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Telmisartan-Induced Alteration of Voltage-Gated Na+ Currents: Integrated Experimental and In Silico Approaches -
Black Hole–Inspired Horizon Model for Neural Signal Dynamics -
Conformational Preferences of the Trypanocidal Drug Benznidazole by DFT-Guided Vibrational Spectroscopy -
Effect of Blue Light on Coaggregation Between Fusobacterium nucleatum and Streptococcus sanguinis
Journal Description
Biophysica
Biophysica
is an international, peer-reviewed, open access journal on applying the methods of physics, chemistry, and math to study biological systems, published bimonthly online by MDPI.
- Open Access— free for readers, with article processing charges (APC) paid by authors or their institutions.
- High Visibility: indexed within ESCI (Web of Science), Scopus, EBSCO, and other databases.
- Rapid Publication: manuscripts are peer-reviewed and a first decision is provided to authors approximately 19.1 days after submission; acceptance to publication is undertaken in 4.7 days (median values for papers published in this journal in the first half of 2026).
- Recognition of Reviewers: APC discount vouchers, optional signed peer review and reviewer names are published annually in the journal.
- Biophysica is a companion journal of IJMS.
Impact Factor:
1.8 (2025);
5-Year Impact Factor:
1.6 (2025)
Latest Articles
Amber Suppressor tRNA-Based Mutagenesis for Positional Semi-Saturated Mutagenesis with Natural Amino Acid Substitutions: An Approach for Mapping Positional Contributions to Protein Function
Biophysica 2026, 6(4), 72; https://doi.org/10.3390/biophysica6040072 - 10 Aug 2026
Abstract
There is a growing interest in methods that illuminate the contributions of individual positions to a protein’s function by site-saturating mutagenesis. However, a commonly used approach for assessing variant libraries with deep mutational scanning relies on readouts of biological fitness, which is influenced
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There is a growing interest in methods that illuminate the contributions of individual positions to a protein’s function by site-saturating mutagenesis. However, a commonly used approach for assessing variant libraries with deep mutational scanning relies on readouts of biological fitness, which is influenced by many protein properties (ligand binding, catalysis, allosteric effector binding, allosteric coupling between effector and substrate, etc.). Biochemical assays are required to distinguish among these factors. To facilitate the generation and biochemical evaluation of the functions of large numbers of substituted positions, we co-express updated plasmids coding a series of amber suppressor tRNA in a high-throughput workflow; these plasmids are available at Addgene. As an example, our goal is to evaluate whether allosteric mechanisms are conserved among homologs. Because homologs often have <50% identity, and up to 30% of a protein’s positions can contribute to allosteric function, we reason that the set of “allosteric” positions likely differs among homologs. Our high-throughput workflow includes the following steps: Step (1) an amber suppressor tRNA-based mutagenesis protocol; Step (2) a robotic system for protein expression/purification and functional assays; and Step (3) a method for aggregating results from multiple substitutions at each position into a composite score.
Full article
(This article belongs to the Special Issue Investigations into Protein Structure: 2nd Edition)
Open AccessArticle
Body Distribution and Occupational Dispersion of Scandium-47 Chloride: Safety Considerations for Radiopharmaceutical Development
by
Haruna Yorifuji, Yoshifumi Shirakami, Tadashi Watabe, Masashi Murakami, Kazuhiro Ooe, Kentaro Hisada, Atsufumi Akai, Sifan Feng, Hidetoshi Kikunaga, Takuya Yokokita, Kazuki Kajiyama, Akina Mitsukai, Atsushi Toyoshima, Takashi Yoshimura, Jens Cardinale, Frederik L. Giesel and Kazuko Kaneda-Nakashima
Biophysica 2026, 6(4), 71; https://doi.org/10.3390/biophysica6040071 - 9 Aug 2026
Abstract
This study investigated the distribution and dispersion of Sc-47 (47Sc), a β-emitting radionuclide that can be produced in large quantities using accelerators. As the stability of labeled compounds inside the body is essential for nuclear medicine therapy, we examined the biodistribution
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This study investigated the distribution and dispersion of Sc-47 (47Sc), a β-emitting radionuclide that can be produced in large quantities using accelerators. As the stability of labeled compounds inside the body is essential for nuclear medicine therapy, we examined the biodistribution of free 47Sc to distinguish it from the distribution of compounds labeled with 47Sc. [47Sc]ScCl3 was administered to normal mice. Body distribution, excretion routes, and contamination of laboratory equipment were also measured. 47Sc remained in the blood for long periods and accumulated mainly in the liver and kidneys because of its binding to plasma proteins. Therefore, 47Sc released from the labeled compounds could potentially cause non-specific liver and kidney damage. Most of the 47Sc was eliminated through feces, whereas some was excreted through the urinary system. 47Sc was found in both the liquid and solid components of the blood. Although animal cages were contaminated with excreta, they could be effectively cleaned by wiping with paper. We also used 47Sc produced by us to label PSMA-617 and verified its performance as a nuclear medicine therapeutic agent. Although [47Sc]Sc-PSMA-617 did not exhibit a high accumulation rate in tumors, it demonstrated antitumor activity. This might suggest the usefulness of 47Sc.
Full article
(This article belongs to the Collection Feature Papers in Biophysics)
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Open AccessArticle
In Vitro Anticancer Activity, Molecular Docking and Structure–Activity Relationship (SAR) Studies of Some Phenylamino Derivatives
by
Nivedya Prasad SreeNilayam, Jayanandan Abhithaj, Sruthi Remeshan, Shyma Makkaramkot, Muthipeedika Nibin Joy, Mallikarjuna R. Guda, Grigory V. Zyryanov and Karickal Raman Haridas
Biophysica 2026, 6(4), 70; https://doi.org/10.3390/biophysica6040070 - 3 Aug 2026
Abstract
We herein report the anticancer activity and molecular docking studies of a series of amide derivatives of two nonsteroidal anti-inflammatory drugs (mefenamic acid and ibuprofen). The hypothesis of drug repurposing has been successfully employed to explore the promising anticancer activity of analogs of
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We herein report the anticancer activity and molecular docking studies of a series of amide derivatives of two nonsteroidal anti-inflammatory drugs (mefenamic acid and ibuprofen). The hypothesis of drug repurposing has been successfully employed to explore the promising anticancer activity of analogs of known anti-inflammatory agents. The compounds have been tested for their inhibitory potential against cervical cancer cell lines by MTT assay using 5-fluorouracil as the reference standard. Among the compounds screened, 3aa [2-(2,3-dimethylamino)phenyl)(1H-indol-1-yl)methanone] and 3ad [2-(2,3-dimethylphenylamino)phenyl)(9H-carbazol-9-yl)methanone] displayed good potency of less than 25 µg/mL half-maximal inhibitory concentration (IC50). The docking analysis has confirmed that molecule 3aa effectively binds to the active site of the target protein CDK2, with a docking score of −9.21 Kcal/mol and a binding energy of −46.44 Kcal/mol, involving a hydrogen bond with Ile 10. The molecule 3ad also exhibited a good glide score of −6.78 Kcal/mol with the binding energy of −45.90 Kcal/mol. As many of the tested compounds displayed promising potency against cervical cancer cell lines, our investigation revealed the importance of drug repurposing in the development of lead molecules in medicinal chemistry.
Full article
(This article belongs to the Special Issue Latest Advances in Molecular Docking Involved in Biophysics)
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Open AccessArticle
Unraveling Novel Prospective Inhibitors of Streptococcus pneumoniae Chorismate Synthase by Pharmacophore Screening, Docking Analysis and Molecular Dynamics Simulation Studies
by
Donanakatte Mallikarjun Anusha, Surjit Bhattacharjee, Gummuluri Meher Unnati, Roopika Azhagisan, Tanos Celmar Costa Franca, Steven R. LaPlante, Ou Zhang and Neelam Mishra
Biophysica 2026, 6(4), 69; https://doi.org/10.3390/biophysica6040069 - 31 Jul 2026
Abstract
Streptococcus pneumoniae is the major causative agent of community-acquired pneumonia, one of the main infectious diseases that causes inflammation in the alveoli and leads to significant morbidity and mortality across various age groups. Current treatments are challenged by multidrug-resistant strains of S. pneumoniae
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Streptococcus pneumoniae is the major causative agent of community-acquired pneumonia, one of the main infectious diseases that causes inflammation in the alveoli and leads to significant morbidity and mortality across various age groups. Current treatments are challenged by multidrug-resistant strains of S. pneumoniae, which has led to the reemergence of pneumonia in recent years; therefore, it is pivotal to identify new drug targets. The enzyme chorismate synthase (CS), involved in the shikimate pathway of S. pneumoniae, aids in the synthesis of vital aromatic amino acids and other metabolites required for bacterial viability. The present study identifies natural compounds that can inhibit CS using an in silico approach, including pharmacophore modeling, virtual screening, molecular docking, ADME analysis, and molecular dynamics (MD) simulations. Our results suggest that the identified compounds can bind effectively to the active site of S. pneumoniae CS (SpCS), exhibiting affinities better than the known inhibitor 1-benzofuran-3-one and close to the enzyme’s natural substrate, 5-enolpyruvylshikimate-3-phosphate (EPSP). This study suggests lead natural compounds as promising candidates for further investigation as potential inhibitors for the treatment of pneumonia, offering a novel strategy to combat this resilient pathogen.
Full article
(This article belongs to the Special Issue Biophysical Insights into Small Molecule Inhibitors)
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Open AccessArticle
A Biophysical and ALARA-Based Comparison of 3D-CRT and IMRT for Spinal Cord Compression
by
Mohammed Elywa, Basma Hawass, Magda Shanafy and Ayat M. Saadeldin
Biophysica 2026, 6(4), 68; https://doi.org/10.3390/biophysica6040068 - 27 Jul 2026
Abstract
Metastatic spinal cord compression (MSCC) requires urgent radiotherapy. However, selecting the optimal technique that balances dosimetric precision with treatment efficiency remains clinically challenging. This study compares four radiotherapy modalities for MSCC—AP-PA with field-in-field, 3D-CRT, 5-field IMRT, and 7-field IMRT—evaluating their precision–efficiency trade-offs and
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Metastatic spinal cord compression (MSCC) requires urgent radiotherapy. However, selecting the optimal technique that balances dosimetric precision with treatment efficiency remains clinically challenging. This study compares four radiotherapy modalities for MSCC—AP-PA with field-in-field, 3D-CRT, 5-field IMRT, and 7-field IMRT—evaluating their precision–efficiency trade-offs and proposing an ALARA-based clinical framework. In this observational dosimetry study, we analyzed treatment plans from 60 consecutive MSCC patients. Four plans were generated per patient (30 Gy/10 fractions). We assessed target coverage (D95%), conformity (Paddick CI), homogeneity (HI), organ-at-risk sparing, and treatment efficiency. The statistical analysis used a repeated-measures ANOVA with Bonferroni correction. IMRT-7 achieved superior dosimetric outcomes, with a target coverage of 95.8% ± 1.5% and a spinal cord dose of 7.4 ± 1.2 Gy—a 70.6% reduction versus AP-PA—but required prolonged sessions (16.9 ± 1.4 min). 3D-CRT provided acceptable coverage (91.2% ± 2.3%) and cord dose (22.8 ± 1.5 Gy) with significantly shorter delivery times (8.7 ± 1.3 min). IMRT-5 offered an intermediate option (cord dose: 8.2 ± 1.3 Gy; session time: 13.4 ± 0.8 min). IMRT benefits were most pronounced in lumbar lesions (68% cord dose reduction) and least in thoracic segments. IMRT offers superior dosimetry but distributes low-dose radiation to larger healthy tissue volumes. Although these doses remain within tolerance, they may conflict with the ALARA principle, whereas 3D-CRT with field-in-field achieves similar coverage and organ sparing in less time. Thus, 3D-CRT is preferred in most palliative settings. However, IMRT or arc therapy becomes essential for re-irradiation or when prior treatment to adjacent levels demands maximal cord sparing. Technique selection should integrate dosimetric goals with clinical context, patient status, and institutional resources.
Full article
(This article belongs to the Special Issue Biophysical Aspects Involved in Cancers: Advances in Physical Treatment Methods and Multimodal Diagnostics)
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Open AccessHypothesis
On the Electrically Driven Transition of a Voltage-Sensitive Ion Channel from Insulator to Ion Conductor
by
H. Richard Leuchtag
Biophysica 2026, 6(4), 67; https://doi.org/10.3390/biophysica6040067 - 27 Jul 2026
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Voltage-sensitive ion channels are glycoprotein macromolecules that carry ion currents across membranes of nerve and muscle fibers. The hypothesis presented helps explain the changes that convert an insulating ion channel into an ion conductor, stating that it undergoes a structural transformation on threshold
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Voltage-sensitive ion channels are glycoprotein macromolecules that carry ion currents across membranes of nerve and muscle fibers. The hypothesis presented helps explain the changes that convert an insulating ion channel into an ion conductor, stating that it undergoes a structural transformation on threshold reduction in the voltage across the membrane. Experimental data show that the excitable membrane is a ferroelectric liquid crystal. The Channel Activation by Electrostatic Repulsion hypothesis proposes the following: electrical attractions between boundary surface charges compress the polar channel into a compact smectic phase with induced dipoles. Critical depolarization eliminates surface charges and dipoles, decreasing the dielectric permittivity of the ion channel. This increases the repulsive electrostatic forces between positively charged residues in the four S4 segments. These forces form a selectivity filter dome and cause a proteinquake to a chiral nematic phase. The selectivity filter allows ions to enter as it strips their hydration waters. The permeant ions occupy hydrogen bonds of ion-conducting helices, displacing protons. Disordered regions between adjacent helices form liquid line defects. In the thermal chaos of physiological temperature, a line defect occasionally connects the inner and outer surfaces, forming a transient ion pathway that carries unpredictable surges of permeant ion currents, as observed in experiments. Tests for this hypothesis are proposed.
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Open AccessArticle
Evaluation of Plate Homogeneity in Cell-Based Potency Assays Using Large Language Models
by
Rok Kosir, Aleksandra Uzar, Luka Brvar and Irena Oven
Biophysica 2026, 6(4), 66; https://doi.org/10.3390/biophysica6040066 - 24 Jul 2026
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Large language models (LLMs) are increasingly applied across drug discovery, yet their role in analytical method development to support quality control in cell-based potency assays remains insufficiently explored. This study evaluates whether general-purpose LLMs can assess plate homogeneity and detect spatial bias using
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Large language models (LLMs) are increasingly applied across drug discovery, yet their role in analytical method development to support quality control in cell-based potency assays remains insufficiently explored. This study evaluates whether general-purpose LLMs can assess plate homogeneity and detect spatial bias using a half-maximal effective concentration (EC50) mapping approach implemented in a 96-well cell-based reporter gene assay. Four independent plates were generated by two analysts on different days and analyzed using a conventional spreadsheet workflow and three LLMs (Google Gemini, ChatGPT, and Microsoft Copilot Analyst) under identical prompt conditions. All approaches consistently identified a statistically significant row-wise positional effect with no significant column-wise effects, supported by one-way analysis of variance (ANOVA), confidence-interval summaries, and heat-map visualizations of raw signal and Z-scores. The dominant top-to-bottom signal gradient was reproducible across individual plates and the averaged dataset. While all LLMs reproduced standard plate quality control (QC) metrics, they differed primarily in workflow completeness, responsiveness to iterative prompting, and in the extent to which additional spatial diagnostics were proposed. Overall, these results suggest that general-purpose LLMs can reproduce conventional plate-effect analyses and may serve as practical analytical companions when guided by structured prompts and complete datasets.
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Open AccessArticle
Analysis of Glucose in Brain Cells and Body Fluids Using Skin Tattoo Painting Wearalble Circuit with Modified Carbon Nanotube Microprobes
by
Kyung Lee, Suw Young Ly, Kwang Jin Choi and Jinhyeok Park
Biophysica 2026, 6(4), 65; https://doi.org/10.3390/biophysica6040065 - 24 Jul 2026
Abstract
In-vivo diabetes detection of glucose was sought using square-wave anodic stripping voltammetry (SW), with bismuth-immobilized carbon nanotube paste electrode (BCE), and skin tattoo painted wearable circuits. The optimum analytical results indicated sensitivity of 0.0781 μg/L peak signals on the BCE. The raw voltammogram
[...] Read more.
In-vivo diabetes detection of glucose was sought using square-wave anodic stripping voltammetry (SW), with bismuth-immobilized carbon nanotube paste electrode (BCE), and skin tattoo painted wearable circuits. The optimum analytical results indicated sensitivity of 0.0781 μg/L peak signals on the BCE. The raw voltammogram was approached within the in vivo detection ranges of 10–90 μg/L, with preconcentration times of 50 s attained. The relative standard deviation was micro ranges under optimum conditions. The analytical detection limit (S/N) was attained at a nano range of 5.5 nM. The handmade microsensor was directly used in vivo on the living fish brain and human urine. The method was applied at real time in vivo, without requiring any pretreatment and other ionic electrolyte solutions. It can be used for medicinal and other materials requiring biological-fluid detection in real time. This study was designed to be suitable for real-time unmanned remote diagnosis and therapeutic drug injection into the body, micro-needle long-term administration, wearable artificial skin tattoo sensor, and real-time control. In addition, the glasses monitor was designed to be suitable for multitasking and multi-user control sensing.
Full article
(This article belongs to the Special Issue Medical Physics and Physiological Measurements: Intelligent Biosensing, Wearables and AI-Driven Quantified Health)
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Open AccessArticle
A Vision-Based Photoanthropometric Approach for Yoga Pose Analysis Using LabVIEW-ML
by
T. P. Kausalya Nandan and S. Saradha Rani
Biophysica 2026, 6(4), 64; https://doi.org/10.3390/biophysica6040064 - 20 Jul 2026
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In this work, we present a novel framework of integrating anthropometric measurement with posture recognition using LabVIEW’s Vision Development Module specifically for yoga poses. Yoga is a practice that originated in India many years ago and is now popular globally, contributing significantly towards
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In this work, we present a novel framework of integrating anthropometric measurement with posture recognition using LabVIEW’s Vision Development Module specifically for yoga poses. Yoga is a practice that originated in India many years ago and is now popular globally, contributing significantly towards balancing the human body and mind. A key challenge is the accurate recognition of yoga poses in real time using contactless techniques. To achieve this, the proposed system works by digitizing yoga poses through anthropometric measurements enhanced through photoanthropometric modeling with Calibrated Bounding Boxes using YOLO version 4 for representing the poses, combined with geometric examinations to normalize bounding box dimensions and proceed for pose variations. The intermediate model developed improves the measurement accuracy, while the final stage handles posture classification in the LabVIEW ML environment for real-time yoga pose recognition. This study focuses on the Tadasana pose. A Microsoft XBOX 360 Kinect sensor was used for capturing the images, which were processed using LabVIEW 2019 Vision IMAQ. An inference model was developed for feature extraction and matching, such that precise posture identification was facilitated with bounding boxes. The experimental results illustrate that the proposed system achieves a pose recognition accuracy, with respect to anthropometric measurements, of 95.4%, thus proving its potential for rehabilitation and health monitoring.
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Open AccessArticle
Standardization and Evaluation of Antispasmodic Activity of Gandhaga Dravagam Using a Rat Ileum Model
by
Kayalvizhi Duraisamy, Visweswaran Shanmugasundaram, Narasimhan Srinivasan, Imad A. Abu-Yousef and Amin F. Majdalawieh
Biophysica 2026, 6(4), 63; https://doi.org/10.3390/biophysica6040063 - 16 Jul 2026
Abstract
Functional gastrointestinal disorders (FGIDs) affect over 40% of the global population and represent a substantial health and economic burden. Gandhaga Dravagam (GD) is a classical Siddha mineral-based distillate prepared from sulfur, potassium nitrate, and alum, traditionally indicated for gastrointestinal complaints such as diarrhea,
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Functional gastrointestinal disorders (FGIDs) affect over 40% of the global population and represent a substantial health and economic burden. Gandhaga Dravagam (GD) is a classical Siddha mineral-based distillate prepared from sulfur, potassium nitrate, and alum, traditionally indicated for gastrointestinal complaints such as diarrhea, indigestion, and colonic spasm. This study aimed to standardize GD using organoleptic and physicochemical evaluation, qualitative acid-radical and basic-radical tests, elemental analysis by Inductively Coupled Plasma-Optical Emission Spectrometry (ICP-OES), and X-ray Diffraction (XRD), as well as to assess its antispasmodic potential against acetylcholine (ACh)-induced contractions in an isolated rat ileum model. GD was a clear acidic liquid (pH 2.05 at 10% aqueous dilution) with a specific gravity of 1.0142 at 25 °C. Qualitative analysis confirmed carbonate, sulfate, phosphate, and nitrate radicals. ICP-OES identified sulfur (501.254 mg/L) as the predominant element, followed by aluminum (155.341 mg/L), potassium (100.121 mg/L), phosphorus (56.341 mg/L), and sodium (1.320 mg/L); arsenic, mercury, lead, manganese, and magnesium were below detection limits. XRD revealed crystalline inorganic phases consistent with the sulfur-, potassium-, and aluminum-based constituents. At a single concentration (2% v/v), GD reduced ACh-induced contractile responses by 40.74–56.25% across all ACh concentrations tested (5–80 µg), indicating a consistent antispasmodic effect. These findings provide a preliminary analytical and pharmacological characterization of GD and warrant further mechanistic, toxicological, and clinical evaluation.
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(This article belongs to the Collection Feature Papers in Biophysics)
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Open AccessReview
Physical Models of Membrane Behavior Based on the Hodgkin–Huxley Formalism
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Paola Romano
Biophysica 2026, 6(4), 62; https://doi.org/10.3390/biophysica6040062 - 13 Jul 2026
Abstract
The electrical behavior of cellular membranes plays a fundamental role in neuronal communication and in many physiological processes involving excitable cells. Mathematical modeling has become an essential tool for understanding the physical mechanisms underlying membrane dynamics and the generation of action potentials. The
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The electrical behavior of cellular membranes plays a fundamental role in neuronal communication and in many physiological processes involving excitable cells. Mathematical modeling has become an essential tool for understanding the physical mechanisms underlying membrane dynamics and the generation of action potentials. The classical Hodgkin–Huxley model represents the cornerstone of conductance-based descriptions of neuronal activity, providing a quantitative framework in which ionic currents across the membrane are represented through nonlinear differential equations. Over the years, numerous extensions of this model have been developed in order to incorporate additional biophysical mechanisms, including dendritic processing, temperature dependence and electromagnetic effects. However, increasing experimental evidence has shown that neuronal activity is intrinsically stochastic due to the probabilistic nature of ion-channel gating and other microscopic processes. As a consequence, stochastic modeling approaches have been introduced to complement deterministic formulations and to capture the variability observed in real neuronal systems. In this review, we focus on a selected class of membrane models grounded in physical or biophysical principles, namely models that describe membrane dynamics through electrical analogies, conductance-based equations, stochastic channel kinetics, or memory-dependent circuit elements. These approaches can be viewed as extensions, reformulations, or generalizations of the Hodgkin–Huxley framework, developed to address specific physiological or computational limitations. The review focuses on the physical and mathematical structure of selected HH-derived models rather than on their experimental validation, and aims to compare representative physically motivated modeling strategies in terms of their assumptions, interpretability, and domains of applicability.
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(This article belongs to the Special Issue Biophysical Methods to Study Membrane Models, Cells, and Tissues)
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Open AccessArticle
Computational Analysis of Microtubule-Mediated Saltatory Neuroelectrical Transmission: A Theoretical Exploration
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Yong Xiao Yang and Bao Ting Zhu
Biophysica 2026, 6(4), 61; https://doi.org/10.3390/biophysica6040061 - 10 Jul 2026
Abstract
It was recently postulated that neural microtubules (neuro-MTs), which are densely packed inside axons and dendrites, are vacuum cylindrical nanotubes that can mediate neuroelectrical transmission with a unique form of quasi-superconductivity. In this work, the behaviors of free electrons inside a theoretical neuro-MT
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It was recently postulated that neural microtubules (neuro-MTs), which are densely packed inside axons and dendrites, are vacuum cylindrical nanotubes that can mediate neuroelectrical transmission with a unique form of quasi-superconductivity. In this work, the behaviors of free electrons inside a theoretical neuro-MT are modeled using computational analysis and calculations. We reveal that neuro-MTs can function as nanosized physiological devices that mediate neuroelectrical transmission with a super-high energy efficiency in a quasi-superconducting manner. Under physiologically relevant conditions, the binding of cytosolic cations (e.g., K+ and Na+) to the surface residues of a neuro-MT triggers its transition from a resting state to an active state, and the rapid dissociation of these cations triggers the opposite. The dipole ring structures of a neuro-MT will help terminate the free electron conduction inside the vacuum tunnel with high efficiency. The proposed neuro-MT-mediated electrical transmission offers a potential mechanistic explanation for the saltatory conduction of action potentials along an axon or a dendrite. This theoretical exploration also offers unique insights into the rational design of biomimetic room-temperature quasi-superconducting materials, such as carbon or silicone-based quasi-superconducting nanotubes.
Full article
(This article belongs to the Topic New Insights into Cytoskeleton)
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Open AccessArticle
ScaleNet: An Imaris XTension for Deep-Learning-Based Per-Scale Quantification of Immune Infiltration in Whole-Mount Vitiligo Mouse Skin
by
Wenxuan Gao, Xuyang Jiang and Yucheng Hu
Biophysica 2026, 6(4), 60; https://doi.org/10.3390/biophysica6040060 - 9 Jul 2026
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Quantifying the spatial distribution of immune cells within intact skin tissue is essential for understanding diseases such as vitiligo, in which CD8+ T cells selectively destroy epidermal melanocytes within the discrete, parallelogram-shaped epidermal compartments of mouse tail skin, which we term scales.
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Quantifying the spatial distribution of immune cells within intact skin tissue is essential for understanding diseases such as vitiligo, in which CD8+ T cells selectively destroy epidermal melanocytes within the discrete, parallelogram-shaped epidermal compartments of mouse tail skin, which we term scales. Existing workflows rely on manual region drawing, which is labor-intensive and operator-dependent. Here we present ScaleNet, a three-stage deep-learning pipeline for automated per-scale quantification of whole-mount immunofluorescent images, implemented as an Imaris XTension to enable seamless integration with existing 3D imaging workflows. ScaleNet (i) encodes a 3D confocal volume as a pseudo-RGB projection that preserves height information lost by standard maximum-intensity projection, (ii) applies two independently trained Detectron2 Mask R-CNN models—one for epidermal scales and one for hair follicles—with sliced inference (SAHI) to segment whole-mount images at full resolution, and (iii) maps the resulting 2D mask back into the Imaris 3D coordinate system to quantify user-defined Spot objects per scale. Applied to vitiligo mice imaging, ScaleNet produced per-scale counts of CD8+ T cells and DCT+ melanocytes, enabling unbiased spatial statistics in the tail epidermis, demonstrating that ScaleNet can provide the quantitative spatial resolution needed to dissect the micro-anatomical dynamics of autoimmune depigmentation.
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Open AccessReview
Platelet-Rich Plasma: Mechanotransduction, Tissue Loading, and Regenerative Repair for Pain Medicine
by
Ahmed I. Anwar, Josephine M. Feeney, Joseph B. Delaney, Christopher L. Robinson, Jamal Hasoon and Alan D. Kaye
Biophysica 2026, 6(4), 59; https://doi.org/10.3390/biophysica6040059 - 9 Jul 2026
Abstract
Musculoskeletal pain is driven by degenerative conditions such as osteoarthritis or intervertebral disk degeneration. This creates a major burden on health systems and patient quality of life. Platelet-rich plasma (PRP) is an orthobiologic that contains platelets and growth factors which promote angiogenesis, modulate
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Musculoskeletal pain is driven by degenerative conditions such as osteoarthritis or intervertebral disk degeneration. This creates a major burden on health systems and patient quality of life. Platelet-rich plasma (PRP) is an orthobiologic that contains platelets and growth factors which promote angiogenesis, modulate inflammation, and support tissue repair. Mechanobiology is central in the healing process, where mechanical loading regulates cellular behavior through mechanotransduction pathways including integrin/FAK and RhoA/ROCK. This use of signaling pathways allows for regeneration along multiple different tissue types. Evidence suggests that PRP and mechanical loading may act together to promote tissue repair, with PRP-derived signals interacting with biomechanical cues to enhance fibroblast activation, remodeling, and regenerative responses. There is variability in PRP preparation, rehabilitation protocols, and tissue-specific responses, which all highlight the need for a more standardized and guided treatment strategy. Understanding the interplay between PRP-derived biologic signaling and mechanobiologic pathways may help inform the development of more standardized, tissue-specific regenerative treatment strategies and could potentially contribute to improved clinical outcomes in patients with musculoskeletal pain.
Full article
(This article belongs to the Special Issue Mechanobiology of Regeneration: From Physical Aspects)
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Open AccessArticle
Bioinspired, Transparent Squid-Derived Eumelanin Surface Films on Quartz for Ultraviolet Shielding
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Shainy Mathew Cheruvathur and Krishna Prasad Nooralabettu
Biophysica 2026, 6(4), 58; https://doi.org/10.3390/biophysica6040058 - 7 Jul 2026
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Developing advanced bioinspired photoprotective barrier from marine resources represents a critical frontier of bioprocessing. This study established a rational design and implementation of effective photoprotective surface-coating eumelanin from ink of an Indian squid (Uroteuthis duvaucelii). The Central Composite Design was developed
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Developing advanced bioinspired photoprotective barrier from marine resources represents a critical frontier of bioprocessing. This study established a rational design and implementation of effective photoprotective surface-coating eumelanin from ink of an Indian squid (Uroteuthis duvaucelii). The Central Composite Design was developed to optimize extraction and functionalization parameters of eumelanin on quartz substrates, strategically developing the matrix for peak optical attenuation within the potential Far-UVC window (220 nm). Translational photoprotective efficacy of the surface, as well as finished eumelanin on quartz surface, was validated by subjecting them to a challenging macro-level biological assay using a hospital-grade 254 nm ultraviolet germicidal source (125 µWcm−2). Quantitative physical dosimetry established that the squid eumelanin coating (A254 = 1.00) reduced internal transmittance to approximately 10%, successfully dampening the incident fluence from 0.225 J cm−2 down to a heavily attenuated 0.0225 J cm−2 at the biological sample plane. While unshielded control indicator microbial strains suffered complete lethal inactivation, the eumelanin barrier maintained exceptional cell viability, yielding biological shielding efficiencies of 98% for Bacillus subtilis, 96% for Staphylococcus aureus, and 92% for Escherichia coli. Characteristic features from FE-SEM, FTIR, and XRD analysis established that this superior photoprotective property is governed by the extensively conjugated, π-π-stacked indolic architecture possessing a characteristic 3.4 Å interlayer d-spacing, which facilitates rapid, non-radiative energy dissipation. This work establishes an effective framework for translating squid biomass into high-value, transparent optical barriers, providing a potential sustainable alternative to synthetic ultraviolet absorbers.
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Open AccessArticle
Temporal Structure of Lightning-Derived Electric Fields and Nonlinear Responses in a Biologically Inspired Excitable System
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Noah Drebing and Naomi Watanabe
Biophysica 2026, 6(4), 57; https://doi.org/10.3390/biophysica6040057 - 5 Jul 2026
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In this study, we investigate how lightning-derived electric-field influences nonlinear excitation dynamics in excitable systems. Cloud-to-ground (CG) lightning observations from the National Lightning Detection Network (NLDN), including event time, location, and peak current, were used to reconstruct realistic lightning-derived electric-field inputs. The electric
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In this study, we investigate how lightning-derived electric-field influences nonlinear excitation dynamics in excitable systems. Cloud-to-ground (CG) lightning observations from the National Lightning Detection Network (NLDN), including event time, location, and peak current, were used to reconstruct realistic lightning-derived electric-field inputs. The electric field distribution was estimated from lightning peak current and propagation distance using a physical formulation, and discrete lightning events were converted into continuous time-dependent forcing signals through Gaussian kernel superposition while preserving their spatiotemporal organization. The resulting electric-field signals were then applied to the FitzHugh–Nagumo (FHN) model, where biologically inspired excitation dynamics were simulated and analyzed using normalized external inputs. The simulations demonstrate that temporally accumulated lightning-derived forcing induces nonlinear transitions between excitation regimes. Stronger peak-current inputs more readily exceed excitation thresholds and produce enhanced responses, including repeated excitation events, whereas weaker inputs generate limited or sub-threshold responses. These results show that excitation dynamics depend not only on electric-field amplitude but also on the temporal accumulation and organization of lightning activity. Furthermore, a spatially extended reaction–diffusion FHN model demonstrates that lightning-induced electric-field attenuation coupled with nonlinear dynamics can generate spatially propagating excitation structures. This physics-based framework provides a conceptual approach for linking naturally occurring electric-field environments with nonlinear excitable-system dynamics. Although the present model does not represent direct physiological coupling, it provides a foundation for exploring how structured environmental electric fields may influence threshold-dependent dynamical responses.
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Mechanistic Modeling of Absorber-Driven Optical Darkening and Long-Timescale Feedback-Mediated Structural Evolution
by
Rashad Hall, To Dang, Daniel B. Erenso and Horace T. Crogman
Biophysica 2026, 6(4), 56; https://doi.org/10.3390/biophysica6040056 - 26 Jun 2026
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Localized optical absorption by nanoscale inclusions can profoundly alter energy deposition in optical traps, giving rise to nonlinear and long-timescale dynamics. Recent experiments have reported the formation of expanding optically darkened regions and episodic plasma-like emission during pulsed near-infrared optical trapping of magnetic
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Localized optical absorption by nanoscale inclusions can profoundly alter energy deposition in optical traps, giving rise to nonlinear and long-timescale dynamics. Recent experiments have reported the formation of expanding optically darkened regions and episodic plasma-like emission during pulsed near-infrared optical trapping of magnetic beads interacting with biological cells. Here, we develop a reduced-order mechanistic model to investigate whether absorber-driven optical–thermal feedback associated with Fe3O4 inclusions is sufficient to reproduce the observed pre-plasma darkening dynamics. The model is constructed progressively from first-principles electromagnetic absorption and pulse-scale thermal diffusion to nonlinear feedback mediated by an evolving optically modified region. Single-pulse and multi-pulse simulations demonstrate that isolated iron-oxide absorbers cool too rapidly to sustain long-timescale thermal accumulation through linear heating alone. However, incorporation of a bubble-mediated optical feedback channel produces bounded growth, partial optical darkening, and slow relaxation dynamics consistent with experimentally observed minute-scale evolution. Electromagnetic absorption was computed using full core–shell Mie theory, yielding absorption cross-sections sufficient to support strong localized optical attenuation under experimentally relevant trapping conditions. The resulting reduced-order feedback framework reproduces stable growth–relaxation cycles, finite transmission plateaus, and self-limited optical darkening without requiring runaway heating or catastrophic cavitation. To evaluate the model quantitatively, simulated transmission dynamics were compared against experimentally measured normalized transmission traces digitized from previously reported optical trapping experiments. The fitted model reproduced the observed finite transmission plateau and slow post-activation relaxation with good agreement ( , RMSE ). These results support the interpretation that experimentally observed optical darkening arises from a feedback-regulated optical–thermal process involving slowly evolving structural modification of the trapping region rather than cumulative thermal storage within isolated absorbers. The present framework provides a quantitatively constrained reduced-order description of feedback-mediated optical darkening under pulsed optical trapping conditions and establishes iron-oxide absorption as a physically plausible ignition mechanism for dark-state formation in the pre-plasma regime.
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HLA Binding Peptide-Based Designing of Non-Spike Universal Nanovaccine Against SARS-CoV-2: A Computational Approach
by
Puja Jaishwal and Satarudra Prakash Singh
Biophysica 2026, 6(4), 55; https://doi.org/10.3390/biophysica6040055 - 25 Jun 2026
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The continuous evolution of the SARS-CoV-2 virus, marked by the emergence of new variants, poses a significant threat to the efficacy of existing vaccines. However, a promising approach to addressing vaccine failure caused by viral mutations (particularly in the spike protein) is the
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The continuous evolution of the SARS-CoV-2 virus, marked by the emergence of new variants, poses a significant threat to the efficacy of existing vaccines. However, a promising approach to addressing vaccine failure caused by viral mutations (particularly in the spike protein) is the development of a variant-proof (conserved), non-spike, multiepitope universal nanostructure vaccine with multifunctionality, biocompatibility, self-adjuvanticity, and structural similarity to pathogens in terms of size and shape. This study aimed to design a self-assembled nanostructure vaccine (SANV) featuring pentameric and trimeric coiled-coil peptide motifs, as well as other functional motifs, including epitopes, TAT, PADRE, and adjuvant. The cytotoxic T lymphocyte (CTL), helper T lymphocyte (HTL), and B lymphocyte (BL) epitopes of SANV were screened from the IEDB with more than 50% individual predicted population coverage (PPC) and fused using linkers to enable self-assembly. The multimerization of the 24 SANV monomers was modeled using the GalaxyHomomer and AlphaFold web servers. Subsequently, the leading SANV constructs with (SANVa9) and without (SANVb6) adjuvant were analyzed for their physicochemical profiles and assessed for antigenicity, allergenicity, solubility, and antioxidant potential. Furthermore, the molecular interactions, specificity, and stability of SANVa9 and SANVb6 with the broadly neutralizing sarbecovirus antibody 5817 and toll-like receptors (TLR2, TLR3, and TLR7) were analyzed using molecular docking and simulation over a 100-nanosecond time scale. Finally, the comparative immune simulation profiles of SANVa9 and SANVb6 with controls indicated stronger, broad-spectrum immune responses that could be translated into in vitro and in vivo studies and warrant further evaluation before clinical use.
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Temperature Distribution and Control in Ultrasound-Based Therapy: An Ex Vivo Study with Bioheat Transfer Modeling
by
Ali Dahaghin, Milad Salimibani and Paria Jahansa
Biophysica 2026, 6(4), 54; https://doi.org/10.3390/biophysica6040054 - 25 Jun 2026
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In therapeutic applications, ultrasound is widely used in physiotherapy, tissue repair, and cancer treatment. Regarding cancer treatment, as an emerging field for technology, significant research efforts have been devoted to the area of ultrasound therapy. The derived energy from beams can be deposited
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In therapeutic applications, ultrasound is widely used in physiotherapy, tissue repair, and cancer treatment. Regarding cancer treatment, as an emerging field for technology, significant research efforts have been devoted to the area of ultrasound therapy. The derived energy from beams can be deposited in tissues not only through heating but also through non-thermal mechanisms, whereby cancer cells are subject to cell death. Ultrasound-induced heating can generate localized temperature elevations within biological tissues, making it a subject of interest for thermal therapeutic applications. Nevertheless, excessive temperature elevations outside the primary exposure region may result in undesirable thermal effects within the surrounding tissue. In this study, we used continuous 3 MHz ultrasound waves at the powers of 0.4 to 1.4 W on ex vivo chicken breast tissue in a water bath to prevent fluctuations in temperature. The process was also numerically modeled with a maximum error of 0.4% from the measured data. Temperature measurements revealed a significant difference between the region of maximum acoustic pressure along the beam axis and deeper tissue locations (in some cases, above 3.5 °C). These findings indicate that temperature gradients can develop within homogeneous tissue during ultrasound exposure, emphasizing the importance of controlling acoustic power and exposure conditions. Moreover, increasing the temperature was significant during the first moments of treatment, which highlights the importance of precise controls for rate and precision in therapy. The numerical simulations also showed that increasing acoustic power elevates tissue temperature while simultaneously producing a less uniform temperature distribution. These observations may be useful for the optimization of future ultrasound-based thermal treatment strategies; however, direct clinical extrapolation requires further investigation using physiologically representative tissue models.
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Open AccessArticle
Magnetic Field-Dependent Changes in ORP and UV Absorption of Lactose Solutions with Different Pretreatment Histories
by
Igor Jerman, Linda Ogrizek and Jonatan Pihir
Biophysica 2026, 6(3), 53; https://doi.org/10.3390/biophysica6030053 - 19 Jun 2026
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Lactose is widely used as a pharmaceutical excipient, yet little is known about how its physicochemical behavior may be influenced by pretreatment history and weak environmental magnetic conditions. In this pilot study, we investigated oxidation–reduction potential (ORP) and UV absorbance of 0.2% aqueous
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Lactose is widely used as a pharmaceutical excipient, yet little is known about how its physicochemical behavior may be influenced by pretreatment history and weak environmental magnetic conditions. In this pilot study, we investigated oxidation–reduction potential (ORP) and UV absorbance of 0.2% aqueous lactose solutions prepared from lactose powders with different pretreatment histories: Active water, Native water, and untreated control. Samples were exposed for 30 min to three static magnetic field conditions: weak geomagnetic field (~4 µT), ambient geomagnetic field (~30 µT), and elevated static field (~750 µT). UV/VIS spectroscopy was performed in the 200–400 nm range, with particular focus on the deep-UV absorption maximum near 200 nm. The strongest differentiation between pretreated samples and control occurred under weak geomagnetic conditions. In this weak-field regime, pretreated lactose solutions showed higher ORP values and a same-direction trend toward increased UV absorbance near 200 nm relative to untreated lactose. Across all samples, both ORP and UV absorbance decreased with increasing magnetic field strength, indicating a consistent field-dependent shift in the overall physicochemical state of the lactose solutions, particularly in redox balance and deep-UV optical response. The same-direction changes in ORP and increased 200 nm absorbance at the group level suggests that weak-field conditions may influence oxidation-related processes, potentially including the formation or stabilization of lactose oxidation products such as lactobionic acid. These findings indicate that lactose-containing aqueous systems may be sensitive to both pretreatment history and low-intensity magnetic environments, with potential implications for pharmaceutical formulation stability, quality control, and biotechnological reproducibility.
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