Biophysica, Volume 5, Issue 2 (June 2025) – 14 articles

An ancient repertoire of ultraviolet (UV)-absorbing pigments which survive today in the phylogenetically oldest extant photosynthetic organisms, the cyanobacteria, point to a direction in evolutionary adaptation of the pigments and their associated biota; from largely UV-C absorbing pigments in the Archean to pigments covering ever more of the longer wavelength UV and visible regions in the Phanerozoic. Since photoprotection is not dependent on absorption, such a scenario could imply selection of photon dissipation rather than photoprotection over the evolutionary history of life, consistent with the thermodynamic dissipation theory of the origin and evolution of life which suggests that the most important hallmark of biological evolution has been the covering of Earth’s surface with organic pigment molecules and water to absorb and dissipate ever more completely the prevailing surface solar spectrum. In this article we compare a set of photophysical, photochemical, biosynthetic, and other inherent properties of the two dominant classes of cyanobacterial UV-absorbing pigments, the mycosporine-like amino acids (MAAs) and scytonemins. We show that the many anomalies and paradoxes related to these biological pigments, for example, their exudation into the environment, spectral coverage of the entire high-energy part of surface solar spectrum, their little or null photoprotective effect, their origination at UV-C wavelengths and then spreading to cover the prevailing Earth surface solar spectrum, can be better understood once photodissipation, and not photosynthesis or photoprotection, is considered as being the important variable optimized by nature. Full article

Ark shells are a group of bivalves that exhibit extraordinary adaptability to the dual environmental pressures of low oxygen and osmotic imbalance. These challenges are particularly pronounced in intertidal zones, where organisms are subjected to rapid and drastic changes in their surroundings. This research investigated the molecular mechanisms that underpin their survival and adaptive strategies, with particular focused on sodium–potassium ATPase (NKA), a pivotal enzyme responsible for maintaining cellular ion transmembrane gradients and ensuring cellular homeostasis under stress conditions. By utilizing genome assemblies and transcriptomics datasets from multiple ark shell species, we successfully identified two distinct NKA-α subunits and two NKA-β subunits, which are essential components of the NKA complex. Moreover, the discovery of a conserved NKA-interacting protein (NKAIN) highlights the complexity and evolutionary significance of the NKA-NKAIN system in ark shells. Phylogenetic analysis revealed a high degree of conservation in the NKA-α and NKA-β subunits across ark shells, suggesting strong selective pressures to preserve their functionality. However, the marked divergence observed between the two NKA-β subunits suggests that they may serve distinct roles in ion transport, potentially specialized for specific environmental conditions or stress responses. Comparative transcriptomic analysis further revealed the regulatory roles of NKA and NKAIN in the adaptive responses to hypoxia and osmotic stress, showing that these genes are dynamically modulated at the transcriptional level in response to environmental challenges. These findings provide a molecular foundation for understanding the osmotic adaptation mechanisms in ark shells and offer novel insights into their ability to thrive in mudflat habitats. This comprehensive exploration of the NKA-NKAIN system not only enhances our understanding of the resilience of ark shells but also provides valuable insights into the molecular and physiological strategies employed by bivalves in intertidal environments. Full article

The system suitability testing of chromatography is an indispensable procedure in pharmaceutical analysis, and it must comply with rules in related pharmacopoeias. An inverse Fourier transform algorithm was developed to accurately evaluate chromatographic features versus a standard Gaussian peak shape. The regular chromatogram is considered a pseudo-frequency spectrum and can be converted to a nominal time signal via inverse Fourier transformation. The system suitability parameters of peak width, theoretical plate number, tailing factor, and noise testing were evaluated using linear regressions directly and compared with the compendial rules. This novel method is simple, accurate, robust, reliable, and efficient for the evaluation of chromatographic peak features. Full article

Proton beam therapy for head and neck cancers traditionally employs a fixed relative biological effectiveness (RBE) of 1.1, which may underestimate actual biological effects in critical structures. This study evaluates how Linear Energy Transfer (LET) optimization could potentially prevent radiation-induced brachial plexopathy (RIBP). (1) Case presentation: A 65-year-old male with stage IVA p16-positive oropharyngeal squamous cell carcinoma received pencil-beam-scanning intensity-modulated proton therapy with concurrent cisplatin. Due to a right level 4 neck node, the high-risk target volume overlapped with the brachial plexus, resulting in a D0.1cc of 70.3 Gy (RBE = 1.1). Four years post-treatment, the patient developed progressive right upper extremity paresthesia, weakness, and dysesthesia. Electromyography revealed myokymia consistent with brachial plexopathy, while MRI showed hyperintensity of the right brachial plexus corresponding to the radiation field. Conservative treatment with pentoxifylline, gabapentin, and physical therapy improved his symptoms. (2) Methods: The original treatment plan was retrospectively analyzed using Monte Carlo dose algorithms and LET-dependent RBE models from McMahon and McNamara. An LET-optimized plan was created to limit LET_d to 2.0 keV/µm in the brachial plexus. (3) Results: The relative biological equivalent (RBE) dose to 0.1cc of the brachial plexus was 77.8 Gy (CGE RBE), exceeding tolerance. The LET-optimized plan reduced the brachial plexus D0.1cc to 59.4 Gy (RBE = 1.1) and 63.2 Gy (CGE RBE), an 18.8% decrease, while maintaining target coverage. LET_d, within the brachial plexus enhancement, decreased from 5.3 to 2.6 keV/μm. (4) Conclusion: This case highlights the potential clinical importance of LET optimization in proton therapy planning, particularly when organs-at-risk overlap with target volumes. By reducing LET_d from 5.3 to 2.6 keV/μm and biological equivalent dose by 18.8%, LET optimization could potentially prevent late toxicities, like RIBP, while maintaining target coverage. Full article

Caenorhabditis elegans is among the most important model organisms. It has been extensively studied from the perspective of life and biomedical sciences. However, no model of growth and metabolism of C. elegans is available in the literature that is based on biothermodynamics and bioenergetics. Such a model would provide insight into growth and metabolism of C. elegans from the perspective of the fundamental laws of nature. In this research, a chemical and thermodynamic characterization of C. elegans is performed, with the determination of empirical formulas, thermodynamic properties of living matter, reactions of biosynthesis, catabolism and metabolism, thermodynamic properties of biosynthesis, catabolism and metabolism, and phenomenological coefficients. Based on the determined properties, a model of the growth and metabolism of C. elegans is developed. The model is used to discuss the metabolism of C. elegans from the aspect of physical chemistry. Full article

The investigation of structure–function relationships in enzyme polysaccharide complexes provides a theoretical foundation for modulating enzyme properties and expanding their industrial applications. In this study, the interaction of cysteine proteases—bromelain, ficin, and papain—with a grafted chitosan–poly(N-vinylpyrrolidone) copolymers, Cs-g-PVP, was examined, and its effect on the catalytic and stability properties of the enzymes was assessed. Molecular docking and Fourier-transform infrared spectroscopy were used to analyze the topology of the resulting complexes and identify macromolecular fragments involved in binding. Based on the obtained results, it was hypothesized that complex formation would lead to a slight reduction in the catalytic activity of cysteine proteases. In vitro studies of the complexes confirmed this hypothesis, showing that the enzymes retained more than 63% of their proteolytic activity while their half-inactivation time during storage increased by up to ~12-fold. The investigated Cs-g-PVP copolymers demonstrated high efficiency as supports for the studied enzymes, capable of retaining up to 100% of the added enzymes. Full article

We present a corrosion-resistant quadrupole ion trap mass spectrometer (QIT-MS) for the direct detection of biosignature gasses in chemically reactive planetary atmospheres, such as Venusian clouds. The system employs a Paul trap with hyperbolic titanium alloy electrodes and alumina spacers for chemical durability and precise ion confinement. An yttria-coated iridium filament serves as the thermionic emitter within a modular electron gun capable of axial and radial ionization. Analytes are introduced through fused silica capillaries and crescent inlets into a miniature pressure cell. The testbed integrates high-voltage RF electronics, pressure-regulated sample delivery, and FPGA-based control for real-time tuning. Continuous operation in 98% sulfuric acid vapor for over three months demonstrated no degradation in emitter or sensor performance. Mass spectra revealed H₂SO₄ fragmentation and thermally induced decomposition up to 425 K. Spectral variations with filament current and electron energy highlight thermal and electron-induced dissociation dynamics. Operational modes include high-resolution scans and selective ion ejection (e.g., CO₂⁺, N₂⁺) to enhance the detection of PH₃⁺, H₂S⁺, and daughter ions. The compact QIT-MS platform is validated for future missions targeting corrosive atmospheres, enabling in situ astrobiological investigations through the detection of biosignature gasses such as phosphine and hydrogen sulfide. Full article

The tetrameric protein transthyretin (TTR) transports the hormone thyroxine in plasma and cerebrospinal fluid. Certain point mutations of TTR, including the Val122Ile mutation investigated here, destabilize the tetramer leading to its dissociation, misfolding, aggregation, and the eventual buildup of amyloid fibrils in the myocardium. Cioffi et al. reported the design and synthesis of a novel TTR kinetic stabilizing ligand, referred to here as TKS14, that inhibited TTR dissociation and amyloid fibril formation. In this study, molecular dynamics simulations were used to investigate the binding of TKS14 and eight TSK14 derivatives to the Val122Ile TTR mutant. For each complex, the ligand’s solvent accessible surface area (SASA), ligand–receptor hydrogen-bonding interactions, and the free energy of ligand-binding to TTR were investigated. The goal of this study was to identify the TSK14 functional groups that contributed to TTR stabilization. TKS14 was found to form a stable, two-point interaction with TTR by hydrogen bonding to Ser-117 residues in the inner receptor binding pocket and interacting through hydrogen bonds and electrostatically with Lys-15 residues near the receptor’s surface. The free energy of TKS14-TTR binding was −18.0 kcal mol⁻¹ and the ligand’s average SASA value decreased by over 80% upon binding to the receptor. The thermodynamic favorability of TTR binding decreased when TKS14 derivatives contained either methyl ester, amide, tetrazole, or N-methyl functional groups that disrupted the above two-point interaction. One derivative in which a tetrazole ring was added to TKS14 was found to form hydrogen bonds with Thr-106, Thr-119, Ser-117, and Lys-15 residues. This derivative had a free energy of TTR binding of −21.4 kcal mol⁻¹. Overall, the molecular dynamics simulations showed that the functional groups within the TKS14 structural template can be tuned to optimize the thermodynamic favorability of ligand binding. Full article

Fungal diseases represent a significant threat to global agriculture, leading to substantial crop losses and endangering food security worldwide. Conventional chemical fungicides, while effective, are increasingly criticized for their detrimental environmental impacts, including soil degradation, water contamination, and the disruption of non-target organisms. Additionally, the overuse of these fungicides has accelerated the emergence of resistant fungal strains, further challenging disease management strategies. In response to these issues, bio-nanofungicides and nano-biofungicides have emerged as a cutting-edge solution, combining biocompatibility, environmental safety, and enhanced efficacy. These advanced formulations integrate bio-based agents, such as microbial metabolites or plant extracts, with nanotechnology to improve their stability, controlled release, and targeted delivery. Chitosan, silica, and silver nanoparticles were extensively studied for their ability to encapsulate bioactive compounds or because of their outstanding antifungal activity, while minimizing environmental residues. Recent studies demonstrated the potential of nano-based fungicides to address critical gaps in sustainable agriculture, with promising applications in integrated pest management systems. Here, we summarize the last advances in the development of bio-nanofungicides and nano-biofungicides and analyze the main differences between them. In addition, challenges such as large-scale production, regulatory approval, and comprehensive risk assessments are discussed. Full article

Cell-based therapy is a promising direction for the treatment of various diseases. However, it is associated with several problems, primarily related to reproducibility and standardization. In this context, the development of new methods for the production of cell-based preparations is of particular relevance. Recently, a novel technology named ‘crossing’ has been developed. It comprises the multi-stage vibrational processing of two closely spaced test tubes containing the initial substance and a neutral carrier (water or lactose). As a result, the neutral carrier acquires some properties of the initial substance, and artificial products, vibrational iterations, are obtained. Some vibrational iterations are also capable of exerting a modifying effect on the initial substance (or its target in the body), changing its physico-chemical/biological properties. Earlier, we demonstrated the possibility of obtaining vibrational iterations from biological molecules (antibodies). In this study, we evaluated the biological effects of vibrational iterations obtained by the crossing technology using cells grown in culture. This work shows that vibrational iterations obtained from CHO-S cell culture affect the ability of CHO-S cells to utilize glucose in the presence of insulin. The data demonstrate the prospect of developing fundamentally new biological drugs based on vibrational iterations, including for the treatment of diabetes mellitus. Full article

Neurodegenerative disorders include Alzheimer’s and Parkinson’s, both of which lead to progressive loss of neurons resulting in the severe loss of cognitive and motor functions. These diseases are among the heavy burdens on global healthcare systems largely because there is no cure, and current treatments apply almost entirely to controlling symptoms rather than disease progression. Recent advances in 3D printing and bioprinting technologies now open the way to overcome these challenges and form patient-specific models and therapeutical tools closely simulating the complex environment of the human brain. It then further illustrates how this technological integration with the aid of 3D printing, coupled with microfabrication and biosensing technologies, transforms drug-screening platforms as well as develops customization in medicine. For example, one can form highly intricate and multi-materially composed structures to better facilitate one’s study or test into some new therapeutic possibilities using methodologies of stereolithography and selective laser sintering. Moreover, 3D printing allows the creation of organ-on-a-chip models that simulate brain-like conditions, which may help identify specific biomarkers and evaluate new options of therapy. On the other hand, bioprinting methods based on neural cells combined with scaffolds mimicking native tissue dramatically transform regenerative medicine. New pathways in neural tissue development and implantable devices are now being brought forth, which can be tailored to the needs of individual patients. These advances bring not only greater precision in terms of the therapy that can be delivered but also 3D printing of implantable microelectrodes able to determine real-time biomarkers responsible for neurodegenerative diseases. Thus, this review highlights the robust impact that might be brought forth on the diagnosis and treatment of these neurodegenerative diseases via 3D printing technologies toward more effective management and personal solutions for healthcare. Full article

The description of the organization of microorganisms in terms of emergent “social” interactions has long been a fascinating and challenging subject, in both biology and sociology. In these organisms, the role of the individual is far less dominant than that of the community, which operates as a sort of superorganism. The coordination is achieved through a communication mechanism known as quorum sensing. Quorum sensing coordinates and regulates various biological aspects of a microbial community, such as the expression of pathogenicity factors, biofilm formation, and the production of secondary metabolites, among others. These processes rely on the coordinated behavior of the entire bacterial population, enabling them to adapt and thrive withing a specific ecological niche under its unique biological, physical and chemical conditions. Finally, quorum sensing also allows the community to control the development of potentially harmful individuals, thus preserving the cooperativeness of the community. This study uses an agent-based quorum sensing model to explore the relationship between metabolic functions and social behavior in bacteria. In particular, we identify two metabolic parameters whose variations provide a broad panorama of possible social characteristics. Furthermore, the proposed QS model allows us to reproduce, at least qualitatively, some experimental results regarding the competition between some strains with different social characteristics. Finally, we examine how an ideal polyculture responds to variations in the metabolic characteristics of its components. Specifically, we identify a particularly stable condition in which the components cooperate to maximize the overall health of the colony. We refer to this state as resonance for life. Full article

This study focuses on biochemical pathways of complex biochemical formation, taking into account various thermodynamic parameters that change as the complexity and molecular weight of complex molecules increase. We conducted a study of the co-direction of changes in thermodynamic quantities such as $lg\left[K_d\right]$, $T\Delta S$, $\Delta (\Delta W)$, and $lg\left(\mathrm{cond}\right(W\left)\right)$ during the transition from a monomer to a dimer and then to a trimer and tetramer. In this work, we assume that the co-direction of changes in thermodynamic quantities as the final molecular formation being achieved signals a higher affinity of molecules among themselves than there is for a biochemical formation, which is characterized by the lack of coordination of the biochemical pathway directions of the final molecular compound. As the studied molecular complexes, we took [LGP2-8dsRNA-LGP2], [VP35]₂-dsRNA-[VP35]₂, and MARV NPcore proteins with peptides and the complex of MJ20 with antigens from the Bundibugyo strain of Ebola virus. Calculations of biochemical reaction paths were conducted. Full article

Within the field of physiology, it is widely recognized that the constant flow of mobile ions across the plasma membrane generates membrane potential in living cells. This understanding is a part of the membrane theory. Despite this, membrane theory does not account for the role of ion adsorption (or desorption) processes in generating membrane potential, even though ion adsorption is a key concept in basic thermodynamics. Presently, the study of physiology lacks integration with thermodynamic principles. The membrane theory posits that living cells can differentiate between Na⁺ and K⁺ by means of channels and pumps. Thus, Na⁺ and K⁺ differentially impact the membrane potential. On the other hand, the Hofmeister effect, an older and less prominent thermodynamic theory, proposes that Na⁺ and K⁺ have varying adsorption levels to biomolecules, potentially accounting for their distinct effects on membrane potential even without the involvement of channels and pumps. This concept, distinct from the traditional membrane theory and grounded in ion adsorption (desorption) alongside the Hofmeister effect, might elucidate the process of membrane potential formation. This ion adsorption (desorption) and Hofmeister effect-based idea relates to the previously overlooked Association-Induction Hypothesis (AIH). Our experimental measurements of membrane potentials using artificial cell models highlight that ion adsorption activity and the Hofmeister effect have a comparable impact on the generation of membrane potential as ion flow in the conventional physiological model, assisted by channels and pumps. Full article