Density Modification Research Articles

Modification factors of the embedding strength dependent on the temperature and load-to-grain angle for two wood species planted in Brazil

This research aims to assess the influence of the temperature and the load-to-grain angle on the embedding strength of the timber of the two most used wood species in Brazil, proposing a continuous function that describes the behaviour of the embedding strength, which can be used in advanced numerical models for estimating the load-bearing capacity of the bolted connections. Embedding tests were carried out with 1400 specimens made according to ASTM D 5764-97a. The experimental program consists of 10 temperature levels and 7 load-to-grain angles for each Pinus elliottii Engelm and Eucalyptus saligna Sm samples. For each combination of one temperature level and one load-to-grain angle, ten specimens were used. The moisture content, density, mean and characteristic embedding strength and modification factor of the characteristic embedding strength were determined. The embedding strength decreases with the increase of the load-to-grain angle and significant differences occur between mean embedding strengths at room temperature (25 °C) and those at elevated temperatures. A fitted model of the modification factor of the characteristic embedding strength was determined for both species. The adjusted coefficients of determination of the models are 0.87 and 0.92 to the Pinus elliottii and Eucalyptus saligna, respectively. These models are continuous functions that can be useful for predicting bolted connections load capacity in advanced numerical models in situations of temperature and load-to-grain angles similar to the ones in this research. They should be used with caution since they present a large variability in their results.

Planned Unit Development (PUD) in Urban Design Project

Since 1960s Bangkok has been under the practices of post-war urban planning, in addition to a series of initial development of comprehensive plans, through four versions of adopted comprehensive plans which were used as urban development controlling tool, while lacking regulations for urban guidance. Planned Unit Development (PUD) is a regulation allowing comprehensive planning and design on a specific large urban area with flexibility for greater livability. This research aims to explore the applicability of PUD in the urban development process of Bangkok. Two conceptual design scenarios for applying PUD were generated providing project feasibility analysis and PUD design guidelines. The research is conducted as an experimental study focusing on the tasks of three variables: scenario generation, feasibility analysis, and urban design and development. The design experimentation result has been stated that it potentially applies PUD on the study site (Pahonyothin 19/1, Bangkok). However, it will require great financial aid and a period of time. With PUD, Bangkok urbanization can reach the stage of urban design that contributes variable benefits such as site planning and design, density modification, providing infrastructures, and circulation improvement. In addition, PUD provides greater ranges of benefits such as carbon reduction, urban heat island mitigation, promoting Transit Oriented Development (TOD), and positioning on SDG 11: Sustainable Cities and Communities. The research output is providing guidelines towards a sustainable 21st century city for Bangkok.

Preparation and application of polyaluminum chloride for demulsification of colloidal biliquid aphron and density modification for DNAPLs

The preparation and application of suitable demulsifiers in the process of density control of DNPALs is in urgent demand. In this study, we prepared a demulsifier -polyaluminum chloride (PACl), for density modifier -colloidal biliquid aphron (CBLA). We found that PACl2 (PACl with [OH]/[Al] = 2) can make CBLA to completely release light organic liquids within 30 min. The prepared PACl was characterized by SEM, XRD, the reaction curve of PACl with ferron reagent, 27Al NMR and charge density test in order to identify the reactive groups and elucidate the demulsification mechanisms. The system achieved 95% demlusification efficiency in acidic environment (pH < 4). The demulsification process followed pseudo-second-order kinetics model. A small amount of aquifer material could promote demulsification due to natural demulsifiers. We also used PACl2 to break CBLA and modify the density of two DNPALs, trichloroethylene (from 1.464 g/cm3 to 0.980 g/cm3), and nitrobenzene (from 1.197 g/cm3 to 0.921 g/cm3). The results show that the density of DNAPL can be reduced to less than that of water, which effectively prevents the downward migration of DNAPLs during remediation process. The findings will improve our understanding of the mechanism of CBLA demulsification and its density modification of DNAPLs for enhanced groundwater remediation.

Density modification of cryo-EM maps.

Density modification uses expectations about features of a map such as a flat solvent and expected distributions of density in the region of the macromolecule to improve individual Fourier terms representing the map. This process transfers information from one part of a map to another and can improve the accuracy ofa map. Here, the assumptions behind density modification for maps from electron cryomicroscopy are examined and a procedure is presented that allows the incorporation of model-based information. Density modification works best in cases where unfiltered, unmasked maps with clear boundaries between the macromolecule and solvent are visible, and where there is substantial noise in the map, both in the region of the macromolecule and the solvent. It also is most effective if the characteristics of the map are relatively constant within regions of the macromolecule and the solvent. Model-based information can be used to improve density modification, but model bias can in principle occur. Here, model bias is reduced by using ensemble models that allow an estimation of model uncertainty. A test of model bias is presented that suggests that even if the expected density in a region of a map is specified incorrectly by using an incorrect model, the incorrect expectations do not strongly affect the final map.

Physicochemical evaluation and Fourier transform infrared spectroscopy characterization of quality protein maize starch subjected to different modifications.

Quality protein maize (QPM) is a biofortified maize rich in lysine and tryptophan, essential amino acids required in human nutrition. This research therefore characterizes native and modified starches from QPM by evaluating the physicochemical properties, Fourier transform infrared spectra (FTIR), and pasting properties. The native QPM starch was modified by oxidation, acetylation, pregelatinization, and acid thinning techniques. The starch yield of native QPM was 43.80%, while that of modified starches were from 88.22 to 98.34%. The moisture content of the native and modified starches was from 4.56 to 9.20 g/100g. Modifications significantly (P ≤ 0.05) reduced the lipid, protein, and amylose contents of the QPM. While the native starch had 0.72 g/cm3 bulk density, modified starches were between 0.59 and 0.88 g/cm3; chemical modification reduced the bulk density and physical modification increased it. In addition, all the modifications except oxidation significantly (P ≤ 0.05) increased water absorption capacity. The oil absorption of the starch samples was increased by modification techniques used with the exception of physical modification. Chemical modification reduced the viscosity of QPM starch while physical modification increased it. The reducing sugar content of the starch was reduced by both the physical and chemical starch modification techniques. Acetylated sample exhibited the highest swelling power while acid‐thinned sample had the least. The major functional groups identified via FTIR were OH, C‐H, C=H, and C≡H. Modifications did not affect the functional groups as all the native and modified starches (except oxidized sample) all have similar spectrum and bands stretch.Practical ApplicationThe study contributes to existing knowledge on valorization of modified starch from quality protein maize. Profiling the chemical attributes of modified starches is especially valuable in novel food processing techniques.

Improvement of cryo-EM maps by density modification.

A density modification procedure for improving maps from single-particle electron cryo-microscopy is presented. The theoretical basis of the method is identical to that of maximum-likelihood density modification, previously used to improve maps from macromolecular X-ray crystallography. Key differences from applications in crystallography are that the errors in Fourier coefficients are largely in the phases in crystallography but in both phases and amplitudes in electron cryo-microscopy, and that half-maps with independent errors are available in electron cryo-microscopy. These differences lead to a distinct approach for combination of information from starting maps with information obtained in the density modification process. The density modification procedure was applied to a set of 104 datasets and improved map-model correlation and increased the visibility of details in many of the maps. The procedure requires two unmasked half-maps and a sequence file or other source of information on the volume of the macromolecule that has been imaged.

Simulating Agriculture in the Community Land Model Version 5

AbstractAgricultural expansion and management have greatly increased global food production and altered Earth's climate by changing physical and biogeochemical properties of terrestrial ecosystems. Few Earth system models represent agricultural management practices due to the complexity of the interactions between human decisions and biological processes on global scales. We describe the new capabilities of representing crop distributions and management in the Community Land Model (CLM) Version 5, which includes time‐varying spatial distributions of major crop types and their management through fertilization and irrigation, and temperature‐based phenological triggers. Including active crop management increases peak growing season gross primary productivity (GPP), increases the amplitude of Northern Hemisphere net ecosystem exchange, and changes seasonal and annual patterns of latent and sensible heat fluxes. The CLM5 crop model simulates the global observed historical trend of crop yields with relative fidelity from 1850 to 1990. Cropland expansion was important for increasing crop production, especially during the first century of the simulations, while fertilization and irrigation were important for increasing yields from 1950 onward. From 1990 to present day, observed crop production continued to increase while CLM5 production levels off, likely because intensification practices are not represented in the model. Specifically, CLM does not currently include increasing planting density, crop breeding and genetic modification, representations of tillage, or other management practices that may also affect crop‐climate and crop‐carbon cycle interactions and alter trends in yields. These results highlight the importance of including crop management in Earth system models, particularly as global data sets for parameterization and evaluation become more readily available.

Mineral particle disintegration model

The study proposes mathematical model for reducing the size of mineral particles in crushing and grinding operations, which is a form of the reflected normal Gaussian – Laplace distribution. The study considers the distribution density modification of the mineral particles depending on the magnitude of the energy impact during grinding. Comparison of the results of computational experiments with the results of laboratory studies confirms the possibility of using the proposed model of disintegration of mineral particles in the development of software modules for the operational evaluation for crushing and (or) grinding of mineral raw materials.

Fragment-based determination of a proteinase K structure from MicroED data using ARCIMBOLDO_SHREDDER

Structure determination of novel biological macromolecules by X-ray crystallography can be facilitated by the use of small structural fragments, some of only a few residues in length, as effective search models for molecular replacement to overcome the phase problem. Independence from the need for a complete pre-existing model with sequence similarity to the crystallized molecule is the primary appeal of ARCIMBOLDO, a suite of programs which employs this ab initio algorithm for phase determination. Here, the use of ARCIMBOLDO is investigated to overcome the phase problem with the electron cryomicroscopy (cryoEM) method known as microcrystal electron diffraction (MicroED). The results support the use of the ARCIMBOLDO_SHREDDER pipeline to provide phasing solutions for a structure of proteinase K from 1.6 Å resolution data using model fragments derived from the structures of proteins sharing a sequence identity of as low as 20%. ARCIMBOLDO_SHREDDER identified the most accurate polyalanine fragments from a set of distantly related sequence homologues. Alternatively, such templates were extracted in spherical volumes and given internal degrees of freedom to refine towards the target structure. Both modes relied on the rotation function in Phaser to identify or refine fragment models and its translation function to place them. Model completion from the placed fragments proceeded through phase combination of partial solutions and/or density modification and main-chain autotracing using SHELXE. The combined set of fragments was sufficient to arrive at a solution that resembled that determined by conventional molecular replacement using the known target structure as a search model. This approach obviates the need for a single, complete and highly accurate search model when phasing MicroED data, and permits the evaluation of large fragment libraries for this purpose.

Spatial Statistical Analysis of the relation in between population density and Human Modification of terrestrial lands at Tabia level in the Tigray Region of Ethiopia

In this study first spatial pattern of the level of human modification of terrestrial lands and second its relation with population density was studied at Taiba level in the Tigray regional state of Ethiopia. For the level of human modification of terrestrial lands global Human Modification dataset (gHM) was used and for population density Gridded Population of the World, Version 4 (GPWv4.11) dataset was used. Both the data set were preprocessed before geostatistical analysis. To measure the distribution pattern Global Moran's I statistics, Cluster and Outlier Analysis (Anselin Local Morans I) statistics was used. To measure the relation between population density and human modification of terrestrial lands geographically weighted regression was used. In the case of first objective the resulting z-score of 50.50, confirm the tabias with high Human Modification of terrestrial lands are highly clustered. In case of second objective the results shows 214 Tabias containing high value and are surrounded by Tabias with high values (HH), 10 Tabias containing high value and is surrounded by Tabias with low values (HL). The relation between population density and human modification of terrestrial lands was found positive with R2= 0.506. This research will help the government and planners for proactive spatial planning to maintain biodiversity and ecosystem function before important environmental values are lost in tabias containing high value and is surrounded by Tabias with high values.

Optimization of electrical conductivity in the Na2O‐P2O5‐AlF3‐SO3 glass system

AbstractWe report on the individual roles of charge carrier density and network modification in sodium ion conducting glasses from the Na2O‐P2O5‐SO3‐AlF3 (NAPFS) system. For this, a broad range of glass compositions was considered across the series of 44Na2O/(56 – x − y)P2O5/xAlF3/ySO3, 47Na2O/(53 − x − y)P2O5/xAlF3/ySO3, and 50Na2O/(50 − x − y)P2O5/xAlF3/ySO3, with x = 8, 12, 16, 20 and y = 0, 5, 7, 10, 12. Impedance spectroscopy was conducted on these glasses at frequencies from 10−2 to 106 Hz and over temperatures from 50 to 250°C, and complemented by structural analyses using Raman spectroscopy and nuclear magnetic resonance data. While the trends in dc conductivity and activation energy follow that of Na2O content (increasing from 44 to 50 mol%), substantial enhancement of conductivity (by about two orders of magnitude) and correspondingly lower activation energy were also found for constant Na2O concentration when adjusting SO3 or AlF3 within specific limits of glass structure.

Surface defects state analysis of laser induced graphene from 4H-SiC

We demonstrate the surface defect type, density and related electrical modification of graphene sheet generated by 193-nm ArF excimer laser irradiation on n-type 4H-SiC. The charge density difference and partial density of states (PDOS) carried out by density functional theory (DFT) calculations predict the graphene with lattice imperfection can induce virtual bound states at the vacancy sites and Fermi level shift compared to perfect graphene. The surface defects density of laser generated graphene is characterized by nanoscale electrical measurements using the conductive atomic force microscope (c-AFM). The corresponding current–voltage (I–V) curves show that the electronic charge transfers, thereby electrical conductivities of laser generated graphene, are influenced by the lattice defects. The defect densities are tunable by change laser fluence and pulse number. This research provides an understanding of the interfacial transport properties between laser generated graphene and 4H-SiC through a detailed analysis of surface defects.

Improved crush energy absorption in 3D woven composites by pick density modification

Although 3D woven composites have exceptional out-of-plane properties, there is a lack of understanding for these materials in crash application in automotive and aerospace industries. To encourage the use of 3D wovens in crashworthy automotive structures, knowledge must be gained so that designers can adjust the highly flexible weave parameters to create tailor-made performance materials. Here we show that fabric pick density causes large changes in progressive failure modes and associated energy absorption, particularly in the dynamic regime, where the quasi-static to dynamic energy absorption loss typical of composites is completely removed. Compression and flexure properties, which are known to be linked to crash performance in composites, are also investigated for these 3D woven layer-to-layer interlock carbon-epoxy composite structures. 3D fabric preforms are manufactured in three different pick densities: 4, 10 & 16 wefts/cm. With a constant warp density of 12 warps/cm from carbon fibres. Increasing the pick density improved specific energy absorption (SEA) even in relatively inefficient progressive failure modes like folding, which has not previously observed in composite materials. SEA values up to 104 J/g (quasi-static) and 93 J/g (dynamic) are recorded. This work shows that minor weft direction (transverse) weave changes can lead to sizeable improvements in warp direction (axial) energy absorption without fundamentally redesigning the weave architecture.

Recent advances in carbon nanotube sponge–based sorption technologies for mitigation of marine oil spills

HypothesisOil spills stemming from supertankers, drilling, and natural events represent a serious problem worldwide due to the potential harms to marine ecosystems and aquatic life. To date, various functional absorbents have been developed to treat spilled oil. Among them, carbon nanotube (CNT)-based aerogels and sponges gained attention due to superior performance in uptake and recovery of various types of oil and organic solvents. CNT aerogel/sponge absorbents are demonstrated for a multitude of merits such as: rapid superhydrophobic/superoleophilic absorption (water contact angle > 150°), high capacity (≥100 mg g−1), large surface area (300–400 m2 g−1)), enhanced strength and flexibility (>95% volume reduction and restoration of pristine morphology at <0.25 MPa stress), mesoporous characteristics with high pore density (pore diameter = 80 nm and >99% porosity), recyclability, and easy surface modification. ExperimentsThis review compares CNT sponge–based absorbents with conventional techniques for remediation/recovery of spilled oil. Typically, synthesis of CNT sponges is performed using chemical vapor deposition (CVD) approach in the presence of a catalyst or using sacrificial removal of template. This work summarizes recent progress in strategies for oil-spill treatment based on CNT sponge techniques. The performance of CNT sponges for oil spill removal was evaluated in terms of their adsorption capacity, compressive stressability, and desorption methods (e.g., heat treatment, burning, or squeezing). FindingsCNT sponges were observed to have high performance for removal of oil spills in terms of key performance metrics. This review offers valuable insights into the current state of CNT-mediated oil-spill cleanup technologies and guidance for future research at the same time. This literature survey would help the stakeholders (researchers, scientists, entrepreneurs, and commercial houses) pursue contamination-free water.

Mask-Based Approach in Phasing and Restoring of Single-Particle Diffraction Data

The development of experimental techniques, in particular the emergence of the X-ray free-electron lasers, allows one to register the scattering from an isolated particle and, thereby, opens a door to the study of a fine three-dimensional structure of non-crystalline biological objects by X-ray diffraction methods. The possibility to measure non-Bragg reflections makes experimental data mutually dependent and essentially simplifies the structure solution. The sampling of experimental scattering data to a sufficiently fine grid makes the structure determination equivalent to phasing of structure factor magnitudes for a 'virtual' crystal with extremely large solvent content. This makes density modification phasing methods especially powerful supposing the object envelope is known. At the same time, such methods may be sensitive to the accuracy of the predefined envelope and completeness of experimental data and may suffer from non-uniqueness of the solution of the phase problem. The mask-based approach is a preliminary phasing method that performs random search for connected object envelopes possessing of the structure factor magnitudes close to the values observed in X-ray experiment. The alignment and averaging of the phase sets corresponding to selected putative envelopes produce an approximate solution of the phase problem. Beside the estimation of unknown phase values this approach allows one to estimate the values of structure factor magnitudes lost in the experiment, e.g. those corresponding to beam-stop shade zone or to oversaturated reflections.

ALEPH: a network-oriented approach for the generation of fragment-based libraries and for structure interpretation.

The analysis of large structural databases reveals general features and relationships among proteins, providing useful insight. A different approach is required to characterize ubiquitous secondary-structure elements, where flexibility is essential in order to capture small local differences. The ALEPH software is optimized for the analysis and the extraction of small protein folds by relying on their geometry rather than on their sequence. The annotation of the structural variability of a given fold provides valuable information for fragment-based molecular-replacement methods, in which testing alternative model hypotheses can succeed in solving difficult structures when no homology models are available or are successful. ARCIMBOLDO_BORGES combines the use of composite secondary-structure elements as a search model with density modification and tracing to reveal the rest of the structure when both steps are successful. This phasing method relies on general fold libraries describing variations around a given pattern of β-sheets and helices extracted using ALEPH. The program introduces characteristic vectors defined from the main-chain atoms as a way to describe the geometrical properties of the structure. ALEPH encodes structural properties in a graph network, the exploration of which allows secondary-structure annotation, decomposition of a structure into small compact folds, generation of libraries of models representing a variation ofa given fold and finally superposition of these folds onto a target structure. These functions are available through a graphical interface designed to interactively show the results of structure manipulation, annotation, fold decomposition, clustering and library generation. ALEPH can produce pictures of the graphs, structures and folds for publication purposes.

SEQUENCE SLIDER: expanding polyalanine fragments for phasing with multiple side-chain hypotheses.

Fragment-based molecular-replacement methods can solve a macromolecular structure quasi-ab initio. ARCIMBOLDO, using a common secondary-structure or tertiary-structure template or a library of folds, locates these with Phaser and reveals the rest of the structure by density modification and autotracing in SHELXE. The latter stage is challenging when dealing with diffraction data at lower resolution, low solvent content, high β-sheet composition or situations in which the initial fragments represent a low fraction of the total scattering or where their accuracy is low. SEQUENCE SLIDER aims to overcome these complications by extending the initial polyalanine fragment with side chains in a multisolution framework. Its use is illustrated on test cases and previously unknown structures. The selection and order of fragments to be extended follows the decrease in log-likelihood gain (LLG) calculated with Phaser upon the omission of each single fragment. When the starting substructure is derived from a remote homolog, sequence assignment to fragments is restricted by the original alignment. Otherwise, the secondary-structure prediction is matched to that found in fragments and traces. Sequence hypotheses are trialled in a brute-force approach through side-chain building and refinement. Scoring the refined models through their LLG in Phaser may allow discrimination of the correct sequence or filter the best partial structures for further density modification and autotracing. The default limits for the number of models to pursue are hardware dependent. In its most economic implementation, suitable for a single laptop, the main-chain trace is extended as polyserine rather than trialling models with different sequence assignments, which requires a grid or multicore machine. SEQUENCE SLIDER has been instrumental in solving two novel structures: that of MltC from 2.7 Å resolution data and that of a pneumococcal lipoprotein with 638 residues and 35% solvent content.

ALIXE: a phase-combination tool for fragment-based molecular replacement.

Fragment-based molecular replacement exploits the use of very accurate yet incomplete search models. In the case of the ARCIMBOLDO programs, consistent phase sets produced from the placement and refinement of fragments with Phaser can be combined in order to increase their signal before proceeding to the step of density modification and autotracing with SHELXE. The program ALIXE compares multiple phase sets, evaluating mean phase differences to determine their common origin, and subsequently produces sets of combined phases that group consistent solutions. In this work, its use on different scenarios of very partial molecular-replacement solutions and its performance after the development of a much-optimized set of algorithms are described. The program is available both standalone and integrated within the ARCIMBOLDO programs. ALIXE has been analysed to identify its rate-limiting steps while exploring the best parameterization to improve its performance and make this software efficient enough to work on modest hardware. The algorithm has been parallelized and redesigned to meet the typical landscape of solutions. Analysis of pairwise correlation between the phase sets has also been explored to test whether this would provide additional insight. ALIXE can be used to exhaustively analyse all partial solutions produced or to complement those already selected for expansion, and also to reduce the number of redundant solutions, which is particularly relevant to the case of coiled coils, or to combine partial solutions from different programs. In each case parallelization and optimization to provide speedup makes its use amenable to typical hardware found in crystallography. ARCIMBOLDO_BORGES and ARCIMBOLDO_SHREDDER now call on ALIXE by default.

IPCAS: a direct-method-based pipeline from phasing to model building and refinement for macromolecular structure determination

A new version (2.0) of the pipeline IPCAS (Iterative Protein Crystal structure Automatic Solution) has been released, in which the program OASIS performs direct-method single-wavelength anomalous diffraction/single isomorphous replacement phasing and direct-method-aided partial-structure extension. IPCAS incorporates the widely used packages CCP4 and PHENIX for locating heavy atoms, density modification, molecular replacement, model building and refinement. Important extensions to the previous version of IPCAS include a resolution screening method for non-crystallographic symmetry searching, an alternate model-building protocol for avoiding premature convergence and direct-method image processing for electron microscopy maps, including single-particle cryo-EM maps. Moreover, a new graphical user interface is provided for controlling and real-time monitoring of the whole dual-space iterative process, which works as a plugin to CCP4i. Applications of the new IPCAS to difficult cases have yielded promising results, including `direct-method phasing and fragment extension' from weak anomalous diffraction signal data and `direct-method-aided partial-structure extension' from low-homology models.

Colloidal biliquid aphron demulsification using polyaluminum chloride and density modification of DNAPLs: optimal conditions and common ion effect.

Dense non-aqueous phase liquids (DNAPLs) entrapped and pooled in aquifers serve as a long term source of groundwater contamination because of their low solubility and high density. Density modification displacement (DMD) with colloidal biliquid aphrons (CBLAs) is a promising approach to prevent DNAPL downward migration during surfactant-based remediation processes. CBLA demulsification and quick release of internal light organic matter is the key to density modification of DNAPLs. In this work, it is reported for the first time that polyaluminum chloride (PAC) could destabilize CBLAs efficiently. The optimum conditions for demulsification of CBLAs by PAC were obtained; the effects of several specific ions in groundwater on demulsification of CBLAs by PAC were investigated. The results indicated that the CBLA was completely demulsified by PAC within 10 minutes and released light organic matter. It recorded the highest demulsification efficiency when the addition ratio (VPAC/VCBLA) was 2 : 1, concentration of PAC was 0.7 g L-1 and the PVR of CBLAs was 8. Most cations (sodium, magnesium and calcium ions) had inhibitory effects on demulsification of CBLAs by PAC with increasing ion concentration, but iron ions had no effect on it. Sulfate anions showed a stronger inhibitory effect on demulsification of CBLAs by PAC compared to chloride ions. With PAC as the demulsifier, CBLAs could be demulsified efficiently, irreversibly modifying the density of trichloroethylene in 5 minutes.