The European Physical Journal. E, Soft Matter[JOURNAL]
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200 papers
Subdiffusion from competition between multi-exponential friction memory and energy barriers.
Klimek A, Dalton BA, Netz RR
Eur Phys J E Soft Matter · 2025 Sep · PMID 40938471 · Full text
Subdiffusion is a hallmark of complex systems, ranging from protein folding to transport in viscoelastic media. However, despite its pervasiveness, the mechanistic origins of subdiffusion remain contested. Here, we analy...
Subdiffusion is a hallmark of complex systems, ranging from protein folding to transport in viscoelastic media. However, despite its pervasiveness, the mechanistic origins of subdiffusion remain contested. Here, we analyze both Markovian and non-Markovian dynamics, in the presence and absence of energy barriers, in order to disentangle the distinct contributions of memory-dependent friction and energy barriers to the emergence of subdiffusive behavior. Focusing on the mean squared displacement (MSD), we develop an analytical framework that connects subdiffusion to multi-scale memory effects in the generalized Langevin equation (GLE), and derive the subdiffusive scaling behavior of the MSD for systems governed by multi-exponential memory kernels. We identify persistence and relaxation timescales that delineate dynamical regimes in which subdiffusion arises from either memory or energy barrier effects. By comparing analytical predictions with simulations, we confirm that memory dominates the overdamped dynamics for barrier heights up to approximately , a regime recently shown to be relevant for fast-folding proteins. Overall, our results advance the theoretical understanding of anomalous diffusion and provide practical tools that are broadly applicable to fields as diverse as molecular biophysics, polymer physics, and active matter systems.
In vivo mimicking multiphase model towards impact of host on avascular tumour growth.
Pramanik AS, Dey B, Raja Sekhar GP
Eur Phys J E Soft Matter · 2025 Sep · PMID 40913660 · Publisher ↗
Tumour growth involves dynamic interactions among tumour cells, extracellular materials, and host tissue. The tumour exerts mechanical stresses on the host tissue and simultaneously experiences compression across the tum...
Tumour growth involves dynamic interactions among tumour cells, extracellular materials, and host tissue. The tumour exerts mechanical stresses on the host tissue and simultaneously experiences compression across the tumour-host interface. This article presents a mathematical model that mimics an in vivo set-up, where an avascular tumour is surrounded by healthy/normal tissue, utilizing conservation principles for the constituents in each region. Tumour and host tissues are separately treated as biphasic mixtures comprising cells and extracellular materials. This study incorporates the diffusion-dominated transport and metabolism of cell-nourishing agents (CNA), such as oxygen, nutrients, and growth factors. The mechanical impact of normal host tissue on tumour growth dynamics while maintaining stress continuity at the tumour-host interface is analysed through numerical simulations. The key findings are that when CNA levels decline below a specific threshold, the tumour cell volume fraction decreases from the periphery to the centre, resulting in necrotic cell death alongside apoptosis. This study indicates that host tissue reduces CNA tension, accelerating tumour necrosis. The increased viscosity of normal host cells indicates stronger intercellular bonds, causing the cells to adhere more tightly and stiffen the host. With increasing viscosity-induced resistance, the host tissue more effectively impedes tumour expansion, thereby slowing tumour growth due to rising compressive stress. Analytical results for a solvable scenario are also provided to explore the comparative behaviour with numerical simulations of the complete model. Furthermore, analytical results indicate that an increased viscosity of normal host tissue may delay the initiation of necrotic cell death.
Fluctuations of local plastic strain in granular media.
Awada I, Bornert M, Langlois V … +1 more , Léopoldès J
Eur Phys J E Soft Matter · 2025 Sep · PMID 40913195 · Publisher ↗
We experimentally study the heterogeneity of strain in a granular medium subjected to oscillatory shear in a rotating drum. Two complementary methods are used. The first method relies on optical imaging and grain trackin...
We experimentally study the heterogeneity of strain in a granular medium subjected to oscillatory shear in a rotating drum. Two complementary methods are used. The first method relies on optical imaging and grain tracking, allowing us to compute some components of the strain tensor and their variance. The second method, diffuse acoustic wave spectroscopy (DAWS), provides the quadratic strain within the bulk. Our results show that strain is spatially heterogeneous, with fluctuations about ten times larger than the mean, primarily dominated by variability at the grain scale. We then analyze in detail the strain fluctuations occurring during the forward and backward branches of the shear stress cycles, along with the intracycle plastic strain resulting from each cycle. Both methods reveal that each shear cycle consists of two consecutive diffusive-like branches, and that the resulting plastic strain fluctuations scale with the mean plastic shear strain. We propose that plastic strain fluctuations result from irreversible strain heterogeneity that increases with applied shear-reflected in forward-backward strain anticorrelations-but is constrained by load-controlled induced memory.
Proportional modulation of proliferation and motility under 2D compressive stress depends on mesenchymal phenotype.
Ben Meriem Z, Meksassi MB, Denais C … +2 more , Guillermet-Guibert J, Delarue M
Eur Phys J E Soft Matter · 2025 Sep · PMID 40900254 · Publisher ↗
Tumor development is accompanied by strong physico-chemical modifications. Among them, compressive stress can emerge in both the epithelial and stromal compartments. Using a simple two-dimensional compression assay which...
Tumor development is accompanied by strong physico-chemical modifications. Among them, compressive stress can emerge in both the epithelial and stromal compartments. Using a simple two-dimensional compression assay which consisted in placing an agarose weight on top of adherent cells, we studied the impact of compressive stress on cell proliferation and motility in different pancreatic cancer cell lines. We observed a proportional reduction of both proliferation and motility in all tested cell types, with genotypes displaying a more "mesenchymal" phenotype (high velocity-to-proliferation ratio) and others related to a more "epithelial" phenotype (low velocity-to-proliferation ratio). Moreover, "mesenchymal" cells seemed more sensitive to compression, a result that was further suggested by a TGF 1 induction of epithelial-to-mesenchymal transition. Finally, we measured that the change in cell proliferation was associated with a change in intracellular macromolecular crowding, which could modulate a plethora of biochemical reactions. Our results together suggest a mechanism in which all biochemical reactions related to proliferation and motility can be modulated by a change in macromolecular crowding, itself depending on the phenotype, leading to differential sensitivity to pressure.
Double-diffusive convection in a plane layer with low thermal conductivity boundaries.
Prokopev S, Lyubimova T
Eur Phys J E Soft Matter · 2025 Aug · PMID 40815431 · Publisher ↗
This study examines double-diffusive convection in a horizontal fluid layer with low thermal conductivity boundaries, where the heat flux is fixed. Using linear stability analysis and nonlinear modeling, the behavior of...
This study examines double-diffusive convection in a horizontal fluid layer with low thermal conductivity boundaries, where the heat flux is fixed. Using linear stability analysis and nonlinear modeling, the behavior of the system is explored under different thermal and concentration gradients. Two instability modes are identified: monotonous and oscillatory. The monotonous mode, exhibiting longwave patterns, dominates when both gradients contribute to instability. The oscillatory mode occurs when the gradients oppose each other, with stability thresholds dependent on system parameters. Nonlinear modeling confirms the linear theory, showing longwave patterns near the instability threshold and oscillatory behavior when gradients are opposed. These findings offer insights into double-diffusive convection in systems with low thermal conductivity boundaries.
Reinforcement learning of a biflagellate model microswimmer.
Bulusu S, Zöttl A
Eur Phys J E Soft Matter · 2025 Aug · PMID 40804567 · Full text
Many microswimmers are able to swim through viscous fluids by employing periodic non-reciprocal deformations of their appendages. Here we use a simple microswimmer model inspired by swimming biflagellates which consists...
Many microswimmers are able to swim through viscous fluids by employing periodic non-reciprocal deformations of their appendages. Here we use a simple microswimmer model inspired by swimming biflagellates which consists of a spherical cell body and two small spherical beads representing the motion of the two flagella. Using reinforcement learning, we identify for different microswimmer morphologies quasi-optimized swimming strokes. For all studied cases, the identified strokes result in symmetric and quasi-synchronized beating of the two flagella beads. Interestingly, the stroke-averaged flow fields are of pusher type, and the observed swimming gaits outperform previously used biflagellate microswimmer models relying on predefined circular flagella-bead motion.
Probing protein-protein interactions with drag flow: a case study of F-actin and tropomyosin.
Bagès C, Chabanon M, Kools W … +8 more , Dos Santos T, Pagès R, Sirkia ME, Leduc C, Houdusse A, Jégou A, Romet-Lemonne G, Wioland H
Eur Phys J E Soft Matter · 2025 Aug · PMID 40802217 · Publisher ↗
Tropomyosins are central regulators of the actin cytoskeleton, controlling the binding and activity of the other actin binding proteins. The interaction between tropomyosin and actin is quite unique: single tropomyosin d...
Tropomyosins are central regulators of the actin cytoskeleton, controlling the binding and activity of the other actin binding proteins. The interaction between tropomyosin and actin is quite unique: single tropomyosin dimers bind weakly to actin filaments but get stabilised by end-to-end attachment with neighbouring tropomyosin dimers, forming clusters which wrap around the filament. Force spectroscopy is a powerful approach for studying protein-protein interactions, but classical methods which usually pull with pN forces on a single protein pair, are not well adapted to tropomyosins. Here, we propose a method in which a hydrodynamic drag force is applied directly to the proteins of interest, by imposing a controlled fluid flow inside a microfluidic chamber. The breaking of the protein bonds is directly visualised with fluorescence microscopy. Using this approach, we reveal that very low forces from 0.01 to 0.1 pN per tropomyosin dimer trigger the detachment of entire tropomyosin clusters from actin filaments. We show that the tropomyosin cluster detachment rate depends on the cytoplasmic tropomyosin isoform (Tpm1.6, 1.7, 1.8) and increases exponentially with the applied force. These observations lead us to propose a cluster detachment model which suggests that tropomyosins dynamically explore different positions over the actin filament. Our experimental setup can be used with many other cytoskeletal proteins, and we show, as a proof-of-concept, that the velocity of myosin-X motors is reduced by an opposing fluid flow. Overall, this method expands the range of protein-protein interactions that can be studied by force spectroscopy.
Optimizing metachronal paddling with reinforcement learning at low Reynolds number.
Bailey AA, Guy RD
Eur Phys J E Soft Matter · 2025 Aug · PMID 40779081 · Full text
Metachronal paddling is a swimming strategy in which an organism oscillates sets of adjacent limbs with a constant phase lag, propagating a metachronal wave through its limbs and propelling it forward. This limb coordina...
Metachronal paddling is a swimming strategy in which an organism oscillates sets of adjacent limbs with a constant phase lag, propagating a metachronal wave through its limbs and propelling it forward. This limb coordination strategy is utilized by swimmers across a wide range of Reynolds numbers, which suggests that this metachronal rhythm was selected for its optimality of swimming performance. In this study, we apply reinforcement learning to a swimmer at zero Reynolds number and investigate whether the learning algorithm selects this metachronal rhythm, or if other coordination patterns emerge. We design the swimmer agent with an elongated body and pairs of straight, inflexible paddles placed along the body for various fixed paddle spacings. Based on paddle spacing, the swimmer agent learns qualitatively different coordination patterns. At tight spacings, a back-to-front metachronal wave-like stroke emerges which resembles the commonly observed biological rhythm, but at wide spacings, different limb coordinations are selected. Across all resulting strokes, the fastest stroke is dependent on the number of paddles; however, the most efficient stroke is a back-to-front wave-like stroke regardless of the number of paddles.
Linear dielectric spectroscopy of a polymer network stabilizing a ferroelectric liquid crystal.
Hanine M, Daoudi A, Hemine J
Eur Phys J E Soft Matter · 2025 Aug · PMID 40773071 · Publisher ↗
In this study, the linear dielectric characterization of a ferroelectric liquid crystal (FLC) stabilized by an anisotropic polymer network (PSFLC) was investigated. The liquid crystal employed in the PSFLC composites exh...
In this study, the linear dielectric characterization of a ferroelectric liquid crystal (FLC) stabilized by an anisotropic polymer network (PSFLC) was investigated. The liquid crystal employed in the PSFLC composites exhibited the chiral smectic C phase (SmC*), with a short helical pitch, a high tilt angle, and a high degree of spontaneous polarization. Dielectric spectroscopy was preceded by polarizing optical microscopy, as well as structural and electro-optical studies on pure FLC and PSFLC composites at different polymer concentrations. These studies enabled the determination of the pitch of the helix, the tilt angle, and the spontaneous polarization as a function of temperature and electric field. In the absence of a DC voltage, the dielectric response indicated the relaxation of the Goldstone mode as well as a reduction in tilt angle, spontaneous polarization and relaxation amplitude as the polymer density increased. By integrating the experimental data with the Landau model, the physical parameters, including the torsional elastic constant and rotational viscosity, were identified for pure FLC and PSFLC films. In addition, the impact of polymer density on these physical parameters was explored.
Simulated interference colors chart from birefringence measurements in lyotropic calamitic nematic-biaxial nematic-discotic nematic phases.
Lüders DD, Akpinar E
Eur Phys J E Soft Matter · 2025 Aug · PMID 40767952 · Publisher ↗
In this study, Nematic Discotic (N)-Nematic Biaxial (N)-Nematic Calamitic (N) phase sequences are investigated for some surfactant-based lyotropic mixtures. From the microscopic analysis point of view, the nematic phases...
In this study, Nematic Discotic (N)-Nematic Biaxial (N)-Nematic Calamitic (N) phase sequences are investigated for some surfactant-based lyotropic mixtures. From the microscopic analysis point of view, the nematic phases, especially N one, are characterized by a methodology we developed to create a resultant image via composition of many microscopic textures (images). The resultant image permits recognizing the N phase bordered by two verticals imaginary lines contrasting two distinct colors. To consolidate our methodology, we simulated the interference colors chart of the samples for the first time via birefringence measurements performed by laser conoscopy technique. The simulated and experimental results are in good accordance.
Mixed convection in thermo-gravitational column: a continuous species separation.
Sioud K, Mojtabi A, Charrier-Mojtabi MC … +2 more , Abdennadher A, Bergeon A
Eur Phys J E Soft Matter · 2025 Aug · PMID 40762784 · Full text
So far, species separation has been achieved in closed vertical thermogravitational columns (TGC). To obtain continuous separation, the initially homogeneous binary solution with a positive thermodiffusion coefficient wa...
So far, species separation has been achieved in closed vertical thermogravitational columns (TGC). To obtain continuous separation, the initially homogeneous binary solution with a positive thermodiffusion coefficient was introduced at a constant volumetric flow rate through one of the two vertical slots of the TGC and retrieved through the opposite slot. This process required the horizontal dimension separating the two slots to be sufficiently large for the mass regime at the exit slot to reach the steady state associated with a vertical stratification of the mass fraction. Analytical resolution and numerical simulations were developed and showed good agreement between theoretical and numerical results.
Local stress-geometry equation of 2D frictionless granular systems.
Zhang X, Dai D, Tang Y
Eur Phys J E Soft Matter · 2025 Jul · PMID 40742693 · Publisher ↗
For a static granular system, the constitutive equation of its stress tensor is of great significance for understanding its mechanical behaviors. Under isostatic state, it can have the form of stress-geometry equation. T...
For a static granular system, the constitutive equation of its stress tensor is of great significance for understanding its mechanical behaviors. Under isostatic state, it can have the form of stress-geometry equation. To investigate the force moment tensor and the stress-geometry equation of a two-dimensional (2D) granular system in theory, we propose some algebraic theories such as the decomposition formula of a second-order tensor and the cross-product of two symmetric tensors for the dyadic space . For a 2D frictionless disk packing, the local stress-geometry equation for a disk with three or four contacts is derived based on the definition of force moments tensor and the equilibrium equation of contact forces. The definition of the geometry tensor in the stress-geometry equation shows complex associations between the contact branch vectors of a disk with three or four contacts. For a disk with four contacts, its local Janssen coefficient can be given from the eigenvalues of its geometry tensor. Discrete element method (DEM) simulations for random frictionless disk packings are performed to verify two local stress-geometry equations in this paper, and the numerical results are in good agreement with the theoretical predictions. The local stress-geometry equations are convenient for obtaining some information about the stress tensors according to the contact structures without knowing the details of the deformations and the intergranular interactions.
The effect of self-induced Marangoni flow on polar-nematic waves in active-matter systems.
Pototsky A, Thiele U
Eur Phys J E Soft Matter · 2025 Jul · PMID 40736612 · Full text
We study the formation of propagating large-scale density waves of mixed polar-nematic symmetry in a colony of self-propelled agents that are bound to move along the planar surface of a thin viscous film. The agents act...
We study the formation of propagating large-scale density waves of mixed polar-nematic symmetry in a colony of self-propelled agents that are bound to move along the planar surface of a thin viscous film. The agents act as an insoluble surfactant, i.e. the surface tension of the liquid depends on their density. Therefore, density gradients generate a Marangoni flow. We demonstrate that for active matter in the form of self-propelled surfactants with local (nematic) aligning interactions such a Marangoni flow nontrivially influences the propagation of the density waves. Upon gradually increasing the Marangoni parameter, which characterises the relative strength of the Marangoni flow as compared to the self-propulsion speed, the density waves broaden while their speed may either increase or decrease depending on wavelength and overall mean density. A further increase in the Marangoni parameter eventually results in the disappearance of the density waves. This may occur either discontinuously at finite wave amplitude via a saddle-node bifurcation or continuously with vanishing wave amplitude at a wave bifurcation, i.e. a finite-wavelength Hopf bifurcation.
Effect of photothermal therapy using PANI-Fe₂O₃-Cys nanocomposites on breast cancer cells with antibacterial activity and cytotoxicity study.
Abdullah HAR, Fahem MQ, Turki ZT … +1 more , Jawad MH
Eur Phys J E Soft Matter · 2025 Jul · PMID 40699542 · Publisher ↗
This study discusses the effect of photothermal therapy using PANI-conductive polymer composites with iron oxide and the amino acid cysteine (Cys) on breast cancer cells. The study focused on the biological and toxicol...
This study discusses the effect of photothermal therapy using PANI-conductive polymer composites with iron oxide and the amino acid cysteine (Cys) on breast cancer cells. The study focused on the biological and toxicological effects associated with the treatment process and its impact on these cancer cells. The materials were prepared using a very simple chemical oxidation method to produce polymer nanoparticles to which iron and cysteine molecules are attached. These composites were used as therapeutic agents in photothermal therapy, which relies primarily on the process of converting light into heat energy to kill cancer cells. The results showed that photothermal therapy using PANI-FeO-Cys composites with near-infrared (NIR) light was significantly more effective in inhibiting breast cancer cells (MDA-MB-231) than using the composites without a laser. Significant changes in the morphology of the cancer cells were observed after treatment, demonstrating the treatment's effectiveness in destroying cancer cells. On the other hand, there was a slight and negligible effect on healthy cells, demonstrating the successful formulation and targeting of the treatment for cancerous tumors. Antibacterial evaluations also demonstrated effective activity against Staphylococcus aureus and Klebsiella bacteria. This study supports the use of composite nanomaterials in photothermal therapy as a targeted treatment for breast cancer, as well as enhancing the effectiveness of this treatment with lasers. It also explains how these materials could be used in future medical applications, particularly in cancer treatment, using methods that are considered less invasive and safer.
Conformational properties of strictly two-dimensional equilibrium polymers.
Wittmer JP, Cavallo A, Johner A
Eur Phys J E Soft Matter · 2025 Jul · PMID 40699456 · Publisher ↗
Two-dimensional monodisperse linear polymer chains are known to adopt for sufficiently large chain lengths N and surface fractions compact configurations with fractal perimeters. We show here by means of Monte Carlo sim...
Two-dimensional monodisperse linear polymer chains are known to adopt for sufficiently large chain lengths N and surface fractions compact configurations with fractal perimeters. We show here by means of Monte Carlo simulations of reversibly connected hard disks (without branching, ring formation and chain intersection) that polydisperse self-assembled equilibrium polymers with a finite scission energy E are characterized by the same universal exponents as their monodisperse peers. Consistently with a Flory-Huggins mean-field approximation, the polydispersity is characterized by a Schulz-Zimm distribution with a susceptibility exponent for all not dilute systems and the average chain length thus increases with an exponent . Moreover, it is shown that for semidilute solutions and for larger densities. The intermolecular form factor F(q) reveals for sufficiently large a generalized Porod scattering with for intermediate wavenumbers q consistently with a fractal perimeter dimension .
Density-dependent cell migration in the absence of social interactions: a case study of Acanthamoeba castellanii.
Ghazi N, Demircigil M, Cochet-Escartin O … +4 more , Chauviat A, Favre-Bonté S, Anjard C, Rieu JP
Eur Phys J E Soft Matter · 2025 Jul · PMID 40699401 · Publisher ↗
Cell migration is often influenced by intercellular or social interactions, ranging from long-range diffusive cues to direct contacts that can trigger biochemical signaling within the cell and affect the cell protruding...
Cell migration is often influenced by intercellular or social interactions, ranging from long-range diffusive cues to direct contacts that can trigger biochemical signaling within the cell and affect the cell protruding activity or direction of turns. Here we study the density-dependent migration of the amoeba Acanthamoeba castellanii (Ac), a unicellular eukaryote that moves without social interactions. Using experiments and mean free path theory, we characterize how collisions affect motility parameters in crowded environments. We identify the collision rate as a key parameter linking cell density to the collision-induced reorientation rate, and we show its consistency across multiple independent approaches. Our findings reveal that the intrinsic migration speed remains constant, while persistence time and effective diffusion are entirely governed by collisions. At high densities, cells exhibit nearly ballistic trajectories between collisions, a behavior rarely reported in eukaryotes. These results establish Ac as a minimal model for motility in the absence of biochemical signaling, with implications for testing behaviors in complex crowded environments and pre-jamming dynamics.
On degree-dependent topological study of line graph of some antiviral COVID-19 drugs.
Das S, Kumari A, Barman J
Eur Phys J E Soft Matter · 2025 Jul · PMID 40659960 · Publisher ↗
A topological index is a numerical value that correlates with a chemical structure. A degree-based topological index of drug molecular structures is beneficial for researchers investigating in the fields of medicals and...
A topological index is a numerical value that correlates with a chemical structure. A degree-based topological index of drug molecular structures is beneficial for researchers investigating in the fields of medicals and pharmaceuticals because it is significant for testing the physicochemical properties of drugs. Graph theory has proven to be quite useful in this field of study. Graph analysis reveals insights into chemical structures. In physical chemistry, a line graph has multiple applications. This article focuses on the topological characterization of a line graph for antiviral COVID-19 drugs, namely Nirmatrelvir, Molnupiravir, Thalidomide, Theaflavin, Remdesivir, Ritonavir, Chloroquine, Hydroxychloroquine, Arbidol and Lopinavir. The computation of degree-based topological indices is carried out using their M-polynomials. Numerical values of topological indices of line graphs and geometric representations of the polynomials are shown graphically. A comparative study between the obtained values of the line graph and the values of an actual graph is presented through numerical and graphical representation. Furthermore, we conduct a QSPR analysis between the degree-based topological indices of the line graph of certain COVID-19 drugs and their physicochemical properties using curvilinear regression models. A comparison is made between the squared correlation coefficients derived from our curvilinear regression models and those obtained from earlier research. These findings may aid the applicability of newly developed drugs of similar kind, in predicting their physicochemical properties and in improving the associated QSPR studies and hence pave a way to improve treatments against the COVID-19 disease.
Label-free metabolic imaging and energy costs in Chlamydomonas.
Boccara M, Wostrikoff K, Bailleuil B … +1 more , Boccara C
Eur Phys J E Soft Matter · 2025 Jul · PMID 40643810 · Full text
We developed a label-free optical microscopy method to study movements of different frequencies and amplitudes within a cell. We use optical transmission tomography (OTT) that operates in transmission, and we record the...
We developed a label-free optical microscopy method to study movements of different frequencies and amplitudes within a cell. We use optical transmission tomography (OTT) that operates in transmission, and we record the changes of signal values of all the pixels of movies taken for a few seconds (dynamic signal). This signal is a metabolic signal in algae as it decreased in the presence of photosystem II inhibitors or when samples were illuminated at wavelengths where the photoreceptors are poorly operative. We used as model organism Chlamydomonas for which mutants are available. We used a mutant deleted of the chloroplastic gene encoding the large subunit of the Rubisco, ΔrbcL. This mutant is unable to fix atmospheric CO and is devoid of pyrenoid. We compared the dynamic signal between wild-type strain and ΔrbcL mutant of Chlamydomonas grown in dark condition and found it to be 5 to 10 times higher. This mutant overproduced starch, and we tempted to associate the metabolic signal to the cost in ATP consumption for building starch. The method is easy to implement and could be very valuable for studies of phytoplankton in situ or virus-infected cells.
Stochastic dynamics in determining fertilization outcomes in plants: effect of gamete number and pollen tube travel path length.
Manzoor A, Mahima, Kachroo P … +2 more , Uma Shaanker R, Sharma AK
Eur Phys J E Soft Matter · 2025 Jul · PMID 40629099 · Publisher ↗
Plants may enhance seed fitness by favoring fertilization by pollen grains with superior genetic qualities. Pistil traits, such as style length and stigmatic area, are thought to influence this selection, but the mechani...
Plants may enhance seed fitness by favoring fertilization by pollen grains with superior genetic qualities. Pistil traits, such as style length and stigmatic area, are thought to influence this selection, but the mechanisms remain unclear. The impact of stochastic factors on pollen germination time variations is also not fully understood. To investigate this, we simulated a biophysical model using the Monte Carlo method to study how gamete number and pollen tube travel path length affect pollen selection. Our results show that longer travel paths (style lengths) and greater pollen loads on the stigma increase the probability of genetically superior pollen fertilizing ovules. It is because longer styles and more pollen load suppress stochastic effects, promoting seed fitness by favoring superior pollen. We also identify a tradeoff between the benefits of increased path length or pollen load and the resource costs incurred.
A python-based novel vertex-edge-weighted modeling framework for enhanced QSPR analysis of cardiovascular and diabetes drug molecules.
Sorgun S, Ullah A
Eur Phys J E Soft Matter · 2025 Jul · PMID 40627270 · Publisher ↗
This study advances the quantitative structure-property relationship analysis by leveraging novel vertex-edge-weighted (VEW) molecular graphs to investigate 19 drug molecules commonly used to treat cardiovascular disease...
This study advances the quantitative structure-property relationship analysis by leveraging novel vertex-edge-weighted (VEW) molecular graphs to investigate 19 drug molecules commonly used to treat cardiovascular diseases and diabetes. The graphs are constructed by assigning weights to vertices and edges based on atomic properties, enabling a detailed and chemically meaningful representation of molecular structures. Python-based programs were developed to compute degree-based topological indices, which were then analyzed through robust linear regression models to uncover correlations with key physicochemical properties. The results reveal strong and consistent relationships between the computed indices and the physicochemical properties, validating the predictive capability of the proposed approach. Notably, the VEW model demonstrates significant improvements in accuracy and correlation strength over traditional unweighted molecular graph models, underscoring its enhanced ability to capture intricate molecular interactions. This work provides novel insights into the utility of degree-based topological indices in drug design, particularly for cardiovascular and diabetic treatments. By bridging theoretical modeling with practical pharmaceutical applications, it lays a solid foundation for optimizing molecular properties, improving drug efficacy, and accelerating the drug development pipeline. These findings reaffirm the growing significance of computational strategies in advancing precision medicine and pharmaceutical innovation.
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