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Membranes
Special Issues
Biological Membranes In Silico—Unraveling Mechanisms Through Molecular Dynamics Simulations
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Biological Membranes In Silico—Unraveling Mechanisms Through Molecular Dynamics Simulations

A special issue of Membranes (ISSN 2077-0375). This special issue belongs to the section "Biological Membranes".

Deadline for manuscript submissions: 30 September 2026 | Viewed by 888

Special Issue Editors

Dr. Haoyuan Jing

E-Mail Website
Guest Editor
1. Center for Cell Dynamics, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
2. Department of Cell Biology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
Interests: membrane dynamics; biological membranes; lipid–protein interactions
Dr. Yanbin Wang

E-Mail Website
Guest Editor
Department of Chemistry, Purdue University, West Lafayette, IN, USA
Interests: protein structure sampling; collective variable discovery; machine learning-aided protein structure prediction

Special Issue Information

Dear Colleagues,

Biological membranes are dynamic, complex systems essential for cellular structure, signaling, and transport. Recent breakthroughs in experimental techniques—such as single-molecule tracking, super-resolution microscopy, and cryo-electron microscopy—have greatly advanced our understanding of biological membranes. These methods have revealed unprecedented detail in membrane ultrastructure, protein complexes, and dynamic behaviors. However, experimental approaches face fundamental trade-offs between spatial and temporal resolution and are constrained by challenges in controlling environmental conditions.

Molecular dynamics (MD) simulations have emerged as a powerful complementary tool, capable of capturing biological processes at atomic resolution and femtosecond timescales, all within a fully controllable virtual environment. MD simulations have provided valuable insights into membrane-associated phenomena, such as membrane protein dynamics; protein–lipid interactions; ion channel and transporter dynamics; membrane fusion and fission; and the biophysical properties of lipid bilayers.

With the rapid advancement of artificial intelligence and increasing access to high-performance GPUs, MD simulations are progressing faster and becoming more sophisticated. AI and machine learning are driving improvements in force field accuracy, enhancing sampling efficiency, predicting plausible reaction pathways, and refining structural models of membrane proteins.

Despite these promising developments, bridging the gap between simplified simulation systems and the complex reality of cellular membranes remains a central challenge. Continued interdisciplinary collaboration will be key to narrowing this divide and unlocking deeper mechanistic insights into membrane biology.

This Special Issue invites original research articles, reviews, and perspective pieces that highlight the latest advancements in MD simulations of biological membranes. Topics may include, but are not limited to, algorithmic innovations, force field development, hybrid modeling approaches, and integrative studies combining simulations with experimental data. Together, we aim to showcase how molecular dynamics is shaping the future of membrane biology.

Dr. Haoyuan Jing
Dr. Yanbin Wang
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 250 words) can be sent to the Editorial Office for assessment.

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. Membranes is an international peer-reviewed open access monthly 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 2200 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

  • molecular dynamics simulation
  • biological membranes
  • membrane protein dynamics
  • lipid–protein interactions
  • membrane fusion and fission
  • ion channels and transporters
  • force field development
  • artificial intelligence in MD
  • membrane biophysics
  • hybrid modeling
  • free-energy landscape sampling
  • kinetics/rare-event sampling
  • Markov-state modeling
  • coarse graining simulation

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Published Papers (1 paper)

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Research

11 pages, 877 KB  
Article
A Study of Liposome Structure Changes with Temperature Using Non-Equilibrium Molecular Dynamics Simulations
by Gary Q. Yang, Weibin Cai and Ying Wan
Membranes 2026, 16(4), 124; https://doi.org/10.3390/membranes16040124 - 31 Mar 2026
Viewed by 518
Abstract
Liposomes, spherical bilayer lipid-containing vesicles, are promising nanocarriers used for constructing drug delivery systems (DDS). Various strategies can be employed to loosen or break the liposome and release drugs as the tumor cells-targeting DDS made of liposomes reach the targeted sites. One of [...] Read more.
Liposomes, spherical bilayer lipid-containing vesicles, are promising nanocarriers used for constructing drug delivery systems (DDS). Various strategies can be employed to loosen or break the liposome and release drugs as the tumor cells-targeting DDS made of liposomes reach the targeted sites. One of the most commonly used strategies is to heat the liposomal DDS by letting the gold nanoparticles or other light-absorbing substances that partition in various portions (inner water core, lipid bilayer or outside) of the liposome absorb light irradiation. Then, which portion can lead to the largest liposome structure change due to the same temperature variation? The answer is essential to aid the design of liposomal DDS; thus, wet lab experiments were carried out. However, even though irradiation-absorbing substances in different portions were irradiated for the same time and with the same irradiation intensity, it was impossible to ensure the three portions have the same temperature increase in the experiments. Furthermore, it is impossible to learn the related micromechanism and molecular-level details of the effects of temperature changes on the liposome structure with experimental methods. The molecular dynamics (MD) method is extensively employed by researchers to obtain in-depth molecular-level insights. Most researchers tend to simulate only a planar lipid bilayer structure, but Amărandi et al. demonstrated that such simplification strategy may give wrong simulation results contrary to the experimental results. Though Jämbeck et al. and Zhu et al. established whole spherical liposome systems with a diameter of about a dozen nanometers and simulated the systems with MD simulations, they did not simulate temperature-relevant properties of the liposome. Therefore, currently there is a lack of research on simulating the structure change in a whole spherical liposome due to temperature variations. So, we established the whole spherical structure of the liposome, simulated how it changes with temperatures and obtained molecular-level research results. It is observed that the temperature increase in the lipid bilayer causes the largest increase in lipid strand sway amplitude, the largest changes in lipid positions, the largest decrease in the distribution density of lipids and water around a lipid and the largest decrease in the interactions between lipids and lipids and between lipids and water, leading to the largest change in the liposome structure. We also studied how the degree of lipid tail unsaturation affects liposome structure changes with temperatures. Due to the C3 kinks in the unsaturated lipid tails, the distribution density of unsaturated lipids is not as high as saturate ones, leading to smaller attraction interactions and consequently larger liposome structure change with temperature. The obtained results are useful for the liposomal DDS design for the purpose of improving DDS performances and delivery outcomes. Full article
(This article belongs to the Special Issue Biological Membranes In Silico—Unraveling Mechanisms Through Molecular Dynamics Simulations)
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