Excluded Volume Research Articles

Thermodynamic complexation mechanism of zinc ion with 8-hydroxyquinoline-5-sulfonic acid in molecular crowding environment

A crowded molecular environment, which is universally observed in biological cells, changes the thermodynamics and kinetics of biochemical reactions compared to bulk solution. Although molecular crowding has received significant attention, a fundamental explanation of the molecular crowding effect based on thermodynamic parameters, including enthalpy (ΔH) and entropy changes (ΔS), is insufficient. Herein, the complexation mechanism of zinc ions with quinolinol derivative in a molecular crowding environment was investigated using polyethylene glycol (PEG) based on the changes in ΔH and ΔS. For 1:1 complexation, which is only promoted by the osmotic pressure effect, ΔH and ΔS decreased with increasing PEG concentration (CPEG) because the number of dehydration molecules decreased. In the 1:2 complexation system, which is affected by the osmotic pressure and volume exclusion effects, no obvious dependences of ΔH and ΔS on CPEG were observed. This is because the osmotic pressure and volume exclusion effects contributed oppositely to ΔH and ΔS. The results presented herein provide fundamental knowledge for protein-metal interactions, and it is expected that these data will attract the attention of many physical chemists and biochemists.

Liquid-hexatic-solid phases in active and passive Brownian particles determined by stochastic birth and death events.

We study the effects of stochastic birth and death processes on the structural phases of systems of active and passive Brownian particles subject to volume exclusion. The total number of particles in the system is a fluctuating quantity, determined by the birth and death parameters and on the activity of the particles. As the birth and death parameters are varied, we find liquid, hexatic, and solid phases. For passive particles, these phases are found to be spatially homogeneous. For active particles, motility-induced phase separation (coexisting hexatic and liquid phases) occurs for large activity and sufficiently small birth rates. We also observe a reentrant transition to the hexatic phase when the birth rate is increased. This results from a balance of an increasing number of particles filling the system, and a larger number of defects resulting from the birth and death dynamics.

Citrate effect on the swelling behaviour and stability of casein microparticles

Casein microparticles obtained from casein micelles by volume exclusion of added pectin and subsequent film drying remain stable in the acidic and neutral pH range, but swell strongly in the basic range. Calcium significantly impacts on the stability and water-binding behavior of phosphorylated caseins and the aggregates and gels formed from them. For a future effective and controlled use as a carrier for bioactive substances, e.g. via the gastrointestinal tract, we therefore investigated how the addition of the calcium chelating agent citrate affects the swelling and stability of the microparticles. Citrate concentrations of 2 mM and above cause a stronger swelling of the microparticles at pH 8, while above 4 mM the second characteristic swelling step starts earlier and thus can also be investigated within the observation time of 120 min. All swelling kinetics can be simulated using seven parameters of a dynamic model, which reproduces the individual swelling steps via volume inflows and outflows into a reservoir. While the rate coefficient for swelling step 1 increases linearly with citrate concentration, no such dependence could be found for swelling step 2. The more citrate is used, the faster the microparticles decompose in turbidity experiments after the addition of sodium dodecyl sulfate, which can be related to a weakening of the hydrophobic interactions.

Molecular dynamics simulation of H2 in amorphous polyethylene system: H2 diffusion in various PE matrices and bubbling during rapid depressurization

Polyethylene (PE) is a candidate liner material for Type IV storage devices. In this case, all-atom molecular dynamics simulations are employed to study the properties of Polyethylene with the presence of H2, including tensile properties, glass transition, diffusion in different PE and bubbling during rapid depressurization. The presence of H2 deteriorates the polyethylene matrix's tensile performance and decreases the glass transition temperature. The branch, side chain and small molecules promote the diffusion of H2 in the amorphous region by introducing more free volume below Tg. With a sufficient length, the length of polymer chain has minor effect on the diffusion of H2. Graphene, as a 2D reinforcement, could decrease the diffusion of H2 but suffers from poor interfacial bonding. Finally, H2 bubble(s) formed from the over-saturated H2 molecule and were observed in both the exclusive and free volume and stabilised at low pressure during rapid depressurization. According to the result obtained in this work, branchless HDPE is expected to give superior performance while the viscosity, which is important during processing, could be tailored by molecular weight. Processing technique leads to orientation is preferred, such as injection moulding.

Effect of Transglutaminase Post-Treatment on the Stability and Swelling Behavior of Casein Micro-Particles.

Casein microparticles are produced by flocculation of casein micelles due to volume exclusion of pectin and subsequent stabilization by film drying. Transglutaminase post-treatment alters their stability, swelling behavior, and internal structure. Untreated particles sediment due to their size and disintegrate completely after the addition of sodium dodecyl sulfate. The fact that transglutaminase-treated microparticles only sediment at comparable rates under these conditions shows that their structural integrity is not lost due to the detergent. Transglutaminase-treated particles reach an equilibrium final size after swelling instead of decomposing completely. By choosing long treatment times, swelling can also be completely suppressed as experiments at pH 11 show. In addition, deswelling effects also occur within the swelling curves, which enhance with increasing transglutaminase treatment time and are ascribed to the elastic network of cross-linked caseins. We propose a structural model for transglutaminase-treated microparticles consisting of a core of uncross-linked and a shell of cross-linked caseins. A dynamic model describes all swelling curves by considering both casein fractions in parallel. The characteristic correlation length of the internal structure of swollen casein microparticles is pH-independent and decreases with increasing transglutaminase treatment time, as observed also for the equilibrium swelling value of uncross-linked caseins.

Regulation of stem cell dynamics through volume exclusion

The maintenance and regeneration of adult tissues rely on the self-renewal of stem cells. Regeneration without over-proliferation requires precise regulation of the stem cell proliferation and differentiation rates. The nature of such regulatory mechanisms in different tissues, and how to incorporate them in models of stem cell population dynamics, is incompletely understood. The critical birth-death (CBD) process is widely used to model stem cell populations, capturing key phenomena, such as scaling laws in clone size distributions. However, the CBD process neglects regulatory mechanisms. Here, we propose the birth-death process with volume exclusion (vBD), a variation of the birth-death process that considers crowding effects, such as may arise due to limited space in a stem cell niche. While the deterministic rate equations predict a single non-trivial attracting steady state, the master equation predicts extinction and transient distributions of stem cell numbers with three possible behaviours: long-lived quasi-steady state (QSS), and short-lived bimodal or unimodal distributions. In all cases, we approximate solutions to the vBD master equation using a renormalized system-size expansion, QSS approximation and the Wentzel–Kramers–Brillouin method. Our study suggests that the size distribution of a stem cell population bears signatures that are useful to detect negative feedback mediated via volume exclusion.

Soft interactions versus hard core repulsions: A journey of cytochrome c from acid-induced denaturation to native protein via pre-molten globule and molten globule conformations exploiting dextran and its monomer glucose

Protein attains its biological functional state in a crowded environment, whereas traditional in vitro experiments are carried out in dilute solutions. In this investigation, synthetic crowders (dextran and glucose) are exploited to investigate the effect of crowding on the conformation of cytochrome c. Protein folding may occur through many non-native intermediate states. Here, the effect of crowder (dextran) and its monomer (glucose) on the structural conformation and stability of cytochrome c (cyt c) has been studied in an acidic environment using various biophysical techniques such as UV–Vis absorbance, circular dichroism, and fluorescence spectroscopy (Trp and ANS fluorescence), dynamic light scattering and interaction experiments using ITC and molecular docking. These techniques show that the cyt c forms a molten globule in the presence of glucose while the pre-molten globule in the presence of the dextran 70. These results suggest that dextran 70 stabilizes the protein due to macromolecular crowding via soft interactions, while glucose due to co-solute engineering exploiting volume exclusion phenomenon as confirmed by ITC experiments. These investigations inferred that crowders protect protein in harsh conditions (acidic pH), which may arise due to various diseased conditions such as acidosis-induced insulin resistance, cardiovascular risks, etc. The current work also has an industrial application to increase the shelf life of therapeutic proteins.

Exclusion volumes of convex bodies in high space dimensions: applications to virial coefficients and continuum percolation

Using the concepts of mixed volumes and quermassintegrals of convex geometry, we derive an exact formula for the exclusion volume v ex(K) for a general convex body K that applies in any space dimension. While our main interests concern the rotationally-averaged exclusion volume of a convex body with respect to another convex body, we also describe some results for the exclusion volumes for convex bodies with the same orientation. We show that the sphere minimizes the dimensionless exclusion volume v ex(K)/v(K) among all convex bodies, whether randomly oriented or uniformly oriented, for any d, where v(K) is the volume of K. When the bodies have the same orientation, the simplex maximizes the dimensionless exclusion volume for any d with a large-d asymptotic scaling behavior of 22d /d 3/2, which is to be contrasted with the corresponding scaling of 2 d for the sphere. We present explicit formulas for quermassintegrals W 0(K), …, W d (K) for many different nonspherical convex bodies, including cubes, parallelepipeds, regular simplices, cross-polytopes, cylinders, spherocylinders, ellipsoids as well as lower-dimensional bodies, such as hyperplates and line segments. These results are utilized to determine the rotationally-averaged exclusion volume v ex(K) for these convex-body shapes for dimensions 2 through 12. While the sphere is the shape possessing the minimal dimensionless exclusion volume, we show that, among the convex bodies considered that are sufficiently compact, the simplex possesses the maximal v ex(K)/v(K) with a scaling behavior of 21.6618…d . Subsequently, we apply these results to determine the corresponding second virial coefficient B 2(K) of the aforementioned hard hyperparticles. Our results are also applied to compute estimates of the continuum percolation threshold η c derived previously by the authors for systems of identical overlapping convex bodies. We conjecture that overlapping spheres possess the maximal value of η c among all identical nonzero-volume convex overlapping bodies for d ⩾ 2, randomly or uniformly oriented, and that, among all identical, oriented nonzero-volume convex bodies, overlapping simplices have the minimal value of η c for d ⩾ 2.

J-aggregation of 5, 10, 15, 20-tetraphenyl-21H, 23H-porphinetetrasulfonic acid in a molecular crowding environment simulated using dextran.

In a molecular crowding environment, different thermodynamics is often observed in a dilute solution. One such example is the promotion of the formation of amyloids, which are causal agents of Alzheimer's disease. Although a considerable number of molecular crowding studies have been reported, its effect remains unclear. In this study, we investigated a J-aggregation of a porphyrin derivative, 5, 10, 15, 20-tetraphenyl-21H,23H-porphinetetrasulfonic acid (TPPS), in a molecular crowding environment simulated by dextran (Dex) in HClO4, HCl, and NaCl solutions. The changes in the number of monomers in the J-aggregate (n) with the concentration of Dex (CDex) depended on the type of solution. No change in n was observed in the NaCl solution, which indicated that the Dex solution did not affect the J-aggregation because of the ionic strength effect. In the HCl solution, the aggregation behavior changed with the pH. Further, at a low pH, the electrostatic interactions promoted J-aggregation by the volume exclusion of Dex, while the aggregation was suppressed at a high pH owing to steric hindrance. A different aggregation mechanism, involving the hydrogen bonding between NH in the center of the TPPS macrocyclic frame and the SO3H and ClO4- functional groups, was responsible for the J-aggregation in the HClO4 solution. Moreover, the n value increased owing to the volume exclusion effect. We expect that this study will be useful for further elucidation of the molecular crowding effect.

Structural and electrostatic properties between pH-responsive polyelectrolyte brushes studied by augmented strong stretching theory.

In this paper, we study electrostatic and structural properties between pH-responsive polyelectrolyte brushes by using a strong stretching theory accounting for excluded volume interactions, the density of polyelectrolyte chargeable sites, and the Born energy difference between the inside and outside of the brush layer. In a free energy framework, we obtain self-consistent field equations to determine electrostatic properties between two pH-responsive polyelectrolyte brushes. We elucidate that in the region between two pH-responsive polyelectrolyte brushes, electrostatic potential at the centerline and osmotic pressure increase not only with excluded volume interaction but also with the density of chargeable sites on a polyelectrolyte molecule. Importantly, we clarify that when two pH-responsive polyelectrolyte brushes approach each other, the brush thickness becomes short and that a large excluded volume interaction and a large density of chargeable sites yield the enhanced contract of polyelectrolyte brushes. In addition, we also demonstrate how the influence of such quantities as pH, the number of Kuhn monomers, the density of charged sites, the lateral separation between adjacent polyelectrolyte brushes, and Kuhn length on the electrostatic and structural properties between the two polyelectrolyte brushes is affected by the exclusion volume interaction. Finally, we investigate the influence of the Born energy difference on the thickness of polyelectrolyte brushes and the osmotic pressure between two pH-responsive polyelectrolyte brushes.

Tailoring Multifunctional and Lightweight Hierarchical Hybrid Graphene Nanoplatelet and Glass Fiber Composites

In this work, hybrid polypropylene (PP)-based composites reinforced with graphene nanoplatelets (GnPs) and glass fiber (GF) were fabricated by injection molding to elucidate how the hybrid approach can produce synergistic effects capable of achieving properties and functionalities not possible in biphasic composites. Synergism between the reinforcements translated to improved mechanical performance, which was attributed to the chemically and/or electrostatically assembled hierarchical structure that facilitates load transfer at the interface while simultaneously tailoring the crystalline microstructure of the matrix by inducing transcrystallization and β-crystal formation. It was demonstrated that there exists an optimal concentration of 0.5 wt % GnP, producing the greatest mechanical properties and synergistic effect, corresponding to the highest degree of crystallinity (∼6% greater than Neat PP) and peak formation of β-crystals within the PP matrix. The greatest synergistic effect was found to be ∼52 and ∼39% for the specific tensile strength and flexural strength, respectively. The same optimal concentration of GnPs was found to produce the highest synergistic effect for thermal conductivity of ∼68% due to the volume exclusion effect induced by the GFs combined with the higher crystallinity of the microstructure, promoting the formation of thermally conductive pathways. Ultimately, the mechanisms contributing to the synergistic effect presented in this work can be used to maximize the performance of hybrid composite systems, giving them the potential to be tailored for a variety of high-performance industrial applications to meet the rising demands for ultra-strong, thermally conductive, and lightweight materials.

Computing time-periodic steady-state currents via the time evolution of tensor network states.

We present an approach based upon binary tree tensor network (BTTN) states for computing steady-state current statistics for a many-particle 1D ratchet subject to volume exclusion interactions. The ratcheted particles, which move on a lattice with periodic boundary conditions subject to a time-periodic drive, can be stochastically evolved in time to sample representative trajectories via a Gillespie method. In lieu of generating realizations of trajectories, a BTTN state can variationally approximate a distribution over the vast number of many-body configurations. We apply the density matrix renormalization group algorithm to initialize BTTN states, which are then propagated in time via the time-dependent variational principle (TDVP) algorithm to yield the steady-state behavior, including the effects of both typical and rare trajectories. The application of the methods to ratchet currents is highlighted, but the approach extends naturally to other interacting lattice models with time-dependent driving. Although trajectory sampling is conceptually and computationally simpler, we discuss situations for which the BTTN TDVP strategy can be beneficial.

An analytical approach to the anomalous density of water

Water, which is essential for the existence of life, has almost a hundred properties that distinguish it from other liquids. In this paper, we will focus on its density, which, unlike the absolute majority of other liquids, increases with increasing temperature in the vicinity of the solid–liquid transition, for a wide range of pressures, including ambient pressure. Our approach will present an analytical thermodynamic formulation for this problem that has, as a novelty, the introduction of a variable exclusion volume. The excluded volume will be considered a thermodynamic variable, that is, it depends on the system's thermal conditions. This approach will be applied to the two-liquid theory of water, which claims that water molecules can be assembled into two different kinds of clusters. At a given state, the relative numbers of these aggregates can be very sensitive to thermal variations, and, as the excluded volume for each of them is different, when their relative number changes, the total excluded volume also changes. We will show how to gather the ideas of a non-constant excluded volume with the two-liquid theory of water into a new, elegant, and non-trivial analytical expression for the density of water. In the end, we compare our expression with experimental data and show that it provides an exact understanding of the anomalous behavior of water density.

Free energies of polymer brushes with mobile anchors in a good solvent calculated with the expanded ensemble method

We explore the free energy of “mobile polymer brushes”: The polymer molecules are not chemically bonded to the particle surface but are rather adsorbed by one end. They can desorb to the equilibrium solution and are able to move laterally along the interface. In a good solvent the prevailing forces in the system (apart from the attraction between the adsorbed anchor and the surface) originate from the entropic repulsion between the individual chains. Here we explore the brushes’ free energy and adsorption equilibrium using Brownian Dynamics in conjunction with Expanded Ensembles Monte Carlo simulations that we adapt making it more suitable for polymer brushes. Expanded Ensembles are employed to calculate the excess chemical potential of a polymer chain as a function of the interfacial lateral density, polymer length, and effective exclusion volume of the segment. The thermodynamic properties are related to the structural features, such as brush height, chain radius of gyration, and the in-plane radial distribution function between the chain anchors. Specific attention is paid to the scaling of the excess chemical potential and brush height with the polymer length and interfacial density as well as its influence on the adsorption equilibrium between interface and the bulk polymer solution.

Crowding-induced protein destabilization in the absence of soft attractions

It is generally assumed that volume exclusion by macromolecular crowders universally stabilizes the native states of proteins and destabilization suggests soft attractions between crowders and protein. Here we show that proteins can be destabilized even by crowders that are purely repulsive. With a coarse-grained sequence-based model, we study the folding thermodynamics of two sequences with different native folds, a helical hairpin and a β-barrel, in a range of crowder volume fractions, φc. We find that the native state, N, remains structurally unchanged under crowded conditions, while the size of the unfolded state, U, decreases monotonically with φc. Hence, for all φc>0, U is entropically disfavored relative to N. This entropy-centric view holds for the helical hairpin protein, which is stabilized under all crowded conditions as quantified by changes in either the folding midpoint temperature, Tm, or the free energy of folding. We find, however, that the β-barrel protein is destabilized under low-T, low-φc conditions. This destabilization can be understood from two characteristics of its folding: 1) a relatively compact U at T<Tm, such that U is only weakly disfavored entropically by the crowders; and 2) a transient, compact, and relatively low-energy nonnative state that has a maximum population of only a few percent at φc=0, but increasing monotonically with φc. Overall, protein destabilization driven by hard-core effects appears possible when a compaction of U leads to even a modest population of compact nonnative states that are energetically competitive with N.

Size-Dependent Interplay of Volume Exclusion Versus Soft Interactions: Cytochrome c in Macromolecular Crowded Environment.

Even though there are a great number of possible conformational states, how a protein generated as a linear unfolded polypeptide efficiently folds into its physiologically active form remained a fascinating and unanswered enigma inside crowded conditions of cells. In this study, various spectroscopic techniques have been exploited to know and understand the effect and mechanism of action of two different sizes of polyethylene glycols, or PEGs (molecular mass ∼10 and ∼20kilo Daltons, kDa), on cytochrome c (cyt c). The outcomes showed that small size of the PEG leads to perturbation of the protein structure, and conversely, large size of the PEG has stabilizing effect on cyt c. Moreover, binding measurements showed that small size of PEG interacts strongly via soft interactions compared to the larger size of PEG, the latter being governed more by excluded volume effect or preferential exclusion from the protein. Overall, this finding suggests that conformations of protein may be influenced in cellular crowded conditions via interactions which depend upon the size of molecule in the environment. This study proposes that both volume exclusion and soft (chemical) interactions governs the protein's conformation and functional activities. The cellular environment's internal architecture as evident from crowder size and shape in this study has a significant role.

Influence of pectin and drying conditions on the structure, stability and swelling behaviour of casein microparticles

Casein microparticles with adjustable swelling properties and stabilities, which are produced under gentle pH and temperature conditions, are of interest as encapsulation systems for bioactive compounds. In the process investigated here, the volume exclusion of pectin causes casein micelles to form aggregates under neutral pH conditions, from which casein microparticles can be produced by film drying. The type of pectin used and the drying conditions significantly influence the stability and swelling behaviour of the casein microparticles. With increasing drying time, the microparticles become more stable and show greater deviations from mono-exponential decomposition after addition of sodium-dodecylsulphate. They are also more stable when dried in pure pectin films rather than in mixed pectin films. While the microparticles from beet and citrus pectin films swell the fastest and the slowest, respectively, those from mixed films show a moderate swelling behaviour with only a weakly pronounced two-step swelling process.

Current Flow in a Cylindrical Nanopore with an Object-Implications for Virus Sensing.

Interest is growing in nanopores as real-time, low-cost, label-free virus size sensors. To optimize their performance, we evaluate how external electric field and ion concentrations and pore wall charges influence currents and object (disk) radius-current relationship using simulations. The physics was described using the Poisson-Nernst-Planck and Navier–Stokes equations. In a charged cylindrical nanopore with a charged disk, elevated external electric field produces higher (and polarity independent) ion concentrations and greater ion current (largely migratory). Elevated external ion concentrations also lead to higher concentrations (mainly away from the pore wall), greater axial electric field especially in the disk-pore wall space, and finally larger current. At low concentrations, current is disk radius independent. The current rises as concentrations increase. Interestingly, the rise is greater for larger disks (except when the pore is blocked mechanically). Smaller cross-sectional area for current flow or volume exclusion of electrolyte by object thus cannot be universally accepted as explanations of current blockage. Ion current rises when pore wall charge density increases, but its direction is independent of charge sign. Current-disk radius relationship is also independent of pore wall charge sign. If the pore wall and disk charges have the same sign, larger current with bigger disk is due to higher counter-ion accumulation in the object-pore wall space. However, if their signs are opposite, it is largely due to elevated axial electric field in the object-pore wall space. Finally in uncharged nanopores, current diminishes when disk radius increases making them better sensors of virus size.

Separation and purification of enveloped and non-enveloped viruses from water samples using an aqueous two-phase system

In this study, a new strategy for enriching viruses in water was developed to improve the detection of viruses in environmental samples. The virus was enriched from water by aqueous two-phase system (ATPS), and the recovery and purification were characterized by tissue culture median infection dose (TCID50) and total protein removal rate. The isolation and purification methods of envelope virus (H1N1) and non-envelope virus (human adenovirus type 5, HAdV-5E) were established and optimized. The results of ATPS were compared with those of membrane filtration, polyethylene glycol precipitation and ultrafiltration. Using ATPS, both viruses were enriched in interphase due to the combined action of volume exclusion and bottom stage salting out. Under the optimum conditions, the recoveries of H1N1 and HAdV-5E were 94.87 ± 2.37% and 96.22 ± 4.71% respectively, and the total protein removal rates were 43.02 ± 5.21% and 71.01 ± 6.34% respectively. Compared with conventional methods, ATPS showed superior performance in recovering virus content and water volume, and the average recoveries were 94.06% (H1N1) and 90.07% (HAdV-5E). Therefore, ATPS had superiorities of high recovery, simple operation and maintaining virus particle activity(Fig. 1).

Effect interfacial size and multiple interface on electromagnetic shielding of silicon rubber/carbon nanotube composites with mixing segregated particles

Controllable distribution of conductive fillers in CPCs, such as segregated distribution, has been applied to improve electromagnetic interference (EMI) shielding effectiveness (SE). In this study, the effect of size and size distribution of segregated particles on electromagnetic shielding performance was explored in polydimethylsiloxane/multi-walled carbon nanotube composites (PDMS/CNT) via regulating the diameter of silicon dioxide (SiO2) particles. Through the addition of segregated SiO2 particles, the volume exclusion effect was introduced into the composites to construct dense conductive networks. With decreasing the size of segregated particles, the EMI SE of the samples enhanced on a whole, because of the increase of interfaces. Furthermore, the SiO2 particles with different diameters mixed to create the composites with multiple interfaces. Micro-micro segregated particles exhibited a synergistic effect when the diameters matched with each other. Nano-micro segregated particles enhanced interfacial polarization to enhance EMI shielding performance, although the conductive networks were damaged by the adhesion of nano-particles on CNTs. On a whole, the addition of single and mixed segregated particles could achieve excellent microwave shielding performance through the volume exclusion effect, the interface regularity, the multiple scattering at the interface, and the mutual interference efficiency.