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EPJ E - Soft Matter and Biological Physics
Journal Prestige (SJR): 0.489  Citation Impact (citeScore): 1 Number of Followers: 3  Hybrid journal (It can contain Open Access articles)ISSN (Print) 1292-8941 - ISSN (Online) 1292-895X Published by Springer-Verlag  [2467 journals]
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- Alignment rule and geometric confinement lead to stability of a vortex in
active flow-
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Abstract: Vortices are hallmarks of a wide range of nonequilibrium phenomena in fluids at multiple length scales. In this work, we numerically study the whirling motion of self-propelled soft point particles confined in circular domain, and aim at addressing the stability issue of the coherent vortex structure. By the combination of dynamical and statistical analysis at the individual particle level, we reveal the persistence of the whirling motion resulting from the subtle competition of activity and geometric confinement. In the stable whirling motion, the scenario of the coexistence of the irregular microscopic motions of individual particles and the regular global whirling motion is fundamentally different from the motion of a vortex in passive fluid. Possible orientational order coexisting with the whirling are further explored. This work shows the stability mechanism of vortical dynamics in active media under the alignment rule in confined space and may have implications in creating and harnessing macroscale coherent dynamical states by tuning the confining geometry. Graphical
PubDate: 2023-01-22
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- Optimizing airborne wind energy with reinforcement learning
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Abstract: Airborne wind energy is a lightweight technology that allows power extraction from the wind using airborne devices such as kites and gliders, where the airfoil orientation can be dynamically controlled in order to maximize performance. The dynamical complexity of turbulent aerodynamics makes this optimization problem unapproachable by conventional methods such as classical control theory, which rely on accurate and tractable analytical models of the dynamical system at hand. Here we propose to attack this problem through reinforcement learning, a technique that—by repeated trial-and-error interactions with the environment—learns to associate observations with profitable actions without requiring prior knowledge of the system. We show that in a simulated environment reinforcement learning finds an efficient way to control a kite so that it can tow a vehicle for long distances. The algorithm we use is based on a small set of intuitive observations and its physically transparent interpretation allows to describe the approximately optimal strategy as a simple list of manoeuvring instructions. Graphical
PubDate: 2023-01-19
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- Impacts of external electric fields on the permeation of glycerol and
water molecules through aquaglyceroporin-7: molecular dynamics simulation
approach-
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Abstract: The aquaglyceroporin-7 (AQP7) protein channels facilitate the permeation of glycerol and water molecules through cell membranes by passive diffusion and play a crucial role in cell physiology. Considering the wide-spirit usage of radiofrequency electromagnetic fields in our daily life, in this study, the effects of constant and GHz electric fields were investigated on the dynamics of glycerol and water molecules inside the AQP7. To this end, four different molecular simulation groups were carried out in the absence and presence of electric fields. The results reveal that the free energy profile of the glycerol permeation inside the channel is reduced in the presence of the field of 0.2 mV/nm and the oscillating field of 10 GHz. In addition, exposing the channel to the electric field of 0.2 mV/nm assisted the water transport through the channel with no considerable effect on channel stability. These observations provide a framework for understanding how such fields could alter normal operation of protein channels, which may lead to disease beginning or being used in disease treatment. Graphical abstract Glycerol and water molecules permeation through the aquaglyceroporin-7 channel can be influenced by application of external electric fields
PubDate: 2023-01-19
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- Marangoni convection in a hybrid nanofluid-filled cylindrical annular
enclosure with sinusoidal temperature distribution-
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Abstract: The current research numerically investigates the Marangoni convection in a cylindrical annulus filled with hybrid nanofluid saturated porous media. The interior and exterior walls are subjected to spatially varying sinusoidal thermal distributions with various amplitude ratios and phase deviations. The limits at the top and bottom are adiabatic. To solve the system of non-dimensional governing equations, the finite difference approach is applied. The main objective of the ongoing study is to investigate the impact of the Marangoni number, nanoparticle volume fraction and the radii ratio on the amplitude ratio and phase deviation. Also, the fluid flow, thermal characteristics, local and average Nusselt numbers are analysed in the hybrid nanofluid-filled vertical cylindrical annulus with magnetic effects. The findings indicate that the sinusoidal temperature promotes multicellular flow in the porous annular region. In the annulus with sinusoidal boundaries, the Marangoni number underperforms while the nanoparticle volume fraction outperforms. Graphic abstract
PubDate: 2023-01-13
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- Inferring turbulent environments via machine learning
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Abstract: The problem of classifying turbulent environments from partial observation is key for some theoretical and applied fields, from engineering to earth observation and astrophysics, e.g., to precondition searching of optimal control policies in different turbulent backgrounds, to predict the probability of rare events and/or to infer physical parameters labeling different turbulent setups. To achieve such goal one can use different tools depending on the system’s knowledge and on the quality and quantity of the accessible data. In this context, we assume to work in a model-free setup completely blind to all dynamical laws, but with a large quantity of (good quality) data for training. As a prototype of complex flows with different attractors, and different multi-scale statistical properties we selected 10 turbulent ‘ensembles’ by changing the rotation frequency of the frame of reference of the 3d domain and we suppose to have access to a set of partial observations limited to the instantaneous kinetic energy distribution in a 2d plane, as it is often the case in geophysics and astrophysics. We compare results obtained by a machine learning (ML) approach consisting of a state-of-the-art deep convolutional neural network (DCNN) against Bayesian inference which exploits the information on velocity and entropy moments. First, we discuss the supremacy of the ML approach, presenting also results at changing the number of training data and of the hyper-parameters. Second, we present an ablation study on the input data aimed to perform a ranking on the importance of the flow features used by the DCNN, helping to identify the main physical contents used by the classifier. Finally, we discuss the main limitations of such data-driven methods and potential interesting applications. Graphical
PubDate: 2022-12-31
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- An optimized recipe for making giant bubbles
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Abstract: Large bubbles are primarily used in physics laboratories to study 2D turbulence, surface wavers, and fundamental properties of soap systems. Outside of physics, blowing large bubbles is also a part of many performances and shows. Both the scientific and artistic communities usually want to get reasonably stable foam films. The purpose of this article is to propose the main physical ingredients needed for an effective recipe to make stable films and bubbles. We propose controlled experiments to measure both the ease of generating a bubble, and its stability in different stabilizing solutions, which we choose by adding the ingredients contained in a bubble artist’s recipe one by one. Our main findings are that (i) the surfactant concentration must not be too high, (ii) the solution must contain long flexible polymer chains to allow for easy bubble generation and (iii) the addition of glycerol provides improved bubble stability by preventing evaporation. Finally, we propose an efficient recipe, which takes into account these considerations. Graphical
PubDate: 2022-12-22
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- Investigation of human β-defensins 1, 2 and 3 in human saliva by
molecular dynamics-
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Abstract: Human β-defensins present in saliva have a broad spectrum of antimicrobial activities that work against infections in oral cavity. To provide a better understanding of these molecules’ properties and functions at the molecular level, we have investigated and compared the important structural properties of human β-defensin-1, -2 and -3 using molecular dynamics simulations. Our results have shown that human β-defensin-3 has a more flexible structure in water than the other two because of its high hydrophilicity, low β-sheet content and high repulsive forces between its charged residues. Moreover, we found that the location of the salt bridges is important in protein's stability in water. Graphical Molecular dynamics simulations of human β-defensins 1, 2 and 3 revealed that the hbd-3 is more flexible in water than hbd-1 and hbd-2.
PubDate: 2022-12-21
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- Sliding friction perturbed by shear ultrasound vibrations: dynamic
lubrication and overaging-
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Abstract: Reduction of the effective static coefficient of friction by shear ultrasound has been shown recently to be due to the partial lubrication of the solid–solid contact. Here, we study the effect of ultrasound perturbation on a multicontact interface at imposed drive velocity. We show that, together with the partial lubrication similar to the static case, ultrasound vibrations enhance structural aging and the emergence of stick–slip. Graphical
PubDate: 2022-12-19
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- UV light sensing and switching applications of dimeric smectic liquid
crystals: comparative calculations-
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Abstract: Two dimeric smectic molecules, namely α-ω-bis (4-n-pentylanilinebenzylidene-4′-oxy) butane (PABO4) and α-ω-bis (4-n-pentylanilinebenzylidene-4′-oxy) pentane (PABO5), have been considered for sensing UV light. The compounds’ optimization process has been performed through B3LYP hybrid functional together with basis set 6-31+G (d) using the input parameters from the crystallographer. The absorption of UV analysis of these compounds has been estimated, and the configuration interaction single-level method has been used to analyse the electronic transition features coupled with the calculation of excited states using semi-empirical Hamiltonian ZINDO. The CNDO/S, INDO/S together with CI approaches, has been utilized for comparative evaluation. The spectral-associated parameters have been summarized. The molecules discussed in this manuscript present several features, viz. the absorption range of the molecules that is sensitive to different wavelengths, the usage in flexible devices, offering the prospect for UV sensors. Further, the switching applications have been explored based on the oscillator strength data in various regions of wavelengths. Graphical abstract
PubDate: 2022-12-15
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- Conditions for the propulsion of a colloid surrounded by a mesoscale phase
separation-
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Abstract: We study a two-dimensional model of an active isotropic colloid whose propulsion is linked to the interactions between solute particles of the bath. The colloid catalyzes a chemical reaction in its vicinity, that yields a local phase separation of solute particles. The density fluctuations of solute particles result in the enhanced diffusion of the colloid. Using numerical simulations, we thoroughly investigate the conditions under which activity occurs, and we establish a state diagram for the activity of the colloid as a function of the parameters of the model. We use the generated data to unravel a key observable that controls the existence and the intensity of activity: The filling fraction of the reaction area. Remarkably, we finally show that propulsion also occurs in three-dimensional geometries, which confirms the interest of this mechanism for experimental applications. Graphic abstract
PubDate: 2022-12-02
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- Dielectric relaxations in a liquid crystal along with thermistor
application-
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Abstract: A thermotropic hydrogen bond liquid crystal ClBAO + 6BAO is synthesized by mixing in equimolar ratios of chlorobenzoic acid and hexyloxybenzoic acid. FTIR studies conform the formation of hydrogen bond between the precursors. This mesogen exhibits nematic phase with long thermal range. DSC thermogram specified the transition temperatures and their respective enthalpy values. Dielectric spectroscopy is performed in the range between 5 Hz and 13 MHz; two types of relaxations, namely type 1 and types 2, are identified and studied extensively. Both of these relaxation are observed to follow Debye relaxation behavior. Type 1 relaxation process, referred as soft mode, is examined at 1 kHz; a mild shift in the relaxation frequency is noticed as temperature decreased. Type 2 relaxation is observed at 9.4 MHz, and the relaxation frequency magnitude shifted to 10.61 MHz with decrement in the temperature. Cole–Cole plots are constructed for both of these relaxation, and the corresponding activation energy is experimentally deduced from the Arrhenius plots. Another interesting observation is the temperature response of this mesogen to resistance. Both positive and negative slopes are identified in thermos-resistive plots thus by modulating the liquid crystal temperature. Perhaps, this is the first report to notice both behaviors in a mono-mesogen segregated by few degrees of temperature. Features of dielectric studies and thermistor applications are discussed in detail. Graphical
PubDate: 2022-12-02
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- Key interaction patterns in proteins revealed by cluster expansion of the
partition function-
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Abstract: The native conformation of structured proteins is stabilized by a complex network of interactions. We analyzed the elementary patterns that constitute such network and ranked them according to their importance in shaping protein sequence design. To achieve this goal, we employed a cluster expansion of the partition function in the space of sequences and evaluated numerically the statistical importance of each cluster. An important feature of this procedure is that it is applied to a dense finite system. We found that patterns that contribute most to the partition function are cycles with even numbers of nodes, while cliques are typically detrimental. Each cluster also gives a contribute to the sequence entropy, which is a measure of the evolutionary designability of a fold. We compared the entropies associated with different interaction patterns to their abundances in the native structures of real proteins. Graphical abstract
PubDate: 2022-11-29
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- A binary/digital approach to amino acid identification and its application
to peptide sequencing and protein identification-
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Abstract: A binary/digital method is proposed in theory for the identification of single amino acids (AAs) in the bulk or with a few molecules from a single binary measurement. Combined with Edman degradation (or other cleaving method), it can be used to sequence a peptide or identify the parent protein from a partial sequence. The approach is centered on the superspecificity property of transfer RNAs (tRNAs). Markedly different from conventional and recent single molecule (SM) sequencing methods based on analog measurements, it changes the analytical question ‘Which AA is it?’ to the much simpler one ‘Is there an AA in the detection space?’. Each of 20 terminal residues cleaved from 20 copies of a peptide enters a different cavity with a unique tRNA; tRNA charging (or binding with AA) occurs only in the cavity with the cognate AA. The bound AA or the AA separated from the tRNA is detected with a single binary measurement; its identity is known from the position of the single high bit in the resulting 20-bit output. Alternatively, a 20-stage pipeline can be used with sparse samples. Detection of the bound AA can be done optically by tagging the AAs with a fluorescent dye, or of the freed AA electrically with a nanopore. Necessary conditions for accurate AA identification are satisfied in principle; related computations and simulation results are presented. A modified version that can be used for de novo sequencing in parallel of large numbers of peptides immobilized on a glass slide with the tRNAs carrying a fluorescent tag is also proposed. Both methods can be used for protein identification from partial sequences containing 2 or 3 AA types by using only the corresponding tRNAs. Experiments may be performed to validate them, followed by translation into practice with existing technology; potential implementation issues are discussed. Graphical Binary/digital amino acid identification for peptide sequencing.
PubDate: 2022-11-29
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- Dynamics of early stages of nose morphogenesis
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Abstract: The formation of sensory organs is an important developmental and evolutionary question. In the context of regenerative medicine also, it is important to know as accurately as possible how sensory organs form. The formation of ears, eyes or nose stems presumably from tissue thickenings called placodes Graham and Shimeld (J Anat 222(1):32–40, 2013), Horie et al. (Nature 560:228–232, 2018) which become these organs after processes termed inductions. However, the origin of the placodes, the mechanism of induction and the overall face organization are not understood. Recently, it has been suggested that there is a physical principle to face organization. Indeed, it has been shown that there exists a pattern of rings and rays in the early blastula which defines the position of face landmarks, especially the ears and eyes Fleury et al. (Second order division in sectors as a prepattern for sensory organs in vertebrate development, 2021), Fleury and Abourachid (Eu Phys J E 45:31, 2022). Tensions in the sectors defined by the intersections of the said rings and rays create the actual face features. I report here that a similar situation exists for the nose. This explains the robustness of face formation in the chordates phylum. By studying nasal pit formation in the chicken embryo by time-lapse (T-L) video microscopy, I show that the nasal placode originates in a narrow sector deformed by tension forces following the biaxial pattern of rings and rays mentioned above. Cells align in the pattern and exert organized forces. Further contractions of the pattern contribute to inducing the nasal pit. The observation of the early pre-pattern of lines which locks the facial features explains readily a number of facts regarding sensory organs. Especially the existence of a lacrimal canal between the eye and the nose Lefevre and Freitag (Semin Ophthalmo l 27(5–6):175–86, 2012), or of a slit connecting the nose to the mouth, the correlation between nose, mouth and eye morphogenesis Dubourg et al. (J Rare Dis 2(8), 2007), the presence of shallow valleys on the nasal and optic vesicles, the medio-lateral asymmetry of nostrils with often a bent slit Liu et al. (PLoS ONE 12: e0181928, 2017), the uneven number of nostrils in many fish Cox (J R Soc Interf 5(23):575–593, 2008) and possibly the transition between agnatha and gnathostomes Gai and Zhu (Chinese Sci Bull 57(31), 2012): all appear under this light, geometrically straightforward. Graphical abstract The nasal pit forms in a sector of tissue which was present on the blastodic (early embryonic stage), and which is projected onto the nasal vesicle during neurulation. The nasal pit forms along a hairpin of tissue. The top part of the hairpin forms the nares, and the bottom part a groove often visible in many animals
PubDate: 2022-11-19
DOI: 10.1140/epje/s10189-022-00245-8
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- Studying the aging of Laponite suspensions using extensional rheology
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Abstract: The effect of aging on the break-up dynamics of Laponite suspensions was studied in an extensional geometry. It was found that samples of increased age undergo stronger necking at the midpoint. The thinning of samples, driven purely by motion of the plates, was compared with standard shear rheology to understand how the dynamics are related to the sample properties. The Laponite suspensions exhibit a growing stress overshoot with monotonically decreasing yield strain as they age. However, it is shown that the thinning curves in extension are only a good indicator of the sample’s static yield stress, being insensitive to its yield strain. These measurements suggest that following an initial linear visco-elastic regime, samples accumulate significant plastic deformations prior to the complete yielding of the sample. The implications of this for the importance of assessing changes to the ductile—brittle nature of samples are also discussed. Graphical abstract
PubDate: 2022-11-16
DOI: 10.1140/epje/s10189-022-00244-9
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- Novel hybrid neuro-fuzzy model to anticipate the heat transfer in a heat
exchanger equipped with a new type of self-rotating tube insert-
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Abstract: In this investigation, a combination of the wingsuit flying search (WFS) and teaching–learning-based optimization (TLBO) algorithms is developed as a new combinatorial optimization algorithm. The proposed combinatorial algorithm is tested over some well-known benchmark functions and then integrated with the artificial neural network (ANN) to construct a novel hybrid model. After that, the obtained hybrid model is employed to anticipate the experimentally obtained values of the average Nusselt number (Nu), average friction coefficient (f) as well as thermal–hydraulic performance ratio (η), in a heat exchanger equipped with a new type of self-rotating tube insert, against governing parameters. The insert is placed in the tube side of the water heater to heat natural gas. The proposed insert consists of various numbers of self-rotating modules. Indeed, the rotating insert is introduced to create effective secondary sweeping flow on the inner side of the tube. Since this type of tube insert simultaneously provides heat transfer enhancement and undesired pressure drop, a thermal–hydraulic performance ratio is defined to consider both of them. The governing parameters are the number of inserts (0 ≤ N ≤ 30), reservoir’s temperature (40 °C ≤ TR ≤ 50 °C) as well as Reynolds number (6 × 103 ≤ Re ≤ 18 × 103). It was found that the WFS–TLBO enhances the effectiveness of the main ANN in anticipating the Nusselt number (Nu), average friction coefficient (f) as well as performance ratio (η). Moreover, introducing the WFS–TLBO algorithm into the neural network provides an enhancement in the effectiveness of the hybrid models based on the single WFS and TLBO algorithms in anticipating the same parameters. Graphical abstract
PubDate: 2022-11-16
DOI: 10.1140/epje/s10189-022-00248-5
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- Tissue mechanics
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PubDate: 2022-11-09
DOI: 10.1140/epje/s10189-022-00240-z
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- Spontaneous multi-scale void formation and closure in densifying
epithelial and fibroblast monolayers from the sub-confluent state-
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Abstract: Using time-lapse phase contrast microscopy, the formation and closure of spontaneously generated voids in the densifying monolayers of isotropic epithelial cells (ECs) and elongated fibroblast cells (FCs) through proliferation from the sub-confluent state are investigated. It is found that, in both types of monolayers after forming a connected network composed of nematic patches with different orientations, numerous multi-scale voids can be spontaneously formed and gradually close with increasing time. The isotropic fluctuations of deformation and crawling of ECs and the anisotropic axial motion/alignment polarizations of FCs are the two keys leading to the following different generic dynamical behaviors. In EC monolayers, voids exhibit irregular boundary fluctuations and easier cell re-orientation of front layer cells (FLCs) surrounding void boundaries. Void closures are mainly through pinching the gap between the opposite fluctuating void boundaries, and the inward crawling of FLCs to reduce void area associated with topological rearrangement to reduce FLC number. In FC monolayers, large voids have piecewise smooth convex boundaries, and cusp-shaped concave boundaries with cells orienting toward the void at cusp tips. The extension of a thin cell bridge from the cusp tip can bisect a large void into smaller voids. For smaller FC voids dominated by convex boundaries, along which cell alignment prohibits inward crawling, the reduction of FLC number through successive outward squeezing of single FLCs by neighboring FLCs sliding along the void boundary plays an important role for topological rearrangement and void closure. Unlike those surrounding artificial wounds in dense EC monolayers, the absence of ring-like purse-strings surrounding EC and FC voids allows topological rearrangements for reducing void perimeter and void area. Graphic
PubDate: 2022-11-08
DOI: 10.1140/epje/s10189-022-00242-x
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- Collective dynamics and shattering of disturbed two-dimensional
Lennard–Jones crystals-
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Abstract: Elucidating collective dynamics in crystalline systems is a common scientific question in multiple fields. In this work, by combination of high-precision numerical approach and analytical normal mode analysis, we systematically investigate the dynamical response of two-dimensional Lennard–Jones crystal as a purely classical mechanical system under random disturbance of varying strength, and reveal rich microscopic dynamics. Specifically, we observe highly symmetric velocity field composed of sharply divided coherent and disordered regions, and identify the order–disorder dynamical transition of the velocity field. Under stronger disturbance, we reveal the vacancy-driven shattering of the crystal. This featured disruption mode is fundamentally different from the dislocation-unbinding scenario in two-dimensional melting. We also examine the healing dynamics associated with vacancies of varying size. The results in this work advance our understanding about the formation of collective dynamics and crystal disruption, and may have implications in elucidating relevant non-equilibrium behaviors in a host of crystalline systems. Graphical abstract Microscopic dynamics and underlying topological defects in the disruption of the Lennard–Jones lattice under random disturbance.
PubDate: 2022-11-01
DOI: 10.1140/epje/s10189-022-00243-w
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- Phenomenological bifurcation in a generally stochastic population model
with Allee effect-
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Abstract: A general population model with Allee effect driven by correlated additive and multiplicative white noises is considered. This paper aims to investigate noise-induced phenomenological bifurcation (P-bifurcation) and the influence of noises on the population model. With the help of Fokker–Planck equation, we obtain the stationary probability distribution (SPD) of the model, and find that the shape of SPD experiences a transition from one structure to another when the noise intensity passes through a critical value, i.e., the P-bifurcation occurs. Moreover, detailed analysis and simulations for stochastic logistic-like models with weak and strong Allee effects show that the correlated noises have complex effects on the eventual distribution of population size. Graphical abstract This paper aims to investigate noise-induced phenomenological bifurcation (P-bifurcation) for a general population model with Allee effect driven by correlated additive and multiplicative white noises. We find that the shape of SPD experiences a transition from one structure to another when the noise intensity passes through a critical value, i.e., the P-bifurcation occurs.
PubDate: 2022-10-29
DOI: 10.1140/epje/s10189-022-00235-w
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