3D Fragments Research Articles

Transition from multi-center fracture to fragmentation statistics under intensive loading

Statistics of transition from damage to fragmentation is studied based on the analysis of multi-scale mechanisms of nucleation and growth of cracks in hollow cylindrical (tubular) specimens made of Al2O3 ceramics. Specimens are loaded by underwater electrical wire explosion. Around 98% of the initial mass of the specimen was recovered as a fragments. The fragments were classified into two types: quasi-two-dimensional (2D) samples, the characteristic size of which d* was greater than (or equal to) the wall thickness of the tube d; and three-dimensional (3D) samples of size d* < d. The analysis of the fragment geometry allows us to determine the mechanisms responsible for the formation of 2D and 3D fragments. The 2D fragments are formed by the large cracks (Mott mechanism) as a result of tube extension in the radial direction. The 3D objects are formed due to instability of fast crack propagation, which leads to microbranching, as was shown in Sharon (1996). The 3D fragments size distribution is governed by the power law, which corresponds to the microbranch distribution. The study of the influence of the initial sample porosity indicates that the distribution of the porosity is described by the power function with an exponent slightly differing from that of the fragments distribution. We suppose that both the initial porosity and crack instability influence the formation of small fragments. The preliminary analysis of the initial porosity of the material shows us that the initial porosity has a direct effect on the formation of 3D fragments. According to the scenario, the initial defects (pores) provide the conditions for multi-site fracture of ceramics under high rate loading.

RAG-3D: a search tool for RNA 3D substructures.

To address many challenges in RNA structure/function prediction, the characterization of RNA's modular architectural units is required. Using the RNA-As-Graphs (RAG) database, we have previously explored the existence of secondary structure (2D) submotifs within larger RNA structures. Here we present RAG-3D—a dataset of RNA tertiary (3D) structures and substructures plus a web-based search tool—designed to exploit graph representations of RNAs for the goal of searching for similar 3D structural fragments. The objects in RAG-3D consist of 3D structures translated into 3D graphs, cataloged based on the connectivity between their secondary structure elements. Each graph is additionally described in terms of its subgraph building blocks. The RAG-3D search tool then compares a query RNA 3D structure to those in the database to obtain structurally similar structures and substructures. This comparison reveals conserved 3D RNA features and thus may suggest functional connections. Though RNA search programs based on similarity in sequence, 2D, and/or 3D structural elements are available, our graph-based search tool may be advantageous for illuminating similarities that are not obvious; using motifs rather than sequence space also reduces search times considerably. Ultimately, such substructuring could be useful for RNA 3D structure prediction, structure/function inference and inverse folding.

Synthesis of functionalized 2-isoxazolines as three-dimensional fragments for fragment-based drug discovery

The design of new sp3 and spiro-enriched fragments has been achieved from 1,3-dipolar cycloaddition between alkenes and chloro-oximes. The selection of reagents was performed to afford a panel of 2-isoxazoline-containing fragments that show desirable three dimensional (3D) characteristics to allow the probing of biologically-relevant chemical space. Principal moments of inertia (PMI) were calculated to evaluate the 3D diversity. The resulting 3D fragments with suitable physicochemical properties, especially a good solubility, will be used to improve the hit rate of our fragment-based screening.

Haptic computer-assisted patient-specific preoperative planning for orthopedic fractures surgery.

The aim of orthopedic trauma surgery is to restore the anatomy and function of displaced bone fragments to support osteosynthesis. For complex cases, including pelvic bone and multi-fragment femoral neck and distal radius fractures, preoperative planning with a CT scan is indicated. The planning consists of (1) fracture reduction-determining the locations and anatomical sites of origin of the fractured bone fragments and (2) fracture fixation-selecting and placing fixation screws and plates. The current bone fragment manipulation, hardware selection, and positioning processes based on 2D slices and a computer mouse are time-consuming and require a technician. We present a novel 3D haptic-based system for patient-specific preoperative planning of orthopedic fracture surgery based on CT scans. The system provides the surgeon with an interactive, intuitive, and comprehensive, planning tool that supports fracture reduction and fixation. Its unique features include: (1) two-hand haptic manipulation of 3D bone fragments and fixation hardware models; (2) 3D stereoscopic visualization and multiple viewing modes; (3) ligaments and pivot motion constraints to facilitate fracture reduction; (4) semiautomatic and automatic fracture reduction modes; and (5) interactive custom fixation plate creation to fit the bone morphology. We evaluate our system with two experimental studies: (1) accuracy and repeatability of manual fracture reduction and (2) accuracy of our automatic virtual bone fracture reduction method. The surgeons achieved a mean accuracy of less than 1mm for the manual reduction and 1.8mm (std [Formula: see text] 1.1mm) for the automatic reduction. 3D haptic-based patient-specific preoperative planning of orthopedic fracture surgery from CT scans is useful and accurate and may have significant advantages for evaluating and planning complex fractures surgery.

Divide-and-conquer quantum mechanical material simulations with exascale supercomputers

Abstract Recent developments in large-scale materials science simulations, especially under the divide-and-conquer method, are reviewed. The pros and cons of the divide-and-conquer method are discussed. It is argued that the divide-and-conquer method, such as the linear-scaling 3D fragment method, is an ideal approach to take advantage of the heterogeneous architectures of modern-day supercomputers despite their relatively large prefactors among linear-scaling methods. Some developments in graphics processing unit (GPU) electronic structure calculations are also reviewed. The accelerators like GPU could be an essential part for the future exascale supercomputing.

X3D Fragment Identifiers — Extending the Open Annotation Model to Support Semantic Annotation of 3D Cultural Heritage Objects over the Web

This paper describes extensions made to the Open Annotation (OA) data model to enable the semantic annotation of points, surface regions and volumetric segments on 3D cultural heritage artefacts. More specifically it describes how the X3D (Extensible 3D Graphics) standard has been adapted to support concise, machine-processable and persistent 3D fragment identifiers. Methods to improve the efficiency of capturing, compressing and processing the X3D fragment identifiers are also described. The proposed X3D extensions are implemented and evaluated using a test-bed of 3D representations of ancient Greek Vases. The advanced annotation and search services that are achievable as a result of combining OA and X3D for the underlying annotation data model are also described. The benefits of this approach are demonstrated by measuring the improvements in file size and response times that are achieved. We also present evaluation results that indicate that the X3D approach combined with innovative run-length encoding (RLE) and innovative processing methods, improves the speed and efficiency of searching, retrieving and rendering annotations on 3D digital objects, over the Web.

Automated building of organometallic complexes from 3D fragments.

A method for the automated construction of three-dimensional (3D) molecular models of organometallic species in design studies is described. Molecular structure fragments derived from crystallographic structures and accurate molecular-level calculations are used as 3D building blocks in the construction of multiple molecular models of analogous compounds. The method allows for precise control of stereochemistry and geometrical features that may otherwise be very challenging, or even impossible, to achieve with commonly available generators of 3D chemical structures. The new method was tested in the construction of three sets of active or metastable organometallic species of catalytic reactions in the homogeneous phase. The performance of the method was compared with those of commonly available methods for automated generation of 3D models, demonstrating higher accuracy of the prepared 3D models in general, and, in particular, a much wider range with respect to the kind of chemical structures that can be built automatically, with capabilities far beyond standard organic and main-group chemistry.

Actinides in irradiated graphite of RBMK-1500 reactor

The activation of graphite in the nuclear power plants is the problem of high importance related with later graphite reprocessing or disposal. The activation of actinide impurities in graphite due to their toxicity determines a particular long term risk to waste management. In this work the activation of actinides in the graphite constructions of the RBMK-1500 reactor is determined by nuclear spectrometry measurements of the irradiated graphite sample from the Ignalina NPP Unit I and by means of numerical modeling using two independent codes SCALE 6.1 (using TRITON-VI sequence) and MCNPX (v2.7 with CINDER). Both models take into account the 3D RBMK-1500 reactor core fragment with explicit graphite construction including a stack and a sleeve but with a different simplification level concerning surrounding graphite and construction of control roads. The verification of the model has been performed by comparing calculated and measured isotope ratios of actinides. Also good prediction capabilities of the actinide activation in the irradiated graphite have been found for both calculation approaches. The initial U impurity concentration in the graphite model has been adjusted taking into account the experimental results. The specific activities of actinides in the irradiated RBMK-1500 graphite constructions have been obtained and differences between numerical simulation results, different structural parts (sleeve and stack) as well as comparison with previous results (Ancius et al., 2005) have been discussed. The obtained results are important for further decommissioning process of the Ignalina NPP and other RBMK type reactors, especially for 244Cm estimation which is a critical parameter contributing to the total alpha activity of the irradiated reactor graphite for approximately 200 years.

Two‐ and Three‐dimensional Rings in Drugs

Using small, flat aromatic rings as components of fragments or molecules is a common practice in fragment-based drug discovery and lead optimization. With an increasing focus on the exploration of novel biological and chemical space, and their improved synthetic accessibility, 3D fragments are attracting increasing interest. This study presents a detailed analysis of 3D and 2D ring fragments in marketed drugs. Several measures of properties were used, such as the type of ring assemblies and molecular shapes. The study also took into account the relationship between protein classes targeted by each ring fragment, providing target-specific information. The analysis shows the high structural and shape diversity of 3D ring systems and their importance in bioactive compounds. Major differences in 2D and 3D fragments are apparent in ligands that bind to the major drug targets such as GPCRs, ion channels, and enzymes.

Iterative Fragment Selection: A Group Contribution Approach to Predicting Fish Biotransformation Half-Lives

There are regulatory needs to evaluate thousands of chemicals for potential hazard and risk with limited available information. An automated method is presented for developing and evaluating Quantitative Structure-Activity Relationships (QSARs) for a range of chemical properties that can be applied for screening level chemical assessments. The method is an integrated algorithm for descriptor generation, data set splitting, cross validation, and model selection. Resulting QSARs are two-dimensional (2D) fragment-based group contribution models. The QSAR development and evaluation method does not require previous expert knowledge for selecting 2D fragments associated with the chemical property of interest. The method includes information on the domain of applicability (structural similarity to the training set) and estimates of the uncertainty in the QSAR predictions. As a demonstration, the method is applied to generate novel QSARs for fish primary biotransformation half-lives (HL(N)). Results from the new HL(N) QSARs are compared to another 2D fragment-based HL(N) QSAR developed with expert judgment, and the predictive powers of the models are found to be similar. The relative merits and limitations of each method are investigated and the new QSAR is found to make comparable predictions with significantly fewer fragments. A coefficient of determination (R(2)) of 0.789 and a root mean squared error (RMSE) of 0.526 were obtained for the training data set and an R(2) of 0.748 and an RMSE of 0.584 were obtained for the validation data set, along with a concordance correlation coefficient (CCC) of 0.857 showing good predictive power.

Route to three-dimensional fragments using diversity-oriented synthesis

Fragment-based drug discovery (FBDD) has proven to be an effective means of producing high-quality chemical ligands as starting points for drug-discovery pursuits. The increasing number of clinical candidate drugs developed using FBDD approaches is a testament of the efficacy of this approach. The success of fragment-based methods is highly dependent on the identity of the fragment library used for screening. The vast majority of FBDD has centered on the use of sp(2)-rich aromatic compounds. An expanded set of fragments that possess more 3D character would provide access to a larger chemical space of fragments than those currently used. Diversity-oriented synthesis (DOS) aims to efficiently generate a set of molecules diverse in skeletal and stereochemical properties. Molecules derived from DOS have also displayed significant success in the modulation of function of various "difficult" targets. Herein, we describe the application of DOS toward the construction of a unique set of fragments containing highly sp(3)-rich skeletons for fragment-based screening. Using cheminformatic analysis, we quantified the shapes and physical properties of the new 3D fragments and compared them with a database containing known fragment-like molecules.

Reassembly of 2D Fragments in Image Reconstruction

Digital images may be considered as collection of pixels. If a single image is divided into more than one part, then these subparts are treated as fragments for an image.Joining of 2D fragments of an in image means we have to reassemble these image’s fragments. The joining of fragments to reconstruct images and objects is a problem associated in several applications, like archeology, medicine, art restoration, and forensics.We mainly focused on 2D Image Reconstruction by joining two 2D fragments. This approach is based on the information generated from the boundary and from the color contents of the two fragments. Local curvature is calculated to obtain transformation independent coordinates. Based on this information comparison is done to obtain maximum matching parts among fragments. Finally longest matching parts can be joined to obtain single image.

Replication origins oriGNAI3 and oriB of the mammalian AMPD2 locus nested in a region of straight DNA flanked by intrinsically bent DNA sites

The aim of this work was to determine whether intrinsically bent DNA sites are present at, or close to, the mammalian replication origins oriGNAI3 and oriB in the Chinese hamster AMPD2 locus. Using an electrophoretic mobility shift assay and in silico analysis, we located four intrinsically bent DNA sites (b1 to b4) in a fragment that contains the oriGNAI3 and one site (b5) proximal to oriB. The helical parameters show that each bent DNA site is curved in a left-handed superhelical writhe. A 2D projection of 3D fragment trajectories revealed that oriGNAI3 is located in a relatively straight segment flanked by bent sites b1 and b2, which map in previously identified Scaffold/Matrix Attachment Region. Sites b3 and b4 are located approximately 2 kb downstream and force the fragment into a strong closed loop structure. The b5 site is also located in an S/MAR that is found just downstream of oriB.

RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures

BackgroundRecent discoveries concerning novel functions of RNA, such as RNA interference, have contributed towards the growing importance of the field. In this respect, a deeper knowledge of complex three-dimensional RNA structures is essential to understand their new biological functions. A number of bioinformatic tools have been proposed to explore two major structural databases (PDB, NDB) in order to analyze various aspects of RNA tertiary structures. One of these tools is RNA FRABASE 1.0, the first web-accessible database with an engine for automatic search of 3D fragments within PDB-derived RNA structures. This search is based upon the user-defined RNA secondary structure pattern. In this paper, we present and discuss RNA FRABASE 2.0. This second version of the system represents a major extension of this tool in terms of providing new data and a wide spectrum of novel functionalities. An intuitionally operated web server platform enables very fast user-tailored search of three-dimensional RNA fragments, their multi-parameter conformational analysis and visualization.DescriptionRNA FRABASE 2.0 has stored information on 1565 PDB-deposited RNA structures, including all NMR models. The RNA FRABASE 2.0 search engine algorithms operate on the database of the RNA sequences and the new library of RNA secondary structures, coded in the dot-bracket format extended to hold multi-stranded structures and to cover residues whose coordinates are missing in the PDB files. The library of RNA secondary structures (and their graphics) is made available. A high level of efficiency of the 3D search has been achieved by introducing novel tools to formulate advanced searching patterns and to screen highly populated tertiary structure elements. RNA FRABASE 2.0 also stores data and conformational parameters in order to provide "on the spot" structural filters to explore the three-dimensional RNA structures. An instant visualization of the 3D RNA structures is provided. RNA FRABASE 2.0 is freely available at http://rnafrabase.cs.put.poznan.pl.ConclusionsRNA FRABASE 2.0 provides a novel database and powerful search engine which is equipped with new data and functionalities that are unavailable elsewhere. Our intention is that this advanced version of the RNA FRABASE will be of interest to all researchers working in the RNA field.

How to observe the oxidation of magnesia‐supported Pd clusters by scanning tunnelling microscopy

AbstractThe structure of adsorbed bare and oxidised Pd9 clusters on a MgO(001) bilayer supported by an Ag(001) surface are studied by density functional theory (DFT). Results for the bare cluster are compared with corresponding calculations of Pd9 on a free‐standing MgO(001) trilayer – a system that already reproduces the adsorption properties of thick MgO films. A 3D double trigonal antiprism is compared to a 2D fragment of a Pd(111) plane. In contrast to the findings for gold clusters, the Pd9 3D ground state on a thick MgO film is still energetically favourable on a thin metal supported MgO film – despite the substantial charge transfer from the metal support to the 2D cluster. Simulated scanning tunnelling microscopy images predict that the oxide formation should be easily detectable for negative bias voltages, since the highest occupied molecular orbitals of both the pristine as well as the oxidised clusters possess a strong Pd(d) contribution localised on the Pd atoms. At positive bias, the nodal structure of delocalised unoccupied orbitals sometimes masks the nuclear positions.magnified image Simulated STM images for (a,d) Pd9@MgO(001)@Ag(001), (b,e) Pd9O2@MgO(001)@Ag(001) and (c,f) Pd9O4@MgO (001)@Ag(001).

Structural fragment clustering reveals novel structural and functional motifs in α-helical transmembrane proteins

BackgroundA large proportion of an organism's genome encodes for membrane proteins. Membrane proteins are important for many cellular processes, and several diseases can be linked to mutations in them. With the tremendous growth of sequence data, there is an increasing need to reliably identify membrane proteins from sequence, to functionally annotate them, and to correctly predict their topology.ResultsWe introduce a technique called structural fragment clustering, which learns sequential motifs from 3D structural fragments. From over 500,000 fragments, we obtain 213 statistically significant, non-redundant, and novel motifs that are highly specific to α-helical transmembrane proteins. From these 213 motifs, 58 of them were assigned to function and checked in the scientific literature for a biological assessment. Seventy percent of the motifs are found in co-factor, ligand, and ion binding sites, 30% at protein interaction interfaces, and 12% bind specific lipids such as glycerol or cardiolipins. The vast majority of motifs (94%) appear across evolutionarily unrelated families, highlighting the modularity of functional design in membrane proteins. We describe three novel motifs in detail: (1) a dimer interface motif found in voltage-gated chloride channels, (2) a proton transfer motif found in heme-copper oxidases, and (3) a convergently evolved interface helix motif found in an aspartate symporter, a serine protease, and cytochrome b.ConclusionsOur findings suggest that functional modules exist in membrane proteins, and that they occur in completely different evolutionary contexts and cover different binding sites. Structural fragment clustering allows us to link sequence motifs to function through clusters of structural fragments. The sequence motifs can be applied to identify and characterize membrane proteins in novel genomes.

Using cellular automata for porous media simulation

A cellular automata (CA) approach is proposed for simulating a fluid flow through porous materials with tortuous channels at pore level. The approach aims to combine CA methods both for constructing computer representation of porous material morphology and for simulating fluid flow through it. Morphology representation is obtained using CA whose evolution exhibits self-organization and results in a stable configuration. The latter is then used for Lattice Gas CA application to simulate fluid flow through a porous material specimen and compute its permeability properties. Special boundary conditions are introduced allowing for different smoothness of solid pore walls surface. The model has been tested on a small 2D fragment in a PC and then implemented to investigate a porous carbon electrode of a hydrogen fuel cell on 128 processors of a multiprocessor cluster.

Fragmentation by electron recombination for HF+ and CF+

Dissociative recombination (DR) is an exothermic process leading to neutralisation and chemical fragmentation in many plasma environments, down to the lowest temperatures. We present results of complex investigations on DR of HF+ and CF+ performed at the TSR storage ring. Beyond the rate coefficient down to meV collision energies also dissociation pathways and geometries have been investigated using full 3D fragment imaging technique. Fragment imaging also provides HF+ rotational structure and fine-structure as well as the HF+ dissociation energy with sub-meV precision.

Automatic Fragment Re-Assembly Method Based on DDTW Match

This paper presents an automatic re-assembly method for matching 3D fragments,which can compute the best match of a pair of broken pieces.To improve speed and accuracy,this paper gives a torsion estimation method based on anti-noise section and a fixed time cost 3D overlap test method.First,the contour curves of fragments are found,then the corner points.Contour curves can be divided into several sub-contours.Second,the torsion sequences are obtained for the DDTW based matching work.Thus,the scale and transformation matrixes can be computed to change size and position of one fragment.Best matching result will be finally chosen according to matching test and extra evaluations.Experiment results show that this method is simple and robust,and can get proper matching results quickly.

Automatic Fragment Re-Assembly Method Based on DDTW Match

This paper presents an automatic re-assembly method for matching 3D fragments,which can compute the best match of a pair of broken pieces.To improve speed and accuracy,this paper gives a torsion estimation method based on anti-noise section and a fixed time cost 3D overlap test method.First,the contour curves of fragments are found,then the corner points.Contour curves can be divided into several sub-contours.Second,the torsion sequences are obtained for the DDTW based matching work.Thus,the scale and transformation matrixes can be computed to change size and position of one fragment.Best matching result will be finally chosen according to matching test and extra evaluations.Experiment results show that this method is simple and robust,and can get proper matching results quickly.