Search Results (33)

In this position paper, we argue that the conventional understanding of ‘information’ (as generally conceived in science, in a digital fashion) is overly simplistic and not consistently applicable to living systems, which are open systems that cannot be reduced to any kind of ‘portion’ (building block) ascribed to the category of quantity. Instead, it is a matter of relationships and qualities in an indivisible analogical (and ontological) relationship between any presumed ‘software’ and ‘hardware’ (information/matter, psyche/soma). Furthermore, in biological systems, contrary to Shannon’s definition, which is well-suited to telecommunications and informatics, any kind of ‘information’ is the opposite of internal entropy, as it depends directly on order: it is associated with distinction and differentiation, rather than flattening and homogenisation. Moreover, the high degree of structural compartmentalisation of living matter prevents its energetics from being thermodynamically described by using a macroscopic, bulk state function. This requires the Second Principle of Thermodynamics to be redefined in order to make it applicable to living systems. For these reasons, any static, bit-related concept of ‘information’ is inadequate, as it fails to consider the system’s evolution, it being, in essence, the organized coupling to its own environment. From the perspective of quantum field theory (QFT), where many vacuum levels, symmetry breaking, dissipation, coherence and phase transitions can be described, a consistent picture emerges that portrays any living system as a relational process that exists as a flux of context-dependent meanings. This epistemological shift is also associated with a transition away from the ‘particle view’ (first quantisation) characteristic of quantum mechanics (QM) towards the ‘field view’ possible only in QFT (second quantisation). This crucial transition must take place in life sciences, particularly regarding the methodological approaches. Foremost because biological systems cannot be conceived as ‘objects’, but rather as non-confinable processes and relationships. Full article

Axis definition plays a key role in the establishment of animal body plans, both in normal development and regeneration. The cnidarian Hydra can re-establish its simple body plan when regenerating from a random cell aggregate or a sufficiently small tissue fragment. At the beginning of regeneration, a hollow cellular spheroid forms, which then undergoes symmetry breaking and de novo body axis definition. In the past, we have published related work in a physics journal, which is difficult to read for scientists from other disciplines. Here, we review our work for readers not so familiar with this type of approach at a level that requires very little knowledge in mathematics. At the same time, we present a few aspects of Hydra biology that we believe to be linked to our work. These biological aspects may be of interest to physicists or members of related disciplines to better understand our approach. The proposed theoretical model is based on fluctuations of gene expression that are triggered by mechanical signaling, leading to increasingly large groups of cells acting in sync. With a single free parameter, the model quantitatively reproduces the experimentally observed expression pattern of the gene ks1, a marker for ‘head forming potential’. We observed that Hydra positions its axis as a function of a weak temperature gradient, but in a non-intuitive way. Supposing that a large fluctuation including ks1 expression is locked to define the head position, the model reproduces this behavior as well—without further changes. We explain why we believe that the proposed fluctuation-based symmetry breaking process agrees well with recent experimental findings where actin filament organization or anisotropic mechanical stimulation act as axis-positioning events. The model suggests that the Hydra spheroid exhibits huge sensitivity to external perturbations that will eventually position the axis. Full article

The class of diamino-naphthalene exhibits antioxidant properties, which are partly related to the relative positions of the two amino groups. This study demonstrates how the reactivity of one of these compounds, 1,5-diamino-naphthalene (DAN), can be adjusted by introducing a single amide bond through a simple thermal coupling with l-pyroglutamic acid (PyroGlu). The solventless thermal reaction between PyroGlu and DAN at 160 °C yielded a new mono-pyroglutanilide compound (PyroDAN) that was characterized using various analytical techniques, including a thermal and infrared analysis, HRMS (ESI), and one- (1D) and two-dimensional (2D) NMR. The optical properties were investigated using UV-Vis and fluorescence spectroscopy. Additionally, two chemical standard assays were used to measure both the antioxidant and pro-oxidant properties of PyroDAN. The molecule has shown nearly negligible pro-oxidant activity, while a mild antioxidant activity is still retained. These findings indicate that the transformation of DAN into a mono-pyroglutanilide derivative breaks the original molecular symmetry and effectively modifies the electronic distribution of the aromatic system, suppressing the oxidant properties while keeping a mild antioxidant activity. Furthermore, the tuneable fluorescent properties of PyroDAN—the mild antioxidant activity and the inhibition of the cytologically harmful pro-oxidant properties—suggest promising applications in bioimaging and other biological fields. Full article

Many physical and biological phenomena are characterized by time asymmetry, and are referred to as irreversible. Time-reversal symmetry breaking is in fact the hallmark of systems operating away from equilibrium and reflects the power dissipated by driving the system away from it. Time asymmetry may manifest in a wide range of time scales; quantifying irreversibility in such systems thus requires methods capable of detecting time asymmetry in a multiscale fashion. In this contribution we review the main algorithmic solutions that have been proposed to detect time irreversibility, and evaluate their performance and limitations when used in a multiscale context using several well-known synthetic dynamical systems. While a few of them have a general applicability, most tests yield conflicting results on the same data, stressing that a “one size fits all” solution is still to be achieved. We conclude presenting some guidelines for the interested practitioner, as well as general considerations on the meaning of multiscale time irreversibility. Full article

We revisit the seminal model of glycolysis first proposed by Sel’kov more than fifty years ago. We investigate the onset of instabilities in biological systems described by the Sel’kov model in order to determine the conditions of the model parameters that lead to bifurcations. We analyze the glycolysis reaction under the circumstances when the diffusivity of both ATP and ADP reactants are taken into account. We estimate the critical value of the model’s single compact dimensionless parameter, which is responsible for the onset of reaction instability and the system’s symmetry breaking. It appears that it leads to spatial inhomogeneities of reactants, leading to the formation of standing waves instead of a homogeneous distribution of ATP molecules. The consequences of this model and its results are discussed in the context of the Warburg effect, which signifies a transition from oxidative phosphorylation to glycolysis that is correlated with the initiation and progression of cancer. Our analysis may lead to the selection of therapeutic interventions in order to prevent the symmetry-breaking phenomenon described in our work. Full article

The refractive index (RI) of biological tissues is a fundamental material parameter that characterizes how light interacts with tissues, making accurate measurement of RI crucial for biomedical diagnostics and environmental monitoring. A Janus sensor (JBS) is designed in this paper, and the photonic spin Hall effect (PSHE) is used to detect subtle changes in RI in biological tissues. The asymmetric arrangement of the dielectric layers breaks spatial parity symmetry, resulting in significantly different PSHE displacements during the forward and backward propagation of electromagnetic waves, thereby realizing the Janus effect. The designed JBS can detect the RI range of 1.3~1.55 RIU when electromagnetic waves are incident along the +z-axis, with a sensitivity of 96.29°/refractive index unit (RIU). In the reverse direction, blood glucose concentrations are identified by the JBS, achieving a sensitivity of 18.30°/RIU. Detecting different RI range from forward and backward scales not only overcomes the limitation that single-scale sensors can only detect a single RI range, but also provides new insights and applications for optical biological detection through high-sensitivity, label-free and non-contact detection. Full article

The Game of Life (GoL) is a paradigmatic computer simulation that exhibits the emergence of complex properties of the whole from relatively simple sets of heuristic rules operating at lower organizational levels. Therefore, it is widely understood as a valuable tool for investigating global properties of evolutionary processes. Cognizant of refined concepts that emerged in recent debates on the central role of historical contingency (historicity) in evolution, we modify the original GoL rules by introducing an updating feedback loop and a probability factor that reflect the degree of historicity in pattern evolution as both stochastic path dependence and sensitivity to initial conditions. We examine this trait in simulations of the emergence and breaking of bilateral and radial symmetries commonly observed in the evolution of life, most prominently as evolving body plans. We show that the implementation of historicity parameters leads to a more realistic sequential and gradual alternating emergence and the breaking of new symmetries than the original set of rules. Apart from its more realistic representations of evolutionary processes, the new approach allows for easier exploration of the parameter space, demonstrates the sequential and gradual emergence and breaking of symmetries, and provides a publicly available and modular simulation tool. We discuss the exploratory potential of the modified GoL platform we designed as an extended thought experiment to study the parameter space defining the historicity of biological processes. Full article

Coupling is a ubiquitous phenomenon observed in various systems, which profoundly alters the original oscillation state of resonant systems and leads to the unique optical properties of metasurfaces. In this study, we introduce a terahertz (THz) tunable coupling metasurface characterized by a four-fold rotation (C₄) symmetry-breaking structural array achieved through the incorporation of vanadium dioxide (VO₂). This disruption of the C₄ symmetry results in dynamically controlled electromagnetic interactions and couplings between excitation modes. The coupling between new resonant modes modifies the peak of electromagnetic-induced transparency (EIT) within the C₄ symmetric metasurfaces, simulating the mutual interference process between modes. Additionally, breaking the C₄ symmetry enhances the mirror asymmetry, and imparts distinct chiral properties in the far-field during the experimental process. This research demonstrates promising applications in diverse fields, including biological monitoring, light modulation, sensing, and nonlinear enhancement. Full article

Binary droplet collision is a basic fluid phenomenon for many spray processes in nature and industry involving lots of discrete droplets. It exists an inherent mirror symmetry between two colliding droplets. For specific cases of the collision between two identical droplets, the head-on collision and the off-center collision, respectively, show the axisymmetric and rotational symmetry characteristics, which is useful for the simplification of droplet collision modeling. However, for more general cases of the collision between two droplets involving the disparities of size ratio, surface tension, viscosity, and self-spin motions, the axisymmetric and rotational symmetry droplet deformation and inner flow tend to be broken, leading to many distinct phenomena that cannot occur for the collision between two identical droplets owing to the mirror symmetry. This review focused on interpreting the asymmetric droplet deformation and the collision-induced internal mixing that was affected by those symmetry breaking factors, such as size ratio effects, Marangoni Effects, non-Newtonian effects, and droplet self-spin motion. It helps to understand the droplet internal mixing for hypergolic propellants in the rocket engineering and microscale droplet reactors in the biological engineering, and the modeling of droplet collision in real combustion spray processes. Full article

Biological symmetry breaking is a mechanism in biosystems that is necessary for human survival, and depends on chemical physics concepts at both microscopic and macroscopic scales. In this work, we present a few mechanisms of the signaling phenomenon that have been studied in various tissues of human origin. We exhibit that anatomical asymmetry in the structure of a membrane can produce a flow of extracellular fluid. Furthermore, we exhibit that membrane asymmetry is a misbalance in the composition of the aqueous phases and interaction forces with the protein trans-membrane. Various biological membranes such as DPPC, DMPC, DLPC, and so on, have considerable electrostatic voltages that extend across the phosphor lipids bilayer. For studying these phenomena, we modeled DPPC, DMPC, and DLPC lipid bilayers with a net charge misbalance across the phospholipids. Because asymmetric membranes create the shifted voltages among the various aqueous tissues, this effect makes the charge misbalances cause a voltage of 1.3 V across the DPPC bilayer and 0.8 V across the DMPC bilayer. This subject exhibits the importance of membrane structures on electrostatic potential gradients. Finally, we exhibited that a quantum effect was created in small parts of the cell’s thickness due to the symmetry breaking of asymmetrical phospholipid bilayers. Full article

As protein is both a structural component and a metabolic intermediary, amino acids play a crucial function in the body. When it comes to proteins, only the L-configuration of chiral amino acids is found. At the molecular level, symmetry is disrupted; however, the scientific basis for this symmetry breaking is not yet known. Enantioanalysis of chiral compounds such as amino acids plays a very important role in the correct diagnosis of illnesses, such as cancer. The enantiomers of glutamine—a chiral amino acid—were investigated in biological samples using a disposable stochastic sensor. The disposable stochastic sensor based on immobilization of maltodextrin (DE 4.0–7.0) on the surface of a disposable sensor based on graphene decorated with Ag was designed, characterized, and validated for screening tests of whole blood and tissue samples. The stochastic sensor was designed using cold plasma deposition of graphene decorated with Ag on plastic material. The sensor was enantioselective, being able to discriminate between the enantiomers of glutamine. High sensitivities were recorded for both enantiomers, while the limits of determination were 100 fmol L⁻¹ for L-glutamine and 1 fmol L⁻¹ for D-glutamine. High recoveries were determined for the assay of one enantiomer in the presence of the other, despite the ratio between the two enantiomers. Full article

Stochastic SIRS models play a key role in formulating and analyzing the transmission of infectious diseases. These models reflect the environmental changes of the diseases and their biological mechanisms. Therefore, it is very important to study the uniqueness and existence of the global positive solution to investigate the asymptotic properties of the model. In this article, we investigate the dynamics of the stochastic SIRS epidemic model with a saturated incidence rate. The effects of both deterministic and stochastic distribution from infectious to susceptible are analyzed. Our findings show that the occurrence of symmetry breaking as a function of the stochastic noise has a significant advantage over the deterministic one to prevent the spread of the infectious diseases. The larger stochastic noise will guarantee the control of epidemic diseases with symmetric Brownian motion. Periodic outbreaks and re-infection may occur due to the existence of feedback memory. It is shown that the endemic equilibrium is stable under some suitable initial conditions, taking advantage of the symmetry of the large amount of contact structure. A numerical method based on Legendre polynomials that converts the given stochastic SIRS model into a nonlinear algebraic system is used for the approximate solution. Finally, some numerical experiments are performed to verify the theoretical results and clearly show the sharpness of the obtained conditions and thresholds. Full article

High-grade serous ovarian carcinoma (HGSC), the most common and aggressive histological type of ovarian cancer, remains the leading cause of cancer-related deaths among females. It is important to develop novel drugs to improve the therapeutic outcomes of HGSC patients, thereby reducing their mortality. Symmetry is one of the most important properties of the biological network, which determines the stability of a biological system. As aberrant gene expression is a critical symmetry-breaking event that perturbs the stability of biological networks and triggers tumor progression, we aim in this study to discover new candidate drugs and predict their targets for HGSC therapy based on differentially expressed genes involved in HGSC pathogenesis. Firstly, 98 up-regulated genes and 108 down-regulated genes were identified from three independent transcriptome datasets. Then, the small-molecule compounds PHA-793887, pidorubicine and lestaurtinib, which target cell-cycle-related processes, were identified as novel candidate drugs for HGSC treatment by adopting the connectivity map (CMap)-based drug repositioning approach. Furthermore, through a topological analysis of the protein–protein interaction network, cell cycle regulators CDK1, TOP2A and AURKA were identified as bottleneck nodes, and their expression patterns were validated at the mRNA and protein expression levels. Moreover, the results of molecular docking analysis showed that PHA-793887, pidorubicine and lestaurtinib had a strong binding affinity for CDK1, TOP2A and AURKA, respectively. Therefore, our study repositioned PHA-793887, pidorubicine and lestaurtinib, which can inhibit cell cycle regulators, as novel agents for HGSC treatment, thereby helping to optimize the therapeutic strategy for HGSC. Full article

Protein complexes perform a diversity of functions in natural biological systems. While computational protein design has enabled the development of symmetric protein complexes with spherical shapes and hollow interiors, the individual subunits often comprise large proteins. Peptides have also been applied to self-assembly, and it is of interest to explore such short sequences as building blocks of large, designed complexes. Coiled-coil peptides are promising subunits as they have a symmetric structure that can undergo further assembly. Here, an α-helical 29-residue peptide that forms a tetrameric coiled coil was computationally designed to assemble into a spherical cage that is approximately 9 nm in diameter and presents an interior cavity. The assembly comprises 48 copies of the designed peptide sequence. The design strategy allowed breaking the side chain conformational symmetry within the peptide dimer that formed the building block (asymmetric unit) of the cage. Dynamic light scattering (DLS) and transmission electron microscopy (TEM) techniques showed that one of the seven designed peptide candidates assembled into individual nanocages of the size and shape. The stability of assembled nanocages was found to be sensitive to the assembly pathway and final solution conditions (pH and ionic strength). The nanocages templated the growth of size-specific Au nanoparticles. The computational design serves to illustrate the possibility of designing target assemblies with pre-determined specific dimensions using short, modular coiled-coil forming peptide sequences. Full article

Homochiral proteins orchestrate biological functions throughout all domains of life, but the origin of the uniform l-stereochemistry of amino acids remains unknown. Here, we describe enantioselective adsorption experiments of racemic alanine and leucine onto homochiral d- and l-quartz as a possible mechanism for the abiotic emergence of biological homochirality. Substantial racemate resolution with enantiomeric excesses of up to 55% are demonstrated to potentially occur in interstitial pores, along grain boundaries or small fractures in local quartz-bearing environments. Our previous hypothesis on the enhanced enantioselectivity due to uranium-induced fission tracks could not be validated. Such capillary tubes in the near-surface structure of quartz have been proposed to increase the overall chromatographic separation of enantiomers, but no systematic positive correlation of accumulated radiation damage and enantioselective adsorption was observed in this study. In general, the natural l-quartz showed stronger enantioselective adsorption affinities than synthetic d-quartz without any significant trend in amino acid selectivity. Moreover, the l-enantiomer of both investigated amino acids alanine and leucine was preferably adsorbed regardless of the handedness of the enantiomorphic quartz sand. This lack of mirror symmetry breaking is probably due to the different crystal habitus of the synthetic z-bar of d-quartz and the natural mountain crystals of l-quartz used in our experiments. Full article