Excluded Volume Research Articles

Comparative analysis of soluble and insoluble dietary fiber on improving the gelation performance and fishy odors of silver carp surimi

This work investigated the effects and mechanisms of soluble and insoluble dietary fiber (SDF and IDF) on the gelation performance and fishy odors of silver carp surimi. The results showed that the gel properties of surimi increased and then decreased with increasing SDF content, and the best gel properties were achieved at 1 wt% SDF. The gel strength, elasticity and deformation resistance of surimi increased in a dose-dependent manner as affected by IDF, but its effect on viscosity and recovery ratio was similar to SDF. Moreover, 2 wt% SDF and 1 wt% IDF reduced the content and odor activity value (OAV) of most fishy compounds in surimi, and the latter was superior to the former. The rheological characteristics indicated that SDF affected the thermal gelation properties of surimi mainly through filling, concentration and volume exclusion, and IDF mainly through filling, concentration and intermolecular interactions between IDF and myofibrillar protein. Additionally, SDF and IDF inhibited the release of fishy odors by improving the gel network structure and their adsorption, but more SDF (2 wt%) promoted the formation of escape channels for odors release. In summary, 1 wt% IDF could simultaneously improve the gelation performance and fishy odors of silver carp surimi.

The extraction of buckwheat protein and its interaction with kappa-carrageenan: Textural, rheological, microstructural, and chemical properties

Current plant-based foods use plant proteins as a key structuring and texturing ingredient. The use of water for extraction can replace conventional protein extraction methods. Water extraction of protein is environmentally friendly and could prevent the loss of protein functionality due to extreme pH changes. This study demonstrates an aqueous extraction method, coupled with ultrasound as pre-treatment, to obtain buckwheat protein (BWPE) and assess its gelling property and composited gel with kappa-carrageenan (k-carr). Textural and rheological analyses showed that the hardness and storage modulus of the composited gel containing 1 % w/w BWPE and 1 % w/w k-carr was 4.2-fold and 100-fold, respectively, higher than k-carr gel at 1 % w/w. Light microscopy showed a mixed bi-continuous gel system, with k-carr reinforcing the protein gel network. Besides volume exclusion effects, chemical bond and FTIR analyses revealed that adding k-carr to BWPE altered the protein's secondary structure and mediated protein denaturation during heating. This results in greater β-sheet content, which creates a more organised gel structure. These results demonstrated that ultrasound-assisted water-extracted BWPE, together with varying concentrations of k-carr, can be used to develop composited gels of tailorable textural and rheological properties to suit different food applications.

MACROMOLECULAR CROWDING AND OTHER IN VITRO MICROENVIRONMENT MODULATORS IN TENOCYTE CULTURES

The term macromolecular crowding is used to describe equilibria and kinetics of biochemical reactions and biological processes that occur via mutual volume exclusion of macromolecules in a highly crowded structureless medium. In vivo, the extracellular space is heavily crowded by a diverse range of macromolecules and thus, biological processes occur rapidly, whilst in vitro, in the absence of macromolecules, the same processes occur very slowly, if they are initiated at all (1-3). This talk will discuss the concept of macromolecular crowding, alone or in combination with other in vitro microenvironment modulators, in tendon engineering context.Acknowledgements: This work has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme, grant agreement No. 866126. This publication has emanated from research supported by grants from Science Foundation Ireland (SFI) under grant number 19/FFP/6982.

ASATrans: Adaptive spatial aggregation transformer for cervical nuclei segmentation on rough edges.

The main characteristic of cervical cytopathy is reflected in the edge shape of nuclei. Existing computer-aided diagnostic techniques can clearly segment individual nuclei, but cannot clearly segment the rough edges of adherent nucleus. Therefore, we propose an effective method (ASATrans) to accurately segment rough cervical nuclei edges by exploring adaptive spatial aggregation methods. ASATrans creates a Multi-Receptive Embedding Layer that samples patches using diverse-scale kernels. This approach provides cross-scale features to each embedding, preventing semantic corruption that might arise from mapping disparate patches to analogous underlying representations. Furthermore, we design Adaptive Pixel Adjustment Block by introducing a long-range dependency and adaptive spatial aggregation. This is achieved through the stratification of the spatial aggregation process into distinct groups. Each group is given an exclusive sampling volume and modulation scale, fostering a collaborative learning paradigm that combines local features and global dependencies. This collaborative approach to feature extraction achieves adaptability, mitigates interference from unnecessary pixels, and allows for better segmentation of edges in the nucleus. Extensive experiments on two cervical nuclei datasets (HRASPP Dataset, ISBI Dataset), demonstrating that our proposed ASATrans outperforms other state-of-the-art methods by a large margin.

Application of the symmetric Poisson-Boltzmann theory to a model colloidal mixture.

A symmetric Poisson-Boltzmann theory is used to analyse the structure of a primitive model colloidal system which contains either 4 or 6 components. The approach symmetrizes the pair distribution function gij(r) between two asymmetric charged species with respect to an interchange of the indices. Good agreement is found with molecular dynamics simulation structural properties when the exclusion volume term is modelled by the Percus-Yevick uncharged hard sphere radial distribution function.

The effect of Ficoll 70 on thermally-induced and chemically-induced conformational transitions of an RTX protein is quantitatively accounted for by a unified excluded volume model.

A unified excluded volume model based upon the effective hard particle approximation is developed and used to quantitatively model previously published experimental measurements of the effect of adding high concentrations of an "inert" polymer, Ficoll 70, on conformational transitions of the toxin protein RCL that are induced by addition of calcium at constant temperature or by increasing temperature in the absence and presence of high calcium concentrations. The best-fit of this model, which accounts quantitatively for all of the published data to within experimental precision, yields an estimate of the volume of solution excluded to Ficoll by each of four identified conformational states of RCL: H - the most compact conformation adopted in the limits of high calcium concentration and low temperature, H* - the conformation adopted in the limits of high calcium concentration and high temperature, A - the conformation adopted in the limits of low (or no) calcium at low temperature, and A* - the conformation adopted in the limits of low calcium and high temperature. Ficoll exclusion volumes increase in the order H < H* < A < A*. These results are discussed in the context of the physiological functions of the RTX proteins, which are involved in the secretion process and the calcium-induced folding of bacterial virulence factors.

Effective patchiness from critical points of a coarse-grained protein model with explicit shape and charge anisotropy.

Colloidal model systems are successful in rationalizing emergent phenomena like aggregation, rheology and phase behaviour of protein solutions. Colloidal theory in conjunction with isotropic interaction models is often employed to estimate the stability of such solutions. In particular, a universal criterion for the reduced second virial coefficient at the critical point is frequently invoked which is based on the behavior of short-range attractive fluids (Noro-Frenkel rule, ). However, if anisotropic models for the protein-protein interaction are considered, e.g. the Kern-Frenkel (KF) patchy particle model, the value of the criterion is shifted to lower values and explicitly depends on the number of patches. If an explicit shape anisotropy is considered, as e.g. in a coarse-grained protein model, the normalization of becomes ambiguous to some extent, as no unique exclusion volume can be defined anymore. Here, we investigate a low-resolution, coarse-grained model for the globular protein bovine serum albumin (BSA) and study effects of charge-anisotropy on the phase diagram (determined by simulations) at the isoelectric point. We present methods of assigning an "effective patchiness" to our protein model by comparing its critical properties to the KF model. We find that doubling the native charges increases the critical temperature Tc by ≈14% and that our BSA model can be compared to a 3 to 5 patch KF model. Finally, we argue that applying existing criteria from colloidal theory should be done with care, due to multiple, physically plausible ways of how to assign effective diameters to shape-anisotropic models.

Evaluation of the Efficiency of a Chitosan Membrane in Removing Gallic Acid from Wastewater Using Adsorption in Batch Mode and Separation by Dead-End Filtration

Abstract: This study assesses the efficacy of adsorption and separation techniques for removing gallic acid (GA) from wastewater using a chitosan membrane (Chi-1.5%). The effect of GA concentration, mass of adsorbent, contact time and pH were investigated. GA adsorption was best fitted by the Freundlich and Langmuir isotherm models, with a correlation coefficient of 0.9972 and 0.9929, respectively. The maximum adsorption capacity of GA (301.70 mg/g) was calculated at pH 8.4 and 303 K. Gibbs free energy was also calculated. The negative value showed that the GA adsorption is spontaneous. On the other hand, the value of activation energy of adsorption (&lt; 7 kJ/mol) indicates that the adsorption is physical in nature. The adsorption kinetics was best fitted by the pseudo-second-order model, and the effect of pH (8.4 and 7.1) on the adsorption is explained by theoretical calculation of the fraction of ions present in solution and their affinity for the membrane. The maximum percentage of GA removal based on a dead-end filtration system was 18.58% at a GA concentration of 300 ppm, pH 8.4 and a pressure of 1 bar. Volume exclusion was found to have a very slight effect on removing GA from the aqueous phase, while adsorption played the main role in removing GA.

Nanopore electrochemical sensors for emerging hazardous pollutants detection

Nanopore electrochemical sensors have been developed to detect various emerging pollutants at the single-molecule level with high sensitivity and specificity due to their high resolution in past three decades, which is of great significance for emerging hazardous pollutants control. Electrochemical detection methods based on nanopore technology are primarily divided into two categories: resistive-pulse and rectification sensing. The main detection mechanism of the resistive-pulse method is based on the volume exclusion effect generated when the analyte enters through the nanopore, and it involves three primary detection strategies. The first approach involves nanopore technology for direct pollutant detection, where pollutant structure and concentration information is assessed based on nanopore-generated ionic current's blockade strength, duration, and frequency. The second strategy relies on weak intermolecular interactions when direct detection of pollutants is challenging. Molecular probes interact with target molecules to enhance detection sensitivity and achieve specific recognition. The third strategy is based on the biological/chemical reaction of pollutant molecules, through indirect detection method to achieve specific detection of target pollutant molecules. Additionally, relies on changes in surface charge polarity or nanopore spatial structure induced by the analyte molecules to achieve the detection of target molecules within the nanopore. This work demonstrates the research progress achieved in the application of nanopore electrochemical sensing technology to high-sensitivity detection of hazardous pollutants, utilizing the unique confined spatial characteristics of nanopores, combined with biorecognition techniques and principles of electrochemical reactions.

Characteristic of the interaction mechanism between soy protein isolate and functional polysaccharide with different charge characteristics and exploration of the foaming properties

The commercial production process will partially damage the foaming properties of soy protein isolate (SPI). Adding functional polysaccharides have a positive effect on the foaming properties of SPI, but the effects are affected by several factors. For this reason, three kinds of polysaccharides with different charges, including chitosan (CS, a cationic polysaccharide), guar gum (GUG, a neutral polysaccharide) and gellan gum (GEG, an anionic polysaccharide), were complexed with SPI at different mass ratios to discuss their interaction mechanism, and the foaming properties of these complexes were preliminarily explored. After complexation, the structure of SPI was further folded and interacted with three polysaccharides mainly through non-covalent bonding. Specifically, SPI and CS interacted through weak electrostatic interaction, volume exclusion effect and hydrogen bonding at a high CS concentration. SPI and GEG interacted through strong electrostatic interaction and hydrogen bonding. However, SPI and GUG interacted only through hydrogen bonding. In addition to SPI/CS10, the foamability of SPI/polysaccharide complexes was significantly lower than single SPI. By contrast, the foam stability of all the complexes was much higher than single SPI, and increased with the increase of the polysaccharide concentration, among which the SPI/GEG complexes showed the highest foam stability. These findings provided the interaction mechanism between SPI and polysaccharides with different charges, and the complexes with outstanding foam stability can be used for improving the stability and texture of aerated foods.

Graphene Oxide-Mediated Regulation of Volume Exclusion and Wettability in Biomimetic Phosphorylation-Responsive Ionic Gates.

Replicating phosphorylation-responsive ionic gates via artificial fluidic systems is essential for biomolecular detection and cellular communication research. However, current approaches to governing the gates primarily rely on volume exclusion or surface charge modulation. To overcome this limitation and enhance ion transport controllability, we introduce graphene oxide (GO) into nanochannel systems, simultaneously regulating the volume exclusion and wettability. Moreover, inspired by (cAMP)-dependent protein kinase A (PKA)-regulated L-type Ca2+ channels, we employ peptides for phosphorylation which preserves them as nanoadhesives to coat nanochannels with GO. The coating boosts steric hindrance and diminishes wettability, creating a substantial ion conduction barrier, which represents a significant advancement in achieving precise ion transport regulation in abiotic nanochannels. Leveraging the mechanism, we also fabricated a sensitive biosensor for PKA activity detection and inhibition exploration. The combined regulation of volume exclusion and wettability offers an appealing strategy for controlled nanofluidic manipulation with promising biomedical applications in diagnosis and drug discovery.

Exact hydrodynamics and onset of phase separation for an active exclusion process

We consider a lattice model of active matter with exclusion and derive its hydrodynamic description exactly. The hydrodynamic limit leads to an integro-differential equation for the density of particles with a given orientation. Volume exclusion results in nonlinear mobility dependent on spatial density. Such models of active matter can support motility-induced phase separation, which occurs despite the absence of attractive interactions. We study the onset of phase separation with linear stability analysis and numerical simulations.

In situ preparation and properties of polyvinyl alcohol/synthetic ribbon-like nanocellulose composites

This study presents a novel approach in which a dual network (DN) composite, comprising polyvinyl alcohol (PVA) and ribbon-like nanocellulose (RC), was synthesized in one step using the volume exclusion effect involved in enzyme-catalyzed cellulose synthesis. Additionally, the impact of PVA as a crowding reagent during enzymatic catalysis on the in situ formation of nanocellulose and its resulting aspect ratio was explored. In contrast, the other two composites were created by incorporating enzyme-catalyzed synthetic block cellulose (BC) and its acid-hydrolyzed regenerated disc-shaped cellulose (DC) into the PVA. Subsequently, the mechanism by which three distinct types of nanocellulose, varying in morphology and size, was explored to elucidate their contributions to enhancing the properties of PVA. The results demonstrated that PVA/RC outperformed PVA/BC and PVA/DC. The elevated aspect ratio and intricate network structure of RCs not only significantly bolster the mechanical robustness of PVA/RC, leading in an 86.40 % surge in tensile strength and a remarkable 277.03 % rise in tensile modulus in comparison to pure PVA, but also induce a slight enhancement in elongation at break. Moreover, the thermal stability and biodegradability of PVA/RC was enhanced. Collectively, this study introduces an innovative strategy for the efficient fabrication of biodegradable composites with enhanced properties.

Dynamic density functional theory for sedimentation processes on complex domains: Modelling, spectral elements, and control problems.

Modelling of many real-world processes, such as drug delivery, wastewater treatment, and pharmaceutical production, requires accurate descriptions of the dynamics of hard particles confined in complicated domains. In particular, when modelling sedimentation processes or systems with driven flows, it is important to accurately capture volume exclusion effects. This work applies Dynamic Density Functional Theory to the evolution of a particle density under diffusion, external forces, particle-particle interaction, and volume exclusion. Using a spectral element framework, for the first time it is possible to include all of these effects in dynamic simulations on complex domains. Moreover, this allows one to apply complicated no-flux, and other non-local, non-linear, boundary conditions. The methodology is also extended to control problems, addressing questions of how to enhance production set-up in industrially-motivated processes. In this work the relevant models are introduced, numerical methods are discussed, and several example problems are solved to demonstrate the methods' versatility. It is shown that incorporating volume exclusion is crucial for simulation accuracy and we illustrate that the choice of boundary conditions significantly impacts the dynamics.

Not Always Sticky: Specificity of Protein Stabilization by Sugars Is Conferred by Protein-Water Hydrogen Bonds.

Solutes added to buffered solutions directly impact protein folding. Protein stabilization by cosolutes or crowders has been shown to be largely driven by protein-cosolute volume exclusion complemented by chemical and soft interactions. By contrast to previous studies that indicate the invariably destabilizing role of soft protein-sugar attractions, we show here that soft interactions with sugar cosolutes are protein-specific and can be stabilizing or destabilizing. We experimentally follow the folding of two model miniproteins that are only marginally stable but in the presence of sugars and polyols fold into representative and distinct secondary structures: β-hairpin or α-helix. Our mean-field model reveals that while protein-sugar excluded volume interactions have a similar stabilizing effect on both proteins, the soft interactions add a destabilizing contribution to one miniprotein but further stabilize the other. Using molecular dynamics simulations, we link the soft protein-cosolute interactions to the weakening of direct protein-water hydrogen bonding due to the presence of sugars. Although these weakened hydrogen bonds destabilize both the native and denatured states of the two proteins, the resulting contribution to the folding free energy can be positive or negative depending on the amino acid sequence. This study indicates that the significant variation between proteins in their soft interactions with sugar determines the specific response of different proteins, even to the same sugar.

Smart Manufacturing Implementation of a Continuous Downstream Precipitation and Filtration Process for Antibody Purification

Abstract Recently, continuous bioprocessing has gained momentum in biomanufacturing and can alleviate many of the hurdles faced in batch or semi-batch operations. Moreover, the parallel development of smart manufacturing (SM) allows the rapid small-scale prototyping and large-scale implementation of continuous bioprocesses. With this background, this paper presents the laboratory-scale implementation of a continuous precipitation-filtration process that can ultimately be used for therapeutic protein capture purification. The experimental setup includes four static mixers, four peristaltic pumps, one hollow fiber dewatering filtration module, and multiple pressure sensors and weigh scales. The system also includes an in-line advanced microscopic particle imaging probe that provides real-time images and derived metrics of the precipitate particle morphologies and a fiber optic 880 nm optical absorbance probe. A polyclonal human serum antibody mixture (hIgG) (10 g/L) was used as a stand-in for a monoclonal antibody therapeutic along with 7 % w/v polyethylene glycol (PEG, volume exclusion agent) and 10 mM zinc chloride (cross-linking agent) as the precipitants to demonstrate the principles of operation and control of a precipitation-based process using SM technology. An integrated input/output (I/O) system was used to acquire pressure, flow rate, and weigh scale data and also to communicate with the pumps to change flow rates in real-time. Edge computers communicate with the I/O system and the imaging probe and host the software layer. The software layer enables real-time data acquisition, data-driven and first-principles model predictions, closed-loop control of precipitate particle morphology using pump flow rate of PEG, and cloud communications with the Clean Energy Smart Manufacturing Innovation Institute Smart Manufacturing Innovation Platform. The paper presents the initial results obtained with this integrated system, demonstrating the potential of SM strategies to enhance the production of life-saving biopharmaceutical products.

Diffusiophoresis of a highly charged rigid colloid in a hydrogel incorporating ion steric interactions

Diffusiophoresis, mediated by an imposed ionic concentration gradient, is a useful technique in directed migration of colloids. Theoretical studies on diffusiophoresis in a polymer hydrogel medium are rather limited owing to the presence of nonlinear terms in the fluid transport equations. The hydrogel creates a hydrodynamic interaction and short-range steric interaction to the dispersing particle and macromolecules. The volume exclusion due to a finite ion size consideration is important in the context of a highly charged particle. In this study, we consider the finite ion size effects on diffusiophoresis of a charged particle with ζ≥1 in a hydrogel medium. The modified ion transport equations coupled with the Brinkman equation for fluid flow and the Poisson equation for electric field are solved numerically in a coupled manner through a control volume approach. Our results based on the Brinkman model incorporating only the hydrodynamic interactions deviate from the existing experimental results. A close comparison with this experimental data is established when the computed mobility is modified to incorporate the short-range steric factor. We have considered the impact of the hindered diffusivity of ions in the gel medium. Our results show that the modification in the ionic diffusivity is significant for low porosity and high charge density situations. The impact of the finite ion size effect is found to be significant when the bulk ionic concentration is large enough to create an electric double layer thinner than the particle size. We have analyzed the size dependency of the mobility in the gel medium. A simplified expression for the mobility in a hydrogel medium is proposed.

Removal of binary and ternary synergistic mixtures of ozone and VOCs by activated carbon filter: Mathematical modelling

Evaluating the activated carbon filter's performance in removing gaseous pollutants is essential to determining the filter maintenance schedule for indoor environments. This paper describes the development of a mathematical model to predict an activated carbon filter's performance for removing mixtures of ozone and volatile organic compounds (toluene and limonene) at their low-level concentrations in typical indoor environments. Mass transfer equations were employed to estimate the filter's dynamic behaviour by including the reaction rates of ozone with carbon surfaces and the reactive volatile organic compound, as well as the adsorption isotherm for a single volatile organic compound or binary mixtures of volatile organic compounds. The reaction rate constant for the ozone-limonene reaction was calculated by fitting the model to the experiment results of their binary mixture at 9 ppm of limonene and 0.1 ppm of ozone. Additionally, the ozone-exposed filters at 0.1 ppm were used to perform adsorption tests to determine the parameters of the Dubinin-Radushkevich isotherm using experimental results at 9, 30, 50, 70, and 90 ppm of volatile organic compounds. The Dubinin-Radushkevich isotherm was extended using the volume exclusion theory to consider the effect of by-products on the removal modelling of the binary mixture of ozone and limonene and the ternary mixture of ozone, limonene, and toluene.The model was able to show the reduced accessibility of the surface of activated carbon for reaction with ozone because of the adsorption of volatile organic compounds and generated by-products (keto-limonene and carvone). The initial influence is of minor magnitude; however, as the surface load intensifies, its significance can progressively amplify over time. Pre-exposing the filter to ozone prior to conducting adsorption tests was able to capture the average change in the adsorption properties of the filter. These considerations in the modelling result in a remarkable predictive capability in determining the breakthrough behaviour of the filter in removing the binary or ternary mixture of ozone and volatile organic compounds at various concentrations. The insignificant effect of the homogeneous reaction between ozone and limonene for the investigated experimental setup was confirmed by comparing the predictions made by the proposed model with those made by another model that considers the homogeneous reaction. Finally, the sensitivity analysis revealed that the model is more sensitive to adsorption isotherm parameters compared to the reaction kinetic parameter between ozone and limonene.

Volume exclusion effects in perovskite charge transport modeling

Due to their flexible material properties, perovskite materials are a promising candidate for many semiconductor devices such as lasers, memristors, LEDs and solar cells. For example, perovskite-based solar cells have recently become one of the fastest growing photovoltaic technologies. Unfortunately, perovskite devices are far from commercialization due to challenges such as fast degradation. Mathematical models can be used as tools to explain the behavior of such devices, for example drift-diffusion equations portray the ionic and electric motion in perovskites. In this work, we take volume exclusion effects on ion migration within a perovskite crystal lattice into account. This results in the formulation of two different ionic current densities for such a drift-diffusion model – treating either the mobility or the diffusivity as density-dependent while the other quantity remains constant. The influence of incorporating each current density description into a model for a typical perovskite solar cell configuration is investigated numerically, through simulations performed using two different open source tools.

Jamming and flocking in the restricted active Potts model.

We study the active Potts model with either site occupancy restriction or on-site repulsion to explore jamming and kinetic arrest in a flocking model. The incorporation of such volume exclusion features leads to a surprisingly rich variety of self-organized spatial patterns. While bands and lanes of moving particles commonly occur without or under weak volume exclusion, strong volume exclusion along with low temperature, high activity, and large particle density facilitates jams due to motility-induced phase separation. Through several phase diagrams, we identify the phase boundaries separating the jammed and free-flowing phases and study the transition between these phases which provide us with both qualitative and quantitative predictions of how jamming might be delayed or dissolved. We further formulate and analyze a hydrodynamic theory for the restricted APM which predicts various features of the microscopic model.