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1.
Langmuir ; 38(39): 11811-11827, 2022 10 04.
Artículo en Inglés | MEDLINE | ID: mdl-36125172

RESUMEN

Polymer micromaterials in a liquid or gel phase covered with a surfactant membrane are widely used materials in pharmaceuticals, cosmetics, and foods. In particular, cell-sized micromaterials of biopolymer solutions covered with a lipid membrane have been studied as artificial cells to understand cells from a physicochemical perspective. The characteristics and phase transitions of polymers confined to a microscopic space often differ from those in bulk systems. The effect that causes this difference is referred to as the cell-size space effect (CSE), but the specific physicochemical factors remain unclear. This study introduces the analysis of CSE on molecular diffusion, nanostructure transition, and phase separation and presents their main factors, i.e., short- and long-range interactions with the membrane surface and small volume (finite element nature). This serves as a guide for determining the dominant factors of CSE. Furthermore, we also introduce other factors of CSE such as spatial closure and the relationships among space size, the characteristic length of periodicity, the structure size, and many others produced by biomolecular assemblies through the analysis of protein reaction-diffusion systems and biochemical reactions.


Asunto(s)
Polímeros , Tensoactivos , Biología , Lípidos , Polímeros/química , Tensoactivos/química
2.
Soft Matter ; 18(39): 7497-7509, 2022 Oct 12.
Artículo en Inglés | MEDLINE | ID: mdl-36156049

RESUMEN

The self-assembly of two-dimensional dodecagonal quasicrystals (DDQCs) from patchy particles is investigated by Brownian dynamics simulations. The patchy particle has a five-fold rotational symmetry pattern described by the spherical harmonics Y55. From the formation of the DDQC obtained by an annealing process, we find the following mechanism. The early stage of the dynamics is dominated by hexagonal structures. Then, nucleation of dodecagonal motifs appears by particle rearrangement, and finally the motifs span the whole system. The transition from the hexagonal structure into the dodecagonal motif is coincident with the collective motion of the particles. The DDQC consists of clusters of dodecagonal motifs, which can be classified into several packing structures. By the analyses of the DDQC under fixed temperature, we find that the fluctuations are characterised by changes in the network of the dodecagonal motifs. Finally we compare the DDQCs assembled from the patchy particle system and isotropic particle system. The two systems share a similar mechanism of the formation and fluctuation of DDQCs.

3.
J Chem Phys ; 156(5): 054901, 2022 Feb 07.
Artículo en Inglés | MEDLINE | ID: mdl-35135257

RESUMEN

We propose an optimization method for the inverse structural design of self-assembly of anisotropic patchy particles. The anisotropic interaction can be expressed by the spherical harmonics of the surface pattern on a patchy particle, and thus, arbitrary symmetries of the patch can be treated. The pairwise interaction potential includes several to-be-optimized parameters, which are the coefficients of each term in the spherical harmonics. We use the optimization method based on the relative entropy approach and generate structures by Brownian dynamics simulations. Our method successfully estimates the parameters in the potential for the target structures, such as square lattice, kagome lattice, and dodecagonal quasicrystal.

4.
Soft Matter ; 16(33): 7667-7675, 2020 Aug 26.
Artículo en Inglés | MEDLINE | ID: mdl-32804175

RESUMEN

We investigate the assembly of dipole-like patchy particles confined to a spherical surface by Brownian dynamics simulations. The surface property of the spherical particle is described by the spherical harmonic Y10, and the orientation of the particle is defined as the uniaxial axis. On a flat space, we observe a defect-free square lattice with nematic order. On a spherical surface, defects appear due to the topological constraint. As for the director field, four defects of winding number +1/2 are observed, satisfying the Euler characteristic. We have found many configurations of the four defects lying near a great circle. Regarding the positional order for the square lattice, eight grain boundary scars proliferate linearly with the sphere size. The positions and orientations of the eight grain boundary scars are strongly related to the four +1/2 defect cores.

5.
J Chem Phys ; 150(18): 184904, 2019 May 14.
Artículo en Inglés | MEDLINE | ID: mdl-31091927

RESUMEN

We investigate the self-propulsive motion of a drop containing an active polar field. The drop demonstrates spontaneous symmetry breaking from a uniform orientational order into a splay or bend instability depending on the types of active stress, namely, contractile or extensile, respectively. We develop an analytical theory of the mechanism of this instability, which has been observed only in numerical simulations. We show that both contractile and extensile active stresses result in the instability and self-propulsive motion. We also discuss asymmetry between contractile and extensile stresses and show that extensile active stress generates chaotic motion even under a simple model of the polarity field coupled with motion and deformation of the drop.

6.
Soft Matter ; 14(17): 3221-3231, 2018 May 02.
Artículo en Inglés | MEDLINE | ID: mdl-29670958

RESUMEN

During the early developmental process of organisms, the formation of left-right laterality requires a subtle mechanism, as it is associated with other principal body axes. Any inherent chiral feature in an egg cell can in principal trigger this spontaneous breaking of chiral symmetry. Individual microtubules, major cytoskeletal filaments, are known as chiral objects. However, to date there lacks convincing evidence of a hierarchical connection of the molecular nature of microtubules to large-scale chirality, particularly at the length scale of an entire cell. Here we assemble an in vitro active layer, consisting of microtubules and kinesin motor proteins, on a glass surface. Upon inclusion of methyl cellulose, the layered system exhibits a long-range active nematic phase, characterized by the global alignment of gliding MTs. This nematic order spans over the entire system size in the millimeter range and, remarkably, allows hidden collective chirality to emerge as counterclockwise global rotation of the active MT layer. The analysis based on our theoretical model suggests that the emerging global nematic order results from the local alignment of MTs, stabilized by methyl cellulose. It also suggests that the global rotation arises from the MTs' intrinsic curvature, leading to preferential handedness. Given its flexibility, this layered in vitro cytoskeletal system enables the study of membranous protein behavior responsible for important cellular developmental processes.


Asunto(s)
Cinesinas/química , Cinesinas/metabolismo , Microtúbulos/metabolismo , Simulación de Dinámica Molecular , Rotación , Estereoisomerismo
7.
Eur Phys J E Soft Matter ; 41(6): 76, 2018 Jun 14.
Artículo en Inglés | MEDLINE | ID: mdl-29926216

RESUMEN

We study how hydrodynamic interactions affect the collective behaviour of active particles suspended in a fluid at high concentrations, with particular attention to lubrication forces which appear when the particles are very close to one another. We compute exactly the limiting behaviour of the hydrodynamic interactions between two spherical (circular) active swimmers in very close proximity to one another in the general setting in both three and (two) dimensions. Combining this with far-field interactions, we develop a novel numerical scheme which allows us to study the collective behaviour of large numbers of active particles with accurate hydrodynamic interactions when close to one another. We study active swimmers whose intrinsic flow fields are characterised by force dipoles and quadrupoles. Using this scheme, we are able to show that lubrication forces when the particles are very close to each other can play as important a role as long-range hydrodynamic interactions in determining their many-body behaviour. We find that when the swimmer force dipole is large, finite clusters and open gel-like clusters appear rather than complete phase separation. This suppression is due to near-field lubrication interactions. For swimmers with small force dipoles, we find surprisingly that a globally polar-ordered phase appears because near-field lubrication rather than long-range hydrodynamics dominates the alignment mechanism. Polar order is present for very large system sizes and is stable to fluctuations with a finite noise amplitude. We explain the emergence of polar order using a minimal model in which only the leading rotational effect of the near-field interaction is included. These phenomena are also reproduced in two dimensions.

8.
J Chem Phys ; 148(13): 134906, 2018 Apr 07.
Artículo en Inglés | MEDLINE | ID: mdl-29626879

RESUMEN

Surface-active molecules supplied from a particle fixed at the water surface create a spatial gradient of the molecule concentration, resulting in Marangoni convection. Convective flow transports the molecules far from the particle, enhancing diffusion. We analytically derive the effective diffusion coefficient associated with the Marangoni convection rolls. The resulting estimated effective diffusion coefficient is consistent with our numerical results and the apparent diffusion coefficient measured in experiments.

9.
J Chem Phys ; 143(1): 014117, 2015 Jul 07.
Artículo en Inglés | MEDLINE | ID: mdl-26156475

RESUMEN

A self-propelled particle in a two-dimensional axisymmetric system, such as a particle in a central force field or confined in a circular region, may show rotational or oscillatory motion. These motions do not require asymmetry of the particle or the boundary, but arise through spontaneous symmetry breaking. We propose a generic model for a self-propelled particle in a two-dimensional axisymmetric system. A weakly nonlinear analysis establishes criteria for determining rotational or oscillatory motion.

10.
Adv Sci (Weinh) ; 11(6): e2308030, 2024 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-38054641

RESUMEN

Cells are small, closed spaces filled with various types of macromolecules. Although it is shown that the characteristics of biochemical reactions in vitro are quite different from those in living cells, the role of the co-existence of various macromolecules in cell-size space remains still elusive. Here, using a constructive approach, it is demonstrated that the co-existence of various macromolecules themselves has the ability to tune protein localization for spatiotemporal regulation and a biochemical reaction system in a cell-size space. Both experimental and theoretical analyses reveal that enhancement of interfacial effects by a large surface-area-to-volume ratio facilitates membrane localization of molecules in the cell-size space, and the interfacial effects are alleviated by competitive binding to lipid membranes among multiple proteins even if their membrane affinities are weak. These results indicate that competition for membrane binding among various macromolecules in the cell-size space plays a role in regulating the spatiotemporal molecular organization and biochemical reaction networks. These findings shed light on the importance of surrounding molecules for biochemical reactions using purified elements in small spaces.


Asunto(s)
Proteínas , Proteínas/química , Transporte de Proteínas
11.
Phys Biol ; 9(4): 046004, 2012 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-22785251

RESUMEN

Cross-linked actomyosin bundles retract when severed in vivo by laser ablation, or when isolated from the cell and micromanipulated in vitro in the presence of ATP. We identify the timescale for contraction as a viscoelastic time τ, where the viscosity is due to (internal) protein friction. We obtain an estimate of the order of magnitude of the contraction time τ ≈ 10-100 s, consistent with available experimental data for circumferential microfilament bundles and stress fibers. Our results are supported by an exactly solvable, hydrodynamic model of a retracting bundle as a cylinder of isotropic, active matter, from which the order of magnitude of the active stress is estimated.


Asunto(s)
Citoesqueleto de Actina/química , Actomiosina/química , Fibras de Estrés/química , Citoesqueleto de Actina/metabolismo , Actomiosina/metabolismo , Adenosina Trifosfato/metabolismo , Animales , Simulación por Computador , Elasticidad , Humanos , Hidrodinámica , Cinética , Micromanipulación , Modelos Biológicos , Fibras de Estrés/metabolismo , Estrés Mecánico , Viscosidad
12.
Phys Rev E ; 106(6-2): 065301, 2022 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-36671103

RESUMEN

Partial differential equations (PDEs) have been widely used to reproduce patterns in nature and to give insight into the mechanism underlying pattern formation. Although many PDE models have been proposed, they rely on the pre-request knowledge of physical laws and symmetries, and developing a model to reproduce a given desired pattern remains difficult. We propose a method, referred to as Bayesian modeling of PDEs (BM-PDEs), to estimate the best dynamical PDE for one snapshot of a objective pattern under the stationary state without ground truth. We apply BM-PDEs to nontrivial patterns, such as quasicrystals (QCs), a double gyroid, and Frank-Kasper structures. We also generate three-dimensional dodecagonal QCs from a PDE model. This is done by using the estimated parameters for the Frank-Kasper A15 structure, which closely approximates the local structures of QCs. Our method works for noisy patterns and the pattern synthesized without the ground-truth parameters, which are required for the application toward experimental data.


Asunto(s)
Teorema de Bayes , Modelos Estadísticos
13.
Sci Adv ; 8(23): eabm8460, 2022 Jun 10.
Artículo en Inglés | MEDLINE | ID: mdl-35675408

RESUMEN

Reaction-diffusion coupling (RDc) generates spatiotemporal patterns, including two dynamic wave modes: traveling and standing waves. Although mode selection plays a substantial role in the spatiotemporal organization of living cell molecules, the mechanism for selecting each wave mode remains elusive. Here, we investigated a wave mode selection mechanism using Min waves reconstituted in artificial cells, emerged by the RDc of MinD and MinE. Our experiments and theoretical analysis revealed that the balance of membrane binding and dissociation from the membrane of MinD determines the mode selection of the Min wave. We successfully demonstrated that the transition of the wave modes can be regulated by controlling this balance and found hysteresis characteristics in the wave mode transition. These findings highlight a previously unidentified role of the balance between activators and inhibitors as a determinant of the mode selection of waves by RDc and depict an unexplored mechanism in intracellular spatiotemporal pattern formations.

14.
ACS Nano ; 16(10): 16853-16861, 2022 10 25.
Artículo en Inglés | MEDLINE | ID: mdl-36214379

RESUMEN

Reaction-diffusion (RD) waves, which are dynamic self-organization structures generated by nanosize molecules, are a fundamental mechanism from patterning in nano- and micromaterials to spatiotemporal regulations in living cells, such as cell division and motility. Although the periods of RD waves are the critical element for these functions, the development of a system to control their period is challenging because RD waves result from nonlinear physical dynamics under far-from-equilibrium conditions. Here, we developed an artificial cell system with tunable period of an RD-driven wave (Min protein wave), which determines a cell division site plane in living bacterial cells. The developed system is based on our finding that Min waves are generated by energy consumption of either ATP or dATP, and the period of the wave is different between these two energy suppliers. We showed that the Min-wave period was modulated linearly by the mixing ratio of ATP and dATP and that it was also possible to estimate the mixing ratio of ATP and dATP from the period. Our findings illuminated a previously unidentified principle to control the dissipative dynamics of biomolecules and, simultaneously, built an important framework to construct molecular robots with spatiotemporal units.


Asunto(s)
Células Artificiales , Difusión , Dinámicas no Lineales , División Celular , Adenosina Trifosfato
15.
Biophys J ; 101(6): L33-5, 2011 Sep 21.
Artículo en Inglés | MEDLINE | ID: mdl-21943439

RESUMEN

The magnitude of traction forces exerted by living animal cells on their environment is a monotonically increasing and approximately sigmoidal function of the stiffness of the external medium. We rationalize this observation using active matter theory, and propose that adaptation to substrate rigidity results from an interplay between passive elasticity and active contractility.


Asunto(s)
Fenómenos Mecánicos , Modelos Biológicos , Animales , Fenómenos Biomecánicos , Línea Celular , Supervivencia Celular , Citoesqueleto/metabolismo , Perros , Transporte de Proteínas
16.
Phys Rev Lett ; 105(26): 268302, 2010 Dec 31.
Artículo en Inglés | MEDLINE | ID: mdl-21231718

RESUMEN

We study self-propulsion of a half-metal coated colloidal particle under laser irradiation. The motion is caused by self-thermophoresis: i.e., absorption of a laser at the metal-coated side of the particle creates local temperature gradient which in turn drives the particle by thermophoresis. To clarify the mechanism, temperature distribution and a thermal slip flow field around a microscale Janus particle are measured for the first time. With measured temperature drop across the particle, the speed of self-propulsion is corroborated with the prediction based on accessible parameters. As an application for driving a micromachine, a microrotor is demonstrated.


Asunto(s)
Coloides/química , Rayos Láser , Movimiento (Física) , Temperatura , Colorantes Fluorescentes/química , Microscopía , Rotación
17.
Bio Protoc ; 10(6): e3561, 2020 Mar 20.
Artículo en Inglés | MEDLINE | ID: mdl-33659532

RESUMEN

The Min system determines the cell division plane of bacteria. As a cue of spatiotemporal regulation, the Min system uses wave propagation of MinD protein (Min wave). Therefore, the reconstitution of the Min wave in cell-sized closed space will lead to the creation of artificial cells capable of cell division. The Min waves emerge via coupling between the reactions among MinD, MinE, and ATP and the differences in diffusion rate on the cell membrane and in the cytoplasm. Because Min waves appear only under the balanced condition of the reaction-diffusion coupling, special attentions are needed towards several technical points for the reconstitution of Min waves in artificial cells. This protocol describes a technical method for stably generating Min waves in artificial cells.

18.
Nanoscale ; 12(22): 11960-11970, 2020 Jun 11.
Artículo en Inglés | MEDLINE | ID: mdl-32458918

RESUMEN

The Min system for determining the cell division position at the center in bacteria has a unique character that uses a protein wave (Min wave) that emerges from its components (MinD and MinE). The Min wave emerges under the coupling of chemical reactions and molecular diffusions of MinDE and appears when the concentrations of MinD and MinE are similar. However, the nanoscale mechanism to determine their concentration ranges has remained elusive. In this study, by using artificial cells as a mimic of cells, we showed that the dominant MinE conformations determined the allowable concentration ranges for the emergence of the Min wave. Furthermore, the deletion of the membrane-binding region of MinE indicated that the region was essential for limiting the concentration ranges to be narrower. These findings illustrate a parameter tuning mechanism underlying complex molecular systems at the nanoscale for spatiotemporal regulation in living cells and show a possibility that the regulation of the equilibrium among molecular conformations can work as a switch for cell division.


Asunto(s)
Proteínas de Escherichia coli , Adenosina Trifosfatasas/genética , Adenosina Trifosfatasas/metabolismo , Proteínas Bacterianas , Proteínas de Ciclo Celular/genética , División Celular , Escherichia coli/metabolismo , Conformación Molecular
19.
Elife ; 82019 07 30.
Artículo en Inglés | MEDLINE | ID: mdl-31358115

RESUMEN

The Min system, a system that determines the bacterial cell division plane, uses changes in the localization of proteins (a Min wave) that emerges by reaction-diffusion coupling. Although previous studies have shown that space sizes and boundaries modulate the shape and speed of Min waves, their effects on wave emergence were still elusive. Here, by using a microsized fully confined space to mimic live cells, we revealed that confinement changes the conditions for the emergence of Min waves. In the microsized space, an increased surface-to-volume ratio changed the localization efficiency of proteins on membranes, and therefore, suppression of the localization change was necessary for the stable generation of Min waves. Furthermore, we showed that the cell-sized space strictly limits parameters for wave emergence because confinement inhibits both the instability and excitability of the system. These results show that confinement of reaction-diffusion systems has the potential to control spatiotemporal patterns in live cells.


Asunto(s)
Proteínas de Ciclo Celular/metabolismo , División Celular , Proteínas de Escherichia coli/metabolismo , Regulación de la Expresión Génica , Modelos Teóricos , Transporte de Proteínas , Análisis Espacio-Temporal
20.
Phys Rev E Stat Nonlin Soft Matter Phys ; 77(6 Pt 1): 061805, 2008 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-18643293

RESUMEN

We investigate theoretically the kinetics of the folding transition of a single semiflexible polymer. In the folding transition, the growth rate decreases with an increase in the number of monomers in the collapsed domain, suggesting that the main contribution to dissipation is from the motion of the domain. In the unfolding transition, the dynamic scaling exponents 1/8 and 1/4 were determined for the disentanglement and relaxation steps, respectively. We performed Langevin dynamics simulations to test our theory. It is found that our theory is in good agreement with simulations. We also propose the kinetics of the transitions in the presence of a hydrodynamic interaction.

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