Physical Sciences

Sort by

Hypothesis
Physical Sciences
Biophysics

Vladimir Trincher

Abstract: In our previously published paper “Solar Intelligence: A Hypothesis on the Electromagnetic Origin of Life”, we proposed a scientific-philosophical hypothesis suggesting that organic life on Earth may have emerged as a resonant response to a highly organized informational impulse originating from external electromagnetic structures. In the present work, we develop this hypothesis further by applying a comparative probabilistic method of analysis: a resonance-induced model of the origin of life is evaluated against the classical scenario of abiogenesis based on probabilistic parameters.The aim of this approach is not empirical verification per se, but the construction of a formalizable model that demonstrates internal logical coherence, physical plausibility, and probabilistic richness. We consider life as a possible result of external informational influence encoded in biological matter, rather than as a purely random chemical autocatalytic sequence. This perspective not only broadens the conceptual framework for the origin-of-life problem but also allows for the formulation of potentially testable hypotheses within the scope of modern physics, biology, and information theory.
Article
Physical Sciences
Biophysics

Islam G Ali,

Issam El Naqa

Abstract: Ultra-high dose rate radiotherapy known as Flash Radiotherapy (FLASH-RT) offers tremendous opportunities to improve the therapeutic ratio of radiotherapy by sparing the normal tissue while maintaining similar tumoricidal efficacy. However, the underlying biophysical basis of the FLASH effect remains under active investigation with several proposed mechanisms involving oxygen depletion, altered free-radical chemistry, and differential biological responses. This article provides an overview of available experimental and computational tools that can be utilized to probe the tumor and normal tissue microenvironment. We analyze in vitro, ex vivo, and in vivo systems used to study FLASH responses. We describe various computational and imaging technologies that can potentially aid in understanding the biophysics of FLASH-RT and lead to safer clinical translational.
Article
Physical Sciences
Biophysics

Seyed Kiarash Sadat Rafiei,

Mahsa Asadi Anar

Abstract: We propose a multilayer geometric model of consciousness based on Recursive Informational Curvature (RIC), in which awareness emerges from curvature dynamics across nested informational manifolds. The model comprises three principal layers: (i) a Fisher layer, encoding unconscious probabilistic inference; (ii) a Finsler layer, capturing direction-sensitive effort and goal-directed cognition; and (iii) a Hermitian layer, modeling recursive symbolic modulation and introspective phase dynamics. Each layer is formalized through a distinct metric and curvature function, and their coupling governs the informational evolution of conscious states. We derive a unifying scalar field, K(t)=α λ(t)-β ∇S(t), where λ(t) represents recursive gain and ∇S(t) the symbolic entropy gradient. Conscious access is predicted to emerge when K(t) exceeds a critical threshold, whereas collapse into unconscious or unstable states occurs when curvature falls below this bifurcation point. Simulations across all three layers reveal the geometric structure of attention, effort, and symbolic cycling, visualizing cognitive dynamics as phase trajectories over recursive curvature fields. We further present an illustrative case study of moral decision-making under cognitive conflict, demonstrating the model’s interpretive capacity. To test empirical feasibility, Appendix B implements a minimal simulation using synthetic EEG-like signals under low- and high-noise regimes. Results confirm that positive curvature corresponds to semantic closure and awareness, while negative curvature indicates collapse into unstable symbolic states. Together, these results suggest that RIC provides a coherent, mathematically grounded framework for unifying cognitive geometry, symbolic dynamics, and informational collapse.
Article
Physical Sciences
Biophysics

András Buzás,

Balázs Sonkodi,

András Dér

Abstract: Heart rate (HRV) is widely considered an important marker of the ANS effects on the heart, and as such, a crucial diagnostic tool in cardiology. There are a number of HRV-descriptors used in medical and research practice, usually without a clear-cut overview about their mutual relationship, which might hamper a proper selection among them, in a particular study. The problem is further complicated by the often-ignored fact that practically all HRV parameters are HR-dependent. Hence, our aim was to perform a comparative statistical analysis of ECG-recordings from a public database, with a focus on the HR-dependence of typical time-, frequency-domain, and nonlinear HRV parameters. We revealed their fundamental connections, that were substantiated by basic mathematical considerations, and were experimentally demonstrated via the analysis of 24-hours ECG-recordings of more than 200 healthy individuals. Wee confirmed the HR-dependence of typical time-domain parameters as RMSSD and SDNN, frequency-domain parameters as the VLF, LF and HF components, and nonlinear indices as sample entropy and DFA exponent. In addition to shedding light on their relationship, we identified a so-far neglected spectral band, VHF, as an important indicator of the SNS activity. We expect our results to be utilized in HRV analysis in both medical and research practice.
Article
Physical Sciences
Biophysics

Yitong Wang,

Peilin Li,

Haoxin Ren,

Yining Li,

Yawen Li,

Yuqi Xia,

Jingyu Zhang,

Peng Zhang

Abstract: Cholesteryl ester deposition in atherosclerosis (AS) plaques drives lipid core formation and plaque instability. Traditional statin drugs lack targeting and cause adverse reactions in some patients. This study proposed a novel laser-targeted therapy strategy based on photon-phonon resonant absorption (PPRA). We assigned the vibrational modes of four cholesteryl esters: cholesteryl linoleate (CLA), cholesteryl oleate (COA), cholesteryl palmitate (CPA), and cholesteryl stearate (CSA) using first-principles density functional theory, and determined the C=O vibration frequencies (1720-1750 cm-1). We suggested using a 52 THz laser to selectively excite C=O bond resonance, thereby achieving effective PPRA. It is predicted to disrupt cholesterol ester intermolecular hydrogen bonds, induce solid or liquid crystalline to liquid phase transitions in lipid cores. Consequently, this enhances the efficiency of esterase hydrolysis and promotes cholesterol reverse transport, which helps alleviate lipid plaque deposition. This method overcomes traditional drug limitations and offers a new physical intervention for laser-targeted therapy of AS.
Article
Physical Sciences
Biophysics

Marco Ruggiero

Abstract: This observational study explores a potential correlation between chanting Nam-Myoho-Renge-Kyo and variations in local natural radioactivity, building on research into consciousness-matter interactions (e.g., PEAR, GCP). Using a RadiaCode 10X instrument in Mesa, Arizona, measurements were continuously conducted to record Counts Per Second (CPS), ambient dose equivalent rate (µSv/h), and energy spectrum during chanting and control periods. The analysis presented here primarily focuses on CPS and spectral data. The cumulative spectrum showed a prominent low-energy peak, likely environmental X-rays. Spectrogram analysis with ImageJ revealed subtle quantitative changes; a representative session showed higher total counts during chanting (498,432 vs 471,680), consistent across other sessions. Visual inspection also suggested increased CPS variability during chanting. Speculatively, these findings hint at a correlation between the focused psycho-physiological state of chanting and subtle alterations in detected radiation patterns, aligning conceptually with consciousness influencing random systems, potentially considered within frontier frameworks like Orch-OR. Study limitations include the single-subject, observational design and inherent radioactivity randomness. Results are preliminary and require cautious interpretation. This work offers initial empirical data on a novel area, suggesting a potential link between chanting and subtle radioactivity variations, contributing to consciousness-matter interaction research. It acknowledges the spiritual depth of the Buddhist practice extends beyond scientific explanation, yet offers this as "actual proof."
Article
Physical Sciences
Biophysics

Abhinav Mishra,

Dipendra Sharma,

Priti Dubey,

S. N. Tiwari

Abstract: Ellipticine, a nitrogen containing compound of plant origin, possesses potent anticancer properties. Mechanism of intercalation into DNA helices and/or topoisomerase II inhibition is ascribed for its pharmaceutical aspects. Multiple biological activities of ellipticine have generated curiosity among researchers belonging to varied disciplines, primarily focussed on unraveling out its mode of action. Employing DFT based B3LYP and functional blended with 6-311 G (d, p) basis function from Gaussian 16 program, electronic parameters and global descriptors of the drug have been examined. A comparative analysis of calculated vibrational assignments of the drug molecule vis-à-vis experimental data from literature has been performed. Again, molecular docking analysis of ellipticine with isomerase transcriptases (PDB ID: 1did, 2ypi and 1xig) has been carried out to understand inhibition activity, binding sites etc.
Article
Physical Sciences
Biophysics

Subhalaxmi Das,

Nikos Ch. Karayiannis,

Supriya Roy

Abstract: Dipalmitoylphosphatidylcholine (DPPC), is one of the key bilayer membranes of the phosphatidylcholine (PC) family which constitutes 40-50% of total cellular phospholipids in mammal cells. In this study, we investigate the behaviour of DPPC subjected to lateral pressures ranging from -200 to 150 bar at 323 K using microseconds-long simulations. We identify, with very high precision and through the employment of diverse metrics, the pressure range for the occurrence of critical phenomena, mainly buckling and rupture. Notably, under compression, the membrane initially thickens, leading to a structural phase transition from a uniformly thick state to an undulated phase between 40 and 50 bar, as gauged by sharp changes in area per lipid and headgroup dispersion. Stretching induces systematic membrane thinning, with rupture becoming probable at -170 bar and certain at -200 bar. Instant application of high pressure, corresponding to high loading, requires longer equilibration times than gradual pressure increments (low loading) and leads to slightly higher rupture probability during stretching. The reverse compression cycle shows pressure hysteresis with a 10-bar shift, while the reverse stretching cycle retraces the pathway. System size has a minimal impact on the trends. Under extreme mechanical stress, particularly near critical phenomena, systems may require up simulation times on the order of microsecond to accurately capture phase behaviour and structural alterations. This work could provide important insights to understand membrane behaviour under extreme conditions, of relevance to numerous biological and technological applications.
Article
Physical Sciences
Biophysics

Shinto Mundackal Francis,

Hugo Sanabria,

Ramakrishna Podila

Abstract: Colloidal quantum dots (QDs) and graphene hybrids have emerged as promising platforms for optoelectronic and biosensing applications due to their unique photophysical and electronic properties. This study investigates the fundamental mechanism underlying the photoluminescence (PL) quenching and recovery in graphene–QD hybrid systems using single-layer graphene field-effect transistors (SLG-FETs) and time-resolved photoluminescence (TRPL) spectroscopy. We demonstrate that PL quenching and its recovery are primarily driven by charge transfer, as evidenced by an unchanged fluorescence lifetime upon quenching. Density functional theory calculations reveal a significant charge redistribution at the graphene–QD interface, corroborating experimental observations. We also provide a simple analytical quantum mechanical model to differentiate charge transfer-induced PL quenching from resonance energy transfer. Furthermore, we leverage the charge transfer mechanism for ultrasensitive biosensing to detect biomarkers such as immunoglobulin G (IgG) at femtomolar concentrations. The sensor’s electrical response, characterized by systematic shifts in the Dirac point of SLG-FETs, confirms the role of analyte-induced charge modulation in PL recovery. Our findings provide a fundamental framework for designing next-generation graphene-based biosensors with exceptional sensitivity and specificity.
Article
Physical Sciences
Biophysics

Yanfang Dong,

Xin Huang,

Wenlu Zhang,

Yu Shao,

Pierre Cloutier,

Yi Zheng,

Leon Sanche

Abstract: Absolute cross sections (ACSs) are needed to estimate cellular damage induced by high energy radiation (HER). Low-energy electrons (LEEs), which are the most numerous secondary particles generated by HER, can trigger hyperthermal reactions in DNA. ACSs for such reactions are essential input parameters to calculate radiobiological effectiveness, particularly in targeted radiotherapy. Using a mathematical model, we generate ACSs from effective damage yields induced by LEE impact on 3,197 base-pair plasmid DNA films. Direct or enzyme-revealed conformational damages, quantified by electrophoresis, provide the first complete set of ACSs for inducing crosslinks, double-strand breaks (DSBs), single-strand breaks, base-damage related crosslinks, non-DSB clustered damages (NDCDs) and isolated base damages. These ACSs are generated across the 1-20 eV range, at one eV intervals. They exhibit a strong energy dependence with maximum values at 10-eV of 3.7 ± 0.8, 3.5 ± 0.6, 45.4 ± 4.1, 2.9 ± 1.1, 5.1 ± 1.4, 54.0 ± 16.4 ×10-15 cm2, respectively. ACSs for DSBs, NDCDs and crosslinks, clearly indicate that lesions threatening cell function and genetic stability can be generated by a single LEE. At 5 and 10 eV, total damage ACSs are 63% and 80% larger, respectively, than those previously determined for the same plasmids bound to arginine, a constituent of histones protecting DNA.
Article
Physical Sciences
Biophysics

Eleonora Alfinito,

Matteo Beccaria

Abstract: The social organization of microorganisms 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 functions as a superorganism. The coordination is achieved through a communication mechanism known as quorum sensing. When the community is healthy, quorum sensing enables it to regulate the development of potentially harmful individuals. This study employs an agent-based quorum sensing model to explore the relationship between metabolic functions and social behavior. It also examines how a polyculture responds to variations in the metabolic characteristics of its components. Finally, 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.
Article
Physical Sciences
Biophysics

Gary Hastings,

Michael Nelson,

Caroline Taylor,

Alex Marchesani,

Wilbur Hudson,

Yi Jiang,

Eric Gilbert

Abstract: Fourier transform infrared (FTIR) spectroscopy can detect biomolecular changes in bacterial cells in response to drugs or other stimuli. To fully develop that area requires an understanding of IR spectral changes associated with the growth of unperturbed cells. Such an understanding is still lacking, however. To address this issue, attenuated total reflectance (ATR) FTIR spectroscopy has been used to probe changes in the composition of Staphylococcus aureus ATCC 6538 cells during exponential growth, with 30-minute time resolution. We find prominent spectral changes associated with proteins, nucleic acids and carbohydrates on evolving from the early (30-120 min) to the late (240-360 min) log phase of growth. Principal component analysis (PCA) shows that spectra obtained for cells during the early and late log phases of growth can be discriminated against with 100% accuracy. Protein-related spectral features are most significant in spectra collected at 30- and 90-minutes post-inoculation and provide a robust basis for temporal differentiation. Spectral changes that occur during the first 30 minutes after inoculation are shown to reverse over the next 30-120 minutes, indicating dynamic adaptations during cellular growth. Overall, we demonstrate a band assignment strategy based on time resolution, underscoring the utility of FTIR spectroscopy in dynamic studies of bacterial cells.
Article
Physical Sciences
Biophysics

Kamolrat Somboon,

Choon-Peng Chng,

Changjin Huang,

Shikhar Gupta

Abstract:

Niacinamide, a derivative of vitamin B3, has been shown to reduce skin pigmentation (i.e. acting as a brightening agent) and inflammatory responses such as dermatitis and acne vulgaris. However, niacinamide is a hydrophilic compound and poor partitioning to the lipid matrix in the uppermost layer of the skin (the stratum corneum or SC) limits its delivery to the skin. This necessitates the use of penetration enhancers to increase its bio-availability. In this study, we used computer simulations to investigate the skin penetration of niacinamide alone and in combination with other brightening agents that are also shown to be skin penetration enhancers, namely Sepiwhite®, bisabolol or sucrose dilaurate. Molecular dynamics simulations were performed to reveal molecular interactions of these brightening agents with a lipid bilayer model that mimics the SC lipid matrix. We observed minimal penetration of niacinamide into the SC lipid bilayer when applied alone or in combination with any one of the three compounds. However, when all three compounds were combined, a notable increase in penetration was observed. We showed 32% increase in the niacinamide diffusivity in the presence of other three brightening agents, which also work as penetration enhancer for niacinamide. These findings suggest that formulations containing multiple brightening agents, which works as penetration enhancers, may improve skin penetration of niacinamide and enhance the effectiveness of the treatment.

Article
Physical Sciences
Biophysics

Vladislav Toronov,

Nima Soltani,

Leeanne Leung,

Rohit Mohindra,

Steve Lin

Abstract: The Coherent Hemodynamic Spectroscopy (CHS) model provides a quantitative framework for modeling cerebral hemodynamics and metabolism, particularly in response to small physiological perturbations. However, in its original approximate formulation it was limited to conditions where parameter changes were constrained to 10–20%, making it unsuitable for modeling extreme physiological disruptions such as cardiac arrest. In this study, we present a detailed discussion of the algorithm using the complete CHS model, which extends the original framework by solving partial differential equations without approximations to handle large non-periodic perturbations. This model was applied to data from a previously published cardiac arrest and cardiopulmonary resuscitation (CPR) study in pigs, where cerebral blood flow changed by 100%. While our prior work demonstrated the utility of this approach for analyzing cerebral microvascular and metabolic parameters, it did not include the algorithmic details necessary for reproducibility and broader application. Here we address this gap by describing the algorithm's workflow, including the use of non-linear multivariate optimization, and its ability to recover multiple physiological variables, such as the capillary and venule oxygen saturations, and parameters, such as the capillary oxygen diffusion rate, and arterial oxygen saturation. The latter can be valuable when the pulse oximetry measurements are unavailable due to unstable, weak or absent pulse. This study underscores the importance of non-linear modeling in advancing the application of CHS to extreme physiological conditions and highlights its potential for translational research and clinical innovation.
Article
Physical Sciences
Biophysics

Nima Soltani,

Rohit Mohindra,

Steve Lin,

Vladislav Toronov

Abstract: Understanding brain oxygen metabolism is crucial for evaluating overall health, par-ticularly in high-stress medical situations such as cardiac arrest and cardiopulmonary resuscitation (CPR). This study focuses on two key indicators of brain oxygen metabo-lism: the cerebral metabolic rate of oxygen (CMRO2) and the oxidation state of redox cytochrome c oxidase (rCCO). Using advanced techniques like hyperspectral near-infrared spectroscopy (hNIRS) and laser doppler flowmetry (LDF), we have con-ducted a comprehensive analysis of their relationship in pigs during and after cardiac arrest and CPR. We investigated both the entire duration of these experiments and specific time intervals, providing a detailed view of how these metrics interact. The data reveals non-linear relationship between rCCO and CMRO2. Our findings contribute to a deeper understanding of how the brain manages oxygen during critical episodes, po-tentially guiding future interventions in neurological care and improving outcomes in emergency medical settings.
Article
Physical Sciences
Biophysics

Raffaele Scafè,

Marco Puccini,

Rosanna Pellegrini,

Roberto Pani

Abstract: The present paper introduces the so-called scintillators footprints, made of schemes showing XRF-escape peaks and their relative emission intensities in the energy range of interest for nuclear medicine SPECT and PET. A footprint describes the suitability of a scintillator for quantitative investigation with the best possible detectabilility. Sixteen scintillation materials have been identified in Literature, characterized by effective atomic number ranging between 22 to 75. The footprints of NaI:Tl and BGO, confirm the best suitability for quantitative spectral analisys at 140.5 keV and 511 keV, respectively. Moreover, for the low-Z eff scintillators like CaF 2 and CMSM, the XRF-escape effect is foresee irrelevant even at 140.5 keV, due to the small energy value of X-ray fluorescences.
Article
Physical Sciences
Biophysics

Maria Sumarokova,

Rais Pavlov,

Tatiana Lavushchenko,

Egor Vasilenko,

Grigory Kozhemyakin,

Oleg Fedorov,

Rodion Molotkovsky,

Pavel Bashkirov

Abstract:

SARS-CoV-2 viral entry requires membrane fusion, facilitated by fusion peptides within its spike protein. While these predominantly hydrophobic peptides insert into target membranes, their precise mechanistic role in membrane fusion remains incompletely understood. Here, we investigate how FP1, the N-terminal fusion peptide sequence, modulates membrane stability and barrier function across various model membrane systems. Through a complementary suite of biophysical techniques—including electrophysiology, fluorescence spectroscopy, and atomic force microscopy—we demonstrate that FP1 significantly promotes pore formation and alters membrane mechanical properties. Our findings reveal that FP1 reduces the energy barrier for membrane defect formation and stimulates the appearance of stable conducting pores, with effects modulated by membrane composition and mechanical stress. The observed membrane-destabilizing activity suggests that beyond its anchoring function, FP1 may facilitate viral fusion by locally disrupting membrane integrity. These results provide mechanistic insights into SARS-CoV-2 membrane fusion mechanisms and highlight the complex interplay between fusion peptides and target membranes during viral entry.

Article
Physical Sciences
Biophysics

Valeria Conti Nibali,

Caterina Branca,

Ulderico Wanderlingh,

Rosaria Verduci,

Elisa Bonaccorso,

Andrea Ciccolo,

Giovanna D’Angelo

Abstract: Water at membrane interfaces is vital for the cellular biological functions, but despite its importance, the structure and function of biological water remain elusive. Here, by studying the OH stretching mode in partially hydrated lipid multilayers by FTIR measurements, relevant information on the water structure at the surface with lipid membranes has been gathered. The water hydrogen-bond network is highly perturbed in the first layers that are in contact with the lipid membrane, exhibiting strong deviations from tetrahedral symmetry and a significant number of defects, such as isolated water molecules and a large number of hydrogen-bonded water dimers in the interfacial region. These findings supports the hypothesis that in phospholipid membranes water chains are formed that are involved in the proton transfer across lipid bilayers by phosphate groups of opposing lipids. Furthermore, we have determined that even at very low hydration levels, a small amount of water is embedded within the confined spaces of the hydrocarbon region of phospholipid bilayers, which could potentially contribute to the structural stability of the lipid membrane.
Review
Physical Sciences
Biophysics

Ahmed Hamraoui

Abstract: Understanding and controlling cell-implant interactions is crucial for enhancing biomaterial performance and reducing post-implantation complications. Among the diverse surface properties that influence these interactions, surface wettability has emerged as a critical factor affecting cell adhesion, migration, proliferation, and differentiation. This review emphasizes the strong correlation between wettability and cell behavior on adhesion surfaces, highlighting its potential as an accessible and effective parameter for surface characterization. Wettability experiments are relatively simple to conduct, offering practical entry points for investigating surface properties. However, misinterpretations of these measurements can lead to erroneous conclusions, especially when directly linking cell responses to surface energy without accounting for other influencing factors. This review aims to bridge the gap between physical chemistry and biological sciences by providing a comprehensive yet accessible resource for biologists and researchers unfamiliar with surface and interface science. By elucidating the principles of wettability, surface energy, and their role in governing cell behavior, we offer insights that help ensure accurate interpretation of experimental results. This understanding prevents oversimplified correlations and fosters more nuanced experimental designs. Additionally, the review outlines key experimental techniques and their relevance to biological responses, enabling researchers to optimize surface properties for biomedical applications. By integrating interdisciplinary knowledge, we not only clarify the molecular mechanisms underlying cell-surface interactions but also empower biologists to leverage these insights in designing advanced biomaterials and implants. This approach ensures meaningful advancements in biomedical science while avoiding pitfalls from incomplete or incorrect interpretations.
Review
Physical Sciences
Biophysics

Igor S. Oliveira,

Guilherme X. Pinheiro,

Maria Luana B. Sa,

Pedro Henrique L.O. Gurgel,

Samuel U. Pizzol,

Rosangela Itri,

Vera B. Henriques,

Thais A. Enoki

Abstract: This mini review intends to highlight the importance of bilayer asymmetry. Biological membranes are complex structures that are a physical barrier separating the external environment from the cellular content. This complex bilayer comprises an extensive lipid repertory, suggesting that the different lipid structures might subserve a role in the membrane. Interestingly, this vast repertory of lipids is asymmetrically distributed between leaflets that form the lipid bilayer. Here, we discuss the properties of the plasma membrane under the view of experimental model membranes, consisting in simplified and controlled in vitro systems. We summarize some crucial features of the exoplasmic (outer) and cytoplasmic (inner) leaflets observed through investigations using symmetric and asymmetric membranes. Symmetric model membranes for the exoplasmic leaflet have a unique lipid composition that might form a coexistence of phases, namely liquid disordered and liquid order phases. These phase domains may appear in different sizes and shapes depending on lipid composition and lipid-lipid interactions. In contrast, symmetric model membranes for the cytoplasmic leaflet form a fluid phase. We discuss the outcomes reported in the literature for asymmetric bilayers, which vary according to lipid compositions and, consequently, reflect to different intra- and inter-leaflet interactions. Interestingly, the asymmetric bilayer could show induced domains in the inner leaflet, or it could decrease the tendency of the outer leaflet to phase separation. If cells regulate the lipid composition of the plasma membrane, they can adjust the existence and sizes of the domains by tuning the lipid composition.

of 5

Prerpints.org logo

Preprints.org is a free preprint server supported by MDPI in Basel, Switzerland.

Subscribe

© 2025 MDPI (Basel, Switzerland) unless otherwise stated