wenhan Guo, Esther Alarcon, Jason E. Sanchez, Chuan Xiao and Lin Li
Cells 2024, 13(24), 2088; https://doi.org/10.3390/cells13242088 - 17 Dec 2024
Cited by 3 | Viewed by 3169
Abstract
Viral capsid assembly is a complex and critical process, essential for understanding viral behavior, evolution, and the development of antiviral treatments, vaccines, and nanotechnology. Significant progress in studying viral capsid assembly has been achieved through various computational approaches, including molecular dynamics (MD) simulations, [...] Read more.
Viral capsid assembly is a complex and critical process, essential for understanding viral behavior, evolution, and the development of antiviral treatments, vaccines, and nanotechnology. Significant progress in studying viral capsid assembly has been achieved through various computational approaches, including molecular dynamics (MD) simulations, stochastic dynamics simulations, coarse-grained (CG) models, electrostatic analyses, lattice models, hybrid techniques, machine learning methods, and kinetic models. Each of these techniques offers unique advantages, and by integrating these diverse computational strategies, researchers can more accurately model the dynamic behaviors and structural features of viral capsids, deepening our understanding of the assembly process. This review provides a comprehensive overview of studies on viral capsid assembly, emphasizing their critical role in advancing our knowledge. It examines the contributions, strengths, and limitations of different computational methods, presents key computational works in the field, and analyzes milestone studies that have shaped current research. Full article
(This article belongs to the Special Issue Computational Biophysics in Cellular Biological Systems)
Show Figures

Figure 1

Back to TopTop