Hysteretic dynamics of active particles in a periodic orienting field

Active motion of living organisms and artificial self-propelling particles has been an area of intense research at the interface of biology, chemistry and physics. Significant progress in understanding these phenomena has been related to the observation that dynamic self-organization in active systems has much in common with ordering in equilibrium condensed matter such as spontaneous magnetization in ferromagnets. The velocities of active particles may behave similar to magnetic dipoles and develop global alignment, although interactions between the individuals might be completely different. In this work, we show that the dynamics of active particles in external fields can also be described in a way that resembles equilibrium condensed matter. It follows simple general laws, which are independent of the microscopic details of the system. The dynamics is revealed through hysteresis of the mean velocity of active particles subjected to a periodic orienting field. The hysteresis is measured in computer simulations and experiments on unicellular organisms. We find that the ability of the particles to follow the field scales with the ratio of the field variation period to the particles'' orientational relaxation time, which, in turn, is related to the particle self-propulsion power and the energy dissipation rate. The collective behaviour of the particles due to aligning interactions manifests itself at low frequencies via increased persistence of the swarm motion when compared with motion of an individual. By contrast, at high field frequencies, the active group fails to develop the alignment and tends to behave like a set of independent individuals even in the presence of interactions. We also report on asymptotic laws for the hysteretic dynamics of active particles, which resemble those in magnetic systems. The generality of the assumptions in the underlying model suggests that the observed laws might apply to a variety of dynamic phenomena from the motion of synthetic active particles to crowd or opinion dynamics.     

On balance laws for fluid-saturated porous media

The space-averaging formalism of Anderson and Jackson is employed to develop a set of balance laws for a multicomponent mixture. The interactions between the mixture components appear as surface integrals in the averaged (or macroscopic) balance laws. These balance laws are used to study the motion of a porous solid; it is shown that the formulations of Herrmann and of Morland are only approximate in that both of these authors neglected the effects of microinertia. The motion of an incompressible Newtonian fluid through a rigid porous matrix is considered, and the assumptions required to recover Darcy's law are discussed. Finally the averaged balance laws are used to derive a first order theory for the motion of fluid-saturated porous media; it is shown that reasonable approximations lead to the balance laws previously derived by Garg, et al. on heuristic grounds.     

Activity pulses induce spontaneous flow reversals in viscoelastic environments

Complex interactions between cellular systems and their surrounding extracellular matrices are emerging as important mechanical regulators of cell functions, such as proliferation, motility and cell death, and such cellular systems are often characterized by pulsating actomyosin activities. Here, using an active gel model, we numerically explore spontaneous flow generation by activity pulses in the presence of a viscoelastic medium. The results show that cross-talk between the activity-induced deformations of the viscoelastic surroundings and the time-dependent response of the active medium to these deformations can lead to the reversal of spontaneously generated active flows. We explain the mechanism behind this phenomenon based on the interaction between the active flow and the viscoelastic medium. We show the importance of relaxation time scales of both the polymers and the active particles and provide a phase space over which such spontaneous flow reversals can be observed. Our results suggest new experiments investigating the role of controlled pulses of activity in living systems ensnared in complex mircoenvironments.     

Numerical simulation of entangled materials mechanical properties

A general approach to simulate the mechanical behaviour of entangled materials submitted to large deformations is described in this paper. The main part of this approach is the automatic creation of contact elements, with appropriate constitutive laws, to take into account the interactions between fibres. The construction of these elements at each increment, is based on the determination of intermediate geometries in each region where two parts of beams are sufficiently close to be likely to enter into contact. Numerical tests simulating a 90% compression of nine randomly generated samples of entangled materials are given. They allow the identification of power laws to represent the evolutions of the compressive load and of the number of contacts.     

Light‐Emitting Transition Metal Dichalcogenide Monolayers under Cellular Digestion

2D materials cover a wide spectrum of electronic properties. Their applications are extended from electronic, optical, and chemical to biological. In terms of biomedical uses of 2D materials, the interactions between living cells and 2D materials are of paramount importance. However, biointerfacial studies are still in their infancy. This work studies how living organisms interact with transition metal dichalcogenide monolayers. For the first time, cellular digestion of tungsten disulfide (WS₂) monolayers is observed. After digestion, cells intake WS₂ and become fluorescent. In addition, these light‐emitting cells are not only viable, but also able to pass fluorescent signals to their progeny cells after cell division. By combining synthesis of 2D materials and a cell culturing technique, a procedure for monitoring the interactions between WS₂ monolayers and cells is developed. These observations open up new avenues for developing novel cellular labeling and imaging approaches, thus triggering further studies on interactions between 2D materials and living organisms.     

Scaling of impact on low fibre-volume glass–polyester laminates

A dimensional analysis approach has been used to develop scaling laws for impact on marine composite materials. An experimental study has been carried out to verify these relationships for the transverse impact of a hemispherical ended impactor on fully clamped circular hand laid-up glass–polyester plates at three different scales. Although the model was a simplified one, the tests showed that it scaled the impact responses well for the elastic response. However, some ‘size effects’ were observed, especially for the damaged response, and further work is required to fully explain the mechanisms behind these effects.     

A computational model for molecular interactions between curved slender fibers undergoing large 3D deformations with a focus on electrostatic,van der Waals,and repulsive steric forces

This contribution proposes the first three-dimensional (3D) beam-beam interaction model for molecular interactions between curved slender fibers undergoing large deformations. While the general model is not restricted to a specific beam formulation, in the present work, it is combined with the geometrically exact beam theory and discretized via the finite element method. A direct evaluation of the total interaction potential for general 3D bodies requires the integration of contributions from molecule or charge distributions over the volumes of the interaction partners, leading to a six-dimensional integral (two nested 3D integrals) that has to be solved numerically. Here, we propose a novel strategy to formulate reduced section-section interaction laws for the resultant interaction potential between a pair of cross-sections of two slender fibers such that only two one-dimensional integrals along the fibers' length directions have to be solved numerically. This section-section interaction potential (SSIP) approach yields a significant gain in efficiency, which is essential to enable the simulation of relevant time and length scales for many practical applications. In a first step, the generic structure of SSIP laws, which is suitable for the most general interaction scenario (eg, fibers with arbitrary cross-section shape and inhomogeneous atomic/charge density within the cross-section) is presented. Assuming circular, homogeneous cross-sections, in a next step, specific analytical expressions for SSIP laws describing short-range volume interactions (eg, van der Waals (vdW) or steric interactions) and long-range surface interactions (eg, Coulomb interactions) are proposed. Besides ready-to-use expressions for the total interaction potential, also the resulting virtual work contributions, its finite element discretizations, as well as a suitable numerical regularization for the limit of zero separation are derived. The validity of the SSIP laws, as well as the accuracy and robustness of the general SSIP approach to beam-beam interactions, is thoroughly verified by means of a set of numerical examples considering steric repulsion, electrostatic, or vdW adhesion.     

Constructor theory of life

Neo-Darwinian evolutionary theory explains how the appearance of purposive design in the adaptations of living organisms can have come about without their intentionally being designed. The explanation relies crucially on the possibility of certain physical processes: mainly, gene replication and natural selection. In this paper, I show that for those processes to be possible without the design of biological adaptations being encoded in the laws of physics, those laws must have certain other properties. The theory of what these properties are is not part of evolution theory proper, yet without it the neo-Darwinian theory does not fully achieve its purpose of explaining the appearance of design. To this end, I apply constructor theory''s new mode of explanation to express exactly within physics the appearance of design, no-design laws, and the logic of self-reproduction and natural selection. I conclude that self-reproduction, replication and natural selection are possible under no-design laws, the only non-trivial condition being that they allow digital information to be physically instantiated. This has an exact characterization in the constructor theory of information. I also show that under no-design laws an accurate replicator requires the existence of a ‘vehicle’ constituting, together with the replicator, a self-reproducer.     

Critical roles for EGFR and EGFR–HER2 clusters in EGF binding of SW620 human carcinoma cells

Epidermal growth factor (EGF) signalling regulates normal epithelial and other cell growth, with EGF receptor (EGFR) overexpression reported in many cancers. However, the role of EGFR clusters in cancer and their dependence on EGF binding is unclear. We present novel single-molecule total internal reflection fluorescence microscopy of (i) EGF and EGFR in living cancer cells, (ii) the action of anti-cancer drugs that separately target EGFR and human EGFR2 (HER2) on these cells and (iii) EGFR–HER2 interactions. We selected human epithelial SW620 carcinoma cells for their low level of native EGFR expression, for stable transfection with fluorescent protein labelled EGFR, and imaged these using single-molecule localization microscopy to quantify receptor architectures and dynamics upon EGF binding. Prior to EGF binding, we observe pre-formed EGFR clusters. Unexpectedly, clusters likely contain both EGFR and HER2, consistent with co-diffusion of EGFR and HER2 observed in a different model CHO-K1 cell line, whose stoichiometry increases following EGF binding. We observe a mean EGFR : EGF stoichiometry of approximately 4 : 1 for plasma membrane-colocalized EGFR–EGF that we can explain using novel time-dependent kinetics modelling, indicating preferential ligand binding to monomers. Our results may inform future cancer drug developments.     

Conduit flow of a fluid through its solid phase and its application to intraglacial channel flow

The physics of water flow within glacier ice is closely examined with special reference to the unsteady flow through intraglacial channels. Starting from general global balance laws in 3-dimensional space 1-dimensional balance laws are derived which are valid for a curved and torded tube-like volume. Following the derivation of the general balance law 1-dimensional forms of the balance of mass, momentum, angular momentum and energy are presented. These laws are then simplified and compared with the theory of Nye. It is found that Nye's equations are strictly valid only for straight conduits with circular cross sections. To close the theory the genera] balance laws are then complemented by phenomenological assumptions. Finally, it is shown how this theory can be used to explain certain simple phenomena in unsteady intraglacial channels. A thorough exploitation of this theory is not attempted, however.     

Advances in nature-guided materials processing

The center of excellence (COE) titled ‘The Creation of Nature-Guided Materials Processing’ has been established in Nagoya University as the 21st Century COE Program supported by Ministry of Education, Culture, Sports, Science and Technology. In the Nature COE, various activities on the education and research are being performed through learning the laws of nature, namely, methods of attaining ‘appearance of the maximum function under the minimum substance and energy consumption’, which the nature and living organisms have acquired through their evolution in long period. Together with such educational programs for PhD students as research incentive, oversea training, and external evaluation programs, an ‘Open-Cluster Program’ was originated for promoting researches proposed by research groups consisting of young researchers in and out of the university and also for fostering them.

The researches are being advanced on materials used for living bodies, mimicking structures which nature or living bodies are forming, and producing materials by mimicking processes to form the structures observed in the nature or the living bodies. In this COE, these researches are conducted by four groups to extend the processes observed in the natural world to a new type of processing, that is, thoroughly examined and rationalized by plunging a scalpel of engineering and to establish a new academic field of materials science and engineering.     

Characterization of zirconium oxynitride films obtained by radio frequency magnetron reactive sputtering

Thin ZrN_xO_y films are deposited on Si (100) substrates by radio frequency (RF) reactive magnetron sputtering of a zirconium target in an argon-oxygen-nitrogen mixture. The Φ_N2/Φ_{(Ar + N2 + O2)} ratio was varied in the range 2.5%-100% while the oxygen flux was kept constant. The films were characterized by combining several techniques: X-ray photoelectron spectroscopy, X-ray diffraction and Secondary Ion Mass Spectroscopy. The relationship between structural and compositional properties and the sputtering parameters was investigated. Increasing nitrogen partial pressure in the gas mixture, a chemical and structural evolution happens. At lowest nitrogen flux, ZrN cubic phase is formed with a very small amount of amorphous zirconium oxynitride. At highest nitrogen flux, only crystalline ZrON phases were found. For the films obtained between these two extremes, a co-presence of ZrN and ZrON can be detected. In particular, chemical analysis revealed the co-presence of ZrO₂, ZrN, ZrON and N-rich zirconium nitride which is correlated with the Φ_N2/Φ_{(Ar + N2 + O2)} values. A zirconium nitride crystal structure with metal vacancies model has been considered in order to explain the different chemical environment detected by X-ray photoelectron spectroscopy measurements. The metal vacancies are a consequence of the deposition rate decreasing due to the target poisoning. It's evident that the growth process is strongly influenced by the zirconium atoms flux. This parameter can explain the structural evolution.     

Structure,formation mechanisms and kinetics of reaction-bonded silicon nitride

This paper reports on models which have been developed to explain the formation mechanism and kinetics of the major microconstituents of reaction-bonded silicon nitride. These models are based on information obtained from a detailed microstructural study during various stages of reaction and a knowledge of the reaction conditions which encourage formation of each particular microconstituent. It has become clear that there are at least two independent mechanisms and that they are governed by independent rate laws. The kinetics of nitridation of a silicon compact is, therefore, the superposition of at least two independent rate laws. Experimental evidence obtained thus far is in good agreement with this hypothesis.     

Interaction of polyelectrolytes and their composites with living cells

Since the layer-wise polyelectrolyte deposition offers the opportunity to modify surfaces for biomedical applications, interactions and toxicity between polyelectrolytes and living cells become interesting. The aim of the present work is to determine the different factors such as contact area, charge, and transplantation site that influence the cell reaction to a specific polymer. We found that toxicity is influenced by all these factors and cannot be tested easily in a model.     

Mechanisms of interpersonal sway synchrony and stability

Here we explain the neural and mechanical mechanisms responsible for synchronizing sway and improving postural control during physical contact with another standing person. Postural control processes were modelled using an inverted pendulum under continuous feedback control. Interpersonal interactions were simulated either by coupling the sensory feedback loops or by physically coupling the pendulums with a damped spring. These simulations precisely recreated the timing and magnitude of sway interactions observed empirically. Effects of firmly grasping another person''s shoulder were explained entirely by the mechanical linkage. This contrasted with light touch and/or visual contact, which were explained by a sensory weighting phenomenon; each person''s estimate of upright was based on a weighted combination of veridical sensory feedback combined with a small contribution from their partner. Under these circumstances, the model predicted reductions in sway even without the need to distinguish between self and partner motion. Our findings explain the seemingly paradoxical observation that touching a swaying person can improve postural control.     

Multiphoton Microscopy of Nonfluorescent Nanoparticles In Vitro and In Vivo

Nanotechnology holds great promise for a plethora of potential applications. The interaction of engineered nanomaterials with living cells, tissues, and organisms is, however, only partly understood. Microscopic investigations of nano‐bio interactions are mostly performed with a few model nanoparticles (NPs) which are easy to visualize, such as fluorescent quantum dots. Here the possibility to visualize nonfluorescent NPs with multiphoton excitation is investigated. Signals from silver (Ag), titanium dioxide (TiO₂), and silica (SiO₂) NPs in nonbiological environments are characterized to determine signal dependency on excitation wavelength and intensity as well as their signal stability over time. Ag NPs generate plasmon‐induced luminescence decaying over time. TiO₂ NPs induce photoluminescent signals of variable intensities and in addition strong third harmonic generation (THG). Optimal settings for microscopic detection are determined and then applied for visualization of these two particle types in living cells, in murine muscle tissue, and in the murine blood stream. Silica NPs produce a THG signal, but in living cells it cannot be discriminated sufficiently from endogenous cellular structures. It is concluded that multiphoton excitation is a viable option for studies of nano‐bio interactions not only for fluorescent but also for some types of nonfluorescent NPs.     

Comparative study of hydrocarbon, fluorocarbon, and aromatic bonded RP-HPLC stationary phases by linear solvation energy relationships.

The retention properties of eight alkyl, aromatic, and fluorinated reversed-phase high-performance liquid chromatography bonded phases were characterized through the use of linear solvation energy relationships (LSERs). The stationary phases were investigated in a series of methanol/water mobile phases. LSER results show that solute molecular size and hydrogen bond acceptor basicity under all conditions are the two dominant retention controlling factors and that these two factors are linearly correlated when either different stationary phases at a fixed mobile-phase composition or different mobile-phase compositions at a fixed stationary phase are considered. The large variation in the dependence of retention on solute molecular volume as only the stationary phase is changed indicates that the dispersive interactions between nonpolar solutes and the stationary phase are quite significant relative to the energy of the mobile-phase cavity formation process. PCA results indicate that one PCA factor is required to explain the data when stationary phases of the same chemical nature (alkyl, aromatic, and fluoroalkyl phases) are individually considered. However, three PCA factors are not quite sufficient to explain the whole data set for the three classes of stationary phases. Despite this, the average standard deviation obtained by the use of these principal component factors are significantly smaller than the average standard deviation obtained by the LSER approach. In addition, selectivities predicted through the LSER equation are not in complete agreement with experimental results. These results show that the LSER model does not properly account for all molecular interactions involved in RP-HPLC. The failure could reside in the V2 solute parameter used to account for both dispersive and cohesive interactions since "shape selectivity" predictions for a pair of structural isomers are very bad.     

Non-linear characteristics of lipid monolayers in relation to the ability to self-organize

It is known that electrostatic interactions strongly influence the growth of condensed phase domains at the main phase transition of lipid membranes. It is demonstrated in this paper that the inclusion of electrostatic interactions into the pressure-area-temperature equation of state provides a much better fit to the observed equilibrium behaviour than the classical van der Waals form. Both of these equations of state predict a region of negative differential compressibility (NDC), which is not described on long time scales because of a competing first-order phase transition. It is shown in this paper that dynamic NDC can account for most of the features of the observed oscillatory behaviour of monolayers at the oil-water interface. Such behaviour may be related to self-organization of spatiotemporal structures in living organisms.     

Theoretical modelling of radiolytic damage of free DNA bases and within DNA macromolecule

The base damages in living cell are the most frequent product of deleterious effect of ionizing radiation. Experimental yields of modified bases determined in free bases and in the double stranded DNA show significant differences in the yields of stable products of radiolytic attack. An attempt to explain these differences is made with the help of theoretical calculations. The relative probabilities of reactions of the most important radiolytic product, OH(*) radical, with individual nucleobases, nucleosides and short DNA oligomers are calculated and compared to available experimental yields of base damages.