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The cytoplasm is densely packed with molecules that contribute to its nonideal behavior. Cytosolic crowding influences chemical reaction rates, intracellular water mobility, and macromolecular complex formation. Overcrowding is potentially catastrophic; to counteract this problem, cells have evolved acute and chronic homeostatic mechanisms that optimize cellular crowdedness. Here, we provide a physiology-focused overview of molecular crowding, highlighting contemporary advances in our understanding of its sensing and control. Long hypothesized as a form of crowding-induced microcompartmentation, phase separation allows cells to detect and respond to intracellular crowding through the action of biomolecular condensates, as indicated by recent studies. Growing evidence indicates that crowding is closely tied to cell size and fluid volume, homeostatic responses to physical compression and desiccation, tissue architecture, circadian rhythm, aging, transepithelial transport, and total body electrolyte and water balance. Thus, molecular crowding is a fundamental physiologic parameter that impacts diverse functions extending from molecule to organism. [ABSTRACT FROM AUTHOR]

During the origin of life, encapsulation of RNA inside vesicles is believed to have been a defining feature of the earliest cells (protocells). The confined biophysical environment provided by membrane encapsulation differs from that of bulk solution and has been shown to increase activity as well as evolutionary rate for functional RNA. However, the structural basis of the effect on RNA has not been clear. Here, we studied how encapsulation of the hairpin ribozyme inside model protocells affects ribozyme kinetics, ribozyme folding into the active conformation, and cleavage and ligation activities. We further examined the effect of encapsulation on the folding of a stem-loop RNA structure and on the formation of a triplex structure in a pH-sensitive DNA switch. The results indicate that encapsulation promotes RNA-RNA association, both intermolecular and intramolecular, and also stabilizes tertiary folding, including the docked conformation characteristic of the active hairpin ribozyme and the triplex structure. The effects of encapsulation were sufficient to rescue the activity of folding-deficient mutants of the hairpin ribozyme. Stabilization of multiple modes of nucleic acid folding and interaction thus enhanced the activity of encapsulated nucleic acids. Increased association between RNA molecules may facilitate the formation of more complex structures and cooperative interactions. These effects could promote the emergence of biological functions in an "RNA world" and may have utility in the construction of minimal synthetic cells.

Biochemical processes within the living cell occur in a highly crowded environment, where macromolecules, first of all proteins and nucleic acids, occupy up to 30% of the volume. The phenomenon of macromolecular crowding is not an exclusive feature of the cytoplasm and can be observed in the densely protein‐packed, nonhomogeneous cellular membranes and at the membrane interfaces. Crowding affects diffusional and conformational dynamics of proteins within the lipid bilayer, alters kinetic and thermodynamic properties of biochemical reactions, and modulates the membrane organization. Despite its importance, the non‐invasive quantification of the membrane crowding is not trivial. Here, we developed a genetically‐encoded fluorescence‐based sensor for probing the macromolecular crowding at the membrane interfaces. Two sensor variants, both composed of fluorescent proteins and a membrane anchor, but differing by flexible linker domains were characterized in vitro, and the procedures for the membrane reconstitution were established. Steric pressure induced by membrane‐tethered synthetic and protein crowders altered the sensors' conformation, causing increase in the intramolecular Förster's resonance energy transfer. Notably, the effect of protein crowders only weakly correlated with their molecular weight, suggesting that other factors, such as shape and charge contribute to the crowding via the quinary interactions. Finally, measurements performed in inner membrane vesicles of Escherichia coli validated the crowding‐dependent dynamics of the sensors in the physiologically relevant environment. The sensors offer broad opportunities to study interfacial crowding in a complex environment of native membranes, and thus add to the toolbox of methods for studying membrane dynamics and proteostasis. [ABSTRACT FROM AUTHOR]

In living cells, the biochemical processes such as energy provision, molecule synthesis, gene expression, and cell division take place in a confined space where the internal chemical and physical conditions are different from those in dilute solutions. The concentrations of specific molecules and the specific reactions and interactions vary for different types of cells, but a number of factors are universal and kept within limits, which we refer to as physicochemical homeostasis. For instance, the internal pH of many cell types is kept within the range of 7.0 to 7.5, the fraction of macromolecules occupies 15%–20% of the cell volume (also known as macromolecular crowding) and the ionic strength is kept within limits to prevent salting-in or salting-out effects. In this article we summarize the generic physicochemical properties of the cytoplasm of bacteria, how they are connected to the energy status of the cell, and how they affect biological processes (Fig.  1). We describe how the internal pH and proton motive force are regulated, how the internal ionic strength is kept within limits, what the impact of macromolecular crowding is on the function of enzymes and the interaction between molecules, how cells regulate their volume (and turgor), and how the cytoplasm is structured. Physicochemical homeostasis is best understood in Escherichia coli , but pioneering studies have also been performed in lactic acid bacteria. [ABSTRACT FROM AUTHOR]

Understanding food materials from the classical realm of physics including soft condensed matter physics has been an area of interest especially in the structural design engineering of food products. The contents of this review would help the reader in understanding the thermodynamics of food polymer, structural design principles, structural hierarchy, steps involved in food structuring, newer structural design technologies, and structure measurement techniques. Understanding the concepts of free volume would help the food engineers and technologists to study the food structural changes, manipulate process parameters and, the optimum amount of nutraceuticals/ingredients to be loaded in the food matrix. Such understanding helps in reducing food ingredient wastage while designing a food product. [ABSTRACT FROM AUTHOR]

Weak polyelectrolytes (WPEs) are responsive materials used as active charge regulators in a variety of applications, including controlled release and drug delivery in crowded bio-related and synthetic environments. In these environments, high concentrations of solvated molecules, nanostructures, and molecular assemblies are ubiquitous. Here, we investigated the effect of high concentrations of non-adsorbing, short chains of poly(vinyl alcohol), PVA, and colloids dispersed by the very same polymers on charge regulation (CR) of poly(acrylic acid), PAA. PVA does not interact with PAA (throughout the full pH range) and thus can be used to examine the role of non-specific (entropic) interactions in polymer-rich environments. Titration experiments of PAA (mainly 100 kDa in dilute solutions, no added salt) were carried out in high concentrations of PVA (13–23 kDa, 5–15 wt%) and dispersions of carbon black (CB) decorated by the same PVA (CB-PVA, 0.2–1 wt%). The calculated equilibrium constant (and p K a ) was up-shifted in PVA solutions by up to ~0.9 units and down-shifted in CB-PVA dispersions by ~0.4 units. Thus, while solvated PVA chains increase the charging of the PAA chains, as compared to PAA in water, CB-PVA particles reduce PAA charging. To investigate the origins of the effect, we analyzed the mixtures using small-angle X-ray scattering (SAXS) and cryo-TEM imaging. The scattering experiments revealed re-organization of the PAA chains in the presence of the solvated PVA but not in the CB-PVA dispersions. These observations clearly indicate that the acid–base equilibrium and the degree of ionization of PAA in crowded liquid environments is affected by the concentration, size, and geometry of seemingly non-interacting additives, probably due to depletion and excluded volume interactions. Thus, entropic effects that do not depend on specific interactions should be taken into consideration when designing functional materials in complex fluid environments. [ABSTRACT FROM AUTHOR]

Proteins in the cellular milieu reside in environments crowded by macromolecules and other solutes. Although crowding can significantly impact the protein folded state stability, most experiments are conducted in dilute buffered solutions. To resolve the effect of crowding on protein stability, we use 19F nuclear magnetic resonance spectroscopy to follow the reversible, two‐state unfolding thermodynamics of the N‐terminal Src homology 3 domain of the Drosophila signal transduction protein drk in the presence of polyethylene glycols (PEGs) of various molecular weights and concentrations. Contrary to most current theories of crowding that emphasize steric protein–crowder interactions as the main driving force for entropically favored stabilization, our experiments show that PEG stabilization is accompanied by significant heat release, and entropy disfavors folding. Using our newly developed model, we find that stabilization by ethylene glycol and small PEGs is driven by favorable binding to the folded state. In contrast, for larger PEGs, chemical or soft PEG–protein interactions do not play a significant role. Instead, folding is favored by excluded volume PEG–protein interactions and an exothermic nonideal mixing contribution from release of confined PEG and water upon folding. Our results indicate that crowding acts through molecular interactions subtler than previously assumed and that interactions between solution components with both the folded and unfolded states must be carefully considered. [ABSTRACT FROM AUTHOR]

We quantify superdiffusive transience for a two-dimensional random walk in which the vertical coordinate is a martingale and the horizontal coordinate has a positive drift that is a polynomial function of the individual coordinates and of the present time. We describe how the model was motivated through an heuristic connection to a self-interacting, planar random walk which interacts with its own centre of mass via an excluded-volume mechanism, and is conjectured to be superdiffusive with a scale exponent 3 / 4. The self-interacting process originated in discussions with Francis Comets. [ABSTRACT FROM AUTHOR]

The screening, the configurational correlations and the interaction correlations in the theory of binary electrolytes are examined, by exploiting the charge conservation and the properties of the equilibrium state. Validity conditions for the linearised Debye–Huckel screened potential are provided. A non-zero ionic radius is employed in order to account for solvation effects, and limitations on the contribution of the ionic radius are derived. A possible stabilisation of the ions in equilibrium positions, arising from counterion configurational correlations, is analysed for associated electrolytes, and the corresponding correlation energy is derived. A van der Waals-type equation is presented for strong electrolytes. Some well-known technical difficulties of the theory of electrolytes are revisited, with emphasis on statistical-dynamical correlations, excluded volume and multiple-boundary conditions. [ABSTRACT FROM AUTHOR]

Protein amyloid fibrils have widespread implications for human health. Over the last twenty years, fibrillation has been studied using a variety of crowding agents to mimic the packed interior of cells or to probe the mechanisms and pathways of the process. We tabulate and review these results by considering three classes of crowding agent: synthetic polymers, osmolytes and other small molecules, and globular proteins. While some patterns are observable for certain crowding agents, the results are highly variable and often depend on the specific pairing of crowder and fibrillating protein. [ABSTRACT FROM AUTHOR]

[Display omitted] • Improvement of the percolation theory based on nanoparticle-dependent parameters. • Defining the aggregation/agglomeration-dependent percolation threshold. • Impact of size and content of nanoparticle clusters on electrical conductivity. • Application of artificial intelligence to predict the main system parameters. • Developing a scaling theory to estimate the electrical conductivity of interphase. The formation of aggregates/agglomerates in polymer nanocomposites is known as an inevitable phenomenon that may affect many physical/mechanical properties. Accordingly, in this study, the impacts of the size and content of nanoparticle clusters on the electrical conductivity of polymer matrices containing spherical nanoparticles were analytically evaluated. To this end, the well-known percolation theory was improved by involving major system parameters, affected by aggregation/agglomeration, reported to be indicative of how electricity may conduct through (e. g. tunneling effect, percolation threshold, content and equivalent electrical conductivity of nanoparticle domains, etc.). The characteristics of the aggregates/agglomerates were estimated via the combination of a devised strategy, representing the structure of clusters, and the fundamentals of the percolation theory. The average electrical conductivity and density of polymer/particle interphase, formed around nanoparticle domains were calculated using a particularly developed scaling theory. Also, the hypothetical relative location of nanoparticle domains to each other was defined by calculating the average nearest distance between them, benchmarked against the tunneling distance. A two-stage validation procedure was conducted using the data elicited from the literature in order to first, evaluate the model efficiency and secondly, assess its predictive capabilities with the aid of an artificial neural network (error < 7 %). [ABSTRACT FROM AUTHOR]

Recent research has increasingly focused on the potential applications of carbon nanotube (CNT) hybrid composites in wearable sensor technologies. Piezoresistivity, which is characterized by the ability to detect alterations in electrical resistance in response to external forces, is a pivotal attribute of resistive sensors. Numerous studies have attempted to improve this performance by incorporating secondary fillers. Despite extensive efforts to comprehend the influence of the dimensions of secondary fillers on electrical conductivity under static and dynamic conditions, notable confusion persists in the literature regarding the comparative analysis of the effects of nano- and microscale secondary fillers. In this study, two distinct sizes of silica particles were introduced as secondary fillers in CNT/polymer composites, followed by a rigorous comparative analysis of their mechanical and electrical properties under static conditions. Furthermore, this study assessed the influence of the silica particle size on the electrical resistance under dynamic tensile conditions, elucidating its impact on the conductive network. [Display omitted] [ABSTRACT FROM AUTHOR]

Weak polyelectrolytes (WPEs) are widely used as pH-responsive materials, pH modulators and charge regulators in biomedical and technological applications that involve multi-component fluid environments. In these complex fluids, coupling between (often weak) interactions induced by micelles, nanoparticles and molecular aggregates modify the pKa as compared to that measured in single component solutions. Here we investigated the effect of coupling between hydrogen bonding and excluded volume interactions on the titration curves and pKa of polyacrylic acid (PAA) in solutions comprising PEO-based micelles (Pluronics and Brij-S20) of different size and volume fraction. Titration experiments of dilute, salt-free solutions of PAA (5 kDa, 30 kDa and 100 kDa) at low degree of polymer ionization (α < 0.25) drive spatial re-organization of the system, reduce the degree of ionization and consequentially increase the pKa by up to ~0.7 units. These findings indicate that the actual degree of ionization of WPEs measured in complex fluids is significantly lower (at a given pH) than that measured in single-component solutions. [ABSTRACT FROM AUTHOR]

Cells are crowded, but proteins are almost always studied in dilute aqueous buffer. We review the experimental evidence that crowding affects the equilibrium thermodynamics of protein stability and protein association and discuss the theories employed to explain these observations. In doing so, we highlight differences between synthetic polymers and biologically relevant crowders. Theories based on hard-core interactions predict only crowding-induced entropic stabilization. However, experiment-based efforts conducted under physiologically relevant conditions show that crowding can destabilize proteins and their complexes. Furthermore, quantification of the temperature dependence of crowding effects produced by both large and small cosolutes, including osmolytes, sugars, synthetic polymers, and proteins, reveals enthalpic effects that stabilize or destabilize proteins.Crowding-induced destabilization and the enthalpic component point to the role of chemical interactions between and among the macromolecules, cosolutes, and water. We conclude with suggestions for future studies. [ABSTRACT FROM AUTHOR]

The excluded volume effect is added to a fractional viscoelastic model for modeling fractal polymers. This reveals a physical connection between the fractional time derivative, fractal geometry, and excluded volume effect. This derivation is a general theoretical framework based on the Scott-Blair fractional model of viscoelasticity when the excluded volume and the hydrodynamic interaction are explicitly taken into account to derive the microscopic stress within the molecular theory of Rouse and Zimm. The methodology extends the generalized molecular theory of Zimm by adding the effect of excluded volume where the new relaxation formulation contains internal state variables that naturally depend on the fractional time derivative of deformation. The modified distribution of the end-to-end vector of a monomer contained within a polymer network is used for pre-averaging approximations of the mobility matrix in the Zimm model. The pre-averaging approximation is important since the mobility matrix is a nonlinear function and it is difficult to explicitly calculate. Through application of thermodynamic laws, we derive the linear fractional model of viscoelasticity based on its spectral dimension, fractal dimension, and the excluded volume parameter for fractal media. This derivation shows how the order of the fractional derivative in the linear fractional model of viscoelasticity is strongly correlated with fractal structure and excluded volume effects. [ABSTRACT FROM AUTHOR]

Protein amyloid fibrils have widespread implications for human health. Over the last twenty years, fibrillation has been studied using a variety of crowding agents to mimic the packed interior of cells or to probe the mechanisms and pathways of the process. We tabulate and review these results by considering three classes of crowding agent: synthetic polymers, osmolytes and other small molecules, and globular proteins. While some patterns are observable for certain crowding agents, the results are highly variable and often depend on the specific pairing of crowder and fibrillating protein.

It is now well appreciated that the crowded intracellular environment significantly modulates an array of physiological processes including protein folding–unfolding, aggregation, and dynamics to name a few. In this work we have studied the dynamics of domain I of the protein human serum albumin (HSA) in its urea-induced denatured states, in the presence of a series of commonly used macromolecular crowding agents. HSA was labeled at Cys-34 (a free cysteine) in domain I with the fluorophore 6-bromoacetyl-2-dimethylaminonaphthalene (BADAN) to act as a solvation probe. In partially denatured states (2–6 M urea), lower crowder concentrations (~ < 125 g/L) induced faster dynamics, while the dynamics became slower beyond 150 g/L of crowders. We propose that this apparent switch in dynamics is an evidence of a crossover from soft (enthalpic) to hard-core (entropic) interactions between the protein and crowder molecules. That soft interactions are also important for the crowders used here was further confirmed by the appreciable shift in the wavelength of the emission maximum of BADAN, in particular for PEG8000 and Ficoll 70 at concentrations where the excluded volume effect is not dominant. [ABSTRACT FROM AUTHOR]

An overview of a hadron resonance gas (HRG) model that includes van der Waals (vdW) interactions between hadrons is presented. Applications of the excluded volume HRG model to heavy-ion collision data and lattice quantum chromodynamics (QCD) equation of state are discussed. A recently developed quantum vdW HRG model is covered as well. Applications of this model in the context of the QCD critical point are elaborated. [ABSTRACT FROM AUTHOR]

Interphase configurations affect conductive properties of carbon fibrous composites (CFCs), specifically the percolation of interphase triggers the dramatic change of conductive properties. It has been a key but unresolved issue how to capture the percolation of soft interphase interacted by anisotropic-shaped carbon fibers and its quantitative effect on the conductivity of CFCs. This work proposes a theoretical framework for the accurate predictions of the excluded volume and percolation threshold of soft interphase and the effective conductivity of CFCs. This framework contains three theoretical models: (1) a coupling scheme between the second virial coefficient theory and Monte Carlo simulations for determining the excluded volumes; (2) an excluded-volume-based percolation model for obtaining the percolation threshold of soft interphase; (3) a continuum percolation-based micromechanical model (CPMM) for predicting the effective conductivity of CFCs with spherocylindrical carbon fibers of high volume fraction and their surrounding interphase percolation. Comparison against numerical and experimental data validates that the theoretical framework can well predict these properties of CFCs. This framework can be regarded as a general scheme that is readily applicable to other core-shell networks. Furthermore, we use the framework to probe various factors effects on the percolation threshold of interphase and electrical conductivity of CFCs. Image 10995 [ABSTRACT FROM AUTHOR]

We investigate a toy model for phase transitions in mixtures of incompressible droplets. The model consists of non-overlapping hypercubes in Z d of sidelengths 2 j , j ∈ N 0 . Cubes belong to an admissible set B such that if two cubes overlap, then one is contained in the other. Cubes of sidelength 2 j have activity z j and density ρ j . We prove explicit formulas for the pressure and entropy, prove a van-der-Waals type equation of state, and invert the density-activity relations. In addition we explore phase transitions for parameter-dependent activities z j (μ) = exp (2 dj μ - E j) . We prove a sufficient criterion for absence of phase transition, show that constant energies E j ≡ λ lead to a continuous phase transition, and prove a necessary and sufficient condition for the existence of a first-order phase transition. [ABSTRACT FROM AUTHOR]

Fluorescent DNA assays are promising in disease diagnosis, environmental monitoring, and drug screening, encompassing both heterogeneous and homogeneous assay types. Nevertheless, heterogeneous assays suffer from tedious washing steps and slow reaction kinetics, whereas homogenous assays require well-designed fluorophore pairs to modulate signal off/on. Herein, we developed a cost-effective and efficient quencher-free fluorescent DNA assay using an aqueous two-phase system (ATPS). Using a strand-displacement reaction, we showed that similar sensing performance could be achieved at a much lower cost. Furthermore, the unique crowding environment in ATPS accelerated strand-displacement reactions by up to six-fold and reduced DNA amplification time from 120 min to 30 min. Our assay demonstrated robust sensing in serum environments and successful detection of miRNA extracted from cells. This innovative assay format has the potential for biosensor development with both heterogeneous readout and rapid reaction kinetics in various applications. [Display omitted] [ABSTRACT FROM AUTHOR]

Understanding mixed stabilizers' ice recrystallization inhibition (IRI) effect is important for ice cream formulation. The IRI effect of cellulose nanocrystals (CNCs) was investigated in the presence of sodium alginate (SA), carboxymethyl cellulose (CMC), polyethylene glycol (PEG), and inulin. Adding low concentrations of SA (≤0.13%) and CMC (≤0.05%) enhanced the IRI effect of CNCs. The enhancement became less at higher concentrations of SA and CMC. Recrystallization was even accelerated with a further increase in concentration of SA (≥0.5%) or CMC (≥0.2%). PEG and inulin had little influence on the IRI effect of CNCs. Rheological analysis of polymer overlap concentration, particle size analysis of CNCs dispersion, and microscopical observation of ice crystals accretion suggested that the dual effects of excluded volume might explain the IRI effect of CNCs in the presence of polymers: (1) adding polymers resulted in the macromolecular crowding, reducing the available volume for CNCs and increasing their effective concentration to interact with ice crystals, and led to an enhanced IRI effect; (2) depletion interaction promoted the aggregation of CNCs and merging of ice crystals, resulting in less enhancement and recrystallization acceleration. Our findings advance our understanding of the IRI effect for mixed stabilizers and are critical to ice cream formulation. [Display omitted] • Anionic polymers at low concentrations enhanced the IRI effect of CNCs. • Anionic polymers at high concentrations reduced the IRI effect of CNCs. • Anionic polymers at much high concentrations accelerated ice recrystallization. • Neutral polymers had little influence on the IRI effect of CNCs. • Dual effects of excluded volume might explain the influences of adding polymer. [ABSTRACT FROM AUTHOR]

How proteins properly fold and maintain solubility at the risk of misfolding and aggregation in the cellular environments still remains largely unknown. Aggregation has been traditionally treated as a consequence of protein folding (or misfolding). Notably, however, aggregation can be generally inhibited by affecting the intermolecular interactions leading to aggregation, independently of protein folding and conformation. We here point out that rigorous distinction between protein folding and aggregation as two independent processes is necessary to reconcile and underlie all observations regarding the combined cellular protein folding and aggregation. So far, the direct attractive interactions (e.g., hydrophobic interactions) between cellular macromolecules including chaperones and interacting polypeptides have been widely believed to mainly stabilize polypeptides against aggregation. However, the intermolecular repulsions by large excluded volume and surface charges of cellular macromolecules can play a key role in stabilizing their physically connected polypeptides against aggregation, irrespective of the connection types and induced conformational changes, underlying the generic intrinsic chaperone activity of cellular macromolecules. Such rigorous distinction and intermolecular repulsive force-driven aggregation inhibition by cellular macromolecules could give new insights into understanding the complex cellular protein landscapes that remain uncharted.

Macromolecular crowding, manifested by high concentrations of proteins and nucleic acids in living cells, significantly influences biological processes such as enzymatic reactions. Studying these reactions in vitro, using agents such as polyetthylene glycols (PEGs) and polyvinyl alcohols (PVAs) to mimic intracellular crowding conditions, is essential due to the notable differences from enzyme behaviors observed in diluted aqueous solutions. In this article, we studied Mycobacterium tuberculosis (Mtb) DNA gyrase under macromolecular crowding conditions by incorporating PEGs and PVAs into the DNA supercoiling reactions. We discovered that high concentrations of potassium glutamate, glycine betaine, PEGs, and PVA substantially stimulated the DNA supercoiling activity of Mtb DNA gyrase. Steady-state kinetic studies showed that glycine betaine and PEG400 significantly reduced the K M of Mtb DNA gyrase and simultaneously increased the V max or k cat of Mtb DNA gyrase for ATP and the plasmid DNA molecule. Molecular dynamics simulation studies demonstrated that PEG molecules kept the ATP lid of DNA gyrase subunit B in a closed or semiclosed conformation, which prevented ATP molecules from leaving the ATP-binding pocket of DNA gyrase subunit B. The stimulation of the DNA supercoiling activity of Mtb DNA gyrase by these molecular crowding agents likely results from a decrease in water activity and an increase in excluded volume., Competing Interests: Conflict of interest The authors declare that they have no conflicts of interest with the contents of this article., (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.)

The article presents classical mechanics approach to thermodynamic properties of molecules at high temperatures which is based on a specific realisation of the idea of excluded volume and in the end avoids the use of second virial coefficient (in contrary to other approaches). The aim of this approach is to remove the negative contribution to the molecular partition function. The influence of the negative part on the partition function is investigated for the ground state of Na molecule. The full molecular partition functions (with bound, resonance and scattering contributions) are compared with the ones with negative contribution excluded. Additionally the applicability of the hard spheres repulsion is investigated and the comparison with an exact free (scattering) contribution is made. [ABSTRACT FROM AUTHOR]

An extended model of the surface energetic attachment (SEA) model is introduced to study the fouling of marine organisms on microtopographic surfaces, taking into account the excluded volume interaction and the attraction between the organisms. It is shown that the excluded volume interaction leads to changes in the site-typed attachment probabilities which increase with the average spore density on the surface. As a result of these changes, the spore density map is flattened under very high density fouling. The attractive interaction on the other hand leads to aggregation of spores and the average aggregate size increased with the strength of attraction. The model can be mapped to a specific experiment to determine the attachment energy parameters. In contrast to various prior empirical approaches, the extended SEA model is rigorous from the statistical mechanics viewpoint, thus it provides a reliable tool for studying complex attachment behaviors of microorganisms on topographic surfaces. [ABSTRACT FROM AUTHOR]

Nanocomposites can be produced by a variety of processes. A common method used in industry is to mix a viscous polymer such as an elastomer compound, with nanofillers in a Brabender mixer or in a calendar. Dispersion has been quantified using a mixing index, D R , that is based on micrographs of reinforced elastomers on the micron-scale. A recently developed technique based on X-ray scattering allows for an alternative nano-scale description of dispersion based on a thermal-dispersion model where an analogy is made between temperature for thermal dispersion and nanocomposite processing conditions such as mixing time, mixing geometry, and viscosity for kinetic dispersion. In this paper the impact of mixing time on dispersion is investigated taking advantage of the van der Waals equation to describe excluded volume and interaction energy in the dispersion. It is found that the thermal-dispersion analogy is well behaved and can determine the wetting time for nano-scale incorporation of filler into elastomer. The nano-scale excluded volume depends only on the filler type and the excess excluded volume seems to be sensitive to the bound rubber layer. The pseudo-interaction energy is strongly dependent on viscosity and polymer chemistry. The thermal-dispersion model offers a novel approach to understanding kinetic dispersion in nanocomposites. Image 1 • Ultra small-angle X-Ray scattering used to quantify nano-scale filler dispersion. • Colloidal analogy relates temperature to time for mechanical mixing of nanofillers. • van der Waals model used to estimate filler excluded volume and interaction energy. • Excluded volume depends strongly on the size of nanofiller particles. • Interaction energy depends on matrix viscosity and relates to filler wetting time. [ABSTRACT FROM AUTHOR]

It is of both theoretical and engineering significance to understand the random packings of non-spherical particles. However, apart from the well-discussed aspect ratio, studies on particle shapes continuously evolved from sphere to ideal polyhedra are still lacking, which represents the roundness effect. In this work, we investigate two packing states, namely random close packing (RCP) and saturated random packing (SRP), of spheropolyhedra (SPP), including three shape families, namely spherotetrahedron (SPT), spherocube (SPC), and spherooctahedron (SPO). We observe a common density peak phenomenon of these two states for all the families with respect to sphericity. Specifically, the RCP densities can reach ~0.746, ~0.750, and ~0.731 for the SPT, SPC, and SPO respectively, comparable with the crystalline density ~0.74 for spheres. Density peaks of the SRP locate at the sphericity ~0.96 for all the families. Additionally, the local structural analysis reveals the complex dependencies of order parameters on the roundness, including positional order q 6 and facet alignment Δ. The SRP states are more random in particle position than orientation. The dimer clusters formed by particles sharing common facets are also explored. We find that the facet number of a single particle is positively correlated with the q 6 yet negatively correlated with the Δ and the cluster ratio for all the polyhedron-like shapes at the RCP. Furthermore, the mechanism of excluded volume can explain the density peak of both the RCP and SRP for all the families and even partly reproduce the general trend of the RCP density for SPT. Unlabelled Image • Random close packing and saturated random packing of spheropolyhedra are studied. • Packing density shows certain universality in relation with sphericity. • Local structural analysis shows peculiarities for the three shape families. [ABSTRACT FROM AUTHOR]

Graphical abstract By depletion flocculation under theoretically determined conditions, Au nanoplates in low yield (<10%) were selectively extracted from a quadruple colloidal mixture. Abstract Au nanoplates represent an emerging class of plasmonic nanostructures of anisotropy that are promising great performance as a probe in biosensing and a building block for nanodevices. In spite of the rapid development of solution-phase synthesis, it has remained an open challenge for colloidal chemists to prepare Au nanoplates in high yield established for their Ag counterparts. This limitation largely compromises the practical use of Au nanoplates in plasmonic applications. Here we report a simple yet versatile approach for efficient purification of Au nanoplates in diverse colloidal mixtures based upon micelle-induced depletion flocculation. By means of calculation on free energy change upon depletion flocculation, we are able to pre-determine the flocculation conditions of different nanoparticles, allowing for predictable nanoparticle precipitation that depends on size and shape. We further demonstrate that the present approach is capable of isolating Au nanoplates of varied sizes in low yield (<10%) in various complex media, including a polyvinylpyrrolidone (PVP)-based colloid solution and a quadruple nanoparticle mixture. This post-synthesis purification method that doesn't rely on professional background suggests wide applicability in extraction of frontier nanostructures at low abundance yet in high demand. [ABSTRACT FROM AUTHOR]

Abstract Understanding the excluded volumes of particles has a great impact on the assessments of continuum percolation and random packing of soft/hard particle systems. The excluded volumes of convex particles have been extensively studied. However, little attention has been paid to the excluded volumes of non-convex particles. In this study, we propose a numerical scheme to investigate the excluded volumes of realistic three-dimensional (3D) non-convex particles. In this numerical scheme, we first reconstruct realistic particles by using X-ray tomography and spherical harmonic series. Subsequently, we triangulate the surfaces of realistic particles and detect the contact between adjacent particles by applying hierarchical detection strategies. Moreover, we present Monte Carlo simulations to obtain the excluded volumes of 3D non-convex particles. Finally, the dependence of the dimensionless excluded volumes on the roughness of surface texture and sphericity of non-convex particles is investigated. The statistical results can be further drawn into assessing the random packing and percolation properties of hard/soft 3D non-convex particle systems. Graphical abstract Unlabelled Image Highlights • A numerical scheme to obtain the excluded volumes of realistic particles is proposed. • Overlap detection between real particles is presented. • Statistical results are in accuracy with theoretical values. • The excluded volume depends on surface roughness and sphericity of real particles. [ABSTRACT FROM AUTHOR]

Abstract We have analyzed chemical equilibria in dimerizing fluids where the pair interactions between monomers and dimers are described by square-well potentials of varying depths and widths. The association is limited by the dimerization stage, in which the dimer is a sphere circumscribed around overlapping monomers. The distances between their centers correspond to the bond lengths. The dissociation energy is considered as a parameter of the theory. Within the statistical-thermodynamic model of the chemical reaction in fluid phase inevitable volume changes in associative equilibria were also taken into account by means of a consistent equation of state (EoS). We show that the attractive part of the intermolecular interaction can manifest itself in deviations of the chemical equilibrium from ideality alternative with temperature. The influence of the attraction and repulsion between monomers and dimers on the position of associative equilibrium is different at high and low temperatures. The stronger the attraction between monomers and (or) the weaker the attraction between associates, the more the equilibrium shifts towards dissociation (especially at moderate temperatures). The changes in density were analyzed as a function of the variation of the square-well depth and width in the associated mixture as well. The increase in the packing fraction is most pronounced with an increase in the width, describing the attraction between the dimers, particularly in the case of small bond lengths. With this, the square-well attraction, in particular between the dimers, contributes to an additional ordering of the fluid. Graphical abstract Unlabelled Image Highlights • The square-well attraction effect on the position of dimerization equilibrium in fluid was analyzed. • The change in the Gibbs free energy at the dimerization of fluid with square-well interaction was shown. • Increase in the attraction between the monomers leads to the shift of equilibrium towards dissociation. • The square-well attraction leads to an increase in the packing fraction, particularly with a small bond length in dimers. • The tendency to the ordering of the mixture manifests rather with a smaller dimer size and larger square wells. [ABSTRACT FROM AUTHOR]

This work presents an analytic study of anomalies observed in the water sound speed. From fundamentals of thermodynamics, we show that the two-liquid model, which assumes that water is composed of two types of clusters, HDL and LDL, whose relative concentration depends on the thermal conditions of the sample, leads straightforwardly to the result that the excluded volume of water can change. From this result, we demonstrate how the parameters determining the water sound speed are modified by the thermal dependent interaction between its clusters, leading to a profile for this property that is typical of water. • Analytic study of anomalies in the water sound speed. • The two-liquid model and consideration of a variable excluded volume and excluded pressure. • Reconsidering the van der Waals' approach to an equation of state. • Propagation of sound in water is affected by the thermal dependent interaction between its clusters. [ABSTRACT FROM AUTHOR]

Aggressive miniaturization in the electronics industry demands more efficient thermal management for electronic devices. Employing the excluded volume approach, we enhanced thermal conductivity (TC) and manipulated heat dissipation in a polymer composite loaded with a thermally conductive filler—graphene nanoplatelets (GNP)—alone or supplemented with a high-volume filler (diamonds). This yielded a maximum bulk TC of 4.5 W m−1K−1 (no compression). The heat dissipation direction could be controlled by compressing (≥50 bars) the wet composite before curing, resulting in an enhancement of the cross-plane thermal conductivity (for thermal-interface materials) to 12.3 W m−1K−1. For non-compressed samples, in-plane thermal conductivity (for circuit board conformal coatings) was dominant (8 Wm−1K−1). Our holistic approach meets diverse thermal management needs. [Display omitted] • The direction of the heat dissipation could be manipulated by compression. • Composites' preparation for various thermal management applications is provided. • Generating excluded volume enhances the thermal conductivity of polymer composites. • Compressed graphene-diamonds composites yield high vertical thermal conductivity. [ABSTRACT FROM AUTHOR]

[Display omitted] • Revisited van Wyk's model on the interfiber spacing for 3D random fiber networks. • Excluded area and excluded volume approaches accounted for low-aspect-ratio fibers. • Relationship between the maximum volume fraction and aspect ratio has been deduced. Understanding the structure–property relationships of random materials is a long-standing problem of great interest as their applications span one of the most diverse fields of science and engineering. Polycrystals, polymer blends, foams, fluidized beds, cermets, rocks, fibrous materials, and composites are notable examples of these materials. In random fiber networks, the apparent disconnect between size effects, intricate porous characteristics, and the stochastic nature of constituents, leading to quasi-heterogeneous features, emphasizes the need to explore beyond their microstructure. Herein, we revisit the pioneering work of van Wyk on the architectural-based interfiber spacing model for random fiber networks established via the excluded area and excluded volume approaches. In van Wyk's original work, the discrepancy between the excluded area and excluded volume frameworks has been ascertained and is now addressed by correlating with classical Bertrand's paradox. Subsequently, the excluded area and excluded volume approaches of the interfiber spacing model have been modified to account for low-aspect-ratio fibers by including the side-side, end-end, and side-end interactions. van Wyk's modified interfiber spacing model for low-aspect-ratio fibers has been compared with the other analytical model, developed for random fiber networks. A simple relationship between the maximum volume fraction and aspect ratio has also been deduced for cylindrical fibers. To demonstrate our analytical model's versatility and wide-ranging applicability, the maximum volume fraction and aspect ratio relationship has been benchmarked with a plethora of analytical models, simulations, and experiments obtained from the literature that resulted in a reasonable agreement. [ABSTRACT FROM AUTHOR]

The interphase region around nanoparticles changes the percolation threshold of long and thin nanoparticles, such as carbon nanotubes (CNT) in polymer nanocomposites. In this paper, the effects of the interphase region on the percolation threshold of nanoparticles and the network fraction are studied. New percolation threshold (φP) is defined by the role of the interphase in the excluded volume of nanoparticles (Vex). Moreover, the influences of filler and interphase size on the percolation volume fraction, the fraction of nanoparticles in the network as well as the volume fraction and relative density of the filler network are investigated. The least ranges of “φP” are obtained by thin and long CNT. Similarly, a thick interphase increases the “Vex” parameter, which causes a positive role in the percolation occurrence. Also, thin CNT and a thick interphase cause the high fraction of the filler network in the nanocomposites.

Biochemical processes within the living cell occur in a highly crowded environment, where macromolecules, first of all proteins and nucleic acids, occupy up to 30% of the volume. The phenomenon of macromolecular crowding is not an exclusive feature of the cytoplasm and can be observed in the densely protein-packed, nonhomogeneous cellular membranes and at the membrane interfaces. Crowding affects diffusional and conformational dynamics of proteins within the lipid bilayer, alters kinetic and thermodynamic properties of biochemical reactions, and modulates the membrane organization. Despite its importance, the non-invasive quantification of the membrane crowding is not trivial. Here, we developed a genetically-encoded fluorescence-based sensor for probing the macromolecular crowding at the membrane interfaces. Two sensor variants, both composed of fluorescent proteins and a membrane anchor, but differing by flexible linker domains were characterized in vitro, and the procedures for the membrane reconstitution were established. Steric pressure induced by membrane-tethered synthetic and protein crowders altered the sensors' conformation, causing increase in the intramolecular Förster's resonance energy transfer. Notably, the effect of protein crowders only weakly correlated with their molecular weight, suggesting that other factors, such as shape and charge contribute to the crowding via the quinary interactions. Finally, measurements performed in inner membrane vesicles of Escherichia coli validated the crowding-dependent dynamics of the sensors in the physiologically relevant environment. The sensors offer broad opportunities to study interfacial crowding in a complex environment of native membranes, and thus add to the toolbox of methods for studying membrane dynamics and proteostasis., (© 2023 The Authors. Protein Science published by Wiley Periodicals LLC on behalf of The Protein Society.)

The intracellular environment represents an extremely crowded milieu, with a limited amount of free water and an almost complete lack of unoccupied space. Obviously, slightly salted aqueous solutions containing low concentrations of a biomolecule of interest are too simplistic to mimic the “real life” situation, where the biomolecule of interest scrambles and wades through the tightly packed crowd. In laboratory practice, such macromolecular crowding is typically mimicked by concentrated solutions of various polymers that serve as model “crowding agents”. Studies under these conditions revealed that macromolecular crowding might affect protein structure, folding, shape, conformational stability, binding of small molecules, enzymatic activity, protein-protein interactions, protein-nucleic acid interactions, and pathological aggregation. The goal of this review is to systematically analyze currently available experimental data on the variety of effects of macromolecular crowding on a protein molecule. The review covers more than 320 papers and therefore represents one of the most comprehensive compendia of the current knowledge in this exciting area.

Eigenvolume effects in the hadron resonance gas (HRG) model are studied for experimental hadronic yields in nucleus–nucleus collisions. If particle eigenvolumes are different for different hadron species, the excluded volume HRG (EV-HRG) improves fits to multiplicity data. In particular, using different mass–volume relations for strange and non-strange hadrons we observe a remarkable improvement in the quality of the fits. This effect appears to be rather insensitive to other details in the schemes employed in the EV-HRG. We show that the parameters found from fitting the data of the ALICE Collaboration in central Pb+Pb collisions at the collision energy s NN = 2.76 TeV entail the same improvement for all centralities at the same collision energy, and for the RHIC and SPS data at lower collision energies. Our findings are put in the context of recent fits of lattice QCD results. [ABSTRACT FROM AUTHOR]

Four types of environmental effects that can affect macromolecular reactions in a living cell are defined: nonspecific intermolecular interactions, side reactions, partitioning between microenvironments, and surface interactions. Methods for investigating these interactions and their influence on target reactions in vitro are reviewed. Methods employed to characterize conformational and association equilibria in vivo are reviewed and difficulties in their interpretation cataloged. It is concluded that, in order to be amenable to unambiguous interpretation, in vivo studies must be complemented by in vitro studies carried out in well-characterized and controllable media designed to contain key elements of selected intracellular microenvironments. [ABSTRACT FROM AUTHOR]