In recent years the scientific advance in biophysics is marked by progress in various research approaches and methods including characterization techniques, theoretical and computational modeling, as well as the application of modern approaches of physics to complex biological systems (and processes). More specifically, the innovation in biophysics is stimulated by the cooperation with related areas, such as biochemistry, physiology, molecular and cell/system biology, with a special focus on the study of the relationship between the structure and function at various biological levels. The Special Issue “Scientific Progress in Biophysics” comprises two review articles and two original research papers that provide important example of recent advancements in biophysics. The article entitled “The role of postural and plantar pressure asymmetries predicting pain in aging adults” (by Svitlana Dikhtyarenko et al.), highlights differences in baropodometry and anthropometrics between sexes, with neck deviation and left knee angle identified as predictors of pain levels. Machine learning analysis evidence that neck left deviation and left knee angle were predictive of participants’ pain levels. The study, that allows us to identify significant variables in a postural analysis, could play an important role in the improvement of people’s quality of life. The review article entitled “Quantum computing meets neural excitability: modeling ion channels and action potentials via membrane biophysics” (by Chitaranjan Mahapatra), evidences how the intersection of quantum computing and membrane biophysics allows to propose innovative quantum algorithms that could revolutionize simulations of ion channel behavior and neuronal signaling. This article evidences how interdisciplinary research work can furnish more efficient and advanced models of neural excitability, by bridging together neuroscience, biophysics, and quantum information science. The article entitled “A low-cost stage-top incubation device for live human cell imaging using rapid prototyping methods” (by Michael Worcester et al.) reports on the production of a do-it-yourself (DIY) device for stage-top incubation with temperature and atmospheric control. The advent of 3D printing technologies may furnish low-cost rapid prototyping approaches with precision comparable to traditional fabrication methods, thus opening the possibility for the in-lab design and production. The review article entitled: “Subcutaneous sustained-release drug delivery system for antibodies and proteins” (by Takayuki Yoshida and Hiroyuki Kojima) discusses the development formulations of drug delivery system (DDS), with particular focus on Subcutaneous (SC) sustained release. The analysis of the biophysical parameters that affect the pharmacokinetics (PK) of SC is an important step for the development and engineering of antibody/protein drugs, especially in view of the reduction of the dosing frequency. Overall, the collection of the articles published in this Special Issue may help to identify the fundamental factors involved in the development of innovative solutions in some specific Biophysical systems by analyzing the main parameters that sensitively influence the design of bio-prototypes and bio-systems, while putting into evidence challenges, limitations, and emerging approaches of the various fields of biotechnology.

Molecular dynamics (MD) and free energy calculations have profoundly altered our strategies for exploring biological and chemical systems at the atomic scale. These computational approaches present a distinctive lens through which to view processes that are frequently unattainable by experimental observation alone, including the prediction of ligand-protein binding affinities and the study of the dynamics of sophisticated biomachinery. In our examination of the complexities surrounding molecular interactions, it is evident that the challenges we face extend beyond mere technical obstacles and present opportunities for innovation. The task of sampling rare events, the substantial computational costs associated with simulating biologically relevant timescales, and the limitations of current empirical potentials for non-standard molecules are just a few of the hurdles that researchers must navigate. Moreover, the simulation of large, multi-component systems, such as membrane environments or entire cellular machineries, introduces additional complexities that require the development of novel approaches and methodologies. This special issue will facilitate readers’ understanding of the vigorous advancements and innovative developments in molecular dynamics and free energy calculations. It gathers top experts who will directly address these challenges, shedding light on the pathway to the next generation of simulation methodologies. The discussions will include AI-driven strategies, automated workflows, and cloud computing platforms, all of which are on the verge of transforming the field. The contributions featured in this special issue clearly demonstrate a domain that is experiencing dynamic and innovative growth. The ‘current limits’ are not merely being tolerated; instead, they are being dismantled through a wave of methodological progress. As we look ahead, the combination of physics-based models with data-driven artificial intelligence, supported by ever more powerful computing resources, signals the dawn of a new era in predictive simulation. The effort to make the computation of intricate molecular events as routine as reading a sequence is already underway, with the advancements showcased here laying the groundwork for a deeper comprehension of molecular systems.

Due to increasing antibiotic resistance and a lack of new antibiotics, alternative treatments are urgently needed. This study investigates photodynamic therapy (PDT), which uses light-activated photosensitizers to produce reactive oxygen species that effectively inactivate bacteria. We evaluated the antibacterial efficacy of PDT against two pathogens that are resistant to current antibiotics, namely Staphylococcus epidermidis (Gram-positive) and Acinetobacter baumannii (Gram-negative), by testing various illumination protocols. The results showed that combining blue light (468 nm) and red light (632 nm) with methylene blue (MB) produced a synergistic effect in bacterial inactivation compared with protocols using either blue or red light individually in combination with methylene blue (MB). Specifically, after just 30 minutes of exposure, S. epidermidis showed a 3.3 log reduction (99.95%), while A. baumannii showed a 3.1 log reduction (99.92%) after 60 minutes. Overall, S. epidermidis was more sensitive to all tested protocols than A. baumannii. We also examined the effects of this protocol on antibiotic susceptibility. For most antibiotics tested, there was no change in the size of the inhibition zones. However, for linezolid, we observed a significant increase in the inhibition zone’s diameter, indicating a possible enhanced susceptibility to this antibiotic.

For centuries, plants have been essential sources of food, shelter, and traditional medicine. With growing antimicrobial resistance and the side effects of modern drugs, there is an urgent need to explore natural remedies as safer therapeutic alternatives. Thus, we aimed to evaluate biological activities, chemical composition, and molecular docking of Elaeis guineensis. Total phenolic content (TPC), total flavonoid content (TFC), radical scavenging activity (DPPH), ferric reducing antioxidant potential (FRAP) assay, α-glucosidase, antimicrobial, gas chromatography mass spectrometry (GCMS), and molecular docking were evaluated. The findings showed average values of 85.23% for DPPH, 57.2 mg/g dry weight for ferric FRAP, 140.4 mg/g Gallic Acid Equivalents for TPC, 120.2 mg/g Quercetin Equivalents (QE) for TFC, along with 65.01 ± 0.2% for α-glucosidase and 14.2 ± 0.2 mm for antimicrobial activity from the ethanol peel extracts. The virtual docking screening showed that compounds 8, 10, and 14 had better binding scores with MolDock scores between −106.05 and −108.94 kcal/mol than that of ciprofloxacin (−105.84 kcal/mol), with hydrogen and hydrophobic bonds playing the most crucial contributions in the molecular interactions. These combined in vitro and in silico findings imply that the peels of E. guineensis are rich in multifunctional phytochemicals that exhibit strong antioxidant, α-glucosidase, and antibacterial inhibitory properties.

In the last decade, complementary metal-oxide semi-conductor (CMOS) cameras became the state-of-the-art technology in many biological applications, and the ability to reach high acquisition rates represents one of the characteristics that outperform previous technologies. In this review, I concentrated on neuronal functional imaging (voltage and/or ions) that requires recording fluorescence from multiples sites of a neuron or of a network at kHz rates to sample signals associated with neuronal excitability. After introducing the physical constrains of this type of imaging and reviewing the technologies used in the past, I analysed how CMOS can address the challenge of neuronal functional imaging. I focused on the characteristics of two CMOS cameras that are in use in my laboratory: DaVinci2K and Kinetix. DaVinci2K achieves high acquisitions rates at 14-bit depth by using parallel processing from 16 sub-sensors whereas Kinetix achieves higher spatiotemporal resolution by sampling fluorescence at 8-bit depth, but at the cost of decreasing the dynamic range which represents a limitation in several experimental scenarios. I present comparable membrane potential imaging recordings of action potentials from the axon initial segment, which were achieved at 20 kHz with the two cameras. Finally, I conclude the review with some perspective considerations on future availability of CMOS cameras that may overcome the performance of present devices and the limitations in developing optimal devices for biological and biomedical applications.

Calcium ions are universal signaling particles used alongside other signaling systems in animal cells. Changes in intracellular calcium concentration trigger vital reactions in different types of eukaryotic cells by acting through molecular calcium sensors. Over several decades, calcium imaging has been developed to study calcium-based signaling pathways. This method visualizes changes in intracellular free calcium using special fluorescent indicators. The retina, a type of nervous tissue in the eye, is responsible for perception, primary processing, and transmission of visual information to the brain. Signal cascades within retinal cells and synaptic transmission between cells play a crucial role in implementing these functions. Calcium plays a significant and diverse role in the functioning of the retina, in both normal and pathological conditions. Studying the fundamental processes of visual perception at the retinal level requires the visualization of changes in intracellular calcium concentration at different time scales, including very rapid changes. Consequently, the calcium imaging method, which was originally developed and used for studying other tissues, has now entered the field of visual neuroscience. While there are currently many examples of calcium imaging being used to study the functioning principles of all major types of retinal cells, adapting this method to the study of this tissue presents a number of difficulties. This review discussed these problems and how to solve them.

The investigation of phytochemicals in plants has garnered substantial interest because of their potential therapeutic applications and pharmaceutical industries. These compounds can interact with biological systems, influencing critical biochemical mechanisms such as apoptosis, cell signaling, and oxidative stress. Therefore, understanding the mechanisms of action of these compounds is crucial to unlock their potential for developing novel agents for pharmaceuticals and health-promoting supplements. Breonadia salicina is a native species distributed throughout tropical and subtropical countries. This plant is used to treat of wounds, ulcers, fevers, headaches, gastrointestinal illness, cancer, arthritis, diabetes, inflammation, and bacterial and fungal infections. The roots were extracted via successive solvent extractions and evaluated for their antioxidant, phytochemical, and anticancer properties, with an emphasis on their apoptotic and underlying potential mechanisms. The ethanolic (REE), aqueous (AQR), ethyl acetate (EAR), and n-butanol (NBR) fractions significantly inhibited HT-29 cancer cells (p < 0.05). The EAR fractions displayed the strongest inhibition (IC₅₀ of 22.5 µg/mL) and promptly triggered early and late apoptosis and cell necrosis (p < 0.001). The EAR fractions demonstrated powerful TFC (19.4 Quercetin/g) activity, with IC₅₀ values of 22 and 25 mg/ml for ABTS and DPPH, respectively. LC‒MS/LC‒HRM analysis revealed several phytochemicals in the EAR fractions that contributed to the potential properties of the plants, including polyphenols, coumarin derivatives, 4,5-dicaffeoylquinic acid, chlorogenic acid, glycosides, and geniposidic acid. Notably, the in-silico cytotoxicity of these phytochemicals revealed the significant cytotoxicity of four potent compounds against six colon cancer cell lines, which presented the greatest interaction with the CDK2 enzyme (− 5.0 kcal/mol). These findings underscore the potential of the identified phytochemicals as promising anticancer or nutraceutical candidates for drug development and in the pharmaceutical industry.