Soft Spheres Research Articles

Electrostatic interactions between cationic dendrimers and anionic model biomembrane

The electrostatic interactions between cationic poly(amidoamine) (PAMAM) dendrimers of different generations, G3, G4, and G6, with net anionic model biomembranes have been predicted by adopting an analytical model based on two dissimilar soft spheres. The influence of bilayer surface charge density, ionic strength, pH, temperature, membrane softness (modeled as changes in bilayer thickness), and dendrimer generation on the attractive interaction was investigated. The attraction was found to decrease with increasing salt concentration, dendrimer charge, and thickness (or softness) of the membrane. On the other hand, the attraction increased with the surface charge density of the membrane, and the size of dendrimer generation. In fact, the attraction was found to be much larger for large generations, like G6 dendrimer that have a higher charge, than it is with small ones like G3 and G4 dendrimers. These results have implications for the use of PAMAM dendrimers as potential gene transfection vectors.

Slow axisymmetric rotation of a soft sphere in a circular cylinder

A semi-analytical study of the creeping flow of an incompressible Newtonian fluid around a soft spherical particle (a hard core covered by a permeable porous layer) rotating about a diameter lying on the axis of a long circular cylinder is presented. To solve the Stokes and Brinkman equations, a solution comprising of the general solutions in spherical and cylindrical coordinates is utilized. The boundary conditions are applied first at the confining cylinder wall through the Fourier transform and then at the particle and hard-core surfaces via a collocation method. Accurate results of the hydrodynamic torque acting on the particle can be obtained for various values of the particle-to-cylinder radius ratio, core-to-particle radius ratio, and ratio of the particle radius to the porous layer’s flow penetration length. The boundary effect of the cylinder on the rotation of the soft particle is significant. The hydrodynamic torque exerted on the confined soft sphere increases with an increase in the particle-to-cylinder radius ratio, and in general remains finite even as the soft particle fills the cylinder. This torque is less than that on an equal-sized hard sphere (or soft sphere having a smaller thickness or lower permeability of its porous layer).

Tetrahedral Liquid‐Crystalline Networks: An A15‐Like Frank–Kasper Phase Based on Rod‐Packing

AbstractThe Pm n cubic and other low‐symmetry Frank–Kasper phases are known to be formed by soft spheres, ranging from metals to block copolymer micelles and colloidal nanoparticles. Here, we report a series of X‐shaped polyphiles composed of sticky rods and two non‐symmetric branched side‐chains, which self‐assemble into the first example of a cubic liquid‐crystalline phase representing a tetrahedral network of rods with a Pm n lattice. It is the topological dual to the Weaire–Phelan foam, being the Voronoi tessellation of the A15 sphere packing, from which this network is obtained by Delaunay triangulation.

Tetrahedral Liquid-Crystalline Networks: An A15-Like Frank-Kasper Phase Based on Rod-Packing.

The Pm 3‾ n cubic and other low‐symmetry Frank–Kasper phases are known to be formed by soft spheres, ranging from metals to block copolymer micelles and colloidal nanoparticles. Here, we report a series of X‐shaped polyphiles composed of sticky rods and two non‐symmetric branched side‐chains, which self‐assemble into the first example of a cubic liquid‐crystalline phase representing a tetrahedral network of rods with a Pm 3‾ n lattice. It is the topological dual to the Weaire–Phelan foam, being the Voronoi tessellation of the A15 sphere packing, from which this network is obtained by Delaunay triangulation.

Particularities of R134a Refrigerant Temperature Variations in a Transient Convective Regime during Vaporization in Rectangular Microchannels.

An analysis of the R134a (tetrafluoroetane) coolant’s non-stationary behavior in rectangular microchannels was conducted with the help of a newly proposed miniature refrigerating machine of our own design and construction. The experimental device incorporated, on the same plate, a condenser, a lamination tube and a vaporizer, all of which integrated rectangular microchannels. The size of the rectangular microchannels was determined by laser profilometry. R-134a coolant vapors were pressurized using a small ASPEN rotary compressor. Using the variable soft spheres (VSS) model, the mean free path, Knudsen and Reynolds numbers, as well as the dimensionless velocity profile can be assessed analytically. In order to determine the average dimensionless temperature drop in the vaporizer’s rectangular microchannels, in non-stationary regime, an analytical solution for incompressible flow with slip at the walls, fully developed flow and laminar regime was used, by aid of an integral transform approach. In the experimental study, the transitional distribution of temperature was tracked while modifying the R134a flow through the rectangular microchannels. Coolant flow was then maintained at a constant, while the amount of heat absorbed by the vaporizer was varied using multiple electric resistors. A comparative analysis of the analytical and experimental values was conducted.

Magnetic Field-Assisted Fast Assembly of Microgel Colloidal Crystals.

Compared with the colloidal crystals (CCs) of hard spheres, large-scale, high-quality CCs of soft microgel spheres are easier to be assembled because they are more tolerant to defects. However, to assemble microgel CCs, a microgel dispersion should first be concentrated and then allowed to crystallize, which is tedious and time-consuming. Herein, we demonstrated that a magnetic poly(N-isopropylacrylamide) (PNIPAM) microgel with an Fe3O4 core and a PNIPAM shell can be assembled into CCs quickly by simply applying an external magnetic field to the diluted microgel dispersions. The resulting CCs are highly ordered as revealed by their iridescent color, laser diffraction pattern, and confocal characterization. They display a sharp Bragg peak on their reflection spectra, which shifts to lower wavelength when heated because of the thermosensitivity of the PNIPAM shell. The magnetic assembly is not only simple and fast but also allows control of the CC structure in both horizontal and vertical directions. Using spatially varying magnetic fields, patterned microgel CCs were facilely assembled. More importantly, magnetic microgel spheres with different sizes can be assembled in a layer-by-layer manner by adding them sequentially, and the thickness of each layer can be simply controlled by the amount of spheres added.

Clarifying Status of Latency in Disaster and Crisis Management through Understanding Core Human Effective Components: Implications for Decreasing Distress, Increasing Resiliency and Better Decision Making Process

The statement of Latency in management Strategy in the Mindset of disaster or crisis managers (management) can cause misunderstanding intentionally or unintentionally in distinguishing a Disaster from a Crisis. Mitigating the consequences depends on whether the cause of the disorder is understood clearly or not! Many serious accidents such as Fukushima, Bhopal, Chernobyl and Three Mile Island show vast consequences, although different but primarily related to a similar factor, which is “Human Deficiency”. Literature shows, although leadership and top management and processes and mechanisms and good strategies are existent, yet problems remain. The fact is that there are fewer studies formulated in this field, from the crisis management strategies point of view, this is the deficiency. The article aims to shed light on the Importance and how to better understand Latency in management Strategy at Management levels, and to better say by the Core Native Human Effective Components (CNHECs) for better knowing and understanding the reality to better act based on the real management strategy in the Mindset (Based on the mind bandwidth). In addition, to understand whether ignoring ignorance is a good management strategy in time of crisis and will it buy time and be effective in not accurate managers or the other way around. Core Native Human Effective Components (CNHECs) are extracted from the Native Human Effective Components (NHECs) that are refined among different Human Effective Components (HECs) based on the literature reviewed in an article recently published by the authors of this article which can help to better understand the latency in management. These components may be generated and be shaped in the crisis managers’ minds’ bandwidth which can be used as a precautionary action to be avoided not to cause more situations that are complex through increase of resiliency and decrease of distress. As a conclusion, we understand that reality may be completely different from what could be assumed, understood and seen. It should be considered that actions are always based on the disaster and crisis Managers’ understanding. For better understanding, the reality we propose a method, Model or a taxonomy that to some extent clarifies and focuses on the statement of latency in management strategy process. This Structure, model or taxonomy shows how and through which windows (Soft, Semi Soft and Hard Spheres) we can get into it and to say how to better understand the function of latency in management strategy by special consideration of CNHECs which can help us to distinguish a crisis from a disaster. It is important to know that by a good Recognition and revealing and also by Better Understanding Core Native Human Effective Components (CNHECs), the disaster and crisis managers can Increase Resiliency and Decrease Distress especially in time of occurrences of different kinds of sudden emergencies generated from different kinds of hazards.

Criticality and marginal stability of the shear jamming transition of frictionless soft spheres.

We study numerically the critical behavior and marginal stability of the shear jamming transition for frictionless soft spheres, observed to occur over a finite range of densities, associated with isotropic jamming for densities above the minimum jamming (J-point) density. Several quantities are shown to scale near the shear jamming point in the same way as the isotropic jamming point. We compute the exponents associated with the small force distribution and the interparticle gap distribution and show that the corresponding exponents are consistent with the marginal stability condition observed for isotropic jamming and with predictions of the mean-field theory of jamming in hard spheres.

Phase Behaviors of ABA Star Polymer and Nanoparticles Confined in a Sphere with Soft Inner Surface.

The phase behaviors of an ABA star polymer and nanoparticles confined in a sphere with soft inner surface, which is grafted with homopolymer brushes have been studied by the self-consistent field theory (SCFT). The morphologies of mixture in the center slice of sphere were focused. Two cases are considered: one is that the nanoparticles interact with the B blocks and the other is that the nanoparticles preferentially wet the B blocks. Under the two conditions, through changing the block ratio of the ABA star polymer, the concentration and radius of the nanoparticles, the phase behaviors of the mixtures confined the soft sphere are studied systematically. With increasing the concentration of nanoparticles, the entropy and the steric repulsive interaction of nanoparticles, and the nanoparticle density distributions along the perpendicular line through the center of sphere are plotted. The phase diagram is also constructed to analyze the effects of the nanoparticle volume fraction and radius on morphologies of ABA star polymers, and to study the effect of confinement on the phase behaviors. The results in this work provide a useful reference for controlling the ordered structures in experiment, which is an effective way to fabricate the newly multifunctional materials.

Advantages of the Rayleigh-Lowe-Andersen thermostat in soft sphere molecular dynamics simulations.

The Rayleigh-Lowe-Andersen thermostat is a momentum-conserving, Galilean-invariant analogue of the Andersen thermostat, like the original (Maxwellian) Lowe-Andersen thermostat. However, the Rayleigh-Lowe-Andersen thermostat remains local even if the fluid density becomes low. By using a minimized thermostat interaction radius we show with a molecular dynamics simulation that the Rayleigh-Lowe-Andersen thermostat affects the natural dynamics of a low-density Lennard-Jones fluid in a minimal fashion. We also show that it is no longer necessary to consider a separate simulation just to determine the optimal value of the thermostat interaction radius. Instead, this value is computed directly during the main simulation run. Because the Rayleigh-Lowe-Andersen thermostat can be combined with the velocity Verlet integration scheme, we expect a widespread applicability of the thermal mechanism presented here.

Contact Lens Prescribing Trends for Keratoconus at an Academic Medical Center: Increased Utilization of Scleral Lenses for Severe Disease.

To describe contact lens prescription trends for patients with keratoconus. Demographics, corneal curvature, visual acuity, and type of contact lens prescribed were reviewed for all patients with keratoconus evaluated in the contact lens service in 2010 and 2020. There were 292 patients in 2010 and 217 in 2020. In 2010, 69% were using corneal gas-permeable lenses (GP), 16% soft toric, 13% hybrid, and 2% soft sphere with no scleral lens (SL). In 2020, 60% were using corneal GP, 22% SL, 12% soft toric, 5% hybrid, and 1% soft sphere. Mean log of minimum angle of resolution visual acuities with manifest refraction were (represented in mean [SD, range]) 0.42 (0.33, 0-1.3) in 2010 and 0.35 (0.33, 0-1.6) in 2020 improving to 0.19 (0.18, 0-1.3; P≤0.01) and 0.13 (0.14, 0-0.60; P<0.01) with contact lenses. Mean keratometry measurement in patients using SLs was 53.0 diopters (D) (9.9, 42.1-84.5), which was steeper than 46.6 D in patient's using all other lens types in 2010 and 2020 (3.9, 40.9-57.9; P<0.01). Scleral lens prescription increased during the past decade; however, corneal GP lenses remain the most frequent lens prescribed for patients with keratoconus in this cohort. Despite being prescribed for patients with the most advanced disease, SLs provide good visual acuity.

Numerical Study on Particle Transport and Placement Behaviors of Ultralow Density Particles in Fracture-Vuggy Reservoirs

Summary A solid/liquid two-phase flow numerical model based on the computational fluid dynamics-discrete element method (CFD-DEM) model was established to study the transport and settlement law of ultralow-density (ULD) particles during the waterdrive channel adjustment of the Tahe carbonate fractured-vuggy reservoir. The mass, momentum, and turbulence equations of the fluid phase were established in Euler coordinates, whereas the particle motion equations were established based on Newton’s second law. The interaction between the ULD particles was described using a soft sphere model, and the water and particle phases were bidirectionally coupled. Meanwhile, virtual experiments were conducted to calibrate the contact parameters of the particles, and parallel plate experiments were performed to validate the model. Using numerical simulations of particle transport behavior in fractures, the process and characteristics of particle transport and placement in fractures are demonstrated, which can be described by the settlement profile angle and equilibrium gap height. According to parameterized simulations, the change law of the settlement profile angle and equilibrium gap height with different parameters such as particle size, pump displacement, and fracture width are demonstrated, which is helpful for the prediction of migration and accumulation of ULD particles in fracture-vuggy reservoirs.

Understanding Adsorption of Organics on Pt(111) in the Aqueous Phase: Insights from DFT Based Implicit Solvent and Statistical Thermodynamics Models.

Adsorption of organics in the aqueous phase is an area which is experimentally difficult to measure, while computational techniques require extensive configurational sampling of the solvent and adsorbate. This is exceedingly computationally demanding, which excludes its routine use. If implicit solvent could be applied instead, this would dramatically reduce the computational cost as configurational sampling of solvent is not needed. Here, using statistical thermodynamic arguments and DFT calculations with implicit solvent models, we show that semiquantitative values for the free energy and entropy change of adsorption in the aqueous phase (ΔGadssolv and ΔSadssolv) for small organics can be calculated, for a range of coverages. We parametrize the soft sphere based solute dielectric cavity to an approximated free energy of solvation for a single Pt atom at the (111) facet, forming upper and lower bounds based on the entropy of water at the aqueous metal interface (ΔGsolv(Pt) = -4.35 to -7.18 kJ mol-1). This captures the decrease in ΔGadssolv compared to the free energy of adsorption in the vacuum phase (ΔGadsvac), while solvent models with electron density based cavities fail to do so. For a range of oxygenated aromatics, the adsorption energetics using horizontal gas phase geometries significantly overestimate ΔGadssolv compared to experiment by ∼100 kJ mol-1, but they agree with ab initio MD simulations using similar geometries. This suggests oxygenated aromatic compounds adsorb perpendicular to the metallic surface, while the ΔGadssolv for vertical geometries of furfural and cyclohexanol agree to within 20 kJ mol-1 of experimental studies. The proposed techniques provide an inexpensive toolset for validation and prediction of adsorption energetics on solvated metallic surfaces, which could be further validated by the future availability of more experimental measurements for the aqueous entropy/free energy of adsorption.

Crack-front model for adhesion of soft elastic spheres with chemical heterogeneity

Adhesion hysteresis can be caused by elastic instabilities that are triggered by surface roughness or chemical heterogeneity. However, the role of these instabilities in adhesion hysteresis remains poorly understood because we lack theoretical and numerical models accounting for realistic roughness. Our work focuses on the adhesion of soft elastic spheres with low roughness or weak heterogeneity, where the indentation process can be described as a Griffith-like propagation of a nearly circular external crack. We discuss how to describe the contact of spheres with chemical heterogeneity that leads to fluctuations in the local work of adhesion. We introduce a variational first-order crack-perturbation model and validate our approach using boundary-element simulations. The crack-perturbation model faithfully predicts contact shapes and hysteretic force-penetration curves, provided that the contact perimeter remains close to a circle and the contact area is simply connected. Computationally, the crack-perturbation model is orders of magnitude more efficient than the corresponding boundary element formulation, allowing for realistic heterogeneity fields.

Avalanche dynamics in sheared athermal particle packings occurs via localized bursts predicted by unstable linear response.

Under applied shear strain, granular and amorphous materials deform via particle rearrangements, which can be small and localized or organized into system-spanning avalanches. While the statistical properties of avalanches under quasi-static shear are well-studied, the dynamics during avalanches is not. In numerical simulations of sheared soft spheres, we find that avalanches can be decomposed into bursts of localized deformations, which we identify using an extension of persistent homology methods. We also study the linear response of unstable systems during an avalanche, demonstrating that eigenvalue dynamics are highly complex during such events, and that the most unstable eigenvector is a poor predictor of avalanche dynamics. Instead, we modify existing tools that identify localized excitations in stable systems, and apply them to these unstable systems with non-positive definite Hessians, quantifying the evolution of such excitations during avalanches. We find that bursts of localized deformations in the avalanche almost always occur at localized excitations identified using the linear spectrum. These new tools will provide an improved framework for validating and extending mesoscale elastoplastic models that are commonly used to explain avalanche statistics in glasses and granular matter.

Eulerian simulation of complex suspensions and biolocomotion in three dimensions

We present a numerical method specifically designed for simulating three-dimensional fluid-structure interaction (FSI) problems based on the reference map technique (RMT). The RMT is a fully Eulerian FSI numerical method that allows fluids and large-deformation elastic solids to be represented on a single fixed computational grid. This eliminates the need for meshing complex geometries typical in other FSI approaches and greatly simplifies the coupling between fluid and solids. We develop a three-dimensional implementation of the RMT, parallelized using the distributed memory paradigm, to simulate incompressible FSI with neo-Hookean solids. As part of our method, we develop a field extrapolation scheme that works efficiently in parallel. Through representative examples, we demonstrate the method's suitability in investigating many-body and active systems, as well as its accuracy and convergence. The examples include settling of a mixture of heavy and buoyant soft ellipsoids, lid-driven cavity flow containing a soft sphere, and swimmers actuated via active stress.

The hydra string method: a novel means to explore potential energy surfaces and its application to granular materials

We present a novel means to understand granular materials, the Hydra String Method (HSM). This is an efficient and autonomous way to trawl an arbitrary potential energy surface (or any similarly high dimensional function) that enumerates the saddle points, minima, and minimum energy paths between them. In doing so, it creates a reduced dimensional network representation of this surface. We also present a series of tests to choose optimized parameters for the application of the HSM. We apply this to the potential energy function of a granular system consisting of a configuration of bi-disperse, frictionless, soft spheres. Future work will make use of the found ensemble of transition pathways to statistically predict the dynamics of a system of grains.

Characterization of Viscoelastic Media Combining Ultrasound and Magnetic-Force Induced Vibrations on an Embedded Soft Magnetic Sphere.

We report a method to locally assess the complex shear modulus of a viscoelastic medium. The proposed approach is based on the application of a magnetic force to a millimeter-sized steel sphere embedded in the medium and the subsequent monitoring of its dynamical response. A coil is used to create a magnetic field inducing the displacement of the sphere located inside a gelatin phantom. Then, a phased-array system using 3 MHz ultrasound probe operating in pulse-echo mode is used to track the displacement of the sphere. Experiments were conducted on several samples and repeated as a function of phantom temperature. The dynamic response of the sphere measured experimentally is in good agreement with Kelvin-Voigt theory. Since the magnetic force is not affected by weak diamagnetic media, our proposal results in an accurate estimation of the force acting on the inclusion. Consequently, the estimated viscoelastic parameters show excellent robustness and the elastic modulus agrees with the measurements using a quasi-static indentation method, obtaining errors below 10% in the whole temperature range. The use of the macroscopic inclusion limits the direct application of this method in a biomedical context, but it provides a robust estimation of the elastic modulus that can be used for material characterization in industrial applications.

One-Step Biosynthesis of Soft Magnetic Bacterial Cellulose Spheres with Localized Nanoparticle Functionalization

Actuated structures are becoming relevant in medical fields; however, they call for flexible/soft-base materials that comply with biological tissues and can be synthesized in simple fabrication steps. In this work, we extend the palette of techniques to afford soft, actuable spherical structures taking advantage of the biosynthesis process of bacterial cellulose. Bacterial cellulose spheres (BCS) with localized magnetic nanoparticles (NPs) have been biosynthesized using two different one-pot processes: in agitation and on hydrophobic surface-supported static culture, achieving core-shell or hollow spheres, respectively. Magnetic actuability is conferred by superparamagnetic iron oxide NPs (SPIONs), and their location within the structure was finely tuned with high precision. The size, structure, flexibility and magnetic response of the spheres have been characterized. In addition, the versatility of the methodology allows us to produce actuated spherical structures adding other NPs (Au and Pt) in specific locations, creating Janus structures. The combination of Pt NPs and SPIONs provides moving composite structures driven both by a magnetic field and a H2O2 oxidation reaction. Janus Pt/SPIONs increased by five times the directionality and movement of these structures in comparison to the controls.

Size and Structure of Empty and Filled Nanocontainer Based on Peptide Dendrimer with Histidine Spacers at Different pH.

Novel peptide dendrimer with Lys-2His repeating units was recently synthesized, studied by NMR (Molecules, 2019, 24, 2481) and tested as a nanocontainer for siRNA delivery (Int. J. Mol. Sci., 2020, 21, 3138). Histidine amino acid residues were inserted in the spacers of this dendrimer. Increase of their charge with a pH decrease turns a surface-charged dendrimer into a volume-charged one and should change all properties. In this paper, the molecular dynamics simulation method was applied to compare the properties of the dendrimer in water with explicit counterions at two different pHs (at normal pH with neutral histidines and at low pH with fully protonated histidines) in a wide interval of temperatures. We obtained that the dendrimer at low pH has essentially larger size and size fluctuations. The electrostatic properties of the dendrimers are different but they are in good agreement with the theoretical soft sphere model and practically do not depend on temperature. We have shown that the effect of pairing of side imidazole groups is much stronger in the dendrimer with neutral histidines than in the dendrimer with protonated histidines. We also demonstrated that the capacity of a nanocontainer based on this dendrimer with protonated histidines is significantly larger than that of a nanocontainer with neutral histidines.