scholarly journals Implicit Modeling of the Impact of Adsorption on Solid Surfaces for Protein Mechanics and Activity with a Coarse-Grained Representation

2020 ◽  
Vol 124 (39) ◽  
pp. 8516-8523
Author(s):  
Nicolas Bourassin ◽  
Marc Baaden ◽  
Elisabeth Lojou ◽  
Sophie Sacquin-Mora
Keyword(s):  
Solid Surfaces ◽  
Coarse Grained ◽  
Protein Mechanics ◽  
Implicit Modeling ◽  
The Impact

scholarly journals Implicit modeling of the impact of adsorption on solid surfaces for protein mechanics and activity with a coarse-grain representation

2020 ◽  
Author(s):  
Nicolas Bourassin ◽  
Marc Baaden ◽  
Elisabeth Lojou ◽  
Sophie Sacquin-Mora
Keyword(s):  
Brownian Dynamics ◽  
Immobilized Enzymes ◽  
Protein Mechanics ◽  
Local Flexibility ◽  
Implicit Modeling ◽  
Dynamics And Function ◽  
Dynamics Simulations ◽  
And Function ◽  
Brownian Dynamics Simulations ◽  
The Impact

AbstractSurface immobilized enzymes play a key role in numerous biotechnological applications such as biosensors, biofuel cells or biocatalytic synthesis. As a consequence, the impact of adsorption on the enzyme structure, dynamics and function needs to be understood on the molecular level as it is critical for the improvement of these technologies. With this perspective in mind, we used a theoretical approach for investigating protein local flexibility on the residue scale that couples a simplified protein representation with an elastic network and Brownian Dynamics simulations. The protein adsorption on a solid surface is implicitly modeled via additional external constraints between the residues in contact with the surface. We first performed calculations on a redox enzyme, bilirubin oxidase (BOD) from M. verrucaria, to study the impact of adsorption on its mechanical properties. The resulting rigidity profiles show that, in agreement with the available experimental data, the mechanical variations observed in the adsorbed BOD will depend on its orientation and its anchor residues (i.e. residues that are in contact with the functionalized surface). Additional calculations on ribonuclease A and nitroreductase shed light on how seemingly stable adsorbed enzymes can nonetheless display an important decrease in their catalytic activity resulting from a perturbation of their mechanics and internal dynamics.

Multiple interactions in riverine biofilms - surfactant adsorption, bacterial attachment and biodegradation

1995 ◽  
Vol 31 (1) ◽  
pp. 61-70 ◽  
Author(s):  
Graham F. White
Keyword(s):  
Organic Pollutants ◽  
Bacterial Attachment ◽  
Solid Surfaces ◽  
Sediment Surface ◽  
Liquid Interfaces ◽  
Polluted Soils ◽  
Biofilm Bacteria ◽  
The Impact ◽  
Multiple Interactions

Many organic pollutants, especially synthetic surfactants, adsorb onto solid surfaces in natural and engineered aquatic environments. Biofilm bacteria on such surfaces make major contributions to microbial heterotrophic activity and biodegradation of organic pollutants. This paper reviews evidence for multiple interactions between surfactants, biodegradative bacteria, and sediment-liquid interfaces. Biodegradable surfactants e.g. SDS, added to a river-water microcosm were rapidly adsorb to sediment surface and stimulated the indigenous bacteria to attach to the sediment particles. Recalcitrant surfactants and non-surfactant organic nutrients did not stimulate attachment Attachment of bacteria was maximal when biodegradation was fastest, and was reversed when biodegradation was complete. Dodecanol, the primary product of SDS-biodegradation, markedly stimulated attachment. When SDS was added to suspensions containing sediment and either known degraders or known non-degraders, only the degraders became attached, and attachment accelerated surfactant biodegradation to dodecanol. These cyclical cooperative interactions have implications for the design of biodegradability-tests, the impact of surfactant adjuvants on biodegradability of herbicides/pesticides formulated with surfactants, and the role of surfactants used to accelerate bioremediation of hydrocarbon-polluted soils.

scholarly journals Review of the relationship between aggregates geology and Los Angeles and micro-Deval tests

2021 ◽  
Vol 80 (3) ◽  
pp. 1963-1980
Author(s):  
Solomon Adomako ◽  
Christian John Engelsen ◽  
Rein Terje Thorstensen ◽  
Diego Maria Barbieri
Keyword(s):  
Los Angeles ◽  
Crystal Size ◽  
Grain Shape ◽  
Mechanical Performance ◽  
Pore Space ◽  
Construction Material ◽  
Engineering Properties ◽  
Coarse Grained ◽  
The Impact ◽  
The Relationship

AbstractRock aggregates constitute the enormous volume of inert construction material used around the globe. The petrologic description as igneous, sedimentary, and metamorphic types establishes the intrinsic formation pattern of the parent rock. The engineering properties of these rocks vary due to the differences in the transformation process (e.g. hydrothermal deposits) and weathering effect. The two most common mechanical tests used to investigate the performance of aggregates are the Los Angeles (LA) and micro-Deval (MD) tests. This study reviewed the geological parameters (including mineralogy, grain and crystal size, grain shape, and porosity) and the relationship to Los Angeles and micro-Deval tests. It was found that high content of primary minerals in rocks (e.g. quartz and feldspar) is a significant parameter for performance evaluation. Traces of secondary and accessory minerals also affect the performance of rocks, although in many cases it is based on the percentage. Furthermore, some studies showed that the effect of mineralogic composition on mechanical strength is not sufficient to draw final conclusions of mechanical performance; therefore, the impact of other textural characteristics should be considered. The disposition of grain size and crystal size (e.g. as result of lithification) showed that rocks composed of fine-grain textural composition of ≤ 1 mm enhanced fragmentation and wear resistance than medium and coarse grained (≥ 1 mm). The effect of grain shape was based on convex and concave shapes and flat and elongated apexes of tested samples. The equidimensional form descriptor of rocks somehow improved resistance to impact from LA than highly flat and elongated particles. Lastly, the distribution of pore space investigated by means of the saturation method mostly showed moderate (R = 0.50) to strong (R = 0.90) and positive correlations to LA and MD tests.

Effect of Welding Processes with High Heat Input on the Microstructure and Toughness of Coarse-Grained Heat-Affected Zone of a High-Strength High-Toughness Steel

2018 ◽  
Vol 937 ◽  
pp. 61-67
Author(s):  
Yu Jie Li ◽  
Jin Wei Lei ◽  
Xuan Wei Lei ◽  
Oleksandr Hress ◽  
Kai Ming Wu
Keyword(s):  
Low Temperature ◽  
Impact Toughness ◽  
Heat Affected Zone ◽  
Heat Input ◽  
High Strength ◽  
High Heat ◽  
Coarse Grained ◽  
Low Temperature Impact Toughness ◽  
The Impact ◽  
Welding Processes

Utilizing submerged arc welding under heat input 50 kJ/cm on 60 mm thick marine engineering structure plate F550, the effect of preheating and post welding heat treatment on the microstructure and impact toughness of coarse-grained heat-affected zone (CGHAZ) has been investigated. The original microstructure of the steel plate is tempered martensite. The yield and tensile strength is 610 and 660 MPa, respectively. The impact absorbed energy at low temperature (-60 °C) at transverse direction reaches about 230~270 J. Welding results show that the preheating at 100 °C did not have obvious influence on the microstructure and toughness; whereas the tempering at 600 °C for 2.5 h after welding could significantly reduce the amount of M-A components in the coarse-grained heat-affected zone and thus improved the low temperature impact toughness.

scholarly journals LABORATORY OBSERVATIONS OF IMPACTS ON COARSE SEDIMENT BEACHES

2011 ◽  
Vol 1 (32) ◽  
pp. 53
Author(s):  
Ian Ball ◽  
Edgar Mendoza-Baldwin ◽  
David Simmonds ◽  
Adrián Pedrozo-Acuña ◽  
Dominic E Reeve
Keyword(s):  
Full Scale ◽  
Impact Pressure ◽  
Coarse Grained ◽  
Laboratory Measurements ◽  
Coarse Sediment ◽  
Full Scale Tests ◽  
The Impact ◽  
Impact Events ◽  
Plunging Breaker

In this paper we present laboratory observations of plunging wave breaker impact pressure responses on a steep coarse-grained beach, extending previous work conducted by Pedrozo-Acuña et al. (2008). Scale laboratory measurements of plunging breaker impact events are reported and compared with the previous full-scale tests. These tests extend the previous relationships to a wider range of surf-similarity parameters and indicate a continued reduction in impact pressure as the transition from plunging impacts to surging impacts is approached. Additional results from scale tests conducted on a smooth impermeable slope also indicate the presence of a maximum impact pressure within the plunging breaker region; however also suggest it may be necessary to include roughness and permeability in the parameterization of the impact pressure.

scholarly journals Impact of a Structure on Durability of Modified Nickel-Base Superalloys in Creep Conditions/ Wpływ Struktury Na Trwałość W Warunkach Pełzania Modyfikowanych Nadstopów Na Bazie Niklu

2014 ◽  
Vol 59 (4) ◽  
pp. 1559-1563 ◽  
Author(s):  
M. Ciesla ◽  
M. Manka ◽  
P. Gradon ◽  
F. Binczyk
Keyword(s):  
Creep Resistance ◽  
Morphological Structure ◽  
Aircraft Engine ◽  
Coarse Grained ◽  
Test Results ◽  
Cast State ◽  
Accelerated Creep ◽  
Nickel Base ◽  
The Impact ◽  
Modification Treatment

Abstract The study assesses the impact of surface and bulk modification and filtration during pouring on a durability under accelerated creep conditions of casts made of IN-713C and MAR-247 nickel superalloys scrap used for manufacturing of aircraft engine parts. The impact of solutionizing (1185°C/2 h) with subsequent ageing (870°C/20 h) on the creep resistance of a casting made from MAR-247 coarse-grained superalloy was also examined. Morphological structure parameters were determined with the use of Met-Ilo software. Macrostructure analysis of casts showed very significant impact of surface modification treatment. Creep test results clearly showed that coarse grained samples of IN-713C and MAR-247 superalloys have higher creep resistance. Moreover alloy MAR-247 had higher creep durability after heat treatment compared to as-cast state.

A mixed contact model for an immersed collision between two solid surfaces

2008 ◽  
Vol 366 (1873) ◽  
pp. 2205-2218 ◽  
Author(s):  
Fu-Ling Yang ◽  
Melany L Hunt
Keyword(s):  
Surface Deformation ◽  
Elastohydrodynamic Lubrication ◽  
Solid Particles ◽  
Solid Surfaces ◽  
Additional Energy ◽  
Collision Model ◽  
Dry Granular Flow ◽  
Wide Range ◽  
The Impact ◽  
Surrounding Liquid

Experimental evidence shows that the presence of an ambient liquid can greatly modify the collision process between two solid surfaces. Interactions between the solid surfaces and the surrounding liquid result in energy dissipation at the particle level, which leads to solid–liquid mixture rheology deviating from dry granular flow behaviour. The present work investigates how the surrounding liquid modifies the impact and rebound of solid spheres. Existing collision models use elastohydrodynamic lubrication (EHL) theory to address the surface deformation under the developing lubrication pressure, thereby coupling the motion of the liquid and solid. With EHL theory, idealized smooth particles are made to rebound from a lubrication film. Modified EHL models, however, allow particles to rebound from mutual contacts of surface asperities, assuming negligible liquid effects. In this work, a new contact mechanism, ‘mixed contact’, is formulated, which considers the interplay between the asperities and the interstitial liquid as part of a hybrid rebound scheme. A recovery factor is further proposed to characterize the additional energy loss due to asperity–liquid interactions. The resulting collision model is evaluated through comparisons with experimental data, exhibiting a better performance than the existing models. In addition to the three non-dimensional numbers that result from the EHL analysis—the wet coefficient of restitution, the particle Stokes number and the elasticity parameter—a fourth parameter is introduced to correlate particle impact momentum to the EHL deformation impulse. This generalized collision model covers a wide range of impact conditions and could be employed in numerical codes to simulate the bulk motion of solid particles with non-negligible liquid effects.

scholarly journals From genomes to systems: the path with yeast

2006 ◽  
Vol 361 (1467) ◽  
pp. 477-482 ◽  
Author(s):  
Stephen G Oliver
Keyword(s):  
Eukaryotic Cell ◽  
Metabolic Control Analysis ◽  
Coarse Grained ◽  
Control Analysis ◽  
Individual Gene ◽  
Metabolic Systems ◽  
Genes Encoding ◽  
Balance Analysis ◽  
Definition Of ◽  
The Impact

Metabolic Control Analysis (MCA) is a conceptual and mathematical formalism that models the relative contributions of individual effectors in a pathway to both the flux through the pathway and the concentrations of individual intermediates within it. To exploit MCA in an initial Systems Biology analysis of the eukaryotic cell, two categories of experiments are required. In category 1 experiments, flux is changed and the impact on the levels of the direct and indirect products of gene action is measured. We have measured the impact of changing the flux on the transcriptome, proteome and metabolome of Saccharomyces cerevisiae . In this whole-cell analysis, flux equates to growth rate. In category 2 experiments, the levels of individual gene products are altered, and the impact on the flux is measured. We have used competition analyses between the complete set of heterozygous yeast deletion mutants to reveal genes encoding proteins with high flux control coefficients. These genes may be exploited, in a top-down analysis, to build a coarse-grained model of the eukaryotic cell, as exemplified by yeast. More detailed modelling requires that ‘natural’ biological systems be identified. The combination of flux balance analysis with both genetics and metabolomics in the definition of metabolic systems is discussed.

High Performance CGM-based Parallel Algorithms for the Optimal Binary Search Tree Problem

2016 ◽  
Vol 8 (4) ◽  
pp. 55-77 ◽  
Author(s):  
Vianney Kengne Tchendji ◽  
Jean Frederic Myoupo ◽  
Gilles Dequen
Keyword(s):  
Parallel Algorithms ◽  
Execution Time ◽  
High Performance ◽  
Scheduling Algorithm ◽  
Search Tree ◽  
Binary Search ◽  
Coarse Grained ◽  
Binary Search Tree ◽  
Parameter Dependent ◽  
The Impact

In this paper, the authors highlight the existence of close relations between the execution time, efficiency and number of communication rounds in a family of CGM-based parallel algorithms for the optimal binary search tree problem (OBST). In this case, these three parameters cannot be simultaneously improved. The family of CGM (Coarse Grained Multicomputer) algorithms they derive is based on Knuth's sequential solution running in time and space, where n is the size of the problem. These CGM algorithms use p processors, each with local memory. In general, the authors show that each algorithms runs in with communications rounds. is the granularity of their model, and is a parameter that depends on and . The special case of yields a load-balanced CGM-based parallel algorithm with communication rounds and execution steps. Alternately, if , they obtain another algorithm with better execution time, say , the absence of any load-balancing and communication rounds, i.e., not better than the first algorithm. The authors show that the granularity has a crucial role in the different techniques they use to partition the problem to solve and study the impact of each scheduling algorithm. To the best of their knowledge, this is the first unified method to derive a set of parameter-dependent CGM-based parallel algorithms for the OBST problem.

Effects of Al, Si and N Content on the Formation of M-A Constituent and HAZ Toughness of Ti-Containing Low-Carbon Steel

2021 ◽  
Vol 1016 ◽  
pp. 42-49
Author(s):  
Kook Soo Bang ◽  
Joo Hyeon Cha ◽  
Kyu Tae Han ◽  
Hong Chul Jeong
Keyword(s):  
Carbon Steel ◽  
Impact Toughness ◽  
Low Carbon Steel ◽  
Charpy Impact ◽  
Coarse Grained ◽  
Low Carbon ◽  
N Content ◽  
Si Content ◽  
The Impact ◽  
Haz Toughness

The present work investigated the effects of Al, Si, and N content on the impact toughness of the coarse-grained heat-affected zone (CGHAZ) of Ti-containing low-carbon steel. Simulated CGHAZ of differing Al, Si, and N contents were prepared, and Charpy impact toughness was determined. The results were interpreted in terms of microstructure, especially martensite-austenite (M-A) constituent. All elements accelerated ferrite transformation in CGHAZ but at the same time increased the amount of M-A constituent, thereby deteriorating CGHAZ toughness. It is believed that Al, Si, and free N that is uncombined with Ti retard the decomposition of austenite into pearlite and increase the carbon content in the last transforming austenite, thus increasing the amount of M-A constituent. Regardless of the amount of ferrite in CGHAZ, its toughness decreased linearly with an increase of M-A constituent in this experiment, indicating that HAZ toughness is predominantly affected by the presence of M-A constituent. When a comparison of the effectiveness is made between Al and Si, it showed that a decrease in Si content is more effective in reducing M-A constituents.

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