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Kahan, Alan, Thomás Fogarty, Jing Li, and Thomas Busch. "Driving Interactions Efficiently in a Composite Few-Body System." Universe 5, no. 10 (2019): 207. http://dx.doi.org/10.3390/universe5100207.
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We study how to efficiently control an interacting few-body system consisting of three harmonically trapped bosons. Specifically, we investigate the process of modulating the inter-particle interactions to drive an initially non-interacting state to a strongly interacting one, which is an eigenstate of a chosen Hamiltonian. We also show that for unbalanced subsystems, where one can individually control the different inter- and intra-species interactions, complex dynamics originate when the symmetry of the ground state is broken by phase separation. However, as driving the dynamics too quickly can result in unwanted excitations of the final state, we optimize the driven processes using shortcuts to adiabaticity, which are designed to reduce these excitations at the end of the interaction ramp, ensuring that the target eigenstate is reached.
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Barcelos, Erika I., Shaghayegh Khani, Mônica F. Naccache, and Joao Maia. "Supervised learning for accurate mesoscale simulations of suspension flow in wall-bounded geometries." Physics of Fluids 34, no. 5 (2022): 053110. http://dx.doi.org/10.1063/5.0086759.
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Herein, we have employed a supervised learning approach combined with Core-Modified Dissipative Particle Dynamics Simulations (CM-DPD) in order to develop and design a reliable physics-based computational model that will be used in studying confined flow of suspensions. CM-DPD was recently developed and has shown promising performance in capturing rheological behavior of colloidal suspensions; however, the model becomes problematic when the flow of the material is confined between two walls. Wall-penetration by the particles is an unphysical phenomenon that occurs in coarse-grained simulations such as Dissipative Particle Dynamics (DPD) that mostly rely on soft inter-particle interactions. Different solutions to this problem have been proposed in the literature; however, no reports have been given on how to deal with walls using CM-DPD. Due to complexity of interactions and system parameters, designing a realistic simulation model is not a trivial task. Therefore, in this work we have trained a Random Forest (RF) for predicting wall penetration as we vary input parameters such as interaction potentials, flow rate, volume fraction of colloidal particles, and confinement ratio. The RF predictions were compared against simulation tests, and a sufficiently high accuracy and low errors were obtained. This study shows the viability and potentiality of ML combined with DPD to perform parametric studies in complex fluids.
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Hubbe, Martin A., Pegah Tayeb, Michael Joyce, et al. "Rheology of nanocellulose-rich aqueous suspensions: A Review." BioResources 12, no. 4 (2017): 9556–661. http://dx.doi.org/10.15376/biores.12.4.hubbe.
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The flow characteristics of dilute aqueous suspensions of cellulose nanocrystals (CNC), nanofibrillated cellulose (NFC), and related products in dilute aqueous suspensions could be of great importance for many emerging applications. This review article considers publications dealing with the rheology of nanocellulose aqueous suspensions in the absence of matrix materials. In other words, the focus is on systems in which the cellulosic particles themselves – dependent on their morphology and the interactive forces between them – largely govern the observed rheological effects. Substantial progress in understanding rheological phenomena is evident in the large volume of recent publications dealing with such issues including the effects of flow history, stratification of solid and fluid layers during testing, entanglement of nanocellulose particles, and the variation of inter-particle forces by changing the pH or salt concentrations, among other factors. Better quantification of particle shape and particle-to-particle interactions may provide advances in future understanding. Despite the very complex morphology of highly fibrillated cellulosic nanomaterials, progress is being made in understanding their rheology, which supports their usage in applications such as coating, thickening, and 3D printing.
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Zhang, Tao, Michelle C. Miller, Yi Zheng, et al. "Macromolecular assemblies of complex polysaccharides with galectin-3 and their synergistic effects on function." Biochemical Journal 474, no. 22 (2017): 3849–68. http://dx.doi.org/10.1042/bcj20170143.
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Although pectin-derived polysaccharides can antagonize galectin function in various pathological disorders, the nature of their binding interactions needs to be better defined for developing them as drugs. Moreover, given their relatively large size and complexity, pectin-derived polysaccharides are also useful as model systems to assess inter-polysaccharide and protein–polysaccharide interactions. Here, we investigated interactions between galectin-3 (Gal-3) and pectin-derived polysaccharides: a rhamnogalacturonan (RG) and two homogalacturonans (HGs). BioLayer Interferometry and fluorescence-linked immunosorbent assays indicate that these polysaccharides bind Gal-3 with macroscopic or apparent KD values of 49 nM, 46 µM, and 138 µM, respectively. 15N-1H heteronuclear single quantum coherence (HSQC) NMR studies reveal that these polysaccharides interact primarily with the F-face of the Gal-3 carbohydrate recognition domain. Even though their binding to Gal-3 does not inhibit Gal-3-mediated T-cell apoptosis and only weakly attenuates hemagglutination, their combination in specific proportions increases activity synergistically along with avidity for Gal-3. This suggests that RG and HG polysaccharides act in concert, a proposal supported by polysaccharide particle size measurements and 13C-1H HSQC data. Our model has HG interacting with RG to promote increased avidity of RG for Gal-3, likely by exposing additional lectin-binding sites on the RG. Overall, the present study contributes to our understanding of how complex HG and RG polysaccharides interact with Gal-3.
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Maity, Tuhin Subhra, Howard M. Fried, and Kevin M. Weeks. "Anti-cooperative assembly of the SRP19 and SRP68/72 components of the signal recognition particle." Biochemical Journal 415, no. 3 (2008): 429–37. http://dx.doi.org/10.1042/bj20080569.
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The mammalian SRP (signal recognition particle) represents an important model for the assembly and role of inter-domain interactions in complex RNPs (ribonucleoproteins). In the present study we analysed the interdependent interactions between the SRP19, SRP68 and SRP72 proteins and the SRP RNA. SRP72 binds the SRP RNA largely via non-specific electrostatic interactions and enhances the affinity of SRP68 for the RNA. SRP19 and SRP68 both bind directly and specifically to the same two RNA helices, but on opposite faces and at opposite ends. SRP19 binds at the apices of helices 6 and 8, whereas the SRP68/72 heterodimer binds at the three-way junction involving RNA helices 5, 6 and 8. Even though both SRP19 and SRP68/72 stabilize a similar parallel orientation for RNA helices 6 and 8, these two proteins bind to the RNA with moderate anti-cooperativity. Long-range anti-cooperative binding by SRP19 and SRP68/72 appears to arise from stabilization of distinct conformations in the stiff intervening RNA scaffold. Assembly of large RNPs is generally thought to involve either co-operative or energetically neutral interactions among components. By contrast, our findings emphasize that antagonistic interactions can play significant roles in assembly of multi-subunit RNPs.
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Goehring, Lucas, Joaquim Li, and Pree-Cha Kiatkirakajorn. "Drying paint: from micro-scale dynamics to mechanical instabilities." Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 375, no. 2093 (2017): 20160161. http://dx.doi.org/10.1098/rsta.2016.0161.
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Charged colloidal dispersions make up the basis of a broad range of industrial and commercial products, from paints to coatings and additives in cosmetics. During drying, an initially liquid dispersion of such particles is slowly concentrated into a solid, displaying a range of mechanical instabilities in response to highly variable internal pressures. Here we summarize the current appreciation of this process by pairing an advection-diffusion model of particle motion with a Poisson–Boltzmann cell model of inter-particle interactions, to predict the concentration gradients in a drying colloidal film. We then test these predictions with osmotic compression experiments on colloidal silica, and small-angle X-ray scattering experiments on silica dispersions drying in Hele–Shaw cells. Finally, we use the details of the microscopic physics at play in these dispersions to explore how two macroscopic mechanical instabilities—shear-banding and fracture—can be controlled. This article is part of the themed issue ‘Patterning through instabilities in complex media: theory and applications.’
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Daumas, F., N. Destainville, C. Millot, A. Lopez, D. Dean, and L. Salomé. "Interprotein interactions are responsible for the confined diffusion of a G-protein-coupled receptor at the cell surface." Biochemical Society Transactions 31, no. 5 (2003): 1001–5. http://dx.doi.org/10.1042/bst0311001.
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The monitoring of the movements of membrane proteins (or lipids) by single-particle tracking enables one to obtain reliable insights into the complex dynamic organization of the plasma membrane constituents. Using this technique, we investigated the diffusional behaviour of a G-protein-coupled receptor. The trajectories of the receptors revealed a diffusion mode combining a short-term rapid confined diffusion with a long-term slow diffusion. A detailed statistical analysis shows that the receptors have a diffusion confined to a domain which itself diffuses, the confinement being due to long-range attractive inter-protein interactions. The existing models of the dynamic organization of the cell membrane cannot explain our results. We propose a theoretical Brownian model of interacting proteins that is consistent with the experimental observations and accounts for the variations found as a function of the domain size of the short-term and long-term diffusion coefficients.
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KOURAKIS, IOANNIS, and PADMA KANT SHUKLA. "NONLINEAR EXCITATIONS IN STRONGLY-COUPLED PLASMA LATTICES: ENVELOPE SOLITONS, KINKS AND INTRINSIC LOCALIZED MODES." International Journal of Bifurcation and Chaos 16, no. 06 (2006): 1711–25. http://dx.doi.org/10.1142/s0218127406015623.
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Ensembles of charged particles (plasmas) are a highly complex form of matter, most often modeled as a many-body system characterized by weak inter-particle interactions (electrostatic coupling). However, strongly-coupled plasma configurations have recently been produced in laboratory, either by creating ultra-cold plasmas confined in a trap or by manipulating dusty plasmas in discharge experiments. In this paper, the nonlinear aspects involved in the motion of charged dust grains in a one-dimensional plasma monolayer (crystal) are discussed. Different types of collective excitations are reviewed, and characteristics and conditions for their occurrence in dusty plasma crystals are discussed, in a quasi-continuum approximation. Dust crystals are shown to support nonlinear kink-shaped supersonic solitary longitudinal excitations, as well as modulated envelope localized modes associated with longitudinal and transverse vibrations. Furthermore, the possibility for intrinsic localized modes (ILMs) — Discrete Breathers (DBs) — to occur is investigated, from first principles. The effect of mode-coupling is also briefly considered. The relation to previous results on atomic chains, and also to experimental results on strongly-coupled dust layers in gas discharge plasmas, is briefly discussed.
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Sanchez-Mondragon, Joel, and Alberto Omar Vazquez-Hernandez. "Solitary wave collisions by double-dam-broken simulations with the MPS method." Engineering Computations 35, no. 1 (2018): 53–70. http://dx.doi.org/10.1108/ec-04-2016-0142.
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Purpose The paper aims to apply a modified version of the MPS method to a double-dam-breaking test in which high dispersion zones and high natural clusterization zones are present, such as when the water column collapses into two sides and the two solitary waves collide, respectively. Design/methodology/approach The work takes advantage of the mixed source term from the cheaper computational version of the moving particle semi-implicit (MPS) method to reduce one step from the MPS classical algorithm. The proposed test can be successfully simulated by applying modifications to the variance parameter in the Laplacian operator and gradient model. Findings The results show stable behavior in dispersion and clusterization zones. Also, the collision and merging produced by solitary waves was successfully simulated. Research limitations/implications The main limitation in this work was the development of a comparison between the obtained results and the simulations with the original cheaper computational version of the MPS, this limitation is due to the overestimation of inter particle repulsive forces from its gradient model. Practical implications The application of solitary waves is of paramount importance in a number of applications, and this stems from the fact that the interaction of solitary waves with ships and other floating structures could generate highly deformed and complex free surface flows. Social implications For future work, the modified version of the MPS method can be applied in flow over sill base simulations, in close and open channels, and in simulating breaking waves to determine impact pressures by using solitary wave propagation. Originality/value The simulation of interaction of large groups of particles as in the case when two solitary waves collide could cause severe instability problems in pressure, causing the computer analysis to stop. MPS classical algorithm takes into account an explicit step that, in this case, may provoke the problem. For this reason, the cheaper version of MPS method is used to correctly simulate solitary wave interactions.
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Leinonen, Ville, Harri Kokkola, Taina Yli-Juuti, et al. "Comparison of particle number size distribution trends in ground measurements and climate models." Atmospheric Chemistry and Physics 22, no. 19 (2022): 12873–905. http://dx.doi.org/10.5194/acp-22-12873-2022.
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Abstract. Despite a large number of studies, out of all drivers of radiative forcing, the effect of aerosols has the largest uncertainty in global climate model radiative forcing estimates. There have been studies of aerosol optical properties in climate models, but the effects of particle number size distribution need a more thorough inspection. We investigated the trends and seasonality of particle number concentrations in nucleation, Aitken, and accumulation modes at 21 measurement sites in Europe and the Arctic. For 13 of those sites, with longer measurement time series, we compared the field observations with the results from five climate models, namely EC-Earth3, ECHAM-M7, ECHAM-SALSA, NorESM1.2, and UKESM1. This is the first extensive comparison of detailed aerosol size distribution trends between in situ observations from Europe and five earth system models (ESMs). We found that the trends of particle number concentrations were mostly consistent and decreasing in both measurements and models. However, for many sites, climate models showed weaker decreasing trends than the measurements. Seasonal variability in measured number concentrations, quantified by the ratio between maximum and minimum monthly number concentration, was typically stronger at northern measurement sites compared to other locations. Models had large differences in their seasonal representation, and they can be roughly divided into two categories: for EC-Earth and NorESM, the seasonal cycle was relatively similar for all sites, and for other models the pattern of seasonality varied between northern and southern sites. In addition, the variability in concentrations across sites varied between models, some having relatively similar concentrations for all sites, whereas others showed clear differences in concentrations between remote and urban sites. To conclude, although all of the model simulations had identical input data to describe anthropogenic mass emissions, trends in differently sized particles vary among the models due to assumptions in emission sizes and differences in how models treat size-dependent aerosol processes. The inter-model variability was largest in the accumulation mode, i.e. sizes which have implications for aerosol–cloud interactions. Our analysis also indicates that between models there is a large variation in efficiency of long-range transportation of aerosols to remote locations. The differences in model results are most likely due to the more complex effect of different processes instead of one specific feature (e.g. the representation of aerosol or emission size distributions). Hence, a more detailed characterization of microphysical processes and deposition processes affecting the long-range transport is needed to understand the model variability.
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Thalamala, Ravi Chandran, A. Venkata Swamy Reddy, and B. Janet. "A Novel Bio-Inspired Algorithm Based on Social Spiders for Improving Performance and Efficiency of Data Clustering." Journal of Intelligent Systems 29, no. 1 (2018): 311–26. http://dx.doi.org/10.1515/jisys-2017-0178.
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Abstract Since the last decade, the collective intelligent behavior of groups of animals, birds or insects have attracted the attention of researchers. Swarm intelligence is the branch of artificial intelligence that deals with the implementation of intelligent systems by taking inspiration from the collective behavior of social insects and other societies of animals. Many meta-heuristic algorithms based on aggregative conduct of swarms through complex interactions with no supervision have been used to solve complex optimization problems. Data clustering organizes data into groups called clusters, such that each cluster has similar data. It also produces clusters that could be disjoint. Accuracy and efficiency are the important measures in data clustering. Several recent studies describe bio-inspired systems as information processing systems capable of some cognitive ability. However, existing popular bio-inspired algorithms for data clustering ignored good balance between exploration and exploitation for producing better clustering results. In this article, we propose a bio-inspired algorithm, namely social spider optimization (SSO), for clustering that maintains a good balance between exploration and exploitation using female and male spiders, respectively. We compare results of the proposed algorithm SSO with K means and other nature-inspired algorithms such as particle swarm optimization (PSO), ant colony optimization (ACO) and improved bee colony optimization (IBCO). We find it to be more robust as it produces better clustering results. Although SSO solves the problem of getting stuck in the local optimum, it needs to be modified for locating the best solution in the proximity of the generated global solution. Hence, we hybridize SSO with K means, which produces good results in local searches. We compare proposed hybrid algorithms SSO+K means (SSOKC), integrated SSOKC (ISSOKC), and interleaved SSOKC (ILSSOKC) with K means+PSO (KPSO), K means+genetic algorithm (KGA), K means+artificial bee colony (KABC) and interleaved K means+IBCO (IKIBCO) and find better clustering results. We use sum of intra-cluster distances (SICD), average cosine similarity, accuracy and inter-cluster distance to measure and validate the performance and efficiency of the proposed clustering techniques.
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Suraj, M. V., A. Talaat, B. C. Dodrill, Y. Wang, J. K. Lee, and P. R. Ohodnicki. "Magnetic characterization of self-assembled nanostructures in cobalt ferrites using first-order reversal curve (FORC) analysis." AIP Advances 12, no. 3 (2022): 035031. http://dx.doi.org/10.1063/9.0000329.
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Magnetic ceramics are important for numerous technologically relevant applications with a detailed understanding of structure, property, and processing inter-relationships playing a critical role in tailoring magnetic properties. Spinel ferrites are a particularly interesting class of magnetic ceramics of chemical formula AB2O4, with applications including biomedical hyperthermia and high frequency electrical power conversion. In this contribution, we seek to investigate a unique class of Co-ferrites in which spinodal decomposition can produce a ferrite nanocomposite with chemistry and stress state fluctuating within the interior of crystalline grains on the nm-scale, resulting in corresponding fluctuations of intrinsic magnetic properties as well as exchange and magnetostatic interactions. Structural and magnetic characterization of spinel ferrite samples are carried out (1) in the as-milled state prior to thermal processing, (2) after chemical and structural homogenization with a thermal calcination step, and (3) in the spinodal decomposed state following a subsequent annealing treatment within the Co-ferrite miscibility gap. Of note is the formation of a wasp-waisted hysteresis loop which emerges for the spinodal decomposed Co-ferrite sample, indicative of more complex magnetization reversal processes at relatively large applied fields than for homogeneous Co-ferrite samples of similar particle size and identical nominal chemistry. First order reversal curve (FORC) analysis is applied to further characterize the magnetization response, and a conventional interpretation of observed features in the FORC contrast is presented to discuss potential dominant magnetization mechanisms. The work described here represents the first application of FORC to spinodal decomposed magnetic ceramics and provides a strong foundation for future investigations seeking to quantitatively describe the impacts of nm-scale chemical, structural, and magnetic fluctuations on magnetization processes in ferrite spinel nanocomposite systems.
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Chandola, Himanshu, Tim E. Williamson, Bruce A. Craig, Alan M. Friedman, and Chris Bailey-Kellogg. "Stoichiometries and affinities of interacting proteins from concentration series of solution scattering data: decomposition by least squares and quadratic optimization." Journal of Applied Crystallography 47, no. 3 (2014): 899–914. http://dx.doi.org/10.1107/s1600576714005913.
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In studying interacting proteins, complementary insights are provided by analyzing both the association model (the stoichiometry and affinity constants of the intermediate and final complexes) and the quaternary structure of the resulting complexes. Many current methods for analyzing protein interactions either give a binary answer to the question of association and no information about quaternary structure or at best provide only part of the complete picture. Presented here is a method to extract both types of information from X-ray or neutron scattering data for a series of equilibrium mixtures containing the initial components at different concentrations. The method determines the association pathway and constants, along with the scattering curves of the individual members of the mixture, so as to best explain the scattering data for the mixtures. The derived curves then enable reconstruction of the intermediate and final complexes. Using simulated solution scattering data for four hetero-oligomeric complexes with different structures, molecular weights and association models, it is demonstrated that this method accurately determines the simulated association model and scattering profiles for the initial components and complexes. Recognizing that experimental mixtures contain static contaminants and nonspecific complexes with the lowest affinities (inter-particle interference) as well as the desired specific complex(es), a new analytical method is also employed to extend this approach to evaluating the association models and scattering curves in the presence of static contaminants, testing both a nonparticipating monomer and a large homo-oligomeric aggregate. It is demonstrated that the method is robust to both random noise and systematic noise from such contaminants, and the treatment of nonspecific complexes is discussed. Finally, it is shown that this method is applicable over a large range of weak association constants typical of specific but transient protein–protein complexes.
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Ledevin, M., N. Arndt, and A. Simionovici. "The rheological behavior of fracture-filling cherts: example of Barite Valley dikes, Barberton Greenstone Belt, South Africa." Solid Earth Discussions 6, no. 1 (2014): 1227–64. http://dx.doi.org/10.5194/sed-6-1227-2014.
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Abstract. A 100 m-thick complex of near-vertical carbonaceous chert dikes marks the transition from the Mendon to Mapepe Formations (3260 Ma) in the Barberton Greenstone Belt, South Africa. Fracturing was intense in this area, as shown by the profusion and width of the dikes (ca. 1 m on average) and by the abundance of completely shattered rocks. The dike-and-sill organization of the fracture network and the upward narrowing of some of the large veins indicate that at least part of the fluid originated at depth and migrated upward in this hydrothermal plumbing system. Abundant angular fragments of silicified country rock are suspended and uniformly distributed within the larger dikes. Jigsaw-fit structures and confined bursting textures indicate that hydraulic fracturing was at the origin of the veins. The confinement of the dike system beneath an impact spherule bed suggests that the hydrothermal circulations were triggered by the impact and located at the external margin of a large crater. From the geometry of the dikes and the petrography of the cherts, we infer that the fluid that invaded the fractures was thixotropic. On one hand, the injection of black chert into extremely fine fractures is evidence for low viscosity at the time of injection; on the other hand, the lack of closure of larger veins and the suspension of large fragments in a chert matrix provide evidence of high viscosity soon thereafter. The inference is that the viscosity of the injected fluid increased from low to high as the fluid velocity decreased. Such rheological behavior is characteristic of media composed of solid and colloidal particles suspended in a liquid. The presence of abundant clay-sized, rounded particles of silica, carbonaceous matter and clay minerals, the high proportion of siliceous matrix and the capacity of colloidal silica to form cohesive 3-D networks through gelation, account for the viscosity increase and thixotropic behavior of the fluid that filled the veins. Stirring and shearing of the siliceous mush as it was injected imparted a low viscosity by decreasing internal particle interactions; then, as the flow rate declined, the fluid became highly viscous as the inter-particulate bonds (siloxane bonds, Si-O-Si) were reconstituted. The gelation of the chert was rapid and the structure persisted at low temperature (T < 200 °C) before fractures were sealed and chert indurated.
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Yi, Xiao Qin, Qing Hai Zeng, and Ying Liang. "Analysis of Motion Process of Incompact Landslip-Collapse Soil." Advanced Materials Research 602-604 (December 2012): 2174–78. http://dx.doi.org/10.4028/www.scientific.net/amr.602-604.2174.
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Simulating motion process of incompact landslip-collapse soil. Monitoring evolution process of average contact force and unbalance force when which are moving. Simulation results indicate that: Process of its motion manifest the macro space position changes, as well as, are the change process about contact stress, unbalance force within the inter particle and single particle movement mechanics etc. Average contact force reflects close degree between particles, fluctuation extent of microscopic parameter and levels of interaction between particles. Microscopic parameters of movement process can be used in the theoretic modeling analysis of complex movement of the incompact soil.
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Ji, Xian Jun, and Guo Qiang Ou. "Numerical Simulation and Analysis of Motion Process of Incompact Soil along Slope." Applied Mechanics and Materials 138-139 (November 2011): 459–65. http://dx.doi.org/10.4028/www.scientific.net/amm.138-139.459.
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Simulating motion process of incompact soil. Monitoring evolution process of average contact force and unbalance force between particles during moving; Recording microscopic parameters and its changing processes, incliding spatial locations, translational rate and rotation rate of specific particle during the moving. Simulation results properly reproduced the whole process of it along slope, which include the starting, moving, piling up. Simulation results indicate that: Process of its motion manifest the macro space position changes, as well as, are the change process about contact stress, unbalance force within the inter particle and single particle movement mechanics etc. Size of average contact force reflects close degree between particles, fluctuation extent of microscopic parameter and levels of interaction between particles. Microscopic parameters of movement process can be used in the theoretic modeling analysis of complex movement of the incompact soil.
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RETKUTE, RENATA, and JAMES P. GLEESON. "ROLE OF INTERACTION ON NOISE-INDUCED TRANSPORT OF TWO COUPLED PARTICLES IN BROWNIAN RATCHET DEVICES." Fluctuation and Noise Letters 06, no. 03 (2006): L263—L277. http://dx.doi.org/10.1142/s0219477506003409.
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The motion of elastically coupled Brownian particles in ratchet-like potentials has attracted much recent interest due to its application to transport processes in many fields, including models of DNA polymers. We consider the influence of the type of interacting force on the transport of two particles in a one-dimensional flashing ratchet. Our aim is to examine whether the common assumption of elastic coupling captures the important features of ratchet transport when the inter-particle forces are more complex. We compare Lennard-Jones type interaction to the classical case of elastically coupled particles. Numerical simulations agree with analytical formulas for the limiting cases where the coupling is very weak or very strong. Parameter values where the Lennard-Jones force is not well approximated by a linearization of the force about the equilibrium distance are identified.
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Patnaik, Sansit, and Fabio Semperlotti. "Variable-order particle dynamics: formulation and application to the simulation of edge dislocations." Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 378, no. 2172 (2020): 20190290. http://dx.doi.org/10.1098/rsta.2019.0290.
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This study presents the application of variable-order (VO) fractional operators to modelling the dynamics of edge dislocations under the effect of a static state of shear stress. More specifically, a particle dynamic approach is used to simulate the microscopic structure of a material where the constitutive atoms or molecules are modelled via discrete masses and their interaction via inter-particle forces. VO operators are introduced in the formulation in order to capture the complex linear-to-nonlinear dynamic transitions following the translation of dislocations as well as the creation and annihilation of bonds between particles. Remarkably, the motion of the dislocation does not require any a priori assumption in terms of either possible trajectory or sections of the model that could undergo the nonlinear transition associated with the creation and annihilation of bonds. The model only requires the definition of the initial location of the dislocations. Results will show that the VO formulation is fully evolutionary and capable of capturing both the sliding and the coalescence of edge dislocations by simply exploiting the instantaneous response of the system and the state of stress. This article is part of the theme issue ‘Advanced materials modelling via fractional calculus: challenges and perspectives’.
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Nanni, Alessandro, Gianni Tinarelli, Carlo Solisio, and Cristina Pozzi. "Comparison between Puff and Lagrangian Particle Dispersion Models at a Complex and Coastal Site." Atmosphere 13, no. 4 (2022): 508. http://dx.doi.org/10.3390/atmos13040508.
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A comparison between a puff atmospheric dispersion model (hereafter: PuM) and a Lagrangian particle model (hereafter: LPM) was conducted for a real case of emissions from an industrial plant, in the context of a complex and coastal site. The PuM’s approach is well-known and widely adopted worldwide, thanks to the authoritative suggestions by the US-EPA for regulatory use as, according to the definitions included in its guidelines, an “alternative” to “preferred” models; LPMs are more advanced models and have gained reliability over the last two decades. Therefore, it is of interest to provide insights into the decision to adopt or recommend, in the field of atmospheric impact assessment, a more advanced, but more knowledge- and resource-intensive, modeling tool, rather than an established albeit less accurate one. An inter-comparison of the two approaches is proposed based on the use of various statistical and comparative parameters with the goal of studying their differences in reproducing maps of ground-level ambient concentration statistics for assessment purposes (annual means, hourly peaks). The models were tested under a year-long simulation. The dispersion from both a point and a volume source, belonging to an existing industrial plant, was analyzed separately. The inter-comparison was performed through the analysis of 2D ground concentration maps, scatterplots, and three classical indices from the 2D maps of annual concentration statistics. To correlate the differences among models with site characteristics, the statistics were analyzed not only globally, but also according to distance from the source, the elevation, and the land-use classification. The analysis shows that around-its-axis plume dispersion in LPM is lower than in PuM over all the land-use types except water surfaces, in agreement with the theoretical basis provided by the models. Because of its more advanced theoretical formulation, e.g., in the interaction of the plume with the complex terrain and the three-dimensional wind field, an LPM used as a comparison term allowed us to highlight the weaknesses of a more traditional approach, such as PuM, in reproducing effects such as plume up-sloping, deflection, channeling, confinement, and wind shear diffusion.
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Yang, J., S. Kook, K. Kim, and C. Kweon. "In-Flame And In-Cylinder Flow/Turbulence Measurements Near The Glow Plug Using Flame Image Velocimetry And Particle Image Velocimetry In An Optical Compression-Ignition Engine." Proceedings of the International Symposium on the Application of Laser and Imaging Techniques to Fluid Mechanics 20 (July 11, 2022): 1–19. http://dx.doi.org/10.55037/lxlaser.20th.94.
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The present study implements two diagnostic methods based on tracking of seeded olive oil droplets (PIV: particle image velocimetry) and pattern changes detected in high-speed flame movies (FIV: flame image velocimetry) in a small-bore optical diesel engine. For each measurement, a total of 100 engine cycles are recorded and processed to address the inherent cyclic variations. The ensemble-averaged flow fields and turbulence intensity distribution extracted from individual cycles via the spatial filtering method are discussed with a particular interest in the influence of glow plug on flow and turbulence, i.e. rigid body and fluid interaction. The PIV results show a swirl flow structure forms and rotates with its centre shifted towards the exhaust side, leading to an asymmetric swirl structure. By comparing a PIV laser plane tilted towards the glow plug and a 10 mm horizontal plane below the cylinder head with no glow flow-plug interaction, it is observed that the flow-plug interaction causes the flow winding around the plug tip to generate complex flow structures and new vortices downstream of the plug. The tilted plane and 10-mm plane show similar bulk flow magnitude distribution patterns; however, the flow-plug interaction generates high turbulence in the tilted plane right downstream of the plug tip where new vortices form, which lasts for a few crank angles. The spatially averaged flow magnitude and turbulence intensity are measured higher in the 10-mm plane where there is no flow-plug interaction, suggesting the increased turbulence is a localised behaviour. The flame-plug interaction is also investigated during the combustion event using the FIV method. The level of flame-plug interaction is adjusted by changing the inter-jet spacing angle of two nozzle holes with one case showing high interaction and the other displaying low interaction. From the FIV measurements, the most significant effect of the flame-plug interaction is observed as the further penetration of the wall bounced flame for the high interaction case. This is due to the glow plug as a rigid body blocking the swirl flow and promoting the flame penetration back towards the centre of the combustion chamber upon the piston-bowl wall impingement. The measured turbulence intensity is also higher thanks to the enhanced wall bounced flame in addition to more significant flame-plug interaction at the interface.
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Lakhbayeva, Zh A., R. S. Taubayeva, S. M. Tazhibayeva, A. A. Barany, and K. B. Musabekov. "Aggregation of Aqueous Kaolin Suspensions in the Presence of Cationic Polyelectrolytes, Anionic Polyelectrolytes and their Mixtures." Eurasian Chemico-Technological Journal 18, no. 2 (2016): 117. http://dx.doi.org/10.18321/ectj432.
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The influence of anionic, cationic synthetic polyelectrolytes and their mixtures on the aggregation of kaolin hydrosuspension has been studied by means of spectrophotometry, electrophoresis and dynamic light scattering (DLS). An enhancement of the flocculating property of the cationic polyelectrolyte FO 4650 in accordance with its consumption increases from 0.77 mg/g to 7.7 mg/g has been found. At these conditions the relative size of floccules (R) increases from 1.0 to 13.0. The increase of the flocculating property accordingly to the increasing charge of anionic polyelectrolyte is observed in mixtures of cationic and anionic polyelectrolytes. The time dependences of R in presence of the weakly charged cationic polyelectrolyte mixtures reach a plateau region. This can be associated with the formation of electrostatic contacts between the solid surface and the polymer mixtures, as well as with stabilizing equilibrium conformation of macromolecules. It has been found that mixtures of oppositely charged polyelectrolytes lead to more efficient aggregation of particles than individual polyelectrolytes. This process is enhanced by the introduction primarily of the cationic polyelectrolyte and then the anionic one (R = 6‒10). Use of the pre-formulated mixtures of polymers leads to the marked increase in degree of particle aggregation (R = 12). The reason is an interaction of kaolin particles with inter-polymer complex formed by electrostatic attraction of oppositely charged polyelectrolytes.
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Brás, Ana, Ana Arizaga, Uxue Agirre, et al. "Chain-End Effects on Supramolecular Poly(ethylene glycol) Polymers." Polymers 13, no. 14 (2021): 2235. http://dx.doi.org/10.3390/polym13142235.
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In this work we present a fundamental analysis based on small-angle scattering, linear rheology and differential scanning calorimetry (DSC) experiments of the role of different hydrogen bonding (H-bonding) types on the structure and dynamics of chain-end modified poly(ethylene glycol) (PEG) in bulk. As such bifunctional PEG with a molar mass below the entanglement mass Me is symmetrically end-functionalized with three different hydrogen bonding (H-bonding) groups: thymine-1-acetic acid (thy), diamino-triazine (dat) and 2-ureido-4[1H]-pyrimidinone (upy). A linear block copolymer structure and a Newtonian-like dynamics is observed for PEG-thy/dat while results for PEG-upy structure and dynamics reveal a sphere and a network-like behavior, respectively. These observations are concomitant with an increase of the Flory–Huggins interaction parameter from PEG-thy/dat to PEG-upy that is used to quantify the difference between the H-bonding types. The upy association into spherical clusters is established by the Percus–Yevick approximation that models the inter-particle structure factor for PEG-upy. Moreover, the viscosity study reveals for PEG-upy a shear thickening behavior interpreted in terms of the free path model and related to the time for PEG-upy to dissociate from the upy clusters, seen as virtual crosslinks of the formed network. Moreover, a second relaxation time of different nature is also obtained from the complex shear modulus measurements of PEG-upy by the inverse of the angular frequency where G’ and G’’ crosses from the network-like to glass-like transition relaxation time, which is related to the segmental friction of PEG-upy polymeric network strands. In fact, not only do PEG-thy/dat and PEG-upy have different viscoelastic properties, but the relaxation times found for PEG-upy are much slower than the ones for PEG-thy/dat. However, the activation energy related to the association dynamics is very similar for both PEG-thy/dat and PEG-upy. Concerning the segmental dynamics, the glass transition temperature obtained from both rheological and calorimetric analysis is similar and increases for PEG-upy while for PEG-thy/dat is almost independent of association behavior. Our results show how supramolecular PEG properties vary by modifying the H-bonding association type and changing the molecular Flory–Huggins interaction parameter, which can be further explored for possible applications.
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Bose, Subhaya, Patrick S. Noerr, Ajay Gopinathan, Arvind Gopinath, and Kinjal Dasbiswas. "Collective States of Active Particles With Elastic Dipolar Interactions." Frontiers in Physics 10 (May 3, 2022). http://dx.doi.org/10.3389/fphy.2022.876126.
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Many types of animal cells exert active, contractile forces and mechanically deform their elastic substrate, to accomplish biological functions such as migration. These substrate deformations provide a mechanism in principle by which cells may sense other cells, leading to long-range mechanical inter–cell interactions and possible self-organization. Here, inspired by cell mechanobiology, we propose an active matter model comprising self-propelling particles that interact at a distance through their mutual deformations of an elastic substrate. By combining a minimal model for the motility of individual particles with a linear elastic model that accounts for substrate-mediated, inter–particle interactions, we examine emergent collective states that result from the interplay of motility and long-range elastic dipolar interactions. In particular, we show that particles self-assemble into flexible, motile chains which can cluster to form diverse larger-scale compact structures with polar order. By computing key structural and dynamical metrics, we distinguish between the collective states at weak and strong elastic interaction strength, as well as at low and high motility. We also show how these states are affected by confinement within a channel geometry–an important characteristic of the complex mechanical micro-environment inhabited by cells. Our model predictions may be generally applicable to active matter with dipolar interactions ranging from biological cells to synthetic colloids endowed with electric or magnetic dipole moments.
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Judge, Russell A., Janani Sridar, Kathryn Tunyasunvunakool, et al. "Structure of the PAPP-ABP5 complex reveals mechanism of substrate recognition." Nature Communications 13, no. 1 (2022). http://dx.doi.org/10.1038/s41467-022-33175-2.
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AbstractInsulin-like growth factor (IGF) signaling is highly conserved and tightly regulated by proteases including Pregnancy-Associated Plasma Protein A (PAPP-A). PAPP-A and its paralog PAPP-A2 are metalloproteases that mediate IGF bioavailability through cleavage of IGF binding proteins (IGFBPs). Here, we present single-particle cryo-EM structures of the catalytically inactive mutant PAPP-A (E483A) in complex with a peptide from its substrate IGFBP5 (PAPP-ABP5) and also in its substrate-free form, by leveraging the power of AlphaFold to generate a high quality predicted model as a starting template. We show that PAPP-A is a flexible trans-dimer that binds IGFBP5 via a 25-amino acid anchor peptide which extends into the metalloprotease active site. This unique IGFBP5 anchor peptide that mediates the specific PAPP-A-IGFBP5 interaction is not found in other PAPP-A substrates. Additionally, we illustrate the critical role of the PAPP-A central domain as it mediates both IGFBP5 recognition and trans-dimerization. We further demonstrate that PAPP-A trans-dimer formation and distal inter-domain interactions are both required for efficient proteolysis of IGFBP4, but dispensable for IGFBP5 cleavage. Together the structural and biochemical studies reveal the mechanism of PAPP-A substrate binding and selectivity.
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Miangolarra, Ander Movilla, and Michele Castellana. "On Non-ideal Chemical-Reaction Networks and Phase Separation." Journal of Statistical Physics 190, no. 1 (2022). http://dx.doi.org/10.1007/s10955-022-03037-8.
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AbstractMuch of the theory on chemical-reaction networks (CRNs) has been developed in the ideal-solution limit, where interactions between the solutes are negligible. However, there is a large variety of phenomena in biological cells and soft-matter physics which appear to deviate from the ideal-solution behaviour. Particularly striking is the case of liquid-liquid phase separation, which is typically caused by inter-particle interactions. Here, we revisit a number of known results in the domain of ideal CRNs, and we generalise and adapt them to arbitrary interactions between the solutes which stem from a given free energy. We start by reviewing the theory of chemical reaction networks, linking it to concepts in statistical physics. Then we obtain a number of new results for non-ideal complex-balanced networks, where the creation and annihilation rates are equal for all chemical complexes which appear as reactants or products in the CRN. Among these is the form of the steady-state probability distribution and Lyapunov functions for such networks. Finally, this allows us to draw a phase diagram for complex-balanced reaction-diffusion systems based on the minimisation of such Lyapunov function, with a rationale similar to that of equilibrium thermodynamics but for systems that may sustain non-equilibrium chemical currents at steady state. In addition, we show that for complex-balanced networks at steady-state, there are no diffusion currents.
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Saeedipour, Mahdi, and Simon Schneiderbauer. "Toward a universal description of multiphase turbulence phenomena based on the vorticity transport equation." Physics of Fluids, July 1, 2022. http://dx.doi.org/10.1063/5.0098824.
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Understanding the evolution of turbulence in multiphase flows remains achallenge due to the complex inter-phase interactions at different scales. This paper attempts to enlighten the multiphase turbulence phenomenon from a new perspective by exploiting the classical concept of vorticity and its role in the evolution of the turbulent energy cascade. We start with the vorticity transport equations for two different multiphase flow formulations, which are one-fluid and two-fluid models. By extending the decaying homogeneous isotropic turbulence (HIT) problem to the multiphase flow context, we performed two highly-resolved simulations of HIT in the presence of (i) a thin interface layer, and (ii) homogeneously distributed solid particle. These two configurations allow for the investigation of interfacial turbulence and particulate turbulence, respectively. Besides the analysis of the global flow characteristic in both cases, we evaluate the spectral contribution of each production/dissipation mechanism in the vorticity transport equation to the distribution of vortical energy (enstrophy) across the scales. We base our discussion on the role of the main inter-phase interaction mechanisms in vorticity transport (i.e. the surface tension for interfacial turbulence and drag force for particulate turbulence), and unveil a similar contribution from these mechanisms to the multiphase turbulence cascade. The results also explain the deviation of kinetic energy and enstrophy spectra of multiphase HIT problems from their single-phase similitudes, confirming the validity of this approach for establishing a universal description of multiphase turbulence.
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Dhaouadi, W., E. Marteau, H. Kolvenbach, et al. "Discrete element modeling of planetary ice analogs: mechanical behavior upon sintering." Granular Matter 24, no. 1 (2021). http://dx.doi.org/10.1007/s10035-021-01167-6.
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AbstractPotentially habitable icy Ocean Worlds, such as Enceladus and Europa, are scientifically compelling worlds in the solar system and high-priority exploration targets. Future robotic exploration of Enceladus and Europa by in-situ missions would require a detailed understanding of the surface material and of the complex lander-surface interactions during locomotion or sampling. To date, numerical modeling approaches that provide insights into the icy terrain’s mechanical behavior have been lacking. In this work, we present a Discrete Element Model of porous planetary ice analogs that explicitly describes the microstructure and its evolution upon sintering. The model dimension is tuned following a Pareto-optimality analysis, the model parameters’ influence on the sample strength is investigated using a sensitivity analysis, and the model parameters are calibrated to experiments using a probabilistic method. The results indicate that the friction coefficient and the cohesion energy density at the particle-scale govern the macroscopic properties of the porous ice. Our model reveals a good correspondence between the macroscopic and bond strength evolutions, suggesting that the strengthening of porous ice results from the development of a large-scale network due to inter-particle bonding. This work sheds light on the multi-scale nature of the mechanics of planetary ice analogs and points to the importance of understanding surface strength evolution upon sintering to design robust robotic systems. Graphic abstract
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Traverso, T., and S. Michelin. "Collective dynamics and rheology of confined phoretic suspensions." Journal of Fluid Mechanics 943 (June 13, 2022). http://dx.doi.org/10.1017/jfm.2022.366.
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Similarly to their biological counterparts, suspensions of chemically active autophoretic swimmers exhibit a non-trivial dynamics involving self-organisation processes as a result of inter-particle interactions. Using a kinetic model for a dilute suspension of autochemotactic Janus particles, we analyse the effect of a confined pressure-driven flow on these collective behaviours and the impact of chemotactic aggregation on the effective viscosity of the active fluid. Four dynamic regimes are identified when increasing the strength of the imposed pressure-driven flow, each associated with a different collective behaviour resulting from the competition of flow- and chemically induced reorientation of the swimmers together with the constraints of confinement. Interestingly, we observe that the effect of the pusher (respectively puller) hydrodynamic signature, which is known to reduce (respectively increase) the effective viscosity of a sheared suspension, is inverted upon the emergence of autochemotactic aggregation. Our results provide new insights into the role of the collective dynamics in complex environments, which are relevant to synthetic as well as biological systems.
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Chugh, Vinit, Shuang Liang, Parsa Yari, Kai Wu, and Jian-Ping Wang. "A method for multiplexed and volumetric-based magnetic particle spectroscopy bioassay: mathematical study." Journal of Physics D: Applied Physics, April 27, 2023. http://dx.doi.org/10.1088/1361-6463/acd0bd.
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Abstract Magnetic particle spectroscopy (MPS) is an emerging biosensing technique that detects target analytes by exploiting the dynamic magnetic responses of magnetic nanoparticles (MNPs). Due to the ease of synthesis and surface chemical functionalization of MNPs, MPS-based bioassays have gained popularity around the globe. One limiting factor for MPS-based assay is the ability to detect multiple analytes simultaneously in a single run, namely, multiplexed bioassay. Several groups have reported the realization of multiplexed bioassays on surface-based MPS platforms by spatially separating reaction areas by using the unique magnetic responses of different MNPs. In this work, we systematically study the magnetization curves (M-H curves) of different types of MNPs and their relationship to the dynamic magnetic responses when subjected to AC magnetic driving fields. Due to the different structures, sizes, and magnetic properties of each kind of MNP, the resulting harmonics are unique. Thus, concurrent quantification (also called “colorization”) of each type of MNP in a mixture is possible by solving the harmonic matrix function. Our results show that the uniqueness of M-H response curves of selected types of MNP and the signal-to-noise ratio (SNR) of the system can affect the accuracy of multiplexed, volumetric-based MPS bioassays. The reported method assumes that each type of MNPs nanoparticles do not interact, and that the magnetic response of the mixture is a linear combination of the responses of each kind of MNP. This assumption may not hold for very dense systems where inter-particle interactions become significant and may require more complex models.
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Gao, Shuxiang, Yunbo Li, Chengrong Ma, Ying Cheng, and Xiaojun Liu. "Emitting long-distance spiral airborne sound using low-profile planar acoustic antenna." Nature Communications 12, no. 1 (2021). http://dx.doi.org/10.1038/s41467-021-22325-7.
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AbstractRecent years have witnessed a rapidly growing interest in exploring the use of spiral sound carrying artificial orbital angular momentum (OAM), toward establishing a spiral-wave-based technology that is significantly more efficient in energy or information delivering than the ordinary plane wave technology. A major bottleneck of advancing this technology is the efficient excitation of far-field spiral waves in free space, which is a must in exploring the use of spiral waves for long-distance information transmission and particle manipulation. Here, we report a low-profile planar acoustic antenna to modulate wavefronts emitted from a near-field point source and achieve far-field spiral airborne sound carrying OAM. Using the holographic interferogram as a 2D modulated artificial acoustic impedance metasurface, we show the efficient conversion from the surface wave into the propagating spiral shape beam both numerically and experimentally. The vortex fields with spiral phases originate from the complex inter-modal interactions between cylindrical surface waves and a spatially-modulated impedance boundary condition. This antenna can open new routes to highly integrated spiral sound emitters that are critical for practical acoustic functional devices.
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Pénzes, Judit J., Hanh T. Pham, Paul Chipman, Emmanuel W. Smith, Robert McKenna, and Peter Tijssen. "Bipartite genome and structural organization of the parvovirus Acheta domesticus segmented densovirus." Nature Communications 14, no. 1 (2023). http://dx.doi.org/10.1038/s41467-023-38875-x.
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AbstractParvoviruses (family Parvoviridae) are currently defined by a linear monopartite ssDNA genome, T = 1 icosahedral capsids, and distinct structural (VP) and non-structural (NS) protein expression cassettes within their genome. We report the discovery of a parvovirus with a bipartite genome, Acheta domesticus segmented densovirus (AdSDV), isolated from house crickets (Acheta domesticus), in which it is pathogenic. We found that the AdSDV harbors its NS and VP cassettes on two separate genome segments. Its vp segment acquired a phospholipase A2-encoding gene, vpORF3, via inter-subfamily recombination, coding for a non-structural protein. We showed that the AdSDV evolved a highly complex transcription profile in response to its multipartite replication strategy compared to its monopartite ancestors. Our structural and molecular examinations revealed that the AdSDV packages one genome segment per particle. The cryo-EM structures of two empty- and one full-capsid population (3.3, 3.1 and 2.3 Å resolution) reveal a genome packaging mechanism, which involves an elongated C-terminal tail of the VP, “pinning” the ssDNA genome to the capsid interior at the twofold symmetry axis. This mechanism fundamentally differs from the capsid-DNA interactions previously seen in parvoviruses. This study provides new insights on the mechanism behind ssDNA genome segmentation and on the plasticity of parvovirus biology.
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Shishova, Elizaveta, Florian Panzer, Martin Werz, and Peter Eberhard. "Reversible inter-particle bonding in SPH for improved simulation of friction stir welding." Computational Particle Mechanics, September 6, 2022. http://dx.doi.org/10.1007/s40571-022-00510-9.
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AbstractFriction stir welding (FSW) is a complex joining process which is governed by multiple intertwined physical phenomena. Besides friction, inelastic heat generation, and heat conduction, it involves high plastic deformations, resulting in a need for a numerical method being able to handle all these. Such a scheme is smoothed particle hydrodynamics (SPH), which is a mesh-free computational technique. Absence of a fixed mesh results in the ability of the method to deal with another challenge of friction stir welding, a coalescence of initially separate workpieces into one due to bonding mechanisms. The background of this phenomenon is a transition from contact between two pieces to one continuum due to enormous changes in several material condition, such as temperature, pressure, strain, and strain rate. This work deals with a new development related to bonding, which will provide deeper understanding about the physical weld formation during FSW. The SPH framework must be extended to consider this bonding mechanism. This involves the bonding criterion definition, the interaction type change, and the SPH–SPH contact formulation. Then, the implementation is tested for two different examples, a compression test and FSW.
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Seifert, Julian, Karin Koch, Melissa Hess, and Annette M. Schmidt. "Magneto-mechanical coupling of single domain particles in soft matter systems." Physical Sciences Reviews, December 4, 2020. http://dx.doi.org/10.1515/psr-2019-0092.
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Abstract Combining inorganic magnetic particles with complex soft matrices such as liquid crystals, biological fluids, gels, or elastomers, allows access to a plethora of magnetoactive effects that are useful for sensing and actuation perspectives, allowing inter alia to explore and manipulate material properties on the nanoscale. The article provides a comprehensive summary of recent advancement on employing magnetic nanoparticles either as tracers for dynamic processes, or as nanoscopic actuating units. By variation of the particle characteristics in terms of size, shape, surface functionality, and magnetic behavior, the interaction between the probe or actuator particles and their environment can be systematically tailored in wide ranges, giving insight into the relevant structure–property relationships.