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EPJ E - Soft Matter and Biological Physics
Journal Prestige (SJR): 0.489  Citation Impact (citeScore): 1 Number of Followers: 3  Hybrid journal (It can contain Open Access articles)ISSN (Print) 1292-8941 - ISSN (Online) 1292-895X Published by Springer-Verlag  [2468 journals]
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- On the force between “rafts”
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Abstract: “Rafts” in the plasma membrane are nanoscopic domains rich in sphingolipids and cholesterol. Groups of them are thought to provide stable platforms for various proteins. How several rafts can form a larger stable platform has yet to be made clear. Here, we show that in the microemulsion theory of rafts, in which they, and the sea in which they float, are characterized by a naturally occurring length, rafts separated by a sea larger than this length will attract one another, thus making the sea smaller. Similarly, if rafts are separated by a sea that is smaller than the characteristic size, they will repel one another thus allowing the sea to increase in size. Such an elastic force can clearly stabilize a platform of many rafts. Graphic abstract
PubDate: 2023-09-22
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- Spin-up flow in ferrofluids: a toy model
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Abstract: It is now more than 50 years since the first observation of ferrofluid spin-up by a rotating magnetic field by the author and R. Moskowitz. The ferrofluid rotated in direction opposite to that of the applied field. The intervening years have seen multiple unsuccessful attempts to explain this phenomenon. A clue was experimentally discovered by J. Popplewell and the author in 1987; rotation direction depends on shape of the ferrofluid meniscus. That notion is studied in further detail in the present work which describes tangential stress generated on the meniscus surface and an analytical expression for torque is developed. Increasing spin rate in smaller diameter vessels is rationalized. In addition, a physical picture of spin-up is introduced. Graphical abstract
PubDate: 2023-09-18
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- Granular convergence as an iterated local map
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Abstract: Abstract Granular convergence is a property of a granular pack as it is repeatedly sheared in a cyclic, quasistatic fashion, as the packing configuration changes via discrete events. Under suitable conditions the set of microscopic configurations encountered converges to a periodic sequence after sufficient shear cycles. Prior work modeled this evolution as the iteration of a pre-determined, random map from a set of discrete configurations into itself. Iterating such a map from a random starting point leads to similar periodic repetition. This work explores the effect of restricting the randomness of such maps in order to account for the local nature of the discrete events. The number of cycles needed for convergence shows similar statistical behavior to that of numerical granular experiments. The number of cycles in a repeating period behaves only qualitatively like these granular studies.
PubDate: 2023-09-18
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- Preparation and stability of pegylated poly(S-alkyl-L-homocysteine)
coacervate core micelles in aqueous media-
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Abstract: We report development and preparation of synthetic polypeptide based, coacervate core polyelectrolyte complex micelles, PCMs, in aqueous media, which were characterized and evaluated for the encapsulation and in vitro release of a model single-stranded RNA, polyadenylic acid, poly(A). Cationic, α-helical polypeptides pegylated at their N-termini, PEG113-b-5bn and PEG113-b-5cn, were designed to form coacervate core PCMs upon mixing with multivalent anions in aqueous media. Sodium tripolyphosphate (TPP) and poly(A) were used as model multivalent anions that allowed optimization of polypeptide composition and chain length for formation of stable, nanoscale PCMs. PEG113-b-5c27 was selected for preparation of PCMs that were characterized under different environmental conditions using dynamic light scattering, atomic force microscopy and cryoelectron microscopy. The PCMs were found to efficiently encapsulate poly(A), were stable at physiologically relevant pH and solution ionic strength, and were able to release poly(A) in the presence of excess polyvalent anions. These PCMs were found to be a promising model system for further development of polypeptide based therapeutic delivery vehicles. Graphical abstract
PubDate: 2023-09-14
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- Electroresponse of weak polyelectrolyte brushes
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Abstract: End-tethered polyelectrolytes are widely used to modify substrate properties, particularly for lubrication or wetting. External stimuli, such as pH, salt concentration, or an electric field, can induce profound structural responses in weak polyelectrolyte brushes, which can be utilized to further tune substrate properties. We study the structure and electroresponsiveness of weak polyacid brushes using an inhomogeneous theory that incorporates both electrostatic and chain connectivity correlations at the Debye–Hückel level. Our calculation shows that a weak polyacid brush swells under the application of a negative applied potential, in agreement with recent experimental observation. We rationalize this behavior using a scaling argument that accounts for the effect of the surface charge. We also show that the swelling behavior has a direct influence on the differential capacitance, which can be modulated by the solvent quality, pH, and salt concentration. Graphical
PubDate: 2023-09-14
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- Renormalized charge and dielectric effects in colloidal interactions: a
numerical solution of the nonlinear Poisson–Boltzmann equation for
unknown boundary conditions-
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Abstract: The Derjaguin–Landau–Verwey–Overbeek (DLVO) theory, introduced more than 70 years ago, is a hallmark of colloidal particle modeling. For highly charged particles in the dilute regime, it is often supplemented by Alexander’s prescription (Alexander et al. in J Chem Phys 80:5776, 1984) for using a renormalized charge. Here, we solve the problem of the interaction between two charged colloids at finite ionic strength, including dielectric mismatch effects, using an efficient numerical scheme to solve the nonlinear Poisson–Boltzmann (NPB) equation with unknown boundary conditions. Our results perfectly match the analytical predictions for the renormalized charge by Trizac and coworkers (Aubouy et al. in J Phys A 36:5835, 2003). Moreover, they allow us to reinterpret previous molecular dynamics (MD) simulation results by Kreer et al. (Phys Rev E 74:021401, 2006), rendering them now in agreement with the expected behavior. We furthermore find that the influence of polarization becomes important only when the Debye layers overlap significantly. Graphical
PubDate: 2023-09-11
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- Fluctuations, structure, and size inside coacervates
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Abstract: Aqueous solutions of oppositely charged macromolecules exhibit the ubiquitous phenomenon of coacervation. This subject is of considerable current interest due to numerous biotechnological applications of coacervates and the general premise of biomolecular condensates. Towards a theoretical foundation of structural features of coacervates, we present a field-theoretic treatment of coacervates formed by uniformly charged flexible polycations and polyanions in an electrolyte solution. We delineate different regimes of polymer concentration fluctuations and structural features of coacervates based on the concentrations of polycation and polyanion, salt concentration, and experimentally observable length scales. We present closed-form formulas for correlation length of polymer concentration fluctuations, scattering structure factor, and radius of gyration of a labelled polyelectrolyte chain inside a concentrated coacervate. Using random phase approximation suitable for concentrated polymer systems, we show that the inter-monomer electrostatic interaction is screened by interpenetration of all charged polymer chains and that the screening length depends on the individual concentrations of the polycation and the polyanion, as well as the salt concentration. Our calculations show that the scattering intensity decreases monotonically with scattering wave vector at higher salt concentrations, while it exhibits a peak at intermediate scattering wave vector at lower salt concentrations. Furthermore, we predict that the dependence of the radius of gyration of a labelled chain on its degree of polymerization generally obeys the Gaussian chain statistics. However, the chain is modestly swollen, the extent of which depending on polyelectrolyte composition, salt concentration, and the electrostatic features of the polycation and polyanion such as the degree of ionization. Graphical abstract
PubDate: 2023-09-08
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- Multiscale micro-architecture of pore space in rocks: size, shape,
deformation and accessibility determined by small-angle neutron scattering
(SANS)-
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Abstract: A brief summary of the evolving applications of small-angle neutron scattering (SANS) to the microstructural research on geological materials in the last few decades is provided, including new developments and possible future directions. This is an account of authors’ view of the interplay between the technical development of SANS instrumentation, methodology and sample environments and the progress of research on the evolution of organic matter, gas adsorption and desorption, fluid transport in the pore space and the microstructure of rocks, based mostly on their own research interests. Graphical abstract
PubDate: 2023-09-08
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- Effect of cholesterol on the mechanical stability of gel-phase
phospholipid bilayers studied by AFM force spectroscopy-
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Abstract: The remarkably low sliding friction of articular cartilage in the major joints such as hips and knees, which is crucial for its homeostasis and joint health, has been attributed to lipid bilayers forming lubricious boundary layers at its surface. The robustness of such layers, and thus their lubrication efficiency at joint pressures, depends on the lipids forming them, including cholesterol which is a ubiquitous component, and which may act to strengthen of weaken the bilayer. In this work, a systematic study using an atomic force microscope (AFM) was carried out to understand the effect of cholesterol on the nanomechanical stability of two saturated phospholipids, DSPC (1,2-distearoyl-sn-glycero-3-phosphatidlycholine) and DPPC (1,2-dipalmitoyl-sn-glycero- phosphatidylcholine), that differ in acyl chain lengths. Measurements were carried out both in water and in phosphate buffer solution (PBS). The nanomechanical stability of the lipid bilayers was quantitatively evaluated by measuring the breakthrough force needed to puncture the bilayer by the AFM tip. The molar fractions of cholesterol incorporated in the bilayers were 10% and 40%. We found that for both DSPC and DPPC, cholesterol significantly decreases the mechanical stability of the bilayers in solid-ordered (SO) phase. In accordance with the literature, the strengthening effect of salt on the lipid bilayers was also observed. For DPPC with 10 mol % cholesterol, the effect of tip properties and the experimental procedure parameters on the breakthrough forces were also studied. Tip radius (2–42 nm), material (Si, Si3N4, Au) and loading rate (40—1000 nm/s) were varied systematically. The values of the breakthrough forces measured were not significantly affected by any of these parameters, showing that the weakening effect of cholesterol does not result from such changes in experimental conditions. As we have previously demonstrated that mechanical robustness improves the tribological performance of lipid layers, this study helps to shed light on the mechanism of physiological lubrication. Graphical abstract Nanoindentation of SDPC bilayers
PubDate: 2023-09-06
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- Structure of microemulsions in the continuous phase channel
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Abstract: Abstract We have studied the microemulsion and lamellar phases of two of the most commonly described systems based on nonionic C12E5 and ionic AOT surfactants. We show that C12E5 is best described by the symmetric disordered open connected lamellar model (DOC-lamellar), contrary to the more commonly employed standard flexible model. In the case of AOT, the bicontinuous microemulsion structure is best described by the standard flexible model at high temperatures. Around room temperature, connected cylinders in a molten cubic crystal phase are the only description which corresponds to the data. In the lamellar phase, around one third of the available surface area is lost in fluctuations and defects. Comparing structurally predictive models with results from conductivity measurements show that salt adsorption in the hydrated ethoxy groups is dominant for C12E5 (nonionic). For AOT, our conductivity measurements clarify the role of tortuosity versus cation absorption.
PubDate: 2023-09-05
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- A molecularly informed field-theoretic study of the complexation of
polycation PDADMA with mixed micelles of sodium dodecyl sulfate and
ethoxylated surfactants-
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Abstract: The self-assembly and phase separation of mixtures of polyelectrolytes and surfactants are important to a range of applications, from formulating personal care products to drug encapsulation. In contrast to systems of oppositely charged polyelectrolytes, in polyelectrolyte-surfactant systems the surfactants micellize into structures that are highly responsive to solution conditions. In this work, we examine how the morphology of micelles and degree of polyelectrolyte adsorption dynamically change upon varying the mixing ratio of charged and neutral surfactants. Specifically, we consider a solution of the cationic polyelectrolyte polydiallyldimethylammonium, anionic surfactant sodium dodecyl sulfate, neutral ethoxylated surfactants (C \(_m\) EO \(_n\) ), sodium chloride salt, and water. To capture the chemical specificity of these species, we leverage recent developments in constructing molecularly informed field theories via coarse-graining from all-atom simulations. Our results show how changing the surfactant mixing ratios and the identity of the nonionic surfactant modulates micelle size and surface charge, and as a result dictates the degree of polyelectrolyte adsorption. These results are in semi-quantitative agreement with experimental observations on the same system. Graphic abstract
PubDate: 2023-09-04
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- Synchrotron X-ray study of intrinsically disordered and polyampholytic Tau
4RS and 4RL under controlled ionic strength-
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Abstract: Aggregated and hyperphosphorylated Tau is one of the pathological hallmarks of Alzheimer’s disease. Tau is a polyampholytic and intrinsically disordered protein (IDP). In this paper, we present for the first time experimental results on the ionic strength dependence of the radius of gyration (Rg) of human Tau 4RS and 4RL isoforms. Synchrotron X-ray scattering revealed that 4RS Rg is regulated from 65.4 to 58.5 Å and 4RL Rg is regulated from 70.9 to 57.9 Å by varying ionic strength from 0.01 to 0.592 M. The Rg of 4RL Tau is larger than 4RS at lower ionic strength. This result provides an insight into the ion-responsive nature of intrinsically disordered and polyampholytic Tau, and can be implicated to the further study of Tau-Tau and Tau-tubulin intermolecular structure in ionic environments. Graphical abstract
PubDate: 2023-08-31
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- Smart design of universally decorated nanoparticles for drug delivery
applications driven by active transport-
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Abstract: Targeting the cell nucleus remains a challenge for drug delivery. Here, we present a universal platform for the smart design of nanoparticle (NP) decoration that is based on: (i) a spacer polymer, commonly biotin-polyethylene-glycol-thiol, whose grafting density and molecular weight can be tuned for optimized performance, and (ii) protein binding peptides, such as cell penetrating peptides (CPPs), cancer-targeting peptides, or nuclear localization signal (NLS) peptides, that are linked to the PEG free-end by universal chemistry. We manifested our platform with two different bromo-acetamide (Br-Ac) modified NLSs. We used cell extract-based and live cell assays to demonstrate the recruitment of dynein motor proteins, which drive the NP active transport toward the nucleus, and the enhancement of cellular and nuclear entry, manifesting the properties of NLS as a CPP. Our control of the NP decoration scheme, and the modularity of our platform, carry great advantages for nano-carrier design for drug delivery applications. Graphical abstract
PubDate: 2023-08-31
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- On the construction of some bioconjugate networks and their structural
modeling via irregularity topological indices-
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Abstract: Bioconjugate networks refer to networks that are formed by connecting different molecules or particles (such as proteins, enzymes, or nanoparticles) through covalent or non-covalent interactions. These networks are often used in various biological and biomedical applications, such as drug delivery, biosensors, and tissue engineering. The specific properties and behavior of these networks depend on the types of molecules used and the nature of their interactions, which can be studied using various computational and experimental techniques. Farnesyl and geranyl groups are types of isoprenoid chains that are commonly found in various biological molecules such as proteins, lipids, and pigments. The addition of these groups to penicillin molecules may alter their physical and chemical properties, such as solubility, stability, and bioavailability. To gain a better understanding of the structure–property relationships of these antibiotics, this study computes various irregularity indices such as the Albertson index, irregularity index, total irregularity index, Randić irregularity index, and other degree-based indices for two types of sensitive bonds of bioconjugate networks. Numerical results and graphical representations are used to illustrate these findings. The obtained results provide valuable insights into the structure–property relationships of penicillins, which will aid in a better understanding of their behavior and developing more effective antibiotics. Graphical abstract
PubDate: 2023-08-21
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- Effect of excitation frequency on dissipation behavior of vibrated
granular balls-
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Abstract: The dissipation behavior of granular balls in a quasi-2D vertically oscillating closed container is studied by the discrete element method with varying excitation frequencies in this work. Combining the dynamic behavior with dissipation effect of vibrated granular balls, the optimal damping effect of the phase transition critical stage between granular density inversion and granular Leidenfrost effect that involves four high damping granular phases (HDGPs) is revealed. Moreover, the high damping granular phases near and away from this phase transition critical stage are compared and analyzed further, which indicates the universal dynamic behavior of dense granular clusters playing the optimal damping effect. Finally, the optimal damping mechanism of granular balls in the quasi-2D closed container is clarified. Graphical abstract Damping properties and motion states of partic
PubDate: 2023-08-18
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- Diffusion coefficients and MSD measurements on curved membranes and porous
media-
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Abstract: We study some geometric aspects that influence the transport properties of particles that diffuse on curved surfaces. We compare different approaches to surface diffusion based on the Laplace–Beltrami operator adapted to predict concentration along entire membranes, confined subdomains along surfaces, or within porous media. Our goal is to summarize, firstly, how diffusion in these systems results in different types of diffusion coefficients and mean square displacement measurements, and secondly, how these two factors are affected by the concavity of the surface, the shape of the possible barriers or obstacles that form the available domains, the sinuosity, tortuosity, and constrictions of the trajectories and even how the observation plane affects the measurements of the diffusion. In addition to presenting a critical and organized comparison between different notions of MSD, in this review, we test the correspondence between theoretical predictions and numerical simulations by performing finite element simulations and illustrate some situations where diffusion theory can be applied. We briefly reviewed computational schemes for understanding surface diffusion and finally, discussed how this work contributes to understanding the role of surface diffusion transport properties in porous media and their relationship to other transport processes. Graphical abstract
PubDate: 2023-08-14
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- Model chromatin flows: numerical analysis of linear and nonlinear
hydrodynamics inside a sphere-
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Abstract: We solve a hydrodynamic model of active chromatin dynamics, within a confined geometry simulating the cell nucleus. Using both analytical and numerical methods, we describe the behavior of the chromatin polymer driven by the activity of motors having polar symmetry, both in the linear response regime as well as in the long-term, fully nonlinear regime of the flows. The introduction of a boundary induces a particular geometry in the flows of chromatin, which we describe using vector spherical harmonics, a tool which greatly simplifies both our analytical and numerical approaches. We find that the long-term behavior of this model in confinement is dominated by steady, transverse flows of chromatin which circulate around the spherical domain. These circulating flows are found to be robust to perturbations, and their characteristic size is set by the size of the domain. This gives us further insight into active chromatin dynamics in the cell nucleus, and provides a foundation for development of further, more complex models of active chromatin dynamics. Graphical abstract
PubDate: 2023-08-04
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- Nonlinear evolution of viscoplastic film flows down an inclined plane
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Abstract: In this article, we experimentally investigate the nonlinear behaviour of a viscoplastic film flow down an inclined plane. We focus on the nonlinear instabilities that appear as roll waves. Roll waves are generated by perturbing a permanent flow of Herschel–Bulkley fluid (Carbopol 980) at low frequencies. To determine the local thickness of the film, we used a laser sensor and a camera to globally capture the transverse shape of the waves. For a regular forcing, the results show the existence of different regimes. First, we observe primary instabilities below the cut-off frequency at the entrance of the channel. After the exponential growth of the wave in the linear regime, we recognise the nonlinear dynamics with the existence of finite amplitude waves. This finite amplitude depends on the frequency, the Reynolds number and the inclination angle. The results show that this instability is supercritical. At moderate Reynolds numbers, the finite 2-D waves become sensitive to transverse perturbations, due to a secondary instability, and become 3-D waves. The experimental results illustrate a phenomenology of viscoplastic film flows similar to Newtonian fluids, except for the capillary waves. Graphical abstract
PubDate: 2023-08-03
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- Super-swelling behavior of stacked lipid bilayer systems
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Abstract: Bilayer systems comprising lipid mixtures are the most well-studied model of biological membranes. While the plasma membrane of the cell is a single bilayer, many intra- and extra-cellular biomembranes comprise stacks of bilayers. Most bilayer stacks in nature are periodic, maintaining a precise water layer separation between bilayers. That equilibrium water separation is governed by multiple inter-bilayer forces and is highly responsive. Biomembranes re-configure inter-bilayer spacing in response to temperature, composition, or mass transport cues. In synthetic bilayer systems for applications in cosmetics or topical treatments, control of the hydration level is a critical design handle. Herein we investigate a binary lipid system that leverages key inter-bilayer forces leading to unprecedented levels of aqueous swelling while maintaining a coherent multilamellar form. We found that combining cationic lipids with bicontinuous cubic phase-forming lipids (lipids with positive Gaussian modulus), results in the stabilization of multilamellar phases against repulsive steric forces that typically lead to bilayer delamination at high degrees of swelling. Using ultra-small-angle X-ray scattering alongside confocal laser scanning microscopy, we characterized various super-swelled states of 1,2-dioleoyl-3-trimethylammonium-propane (DOTAP) and glycerol monooleate (GMO) lipids, as well as other analogous systems, at varied concentration and molar ratios. Through these experiments we established swelling profiles of various binary lipid systems that were near-linear with decreasing lipid volume fraction, showing maximum swelling with periodicity well above 200 nanometers. Graphic abstract Confocal fluorescence micrograph of super-swelled multilamellar structures in 90GMOD sample at 25 mM concentration. Inset plot shows intensity profile of orange line, with pink triangles indicating maxima.
PubDate: 2023-08-03
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- Charge fluctuations in charge-regulated systems: dependence on statistical
ensemble-
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Abstract: We investigate charge regulation of nanoparticles in concentrated suspensions, focusing on the effect of different statistical ensembles. We find that the choice of ensemble does not affect the mean charge of nanoparticles, but significantly alters the magnitude of its fluctuation. Specifically, we compared the behaviors of colloidal charge fluctuations in the semi-grand canonical and canonical ensembles and identified significant differences between the two. The choice of ensemble—whether the system is isolated or is in contact with a reservoir of acid and salt—will, therefore, affect the Kirkwood–Shumaker fluctuation-induced force inside concentrated suspensions. Our results emphasize the importance of selecting an appropriate ensemble that accurately reflects the experimental conditions when studying fluctuation-induced forces between polyelectrolytes, proteins, and colloidal particles in concentrated suspensions. Graphical abstract
PubDate: 2023-07-31
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