Real 3D Structures Research Articles

Novel connectivity tensor for a systematic assessment of topology and anisotropy of real membranes and microporous structures

In this work, an original and complete systematic topological assessment of anisotropy, connectivity and tortuosity of real 3D porous structures is presented. Several novelties are introduced here, like: the definition of the Average Effective Diffusivity Tensor (AEDT), allowing us to assess the desired topological parameters, the novel concept of connectivity tensor based on the inverse of the (diagonal) tortuosity tensor, the development of a new procedure of digital reconstruction of real 3D structures for CFD purpose, and a novel methodology for the connectivity tensor calculation, which avoids time-dependent diffusivities. After a detailed explanation of methodology and related validation using well-known 3D structures, we analyse two different real digitally-reconstructed 3D structures: LTL zeolite and clinoptilolite. As key-result, the internal voids distribution is characterised in terms of several existing and new topological parameters, all obtained from the mathematical properties of tortuosity and connectivity tensors. Among them, particular useful are the here-defined directionality factors, which indicate the preferential diffusional paths. The proposed approach is relatively easy and can be effectively applied not only to characterise existing materials, but also to design novel ones (in form of catalysts, selective membranes and/or adsorbents) with desired and predictable topological and mass transport properties.

Effect of permeability heterogeneity on the dissolution process during carbon dioxide sequestration in saline aquifers: two-and three-dimensional structures

The convection–diffusion process of carbon dioxide (CO2) dissolution in a saline reservoir is investigated to shed light on the effects of the permeability heterogeneity. Using sequential Gaussian simulation method, random permeability fields in two and three-dimension (2D and 3D) structures are generated. Quantitative (average amount of the dissolved CO2 and dissolution flux) and qualitative (pattern of the dissolved CO2 and velocity streamlines) measurements are used to investigate the results. A 3D structure shows a slightly higher dissolution flux than a 2D structure in the homogeneous condition. Results in the random permeability fields in 2D indicates an increase in the standard deviation of the permeability nodes enhances the dissolution efficiency, fluctuations in CO2 dissolution flux, separation between the different realizations from the same input parameters, and tendency toward more jagged convective fingers’ shape. Furthermore, the distance between the permeability nodes increases the convective fingers’ dissolution efficiency and jagged structure. The degree of freedom in 3D structures results in a higher chance of escaping from the low permeability zones and reduces the interactions between convective fingers in 3D systems. With the same variance and correlation length between permeability nodes, connectivity between high permeable zones in 3D cases are less than that of 2D cases; therefore, 2D realizations overestimate the dissolution flux of real heterogeneous 3D structures, which should be considered carefully.Article HighlightsCO2 sequestration in two and three dimensional heterogeneous saline aquifers are investigated.3D structures in homogeneous conditions show higher dissolution than 2D structures.2D realizations overestimates the dissolution flux over real heterogeneous 3D reservoirs.

Experimental and finite element simulation of natural rubber foams using real 3D structures

Natural rubber (NR) foams were prepared via a one-step foaming process, the effect of density and morphology on micro-level and macro-level mechanical properties was studied. In particular, experimental data were used to validate different numerical models based on actual three-dimensional (3D) foam structures built using a combination of 2D scanning electron microscopy (SEM) images. Then the uniaxial compression behavior was simulated at two levels (micro-scale and macro-scale) with finite element methods (FEM). The FEM results were finally compared with experimental data and different hyper-elastic models. SEM images showed that increasing the relative foam density from 0.3 to 0.5 led to a 55% decrease in cell size and a 1000% increase in cell number. The real 3D structures showed that foams with higher density have a more homogenous structure with lower structural defects or cell connections. The results also revealed that FEM at the macroscopic level is in good agreement with experimental results, especially for high density foams. On the other hand, FEM at the microscopic level showed that the maximum stress concentration and related micro-strain substantially decreased with increasing foam density.

PRISMOID: a comprehensive 3D structure database for post-translational modifications and mutations with functional impact.

Post-translational modifications (PTMs) play very important roles in various cell signaling pathways and biological process. Due to PTMs' extremely important roles, many major PTMs have been studied, while the functional and mechanical characterization of major PTMs is well documented in several databases. However, most currently available databases mainly focus on protein sequences, while the real 3D structures of PTMs have been largely ignored. Therefore, studies of PTMs 3D structural signatures have been severely limited by the deficiency of the data. Here, we develop PRISMOID, a novel publicly available and free 3D structure database for a wide range of PTMs. PRISMOID represents an up-to-date and interactive online knowledge base with specific focus on 3D structural contexts of PTMs sites and mutations that occur on PTMs and in the close proximity of PTM sites with functional impact. The first version of PRISMOID encompasses 17145 non-redundant modification sites on 3919 related protein 3D structure entries pertaining to 37 different types of PTMs. Our entry web page is organized in a comprehensive manner, including detailed PTM annotation on the 3D structure and biological information in terms of mutations affecting PTMs, secondary structure features and per-residue solvent accessibility features of PTM sites, domain context, predicted natively disordered regions and sequence alignments. In addition, high-definition JavaScript packages are employed to enhance information visualization in PRISMOID. PRISMOID equips a variety of interactive and customizable search options and data browsing functions; these capabilities allow users to access data via keyword, ID and advanced options combination search in an efficient and user-friendly way. A download page is also provided to enable users to download the SQL file, computational structural features and PTM sites' data. We anticipate PRISMOID will swiftly become an invaluable online resource, assisting both biologists and bioinformaticians to conduct experiments and develop applications supporting discovery efforts in the sequence-structural-functional relationship of PTMs and providing important insight into mutations and PTM sites interaction mechanisms. The PRISMOID database is freely accessible at http://prismoid.erc.monash.edu/. The database and web interface are implemented in MySQL, JSP, JavaScript and HTML with all major browsers supported.

Comprehensive study of the interactions between the critical dimensionless numbers associated with multiphase flow in 3D porous media

Multiphase flow in porous media is of great interest in many engineering applications, such as geologic carbon sequestration, enhanced oil recovery, and groundwater contamination and remediation. In order to advance the fundamental understanding of multiphase flow in complex three-dimensional (3D) porous media, the interactions between the critical dimensionless numbers, including the contact angle, viscosity ratio, and capillary (Ca) number, were investigated using X-ray micro-computed tomography (micro-CT) scanning and lattice Boltzmann (LB) modeling. In this study, the 3D pore structure information was extracted from micro-CT images and then used as interior boundary conditions of flow modeling in a pore-scale LB simulator to simulate multiphase flow within the pore space. A Berea sandstone sample was scanned and then two-phase flow LB simulations were performed based on the micro-CT images. The LB-simulated water/CO2 distributions agreed well with the micro-CT scanned images. Simulation results showed that a decreasing contact angle causes a decrease in wetting-fluid relative permeability and an increase in non-wetting fluid relative permeability. A rising Ca number increases both wetting and non-wetting fluid relative permeabilities. An increasing viscosity ratio (the ratio of non-wetting fluid viscosity to wetting fluid viscosity) facilitates the increase of non-wetting fluid relative permeability and mitigates the reduction of wetting fluid relative permeability, when the contact angle decreases continuously. The primary novel finding of this study is that the viscosity ratio affects the rate of change of the relative permeability curves for both phases when the contact angle changes continuously. To the best of our knowledge, it is the first time that comprehensive interactions between these dimensionless numbers are demonstrated in a sandstone sample based on real 3D structures. We also investigated the role of the changes of flow direction and sample location on relative permeability curves. Simulation results showed that the change in non-wetting fluid relative permeability was larger when the flow direction was switched from vertical to horizontal, which indicated that there was stronger anisotropy in larger pore networks that were primarily occupied by the non-wetting fluid.

DREM2: a facile fabrication strategy for freestanding three dimensional silicon micro- and nanostructures by a modified Bosch etch process

Three dimensional (3D) silicon micro- and nanostructures enable novel functionalities and better device performances in various fields. Fabrication of real 3D structures in a larger scale and wider applications has been proven to be limited by the technical difficulties during the fabrication process, which normally requires multiple process steps and techniques. Direct top-down fabrication processes by modifying a plasma etch process have been proposed and studied in previous studies. However, the repeatability, size uniformity and the maximal number of stacked layers were limited. Here we report a facile single run fabrication strategy for three dimensional silicon micro- and nanostructures. A good uniformity of suspended layer thickness has to be achieved and up to 10 stacked layers have been fabricated in a single run without other additional steps or post-process procedures. This is enabled by a modified multiplexed Bosch etch process, so called DREM (deposit, remove, etch, multistep), while the DREM etch is used to transfer the patterns into silicon, an extra isotropic etch creates a complete undercut and thus freestanding structures come into form. This method is easy to program and provides well-controlled etch profiles.

3D free forms in c-Si via grayscale lithography and RIE

A grayscale technology process for structuring of true 3D shapes into crystalline silicon (c-Si) has been developed. The process combines maskless grayscale lithography and an optimized RIE process. To achieve a 1:1 transfer of the 3D photoresist patterns into c-Si, the RIE process was optimized for a selectivity of S=1 and an anisotropy Af close to one. Suitable process conditions of the RIE process are defined by SF6 flowrate of 3sccm, CHF3 flowrate of 35sccm, a RF power of 100W, a temperature of 10°C and a pressure of 10mTorr. The 3D pattern transfer is demonstrated at special test structures as well as at real 3D structures such as pyramids. The developed process allows a direct transfer from 3D CAD data via maskless grayscale lithography using Heidelberg Instrument DWL66FS to c-Si 3D structures. The pattern transfer accuracy is about 5% in respect to the 3D CAD data.

Modeling Microbial Decomposition in Real 3D Soil Structures Using Partial Differential Equations

Partial Differential Equations (PDEs) have been already widely used to simulate various complex phenomena in porous media. This paper is one of the first attempts to apply PDEs for simulating in real 3D structures. We apply this scheme to the specific case study of the microbial decomposition of organic matter in soil pore space. We got a 3D geometrical representation of the pore space relating to a network of volume primitives. A mesh of the pore space is then created by using the network. PDEs system is solved by free finite elements solver Freefem3d in the particular mesh. We validate our PDEs model to experimental data with 3D Computed Tomography (CT) images of soil samples. Regarding the current state of art on soil organic matter decay models, our approach allows taking into account precise 3D spatialization of the decomposition process by a pore space geometry description.

Scalable Numerical Tools for Flow and Pressure Drop Computation in Fibrous Filter Media

AbstractThe prediction of flow behavior and pressure drop in fibrous filter media is challenging due to the complexity of the nonuniform fiber structure. Numerical calculation tools can considerably contribute to pressure drop determination for inhomogeneous filter structures. A numerical solution approach based on the finite element method to simulate 2D and 3D filter structures is considered. As numerical examples, computer designed homogeneous and inhomogeneous 2D cases where the numerical approach is validated by analytical models are investigated. Furthermore, the capability of the numerical method to simulate real 3D structures corresponding to more than 25 million degrees of freedom of the related algebraic system is demonstrated. The large systems involved require the use of dedicated techniques related to high performance computing.

Thermomechanical design in the automotive industry

ABSTRACTIn this paper thermomechanical fatigue assessment in the automotive industry is discussed. The design strategy is based upon a consistent approach of the thermomechanical loading, the mechanical constitutive law of the material, the damage parameters and the fatigue strength criteria. The good understanding of these different steps allows one to perform predictive calculations of automotive parts subjected to thermomechanical loading. The main hypotheses and modelling choices are presented and results are illustrated by a series of computations on real 3D structures. Cracked area and lifetime prediction are described in the case of aluminium alloy cylinder heads subjected to transient thermal loadings.

High aspect ratio, 3D structuring of photoresist materials by ion beam LIGA

IB-LIGA (Ion Beam Lithographie, Galvanoformung and Abformung) is a new technique for the 3D structuring of photoresist materials. It is a direct-write (maskless) technique that uses high energy (0.5–3.5 MeV) light ions (protons or helium ions) for the irradiation of photoresist materials. At CAFI (Centre d’Analyse par Faisceau Ionique), the IB-LIGA technique has been implemented. The experimental parameters for irradiation and the subsequent development have been optimised for PMMA. The results obtained so far are presented. These results include irradiations with different beam energies to control the depth, different sample tilt angles to produce sloping structures, and production of walls by moving the sample. Real 3D structures can be obtained in this way as shown in the examples. These examples show that structures in PMMA can be obtained with smooth near 90° side walls and bottom surfaces with low roughness. High aspect ratios have also been obtained, the current maximum is about 40. An ion-beam focussing system has recently been installed at CAFI, to produce ion-beams with sub-micrometer dimensions which can be accurately scanned in an arbitrary pattern over an area of 2.5×2.5 mm.

Principles of agonism: undressing efficacy.

As the temperature and humidity rose in the auditorium during the heat-wave of the Italian alps, it became evident that, in fact, more was revealed of the bodies of certain distinguished pharmacologists than of the true nature of Stephenson's efficacy.Nevertheless, real 3D structures of receptors in their empty, apo-, form as well as in their holo-forms, i.e. in complex with different ligands: agonists, partial agonists, antagonists, etc. are currently becoming available, at least in the nuclear receptor field (Fig. 2Fig. 2). Thus, we are rapidly approaching a long-awaited point in time where pharmacologists and medicinal chemists can relate theoretical pharmacological concepts directly to 3D structures. This could soon be the case even for 7TM receptors. On the day of the meeting the structural basis for activation of the G protein, Ras, by the nucleotide exchange factor, Sos, was published[10xBorlack-Sjodin, P.A., Margerit, S.M., Bar-Sagi, D., and Kuriyan, J. Nature. 1998; 394: 337–343Crossref | PubMed | Scopus (430)See all References[10]. The `loosening' of the GDP (corresponding to efficacy—see above) was clearly shown to be achieved through two antiparallel helices extending from the Sos molecule and interacting with a switch domain on the G protein. It could be relevant that the main G protein-interacting domain of 7TM receptors also is represented by two antiparallel helices, i.e. the intracellular extensions of TM5 and TM6 (Ref. [11xAltenbach, C. et al. Biochemistry. 1995; 35: 12470–12478Crossref | Scopus (263)See all References[11]; Fig. 1Fig. 1).

Theoretical study of the thermochemistry of sulfur molecular crystals II. Lowest energy allotropes of polymeric ω-sulfurs

Extended Huckel theory (for the repulsive part of the energy) and a method derived from classical perturbation expansions (for the long-range attractive part of the energy) were combined and the adequate parametrization has been set up in Part I. In this first part of the series, the method has been tested with success on ω-sulfur and on an example of two interacting helices. Here, we apply this method to determine the lowest energy conformations for all 1D, 2D and real 3D structures of polymeric ω-sulfurs considered from our structural hypotheses. We examine how considerations on the intermolecular repulsive interactions can lead to reliable structural information. Of course, the dispersive (attractive) part of the energy (including dipole-dipole, dipole-quadrupole and three-body terms) is necessary to determine quantitatively the stability of these sulfur structures. We find that ω2-sulfur is more stable than ω1-sulfur, where each of these helical chains is built up from a three-atom unit cell. For both 3D allotropes, the calculated enthalpy of sublimation is in good agreement with the experimental values.

Controlled topography production—true 3D simulation and experiment

A true 3D computer program, named DINESE, has been developed to simulate the evolution of real 3D structures during erosion and deposition. It is based on the generalized Huygens reconstruction formalism of surface evolution and can predict the evolution of any surface of the form z = f( x, y) resulting from any erosion or deposition process. True 3D computer simulations of a number of cases are presented and compared with experiment. The powers of the simulation method are further demonstrated by a series of sequential predictive simulations resulting in a desired topography which is then verified experimentally under the same sequence of conditions. Specifically, the evolution of different Si 3N 4 structures during ion beam etching with Ar ions under different erosion conditions has been studied both numerically and experimentally.