Machine learning approach for recognition and morphological analysis of isolated astrocytes in phase contrast microscopy.

Astrocytes are glycolytically active cells in the central nervous system playing a crucial role in various brain processes from homeostasis to neurotransmission. Astrocytes possess a complex branched morphology, frequently examined by fluorescent microscopy. However, staining and fixation may impact the properties of astrocytes, thereby affecting the accuracy of the experimental data of astrocytes dynamics and morphology. On the other hand, phase contrast microscopy can be used to study astrocytes morphology without affecting them, but the post-processing of the resulting low-contrast images is challenging. The main result of this work is a novel approach for recognition and morphological analysis of unstained astrocytes based on machine-learning recognition of microscopic images. We conducted a series of experiments involving the cultivation of isolated astrocytes from the rat brain cortex followed by microscopy. Using the proposed approach, we tracked the temporal evolution of the average total length of branches, branching, and area per astrocyte in our experiments. We believe that the proposed approach and the obtained experimental data will be of interest and benefit to the scientific communities in cell biology, biophysics, and machine learning.

Influence of anomalous agents on the dynamics of an active system.

Swarming behavior in systems of self-propelled particles, whether biological or artificial, has received increased attention in recent years. Here, we show that even a small number of particles with anomalous behavior can change dramatically collective dynamics of the swarming system and can impose unusual behavior and transitions between dynamic states. Our results pave the way to practical approaches and concepts of multiagent dynamics in groups of flocking animals: birds, insects, and fish, i.e., active and living soft matter.

Current progress and challenges in the development of brain tissue models: How to grow up the changeable brain in vitro?

In vitro modeling of brain tissue is a promising but not yet resolved problem in modern neurobiology and neuropharmacology. Complexity of the brain structure and diversity of cell-to-cell communication in (patho)physiological conditions make this task almost unachievable. However, establishment of novel in vitro brain models would ultimately lead to better understanding of development-associated or experience-driven brain plasticity, designing efficient approaches to restore aberrant brain functioning. The main goal of this review is to summarize the available data on methodological approaches that are currently in use, and to identify the most prospective trends in development of neurovascular unit, blood-brain barrier, blood-cerebrospinal fluid barrier, and neurogenic niche in vitro models. The manuscript focuses on the regulation of adult neurogenesis, cerebral microcirculation and fluids dynamics that should be reproduced in the in vitro 4D models to mimic brain development and its alterations in brain pathology. We discuss approaches that are critical for studying brain plasticity, deciphering the individual person-specific trajectory of brain development and aging, and testing new drug candidates in the in vitro models.

Inertia changes evolution of motility-induced phase separation in active matter across particle activity.

The effects of inertia in active matter and motility-induced phase separation (MIPS) have attracted growing interest but still remain poorly studied. We studied MIPS behavior in the Langevin dynamics across a broad range of particle activity and damping rate values with molecular dynamic simulations. Here we show that the MIPS stability region across particle activity values consists of several domains separated by discontinuous or sharp changes in susceptibility of mean kinetic energy. These domain boundaries have fingerprints in the system's kinetic energy fluctuations and characteristics of gas, liquid, and solid subphases, such as the number of particles, densities, or the power of energy release due to activity. The observed domain cascade is most stable at intermediate damping rates but loses its distinctness in the Brownian limit or vanishes along with phase separation at lower damping values.

Diffusion mobility increases linearly on liquid binodals above triple point.

Self-diffusion in fluids has been thoroughly studied numerically, but even for simple liquids just a few scaling relationships are known. Relations between diffusion, excitation spectra, and character of the interparticle interactions remain poorly understood. Here, we show that diffusion mobility of particles in simple fluids increases linearly on the liquid branch of the liquid-gas binodal, from the triple point almost up to the critical point. With molecular dynamics simulations, we considered bulk systems of particles interacting via a generalised Lennard-Jones potential, as well as ethane. Using a two-oscillator model for the analysis of excitations, we observed that the mobility (inverse diffusion) coefficient on the liquid-gas binodal increases linearly above the triple point until the dispersion of high-frequency spectra has a solid-like (oscillating) shape. In terms of a separate mode analysis (of longitudinal and transverse modes), this corresponds to crossed modes in the intermediate range of wavenumbers q, between the hydrodynamic regime (small q) and the regime of individual particle motion (large q). The results should be interesting for a broad community in physics and chemistry of fluids, since self-diffusion is among the most fundamental transport phenomena, important for prospective chemical technologies, micro-, nanofluidics, and biotechnologies.

Interacting Oscillators with Fluctuating Coupling: Mode Mixing without Cross-Correlations.

Coupled oscillators are one of the basic models in nonlinear dynamics. Here, we study numerically and analytically the spectra of two harmonic oscillators with stochastically fluctuating coupling and driving forces reproducing a thermostat. We show that, even at small coupling, vanishing on average, the oscillation spectra exhibit mixing, even though no cross-correlations exists between the oscillators. Our results reveal a new mechanism of mode mixing for stochastically uncorrelated systems that is crucial for analysis of spectra in various systems, from simple liquids to living systems.

The role of attraction in the phase diagrams and melting scenarios of generalized 2D Lennard-Jones systems.

Monolayer and two-dimensional (2D) systems exhibit rich phase behavior, compared with 3D systems, in particular, due to the hexatic phase playing a central role in melting scenarios. The attraction range is known to affect critical gas-liquid behavior (liquid-liquid in protein and colloidal systems), but the effect of attraction on melting in 2D systems remains unstudied systematically. Here, we have revealed how the attraction range affects the phase diagrams and melting scenarios in a 2D system. Using molecular dynamics simulations, we have considered the generalized Lennard-Jones system with a fixed repulsion branch and different power indices of attraction from long-range dipolar to short-range sticky-sphere-like. A drop in the attraction range has been found to reduce the temperature of the gas-liquid critical point, bringing it closer to the gas-liquid-solid triple point. At high temperatures, attraction does not affect the melting scenario that proceeds through the cascade of solid-hexatic (Berezinskii-Kosterlitz-Thouless) and hexatic-liquid (first-order) phase transitions. In the case of dipolar attraction, we have observed two triple points inherent in a 2D system: hexatic-liquid-gas and crystal-hexatic-gas, the temperature of the crystal-hexatic-gas triple point is below the hexatic-liquid-gas triple point. This observation may have far-reaching consequences for future studies, since phase diagrams determine possible routes of self-assembly in molecular, protein, and colloidal systems, whereas the attraction range can be adjusted with complex solvents and external electric or magnetic fields. The results obtained may be widely used in condensed matter, chemical physics, materials science, and soft matter.

2D colloids in rotating electric fields: A laboratory of strong tunable three-body interactions.

Many-body forces play a prominent role in structure and dynamics of matter, but their role is not well understood in many cases due to experimental challenges. Here, we demonstrate that a novel experimental system based on rotating electric fields can be utilised to deliver unprecedented degree of control over many-body interactions between colloidal silica particles in water. We further show that we can decompose interparticle interactions explicitly into the leading terms and study their specific effects on phase behaviour. We found that three-body interactions exert critical influence over the phase diagram domain boundaries, including liquid-gas binodal, critical and triple points. Phase transitions are shown to be reversible and fully controlled by the magnitude of external rotating electric field governing the tunable interactions. Our results demonstrate that colloidal systems in rotating electric fields are a unique laboratory to study the role of many-body interactions in physics of phase transitions and in applications, such as self-assembly, offering exciting opportunities for studying generic phenomena inherent to liquids and solids, from atomic to protein and colloidal systems.

Entropy of simple fluids with repulsive interactions near freezing.

Among different thermodynamic properties of liquids, the entropy is one of the hardest quantities to estimate. Therefore, the development of models allowing accurate estimations of the entropy for different mechanisms of interatomic interactions represents an important problem. Here, we propose a method for estimating the excess entropy of simple liquids not too far from the liquid-solid phase transition. The method represents a variant of cell theory, which particularly emphasizes relations between liquid state thermodynamics and collective modes properties. The method is applied to calculate the excess entropy of inverse-power-law fluids with ∝r-n repulsive interactions. The covered range of potential softness is extremely wide, including the very soft Coulomb (n = 1) case, much steeper n = 6 and n = 12 cases, and the opposite hard-sphere interaction limit (n = ∞). An overall reasonably good agreement between the method's outcome and existing "exact" results is documented at sufficiently high fluid densities. Its applicability condition can be conveniently formulated in terms of the excess entropy itself. The method is also applied to the Lennard-Jones potential but demonstrates considerably lower accuracy in this case. Our results should be relevant to a broad range of liquid systems that can be described with isotropic repulsive interactions, including liquid metals, macromolecular systems, globular proteins, and colloidal suspensions.

Mean-field model of melting in superheated crystals based on a single experimentally measurable order parameter.

Melting is one of the most studied phase transitions important for atomic, molecular, colloidal, and protein systems. However, there is currently no microscopic experimentally accessible criteria that can be used to reliably track a system evolution across the transition, while providing insights into melting nucleation and melting front evolution. To address this, we developed a theoretical mean-field framework with the normalised mean-square displacement between particles in neighbouring Voronoi cells serving as the local order parameter, measurable experimentally. We tested the framework in a number of colloidal and in silico particle-resolved experiments against systems with significantly different (Brownian and Newtonian) dynamic regimes and found that it provides excellent description of system evolution across melting point. This new approach suggests a broad scope for application in diverse areas of science from materials through to biology and beyond. Consequently, the results of this work provide a new guidance for nucleation theory of melting and are of broad interest in condensed matter, chemical physics, physical chemistry, materials science, and soft matter.

Diagrammatics of tunable interactions in anisotropic colloids in rotating electric or magnetic fields: New kind of dipole-like interactions.

Anisotropic particles are widely presented in nature, from colloidal to bacterial systems, and control over their interactions is of crucial importance for many applications, from self-assembly of novel materials to microfluidics. Placed in rapidly rotating external electric fields, colloidal particles attain a tunable long-range and many-body part in their interactions. For spherical colloids, this approach has been shown to offer rich capabilities to construct the tunable interactions via designing the internal structure of particles and spatial hodographs of external rotating fields, but in the case of anisotropic particles, the interactions remain poorly understood. Here, we show that tunable interactions between anisotropic rod-like and spheroidal colloidal particles in rotating electric or magnetic fields can be calculated and analyzed with the diagrammatic technique we developed in the present work. With this technique, we considered an in-plane rotating electric field, obtained the long-range asymptotics of the anisotropic interactions, calculated the tunable interactions between particles rotating synchronously, and found conditions for rotator repulsion. We compared the mechanisms providing tunable interactions to those for orientational (Keesom), induction (Debye), and dispersion (London) interactions in molecular systems and found that the tunable interactions between anisotropic particles represent a novel kind of dipole-like interaction. The method can be directly generalized for magnetically induced interactions, 3D systems, and fields with spatial hodographs. The results provide significant advance in theoretical methods for tunable interactions in colloids and, therefore, are of broad interest in condensed matter, chemical physics, physical chemistry, materials science, and soft matter.

Core-shell particles in rotating electric and magnetic fields: Designing tunable interactions via particle engineering.

Tunable interactions between colloidal particles, governed by external rotating electric or magnetic fields, yield rich capabilities for prospective self-assembly technologies of materials and fundamental particle-resolved studies of phase transitions and transport phenomena in soft matter. However, the role of the internal structure of colloidal particles in the tunable interactions has never been systematically investigated. Here, we study the tunable interactions between composite particles with core-shell structure in a rotating electric field and show that the engineering of their internal structure provides an effective tool for designing the interactions. We generalized an integral theory and studied the tunable interactions between core-shell particles with homogeneous cores (layered particles) and cores with nano-inclusions to reveal the main trends in the interactions influenced by the structure. We found that depending on the materials of the core, shell, and solvent, the interactions with the attractive pairwise part and positive or negative three-body part can be obtained, as well as pairwise repulsion with attractive three-body interactions (for triangular triplets). The latter case is observed for the first time, being unattainable for homogeneous particles but feasible with core-shell particles: Qualitatively similar interactions are inherent to charged colloids (repulsive pairwise and attractive three-body energies), known as a model system of globular proteins. The methods and conclusions of our paper can be generalized for magnetic and 3D colloidal systems. The results make a significant advance in the analysis of tunable interactions in colloidal systems, which are of broad interest in condensed matter, chemical physics, physical chemistry, materials science, and soft matter.

Collective excitations in active fluids: Microflows and breakdown in spectral equipartition of kinetic energy.

The effect of particle activity on collective excitations in active fluids of microflyers is studied. With an in silico study, we observed an oscillating breakdown of equipartition (uniform spectral distribution) of kinetic energy in reciprocal space. The phenomenon is related to short-range velocity-velocity correlations that were realized without forming of long-lived mesoscale vortices in the system. This stands in contrast to well-known mesoscale turbulence operating in active nematic systems (bacterial or artificial) and reveals the features of collective dynamics in active fluids, which should be important for structural transitions and glassy dynamics in active matter.

From soft- to hard-sphere fluids: Crossover evidenced by high-frequency elastic moduli.

The conventional (Zwanzig-Mountain) expressions for instantaneous elastic moduli of simple fluids predict their divergence as the limit of hard-sphere (HS) interaction is approached. However, elastic moduli of a true HS fluid are finite. Here we demonstrate that this paradox reveals the soft-to-hard-sphere crossover in fluid excitations and thermodynamics. With extensive in silico study of fluids with repulsive power-law interactions (∝r^{-n}), we locate the crossover at n≃10-20 and develop a simple and accurate model for the HS regime. The results open prospects to deal with the elasticity and related phenomena in various systems, from simple fluids to melts and glasses.

Programmable Soft-Matter Electronics.

The hydrogels of the polyelectrolytes polyethylenimine and poly(acrylic acid) are used to form a thin-layer interface on the gallium-indium eutectic alloy's surface. The proposed method of gradually increasing the applied voltage reveals the possibility of formation of electronic components: diode, capacitor, resistor, and memristor. The components can be changed to each other many times. A multilayer perceptron model with one hidden layer and 12 nodes allows identifying hydrogels' composition and automatically setting the desired architecture of electronic components. The design of electronic components makes it possible to easy-to-produce new electronic parts and programmable soft-matter electronics.

Universal Effect of Excitation Dispersion on the Heat Capacity and Gapped States in Fluids.

The change in dispersion of high-frequency excitations in fluids, from an oscillating solidlike to a monotonic gaslike one, is shown for the first time to affect thermal behavior of heat capacity and the q-gap width in reciprocal space. With in silico study of liquified noble gases, liquid iron, liquid mercury, and model fluids, we established universal bilinear dependence of heat capacity on q-gap width, whereas the crossover precisely corresponds to the change in the excitation spectra. The results open novel prospects for studies of various fluids, from simple to molecular liquids and melts.

Colloids in rotating electric and magnetic fields: designing tunable interactions with spatial field hodographs.

Opening a way to designing tunable interactions between colloidal particles in rotating electric and magnetic fields provides rich opportunities both for fundamental studies of phase transitions and engineering of soft materials. Spatial hodographs, showing the distribution of the field magnitude and orientation, allow the adjustment of interactions and can be an extremely potent tool for prospective experiments, but remain unstudied systematically. Here, we calculate the tunable interactions between spherical particles in rhodonea, conical, cylindrical, and ellipsoidal field hodographs, as the most experimentally important cases. We discovered that spatial hodographs are reduced to each other, providing a plethora of interactions, e.g., repulsive, attractive, barrier-like, and double-scale repulsive ones. Complementing the "magic" conical angle, the "magic" compression and ellipticity of cylindrical and ellipsoidal hodographs are introduced. In the "magic" hodographs, the interactions become spatially isotropic and attain dispersion-force-like asymptotic (the same for pairwise and many-body energies), being attractive or repulsive, if the particle permittivity is larger or smaller than that of the solvent. With the diagrammatic method and numerical calculations, we obtained physically meaningful fits to the many-body tunable potentials for silica (iron oxide) particles in deionised water in the rotating electric (magnetic) fields. Our results provide essential guidance for future experiments and simulations of colloidal liquids, crystals, gels, and glasses, important for a broad range of problems in condensed matter, chemical physics, physical chemistry, materials science, and soft matter.

Strange attractors induced by melting in systems with nonreciprocal effective interactions.

Newton's third law-the action-reaction symmetry-can be violated for effective interbody forces in open and nonequilibrium systems that are ubiquitous in areas as diverse as complex plasmas, colloidal suspensions, active and living soft matter, and social behavior. While studying monolayer complex plasma (confined charged particles in an ionized gas) with nonreciprocal interactions mediated by plasma flows, in silico we found that an interplay between melting and thermal activation drastically transforms the collective dynamics: the order-disorder transition modifies the system's thermal steady state so that the crystal tends to melt, whereas the fluid tends to freeze, jumping chaotically between the two states. We identified this collective chaotic behavior as strange attractors formed in a monolayer complex plasma and link the strange attractor behavior to the specifics of interparticle interactions.

Direct Experimental Evidence of Longitudinal and Transverse Mode Hybridization and Anticrossing in Simple Model Fluids.

A significant number of key properties of condensed matter are determined by the spectra of elementary excitations and, in particular, collective vibrations. However, the behavior and description of collective modes in disordered media (e.g., liquids and glasses) remains a challenging area of modern condensed matter science. Recently, anticrossing between longitudinal and transverse modes was predicted theoretically and observed in molecular dynamics simulations, but this fundamental phenomenon has never been observed experimentally. Here we demonstrate the mode anticrossing in a simple Yukawa fluid constructed from charged microparticles in weakly ionized gas. Theory, simulations, and experiments show clear evidence of mode anticrossing that is accompanied by mode hybridization and strong redistribution of the excitation spectra. Our results provide a significant advance in understanding excitations of fluids, opening new perspectives for studies of dynamics, thermodynamics, and transport phenomena in a wide variety of systems from noble-gas fluids and metallic melts to strongly coupled plasmas and molecular and complex fluids.

Tick-Borne Encephalitis Electrochemical Detection by Multilayer Perceptron on Liquid-Metal Interface.

This work depicts an electrochemical hydrogel-eutectic gallium indium alloy interface for the detection of tick-borne encephalitis (TBE) virus. This interface allows recording of nonlinear current-voltage responses, depending on the composition of the hydrogel. The current-voltage data for the machine learning model are trained by a multilayer perceptron. This model accurately recognizes the TBE antibody, antigen, and an antibody-antigen complex in mixture with interfering bovine serum albumin with 93% accuracy. Thus, this interface can be used as a convenient method for expressed viruses and pathogens detection.