Eur Phys J E Soft Matter
· 2024 Jun · PMID 38913273
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We report high-resolution calorimetric, optical and dielectric studies on two Schiff's based liquid crystalline materials, 4O.5 and 5O.5, which exhibit multiple phase transitions. The study goes beyond the commonly studi...We report high-resolution calorimetric, optical and dielectric studies on two Schiff's based liquid crystalline materials, 4O.5 and 5O.5, which exhibit multiple phase transitions. The study goes beyond the commonly studied isotropic-to-nematic (I-N) and nematic-to-smectic A (N-SmA) phase transitions and explores higher-order smectic phase transitions. The critical exponent, α values, for different phase transitions has been explored. For the I-N, N-SmA, SmA-SmC, SmC-SmF, SmF-CrG and SmB-CrG transitions, α values close to 0.5 and amplitude ratios A/A ~ 1.6 and D/D ~ 1 indicate a first-order nature. Notably, for the SmA-SmB transition, although α (≈ 0.64) is larger than the tricritical value of 0.5, A/A ~ 1.2 and D/D ~ 1, and the study reports an order parameter critical exponent (β) of 0.26 ± 0.002, which supports a tricritical nature for this transition. Importantly, the ratios of A/A and D/D are found to have similar values across all three-measurement methods, indicating consistency and agreement among these methods.
Eur Phys J E Soft Matter
· 2024 Jun · PMID 38900310
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The number of topological defects in the shear flow of active nematic fluids is numerically investigated in this study. The evolution of the flow state of extensile active nematic fluids is explored by increasing the act...The number of topological defects in the shear flow of active nematic fluids is numerically investigated in this study. The evolution of the flow state of extensile active nematic fluids is explored by increasing the activity of active nematic fluids. Evidently, medium-activity active nematic fluids exhibit a highly ordered vortex lattice fluid state. However, high-activity active nematic fluids exhibit a meso-scale turbulent flow accompanied by topological defects. The number of topological defects (N) increases with increasing shear Reynolds number (Re). Fluid viscosity strongly influences N, while the influence of fluid density is relatively weak. N decreases with increasing activity length scale (l) value. A small Re value strongly influences N, whereas a large l value only weakly influences N. As the activity increases, N in contractile active nematic fluids becomes larger than that of extensile active nematic fluids.
Jyothish K, Santiago R, Govardhan S
… +1 more, Hayat S
Eur Phys J E Soft Matter
· 2024 Jun · PMID 38890172
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Trigonal triphenylenoids (TTPs) are a fascinating class of organic molecules with unique structural and electronic properties. Their diverse applications, ranging from organic electronics to nonlinear optics, have spurre...Trigonal triphenylenoids (TTPs) are a fascinating class of organic molecules with unique structural and electronic properties. Their diverse applications, ranging from organic electronics to nonlinear optics, have spurred significant research interest in understanding their physicochemical behavior. Topological indices, mathematical descriptors derived from the molecular graph, offer valuable insights into the structural complexity and potential properties of TTPs. This work focuses on exploring the utility of degree-based topological indices in characterizing and predicting the properties of trigonal triphenylenoids. We systematically calculate various degree-based topological indices, for a diverse set of TTPs with varying substituents and topologies. The relationships between these indices and key physicochemical properties, such as HOMO-LUMO energy gap, thermodynamic stability, and reactivity are investigated using statistical and machine learning approaches. We identify significant correlations between specific degree-based indices and different properties, allowing for potential prediction of these properties based solely on the topological information.
Eur Phys J E Soft Matter
· 2024 Jun · PMID 38880801
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In recent years, the problem of traffic congestion has become increasingly serious, and research on traffic system control has become a new hotspot. Studying the bifurcation characteristics of traffic flow systems and de...In recent years, the problem of traffic congestion has become increasingly serious, and research on traffic system control has become a new hotspot. Studying the bifurcation characteristics of traffic flow systems and designing control schemes for unstable support points can alleviate traffic congestion from a new perspective. This article improves the full speed differential model considering strong wind models from the perspective of bifurcation control to adjust traffic flow. This article theoretically proves the existence conditions of Hopf bifurcation and saddle node bifurcation in the model and finds the stability mutation point of the transportation system stability. A nonlinear system feedback controller was designed for unstable bifurcation points using Chebyshev polynomial approximation and random feedback control methods. Without changing the system equilibrium point, the advance, delay, and elimination of Hopf bifurcation were achieved, and the abrupt behavior of the transportation system was controlled, thereby alleviating traffic congestion. This article explains the changes in the stability of complex transportation systems from the perspective of bifurcation analysis, which can better capture the characteristics of traffic flow. By adjusting the control parameters in the feedback controller, the influence of boundary conditions on the stability of the transportation system is fully described, and the influence of unstable focal points and saddle points on the system is suppressed, thereby slowing down the traffic flow. In addition, unstable bifurcation points can be eliminated, and the Hopf bifurcation can be controlled to advance, delay, and disappear, thereby achieving control over the stable behavior of the transportation system. This helps alleviate traffic congestion and also helps describe actual traffic phenomena.
Adorjáni B, Libál A, Reichhardt C
… +1 more, Reichhardt CJO
Eur Phys J E Soft Matter
· 2024 Jun · PMID 38844720
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We examine run-and-tumble disks in two-dimensional systems where the particles also have a Magnus component to their dynamics. For increased activity, we find that the system forms a motility-induced phase-separated (MIP...We examine run-and-tumble disks in two-dimensional systems where the particles also have a Magnus component to their dynamics. For increased activity, we find that the system forms a motility-induced phase-separated (MIPS) state with chiral edge flow around the clusters, where the direction of the current is correlated with the sign of the Magnus term. The stability of the MIPS state is non-monotonic as a function of increasing Magnus term amplitude, with the MIPS region first extending down to lower activities followed by a break up of MIPS at large Magnus amplitudes into a gel-like state. We examine the dynamics in the presence of quenched disorder and a uniform drive and find that the bulk flow exhibits a drive-dependent Hall angle. This is a result of the side jump effect produced by scattering from the pinning sites and is similar to the behavior found for skyrmions in chiral magnets with quenched disorder.
Eur Phys J E Soft Matter
· 2024 Jun · PMID 38831117
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Small-Angle Scattering (SAS), encompassing both X-ray (SAXS) and Neutron (SANS) techniques, is a crucial tool for structural analysis at the nanoscale, particularly in the realm of biological macromolecules. This paper e...Small-Angle Scattering (SAS), encompassing both X-ray (SAXS) and Neutron (SANS) techniques, is a crucial tool for structural analysis at the nanoscale, particularly in the realm of biological macromolecules. This paper explores the intricacies of SAS, emphasizing its application in studying complex biological systems and the challenges associated with sample preparation and data analysis. We highlight the use of neutron-scattering properties of hydrogen isotopes and isotopic labeling in SANS for probing structures within multi-subunit complexes, employing techniques like contrast variation (CV) for detailed structural analysis. However, traditional SAS analysis methods, such as Guinier and Kratky plots, are limited by their partial use of available data and inability to operate without substantial a priori knowledge of the sample's chemical composition. To overcome these limitations, we introduce a novel approach integrating -SAS, a computational method for simulating SANS with CV, with machine learning (ML). This approach enables the accurate prediction of scattering contrast in multicomponent macromolecular complexes, reducing the need for extensive sample preparation and computational resources. -SAS, utilizing Monte Carlo methods, generates comprehensive datasets from which structural invariants can be extracted, enhancing our understanding of the macromolecular form factor in dilute systems. The paper demonstrates the effectiveness of this integrated approach through its application to two case studies: Janus particles, an artificial structure with a known SAS intensity and contrast, and a biological system involving RNA polymerase II in complex with Rtt103. These examples illustrate the method's capability to provide detailed structural insights, showcasing its potential as a powerful tool for advanced SAS analysis in structural biology.
Eur Phys J E Soft Matter
· 2024 Jun · PMID 38829470
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In the field of biomimetics, the tiny riblet structures inspired by shark skin have been extensively studied for their drag reduction properties in turbulent flows. Here, we show that the ridged surface texture of anothe...In the field of biomimetics, the tiny riblet structures inspired by shark skin have been extensively studied for their drag reduction properties in turbulent flows. Here, we show that the ridged surface texture of another swimming creature in the ocean, i.e., the scallops, also has some friction drag reduction effect. In this study, we investigated the potential drag reduction effects of scallop shell textures using computational fluid dynamics simulations. Specifically, we constructed a conceptual model featuring an undulating surface pattern on a conical shell geometry that mimics scallop. Simulations modeled turbulent fluid flows over the model inserted at different orientations relative to the flow direction. The results demonstrate appreciable friction drag reduction generated by the ribbed hierarchical structures encasing the scallop, while partial pressure drag reduction exhibits dependence on alignment of scallop to the predominant flow direction. Theoretical mechanisms based on classic drag reduction theory in turbulence was established to explain the drag reduction phenomena. Given the analogous working environments of scallops and seafaring vessels, these findings may shed light on the biomimetic design of surface textures to enhance maritime engineering applications. Besides, this work elucidates an additional evolutionary example of fluid drag reduction, expanding the biological repertoire of swimming species.
O'Callaghan JA, Kamat NP, Vargo KB
… +3 more, Chattaraj R, Lee D, Hammer DA
Eur Phys J E Soft Matter
· 2024 Jun · PMID 38829453
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In this study, we demonstrate the fabrication of polymersomes, protein-blended polymersomes, and polymeric microcapsules using droplet microfluidics. Polymersomes with uniform, single bilayers and controlled diameters ar...In this study, we demonstrate the fabrication of polymersomes, protein-blended polymersomes, and polymeric microcapsules using droplet microfluidics. Polymersomes with uniform, single bilayers and controlled diameters are assembled from water-in-oil-in-water double-emulsion droplets. This technique relies on adjusting the interfacial energies of the droplet to completely separate the polymer-stabilized inner core from the oil shell. Protein-blended polymersomes are prepared by dissolving protein in the inner and outer phases of polymer-stabilized droplets. Cell-sized polymeric microcapsules are assembled by size reduction in the inner core through osmosis followed by evaporation of the middle phase. All methods are developed and validated using the same glass-capillary microfluidic apparatus. This integrative approach not only demonstrates the versatility of our setup, but also holds significant promise for standardizing and customizing the production of polymer-based artificial cells.
Gannavarapu A, Arzash S, Muntz I
… +4 more, Shivers JL, Klianeva AM, Koenderink GH, MacKintosh FC
Eur Phys J E Soft Matter
· 2024 May · PMID 38802588
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Fibrous networks such as collagen are common in biological systems. Recent theoretical and experimental efforts have shed light on the mechanics of single component networks. Most real biopolymer networks, however, are c...Fibrous networks such as collagen are common in biological systems. Recent theoretical and experimental efforts have shed light on the mechanics of single component networks. Most real biopolymer networks, however, are composites made of elements with different rigidity. For instance, the extracellular matrix in mammalian tissues consists of stiff collagen fibers in a background matrix of flexible polymers such as hyaluronic acid (HA). The interplay between different biopolymer components in such composite networks remains unclear. In this work, we use 2D coarse-grained models to study the nonlinear strain-stiffening behavior of composites. We introduce a local volume constraint to model the incompressibility of HA. We also perform rheology experiments on composites of collagen with HA. Theoretically and experimentally, we demonstrate that the linear shear modulus of composite networks can be increased by approximately an order of magnitude above the corresponding moduli of the pure components. Our model shows that this synergistic effect can be understood in terms of the local incompressibility of HA, which acts to suppress density fluctuations of the collagen matrix with which it is entangled.
Eur Phys J E Soft Matter
· 2024 May · PMID 38787519
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Sessile drying droplets manifest distinct morphological patterns, encompassing diverse systems, viz., DNA, proteins, blood, and protein-liquid crystal (LC) complexes. This study employs an integrated methodology that com...Sessile drying droplets manifest distinct morphological patterns, encompassing diverse systems, viz., DNA, proteins, blood, and protein-liquid crystal (LC) complexes. This study employs an integrated methodology that combines drying droplet, image texture analysis (features from First Order Statistics, Gray Level Co-occurrence Matrix, Gray Level Run Length Matrix, Gray Level Size Zone Matrix, and Gray Level Dependence Matrix), and statistical data analysis (Generalized Additive Modeling and K-means clustering). It provides a comprehensive qualitative and quantitative exploration by examining LC-protein droplets at varying initial phosphate buffered concentrations (0x, 0.25x, 0.5x, 0.75x, and 1x) during the drying process under optical microscopy with crossed polarizing configuration. Notably, it unveils distinct LC-protein textures across three drying stages: initial, middle, and final. The Generalized Additive Modeling (GAM) reveals that all the features significantly contribute to differentiating LC-protein droplets. Integrating the K-means clustering method with GAM analysis elucidates how textures evolve through the three drying stages compared to the entire drying process. Notably, the final drying stage stands out with well-defined, non-overlapping clusters, supporting the visual observations of unique LC textures. Furthermore, this paper contributes valuable insights, showcasing the efficacy of drying droplets as a rapid and straightforward tool for characterizing and classifying dynamic LC textures.
Eur Phys J E Soft Matter
· 2024 May · PMID 38782771
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We present a scheme for producing tunable active dynamics in a self-propelled robotic device. The robot moves using the differential drive mechanism where two wheels can vary their instantaneous velocities independently....We present a scheme for producing tunable active dynamics in a self-propelled robotic device. The robot moves using the differential drive mechanism where two wheels can vary their instantaneous velocities independently. These velocities are calculated by equating robot's equations of motion in two dimensions with well-established active particle models and encoded into the robot's microcontroller. We demonstrate that the robot can depict active Brownian, run and tumble, and Brownian dynamics with a wide range of parameters. The resulting motion analyzed using particle tracking shows excellent agreement with the theoretically predicted trajectories. Later, we show that its motion can be switched between different dynamics using light intensity as an external parameter. Intriguingly, we demonstrate that the robot can efficiently navigate through many obstacles by performing stochastic reorientations driven by the gradient in light intensity towards a desired location, namely the target. This work opens an avenue for designing tunable active systems with the potential of revealing the physics of active matter and its application for bio- and nature-inspired robotics.
Eur Phys J E Soft Matter
· 2024 May · PMID 38753070
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We investigate the self-propulsion of an inertial active particle confined in a two-dimensional harmonic trap. The particle is suspended in a non-Newtonian or viscoelastic suspension with a friction kernel that decays ex...We investigate the self-propulsion of an inertial active particle confined in a two-dimensional harmonic trap. The particle is suspended in a non-Newtonian or viscoelastic suspension with a friction kernel that decays exponentially with a time constant characterizing the memory timescale or transient elasticity of the medium. By solving the associated non-Markovian dynamics, we identify two regimes in parameter space distinguishing the oscillatory and non-oscillatory behavior of the particle motion. By simulating the particle trajectories and exactly calculating the steady-state probability distribution functions and mean square displacement; interestingly, we observe that with an increase in the memory time scale, the effective temperature of the environment increases. As a consequence, the particle becomes energetic and spread away from the center, covering larger space inside the confinement. On the other hand, with an increase in the duration of the activity, the particle becomes trapped by the harmonic confinement.
Barrio-Zhang H, Ruiz-Gutiérrez É, Orejon D
… +2 more, Wells GG, Ledesma-Aguilar R
Eur Phys J E Soft Matter
· 2024 May · PMID 38735905
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The motion of droplets on solid surfaces in response to an external gradient is a fundamental problem with a broad range of applications, including water harvesting, heat exchange, mixing and printing. Here we study the...The motion of droplets on solid surfaces in response to an external gradient is a fundamental problem with a broad range of applications, including water harvesting, heat exchange, mixing and printing. Here we study the motion of droplets driven by a humidity gradient, i.e. a variation in concentration of their own vapour in the surrounding gas phase. Using lattice-Boltzmann simulations of a diffuse-interface hydrodynamic model to account for the liquid and gas phases, we demonstrate that the droplet migrates towards the region of higher vapour concentration. This effect holds in situations where the ambient gradient drives either the evaporation or the condensation of the droplet, or both simultaneously. We identify two main mechanisms responsible for the observed motion: a difference in surface wettability, which we measure in terms of the Young stress, and a variation in surface tension, which drives a Marangoni flow. Our results are relevant in advancing our knowledge of the interplay between gas and liquid phases out of thermodynamic equilibrium, as well as for applications involving the control of droplet motion.
Timmanaikar ST, Hayat S, Hosamani SM
… +1 more, Banu S
Eur Phys J E Soft Matter
· 2024 May · PMID 38735010
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Coumarins, a subgroup of colorless and crystalline oxygenated heterocyclic compounds originally discovered in the plant Dipteryx odorata, were the subject of a recent study investigating their quantitative structure-acti...Coumarins, a subgroup of colorless and crystalline oxygenated heterocyclic compounds originally discovered in the plant Dipteryx odorata, were the subject of a recent study investigating their quantitative structure-activity relationship (QSAR) in cancer pharmacotherapy. This study utilized graph theoretical molecular descriptors, also known as topological indices, as a numerical representation method for the chemical structures embedded in molecular graphs. These descriptors, derived from molecular graphs, play a pivotal role in quantitative structure-property relationship (QSPR) analysis. In this paper, intercorrelation between the Balban index, connective eccentric index, eccentricity connectivity index, harmonic index, hyper Zagreb index, first path Zagreb index, second path Zagreb index, Randic index, sum connectivity index, graph energy and Laplacian energy is studied on the set of molecular graphs of coumarins. It is found that the pairs of degree-based indices are highly intercorrelated. The use of these molecular descriptors in structure-boiling point modeling was analyzed. Finally, the curve-linear regression between considered molecular descriptors with physicochemical properties of coumarins and coumarin-related compounds is obtained.
Eur Phys J E Soft Matter
· 2024 May · PMID 38720027
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The aggregation or clustering of proteins and other macromolecules plays an important role in the formation of large-scale molecular assemblies within cell membranes. Examples of such assemblies include lipid rafts, and...The aggregation or clustering of proteins and other macromolecules plays an important role in the formation of large-scale molecular assemblies within cell membranes. Examples of such assemblies include lipid rafts, and postsynaptic domains (PSDs) at excitatory and inhibitory synapses in neurons. PSDs are rich in scaffolding proteins that can transiently trap transmembrane neurotransmitter receptors, thus localizing them at specific spatial positions. Hence, PSDs play a key role in determining the strength of synaptic connections and their regulation during learning and memory. Recently, a two-dimensional (2D) diffusion-mediated aggregation model of PSD formation has been developed in which the spatial locations of the clusters are determined by a set of fixed anchoring sites. The system is kept out of equilibrium by the recycling of particles between the cell membrane and interior. This results in a stationary distribution consisting of multiple clusters, whose average size can be determined using an effective mean-field description of the particle concentration around each anchored cluster. In this paper, we derive corrections to the mean-field approximation by applying the theory of diffusion in singularly perturbed domains. The latter is a powerful analytical method for solving two-dimensional (2D) and three-dimensional (3D) diffusion problems in domains where small holes or perforations have been removed from the interior. Applications range from modeling intracellular diffusion, where interior holes could represent subcellular structures such as organelles or biological condensates, to tracking the spread of chemical pollutants or heat from localized sources. In this paper, we take the bounded domain to be the cell membrane and the holes to represent anchored clusters. The analysis proceeds by partitioning the membrane into a set of inner regions around each cluster, and an outer region where mean-field interactions occur. Asymptotically matching the inner and outer stationary solutions generates an asymptotic expansion of the particle concentration, which includes higher-order corrections to mean-field theory that depend on the positions of the clusters and the boundary of the domain. Motivated by a recent study of light-activated protein oligomerization in cells, we also develop the analogous theory for cluster formation in a three-dimensional (3D) domain. The details of the asymptotic analysis differ from the 2D case due to the contrasting singularity structure of 2D and 3D Green's functions.
Eur Phys J E Soft Matter
· 2024 May · PMID 38704810
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In this work, we study the polarization time series obtained from experimental observation of a group of zebrafish (Danio rerio) confined in a circular tank. The complex dynamics of the individual trajectory evolution le...In this work, we study the polarization time series obtained from experimental observation of a group of zebrafish (Danio rerio) confined in a circular tank. The complex dynamics of the individual trajectory evolution lead to the appearance of multiple characteristic scales. Employing the Multifractal Detrended Fluctuation Analysis (MF-DFA), we found distinct behaviors according to the parameters used. The polarization time series are multifractal at low fish densities and their average scales with . On the other hand, they tend to be monofractal, and their average scales with for high fish densities. These two regimes overlap at critical density , suggesting the existence of a phase transition separating them. We also observed that for low densities, the polarization velocity shows a non-Gaussian behavior with heavy tails associated with long-range correlation and becomes Gaussian for high densities, presenting an uncorrelated regime.
Eur Phys J E Soft Matter
· 2024 Apr · PMID 38676815
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We develop a two-timing perturbation analysis to provide quantitative insights on the existence of temporal ratchets in an exemplary system of a particle moving in a tank of fluid in response to an external vibration of...We develop a two-timing perturbation analysis to provide quantitative insights on the existence of temporal ratchets in an exemplary system of a particle moving in a tank of fluid in response to an external vibration of the tank. We consider two-mode vibrations with angular frequencies and , where is a rational number. If is a ratio of odd and even integers (e.g., ), the system yields a net response: here, a nonzero time-average particle velocity. Our first-order perturbation solution predicts the existence of temporal ratchets for . Furthermore, we demonstrate, for a reduced model, that the temporal ratcheting effect for and appears at the third-order perturbation solution. More importantly, we find closed-form formulas for the magnitude and direction of the induced net velocities for these values. On a broader scale, our methodology offers a new mathematical approach to study the complicated nature of temporal ratchets in physical systems.
Eur Phys J E Soft Matter
· 2024 Apr · PMID 38619676
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We use Gürsey's statistical mechanics of a one-dimensional fluid to find a formula for the ratio in the transport of hard spheres across a membrane through a narrow channel that can accommodate molecular movement only i...We use Gürsey's statistical mechanics of a one-dimensional fluid to find a formula for the ratio in the transport of hard spheres across a membrane through a narrow channel that can accommodate molecular movement only in single file. is the membrane permeability for osmotic flow and the permeability for exchange across the membrane in the absence of osmotic flow. The deviation of the ratio from unity indicates the degree of cooperative transport relative to ordinary diffusion of independent molecules. In contrast to an early idea that must be equal to the number of molecules in the channel, regardless of the physical nature of the interactions among the molecules, we find a functional dependence on the fractional occupancy of the length of the channel by the hard spheres. We also attempt a random walk calculation for individually, which gives a result for as well when combined with the ratio.
Eur Phys J E Soft Matter
· 2024 Apr · PMID 38613716
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To gain insights into the mechanisms of free surface oscillation in a rotating mixing container, we observe the free surface deformation and measure the torque acting on the bar. The container was half-filled with liquid...To gain insights into the mechanisms of free surface oscillation in a rotating mixing container, we observe the free surface deformation and measure the torque acting on the bar. The container was half-filled with liquids. Periodic surface oscillation occurs. At the rotational speed where the amplitude of the oscillation reaches its maximum, the time-averaged torque also takes the local maximum values. To account for the sloshing mechanism, an equation of motion is derived using the Lagrangian mechanics; we found that the sloshing occurs when the collision frequency of bar on the surface is consistent with the natural frequency of the system and the damping coefficient is sufficiently smaller than unity. The time-averaged torque increases when the sloshing becomes violent. We conclude that the hydrodynamics of oscillation is successfully modeled using point-mass mechanics, and thus we can reasonably capture the rotation speed at which violent oscillation occurs.