Tetrahedral Particles Research Articles

TET peptidases: A family of tetrahedral complexes conserved in prokaryotes.

The TET peptidases are large polypeptide destruction machines present among prokaryotes. They form 12-subunits hollow tetrahedral particles, and belong to the family of M42 metallo-peptidases. Structural characterization of various archaeal and bacterial complexes has revealed a unique mechanism of internal compartmentalization and peptide trafficking that distinguishes them from the other oligomeric peptidases. Different versions of the TET complex often co-exist in the cytosol of microorganisms. In depth enzymatic studies have revealed that they are non-processive cobalt-activated aminopeptidases and display contrasting substrate specificities based on the properties of the catalytic chambers. Recent studies have shed light on the assembly mechanism of homo and hetero-dodecameric TET complexes and shown that the activity of TET aminopeptidase towards polypeptides is coupled with its assembly process. These findings suggested a functional regulation based on oligomerization control invivo. This review describes a current knowledge on M42 TET peptidases biochemistry and discuss their possible physiological roles. This article is a part of the Special Issue entitled: «A potpourri of proteases and inhibitors: from molecular toolboxes to signalling scissors».

Random packing of tetrahedral particles using the polyhedral discrete element method

The random packing of tetrahedral particles is studied by applying the discrete element method (DEM), which simulates the effects of friction, height ratio, and eccentricity. The model predictions are analyzed in terms of packing density and coordination number (CN). It is demonstrated that friction has the maximal effect on packing density and mean CN among the three parameters. The packing density of the regular tetrahedron is 0.71 when extrapolated to a zero friction effect. The shape effects of height ratio and eccentricity show that the regular tetrahedron has the highest packing density in the family of tetrahedra, which is consistent with what has been reported in the literature. Compared with geometry-based packing algorithms, the DEM packing density is much lower. This demonstrates that the inter-particle mechanical forces have a considerable effect on packing. The DEM results agree with the published experimental results, indicating that the polyhedral DEM model is suitable for simulating the random packing of tetrahedral particles.

Preparation of Pd Nanoparticles with Tetrahedral, Spherical, Plate, and Feather Shapes by Capping with 1-Pentyl Isocyanide

In this study, we synthesized n-alkyl-isocyanide-protected palladium colloidal nanoparticles with different shapes. The 1-pentyl-isocyanide-protected Pd nanoparticles prepared by the reduction of the Pd complex with ethylene glycol had various geometric shapes. Transmission electron micrographs showed that tetrahedral particles were predominant, although some spherical, plate-, and feather-shaped particles were also observed. The enriched nanotetrahedra were isolated as a black powder by reprecipitation with methanol–chloroform and the particle size was controlled by the reaction conditions.

Influence of patch-size variability on the crystallization of tetrahedral patchy particles.

The understanding of disorder effects on crystallization is of fundamental and technological importance. It is well established by both theory and experiment that particle-size polydispersity hinders crystallization for isotropically interacting particles. Here, we address the effects of patch variability in a model for tetrahedral colloids, where polydispersity is introduced independently on the size, position, and strength of the attractive patches. Our simulations indicate that, unlike particle-size polydispersity, angular polydispersity has a minor impact on the crystallization properties of tetrahedral colloidal particles. Particles with angular polydispersity well within current experimental possibilities fully retain their crystallization properties, a result which should encourage the realization of colloidal crystals in experiment.

Free falling and rising of spherical and angular particles

Direct numerical simulations of freely falling and rising particles in an infinitely long domain, with periodic lateral boundary conditions, are performed. The focus is on characterizing the free motion of cubical and tetrahedral particles for different Reynolds numbers, as an extension to the well-studied behaviour of freely falling and rising spherical bodies. The vortical structure of the wake, dynamics of particle movement, and the interaction of the particle with its wake are studied. The results reveal mechanisms of path instabilities for angular particles, which are different from those for spherical ones. The rotation of the particle plays a more significant role in the transition to chaos for angular particles. Following a framework similar to that of Mougin and Magnaudet [“Wake-induced forces and torques on a zigzagging/spiralling bubble,” J. Fluid Mech. 567, 185–194 (2006)], the balance of forces and torques acting on particles is discussed to gain more insight into the path instabilities of angular particles.

Erasing no-man's land by thermodynamically stabilizing the liquid-liquid transition in tetrahedral particles.

One of the most controversial hypotheses for explaining the origin of the thermodynamic anomalies characterizing liquid water postulates the presence of a metastable second-order liquid-liquid critical point [1] located in the “no-man’s land” [2]. In this scenario, two liquids with distinct local structure emerge near the critical temperature. Unfortunately, since spontaneous crystallization is rapid in this region, experimental support for this hypothesis relies on significant extrapolations, either from the metastable liquid or from amorphous solid water [3, 4]. Although the liquid-liquid transition is expected to feature in many tetrahedrally coordinated liquids, including silicon [5], carbon [6] and silica, even numerical studies of atomic and molecular models have been unable to conclusively prove the existence of this transition. Here we provide such evidence for a model in which it is possible to continuously tune the softness of the interparticle interaction and the flexibility of the bonds, the key ingredients controlling the existence of the critical point. We show that conditions exist where the full coexistence is thermodynamically stable with respect to crystallization. Our work offers a basis for designing colloidal analogues of water exhibiting liquid-liquid transitions in equilibrium, opening the way for experimental confirmation of the original hypothesis.

Excluded volumes of clusters in tetrahedral particle packing

Abstract We investigate the excluded volumes of clusters in tetrahedral particle packing using an ideal tetrahedron model and Monte Carlo simulation. Both the influences of the size and topology of clusters on the excluded volume are studied. We find that the excluded volumes of the dimer composed of two tetrahedra and the wagon wheel composed of five tetrahedra are relatively lower than other cluster forms. For large clusters, the excluded volume decreases when the topology of a cluster approaches the wagon-wheel geometry. The results give an explanation to the cluster distribution which demonstrates that the dimer and wagon wheel are the dominative cluster forms in the packing structure of tetrahedra.

Particles-bridging the Gap between Solids and Fluids

Meshless particle methods, a group of simulation approaches that gains attention in the recent years in engineering and physics, are in the focus of this article. By means of application examples from different engineering contexts, we demonstrate how such methods, especially smoothed particle hydrodynamics and the discrete element method can be used as valuable numerical simulation tools, e.g., in design processes. We provide a simulation example from rock mechanics that demonstrates how the breakage of granite material can be simulated using an enhanced discrete element method approach. The simulation of very soft granular matter based on deformable tetrahedral particle elements, as it might be useful for the simulation of e.g. silicon materials, is another example that emphasizes the flexibility of particle methods. Moreover, we show how cutting processes may be investigated using a smoothed particle hydrodynamic based simulation approach for elasto-plastic solids. Finally, we provide examples for the application of smoothed particle hydrodynamic fluid-multibody simulations to co-simulate sloshing processes.

Formation of Tetrapod-Shaped Nanowires in the Gas Phase During the Synthesis of ZnO Nanostructures by Carbothermal Reduction

We experimentally confirmed that charged ZnO nanoparticles were generated abundantly in the gas phase using a differential mobility analyzer (DMA). When they were size-selected by the DMA and captured on a grid for transmission electron microscopy, particles of 10 nm had a rod or tetrahedron shape, while particles larger than 10 nm tended to have a tetrapod shape. The tetrahedral particles seemed to be a seed for the growth of tetrapod nanowires. Although the growth of a tetrahedron shape enclosed by a close-packed plane (0002) of the hexagonal close-packed ZnO can be explained by the classical crystal growth theory, the growth of tetrapod nanowires can be better explained by the building block of charged nanoparticles generated in the gas phase.

Effect of Particle Shape on Capillary Forces Acting on Particles at the Air–Water Interface

The capillary forces exerted by moving air-water interfaces can dislodge particles from stationary surfaces. The magnitude of the capillary forces depends on particle shape, orientation, and surface properties, such as contact angle and roughness. The objective was to quantify, both experimentally and theoretically, capillary force variations as an air-water interface moves over the particles. We measured capillary forces as a function of position, i.e., force-position curves, on particles of different shape by using force tensiometry. The particles (5 mm nominal size) were made of polyacrylate and were fabricated using a 3D printer. Experimental measurements were compared with theoretical calculations. We found that force-position curves could be classified into in three categories according to particle shapes: (1) curves for particles with round cross sections, such as spheroidal particles, (2) curves for particles with fixed cross sections, such cylindrical or cubical particles, and (3) curves for particles with tapering cross sections, such as prismatic or tetrahedral particles. Spheroidal particles showed a continuously varying capillary force. Cylindrical or cubical particles showed pronounced pinning of the air-water interface line at edges. The pinning led to an increased capillary force, which was relaxed when the interface snapped off from the edges. Particles with tapering cross section did not show pinning and showed reduced capillary forces as the air-water interface line perimeter and displacement cross section continuously decrease when the air-water interface moved over the particles.

Silver nanoparticles enhance Pseudomonas aeruginosa PAO1 biofilm detachment

Objectives: Silver nanoparticles (AgNPs) with a size ranging from 7 to 70 nm were synthesized using the ascorbic acid-citrate seed-mediated growth approach at room temperature.Methods: The 8 nm silver particles were prepared using gallic acid in alkaline conditions and used as seed to prepare AgNPs.Results: The presence of ascorbic acid and citrate allows the regulation of size and size distribution of the nanoparticles. The increase in free silver ion-to-seed ratio (Ag+/Ag0) resulted in changes of particle shape from spherical to pseudo-spherical and minor cylindrical shape. Further, a repetitive seeding approach resulted in the formation of pseudo-spherical particles with higher polydispersity index and minor distributions of tetrahedral particles. Citrate-capped AgNPs were stable and did not agglomerate upon centrifugation. The effect of AgNPs on biofilm reduction was evaluated using static culture on 96-well microtiter plates. Results showed that AgNPs with the smallest average diameter were most effective in the reduction of Pseudomonas aeruginosa biofilm colonies, which accounted for 90% of removal.Conclusion: The biofilm removal activities of the nanoparticles were found to be concentration-independent particularly for the concentration within the range of 80–200 µg/mL.

Quasi-random packing of tetrahedra

We present a new order metric for tetrahedral particle packing, which is observed to have a strong linear correlation with the packing density. We propose the concept of quasi-random packing to represent the hierarchical random packing structure of clusters. We also find that the nematic order of clusters can be used to classify the ordered and disordered packing of tetrahedra, which is also an indicator for quasi-random packing.

Beneficial Effects of Microwave-Assisted Heating versus Conventional Heating in Noble Metal Nanoparticle Synthesis

An extensive comparative study of the effects of microwave versus conventional heating on the nucleation and growth of near-monodisperse Rh, Pd, and Pt nanoparticles has revealed distinct and preferential effects of the microwave heating method. A one-pot synthetic method has been investigated, which combines nucleation and growth in a single reaction via precise control over the precursor addition rate. Using this method, microwave-assisted heating enables the convenient preparation of polymer-capped nanoparticles with improved monodispersity, morphological control, and higher crystallinity, compared with samples heated conventionally under otherwise identical conditions. Extensive studies of Rh nanoparticle formation reveal fundamental differences during the nucleation phase that is directly dependent on the heating method; microwave irradiation was found to provide more uniform seeds for the subsequent growth of larger nanostructures of desired size and surface structure. Nanoparticle growth kinetics are also markedly different under microwave heating. While conventional heating generally yields particles with mixed morphologies, microwave synthesis consistently provides a majority of tetrahedral particles at intermediate sizes (5-7 nm) or larger cubes (8+ nm) upon further growth. High-resolution transmission electron microscopy indicates that Rh seeds and larger nanoparticles obtained from microwave-assisted synthesis are more highly crystalline and faceted versus their conventionally prepared counterparts. Microwave-prepared Rh nanoparticles also show approximately twice the catalytic activity of similar-sized conventionally prepared particles, as demonstrated in the vapor-phase hydrogenation of cyclohexene. Ligand exchange reactions to replace polymer capping agents with molecular stabilizing agents are also easily facilitated under microwave heating, due to the excitation of polar organic moieties; the ligand exchange proceeds with excellent retention of nanoparticle size and structure.

Shape effects on the random-packing density of tetrahedral particles

Regular tetrahedra have been demonstrated recently giving high packing density in random configurations. However, it is unknown whether the random-packing density of tetrahedral particles with other shapes can reach an even higher value. A numerical investigation on the random packing of regular and irregular tetrahedral particles is carried out. Shape effects of rounded corner, eccentricity, and height on the packing density of tetrahedral particles are studied. Results show that altering the shape of tetrahedral particles by rounding corners and edges, by altering the height of one vertex, or by lateral displacement of one vertex above its opposite face, all individually have the effect of reducing the random-packing density. In general, the random-packing densities of irregular tetrahedral particles are lower than that of regular tetrahedra. The ideal regular tetrahedron should be the shape which has the highest random-packing density in the family of tetrahedra, or even among convex bodies. An empirical formula is proposed to describe the rounded corner effect on the packing density, and well explains the density deviation of tetrahedral particles with different roundness ratios. The particles in the simulations are verified to be randomly packed by studying the pair correlation functions, which are consistent with previous results. The spherotetrahedral particle model with the relaxation algorithm is effectively applied in the simulations.

Probing Higher Order Surface Plasmon Modes on Individual Truncated Tetrahedral Gold Nanoparticle Using Cathodoluminescence Imaging and Spectroscopy Combined with FDTD Simulations

We report the spatial maps of the localized surface plasmon resonances associated photon emission in a truncated tetrahedral gold nanoparticle on a silicon substrate. Site-specific cathodoluminescence spectroscopy and imaging in a scanning electron microscope shows stronger photon emission in the visible range near the tips of the particle in contact with the substrate compared to the edges of the particle. Strong local field variations on a length scale as short as 19 nm are resolved. We also perform FDTD simulations of both the spectra and, for the first time, the full cathodoluminescence images. Excellent agreement is obtained with the experimental results, and the detailed information available from the simulated results makes it possible to identify the signature of out-of-plane higher order modes in the truncated tetrahedral gold particle.

Synthesis, morphology, and optical properties of CuI microcrystals

We have studied the effect of synthesis conditions on the luminescence spectra of ultrafine CuI powders. The results demonstrate that synthesis conditions (the reductant of Cu2+, the anion of the copper(II) salt, initial solution concentrations, and the presence of a stabilizer) influence the size and shape of the forming CuI particles and, accordingly, their luminescence spectrum. The highest luminescence intensity near λmax ≅720 nm (λex ≅ 370 nm) is offered by regularly shaped tetrahedral particles 1.1–1.2 μm in average size.

Self and collective correlation functions in a gel of tetrahedral patchy particles

We discuss the results of intensive Brownian dynamics simulations of a simple model of tetrahedral patchy particles in the optimal network density region. This choice allows us to investigate the evolution of the structure and of the dynamics in a wide range of temperatures without encountering any phase separation. The slowing down of the dynamics in this model system is driven by the progressive bond formation and the increasing bond lifetime. Although dynamical arrest is different from the glass case, where excluded volume interactions are dominant, the decay of the self- and collective correlation functions of the resulting fluid bears similarities with that observed in glassy systems.

Synthesis of hydrotalcite-supported shape-controlled Pd nanoparticles by a precipitation–reduction method

A Pd catalyst supported on a layered double hydroxide (LDH or hydrotalcite-like material) has been synthesized in a one step reaction using a precipitation–reduction method in which hydrolysis of hexamethylenetetramine was used to both precipitate the LDH by virtue of the resulting increase in pH and provide formaldehyde which reduces the Pd 2+ precursor to Pd 0. The resulting Pd nanoparticles were mostly tetrahedral in shape, and were highly dispersed on the surface of the LDH. After introducing a capping agent during the synthesis, the morphology of the Pd particles changed to truncated octahedral, although a similar high degree of dispersion was obtained. Compared with a conventional impregnated catalyst composed of pseudo-spherical Pd particles, catalysts prepared by the new method showed both higher activity and selectivity in the hydrogenation of acetylene. The enhanced activity is due to the specific morphology of the Pd particles, which results in their higher dispersion, while the higher selectivity is attributed to the Pd–C phase formed in the catalyst during the reaction. Furthermore, compared with the truncated octahedral Pd particles enclosed by (1 1 1) and (1 0 0) facets, the tetrahedral particles with only (1 1 1) facets exposed showed higher ethylene selectivity, suggesting that the Pd (1 1 1) facet is the preferred facet in the selective hydrogenation of acetylene to ethylene.

Polyhedral Particles Hopper Flowrate Predictions using Discrete Element Method

Discrete, or Distinct, element modelling, DEM, is used to investigate the effect of particle shape on hopper flowrate. Firstly, simulation results using a model based on spherical particles are validated against solid discharge rates predicted by the modified Beverloo equation. The validated model is then used to investigate the shape effects on discharge rate from a flat bottomed rectangular hopper. Two regular rounded polyhedral particles are studied. The discharge rate varies significantly with particle shape. A reduction on flowrate of up to 49% and 41% is observed for tetrahedral and octahedral particles, respectively. The effects of friction, cohesion, and damping on flowrate are also investigated with DEM.

Nucleation barriers in tetrahedral liquids spanning glassy and crystallizing regimes

Crystallization and vitrification of tetrahedral liquids are important both from a fundamental and a technological point of view. Here, we study via extensive umbrella sampling Monte Carlo computer simulations the nucleation barriers for a simple model for tetrahedral patchy particles in the regime where open tetrahedral crystal structures (namely, cubic and hexagonal diamond and their stacking hybrids) are thermodynamically stable. We show that by changing the angular bond width, it is possible to move from a glass-forming model to a readily crystallizing model. From the shape of the barrier we infer the role of surface tension in the formation of the crystalline clusters. Studying the trends of the nucleation barriers with the temperature and the patch width, we are able to identify an optimal value of the patch size that leads to easy nucleation. Finally, we find that the nucleation barrier is the same, within our numerical precision, for both diamond crystals and for their stacking forms.