scholarly journals Promiscuous esterases counterintuitively are less flexible than specific ones

2020 ◽  
Author(s):  
Christina Nutschel ◽  
Cristina Coscolín ◽  
Daniel Mulnaes ◽  
Benoit David ◽  
Manuel Ferrer ◽  
...  
Keyword(s):  
Structural Dynamics ◽  
Sequence Space ◽  
Specific Activity ◽  
Experimental Information ◽  
Point Of View ◽  
Structural Flexibility ◽  
Computationally Efficient ◽  
Application Point ◽  
Substrate Promiscuity ◽  
Molecular Origin

AbstractUnderstanding mechanisms of promiscuity is increasingly important from a fundamental and application point of view. As to enzyme structural dynamics, more promiscuous enzymes generally have been recognized to also be more flexible. However, examples for the opposite received much less attention. Here, we exploit comprehensive experimental information on the substrate promiscuity of 147 esterases tested against 96 esters together with computationally efficient rigidity analyses to understand the molecular origin of the observed promiscuity range. Unexpectedly, our data reveal that promiscuous esterases are significantly less flexible than specific ones, are significantly more thermostable, and have a significantly increased specific activity. These results may be reconciled with a model according to which structural flexibility in the case of specific esterases serves for conformational proofreading. Our results signify that esterase sequence space can be screened by rigidity analyses for promiscuous esterases as starting points for further exploration in biotechnology and synthetic chemistry.

scholarly journals Multiple Haplotype Reconstruction from Allele Frequency Data

2020 ◽  
Author(s):  
Marta Pelizzola ◽  
Merle Behr ◽  
Housen Li ◽  
Axel Munk ◽  
Andreas Futschik
Keyword(s):  
Allele Frequency ◽  
Real Data ◽  
Coefficient Matrix ◽  
Point Of View ◽  
Design Matrix ◽  
Frequency Data ◽  
Computationally Efficient ◽  
Regression Problem ◽  
Allele Frequency Data ◽  
Multiple Samples

AbstractSince haplotype information is of widespread interest in biomedical applications, effort has been put into their reconstruction. Here, we propose a new, computationally efficient method, called haploSep, that is able to accurately infer major haplotypes and their frequencies just from multiple samples of allele frequency data. Our approach seems to be the first that is able to estimate more than one haplotype given such data. Even the accuracy of experimentally obtained allele frequencies can be improved by re-estimating them from our reconstructed haplotypes. From a methodological point of view, we model our problem as a multivariate regression problem where both the design matrix and the coefficient matrix are unknown. The design matrix, with 0/1 entries, models haplotypes and the columns of the coefficient matrix represent the frequencies of haplotypes, which are non-negative and sum up to one. We illustrate our method on simulated and real data focusing on experimental evolution and microbial data.

Rough Sets and Approximate Reasoning

2014 ◽  
pp. 180-228 ◽  
Author(s):  
B. K. Tripathy
Keyword(s):  
Fuzzy Logic ◽  
Fuzzy Sets ◽  
Rough Sets ◽  
Intuitionistic Fuzzy Sets ◽  
Point Of View ◽  
Approximate Reasoning ◽  
Human Reasoning ◽  
Intuitionistic Fuzzy ◽  
Application Point ◽  
Future Work

Several models have been introduced to capture impreciseness in data. Fuzzy sets introduced by Zadeh and Rough sets introduced by Pawlak are two of the most popular such models. In addition, the notion of intuitionistic fuzzy sets introduced by Atanassov and the hybrid models obtained thereof have been very fruitful from the application point of view. The introduction of fuzzy logic and the approximate reasoning obtained through it are more realistic as they are closer to human reasoning. Equality of sets in crisp mathematics is too restricted from the application point of view. Therefore, extending these concepts, three types of approximate equalities were introduced by Novotny and Pawlak using rough sets. These notions were found to be restrictive in the sense that they again boil down to equality of sets and also the lower approximate equality is artificial. Keeping these points in view, three other types of approximate equalities were introduced by Tripathy in several papers. These approximate equalities were further generalised to cover the approximate equalities of fuzzy sets and intuitionistic fuzzy sets by him. In addition, considering the generalisations of basic rough sets like the covering-based rough sets and multigranular rough sets, the study has been carried out further. In this chapter, the authors provide a comprehensive study of all these forms of approximate equalities and illustrate their applicability through several examples. In addition, they provide some problems for future work.

scholarly journals Implicit max-stable extremal integrals

Extremes ◽  
2020 ◽  
Author(s):  
D. Kremer
Keyword(s):  
Loss Function ◽  
Open Problem ◽  
Stochastic Integral ◽  
Extreme Values ◽  
Stable Distributions ◽  
Extreme Value ◽  
Point Of View ◽  
Extreme Value Distributions ◽  
Application Point ◽  
Deterministic Function

Abstract Recently, the notion of implicit extreme value distributions has been established, which is based on a given loss function f ≥ 0. From an application point of view, one is rather interested in extreme loss events that occur relative to f than in the corresponding extreme values itself. In this context, so-called f -implicit α-Fréchet max-stable distributions arise and have been used to construct independently scattered sup-measures that possess such margins. In this paper we solve an open problem in Goldbach (2016) by developing a stochastic integral of a deterministic function g ≥ 0 with respect to implicit max-stable sup-measures. The resulting theory covers the construction of max-stable extremal integrals (see Stoev and Taqqu Extremes 8, 237–266 (2005)) and, at the same time, reveals striking parallels.

Positron Lifetime Calculation for Plastic Deformed Nanocrystalline Copper

2017 ◽  
Vol 373 ◽  
pp. 31-34
Author(s):  
Kai Zhou ◽  
Ting Zhang
Keyword(s):  
Positron Annihilation ◽  
Deformation Mechanism ◽  
Positron Lifetime ◽  
Experimental Information ◽  
Point Of View ◽  
Nanocrystalline Copper ◽  
Mean Grain Size ◽  
Positron Lifetimes ◽  
Boundary Deformation

Positron lifetime calculation has been performed on a computer-generated nanocrystalline copper with a mean grain size of 9.1 nm during its deformation. For the undeformed and deformed nanocrystalline copper, calculated positron lifetimes are around 157 ps which come from the positron annihilation in the free volume in grain boundaries. Due to the grain-boundary deformation mechanism, no vacancies or vacancy clusters will be induced in grains during the plastic deformation of the nanocrystalline copper, which is different to the deformation of the conventional polycrystal. From this point of view, in-situ positron annihilation measurements can provide important experimental information on the deformation mechanism of nanocrystalline metals.

Modeling of Combustor and Turbine Vane Interaction

2019 ◽  
Author(s):  
Ishan Verma ◽  
Laith Zori ◽  
Jaydeep Basani ◽  
Samir Rida
Keyword(s):  
Swirling Flow ◽  
Guide Vane ◽  
Primary Objective ◽  
Point Of View ◽  
Computationally Efficient ◽  
Joint Simulation ◽  
Chemically Reacting ◽  
Combined Simulation ◽  
Aero Engines ◽  
Nozzle Guide

Abstract Modern aero-engines are characterized by compact components (fan, compressor, combustor, and turbine). Such proximity creates a complex interaction between the components and poses a modeling challenge due to the difficulties in identifying a clear interface between components since they are usually modeled separately. From a numerical point of view, the simulation of a complex compact aero-engine system requires interaction between these individual components, especially the combustor-turbine interaction. The combustor is characterized by a subsonic chemically reacting and swirling flow while the high-pressure turbine (HPT) stage has flow which is transonic. Furthermore, the simulation of combustor-turbine interactions is more challenging due to aggressive flow conditions such as non-uniform temperature, non-uniform total-pressure, strong swirl, and high turbulence intensity. The simulation of aero-engines, where combustor-turbine interactions are important, requires a methodology that can be used in a real engine framework while ensuring numerical requirements of accuracy and stability. Conventionally, such a simulation is carried out using one of the two approaches: a combined simulation (or joint-simulation) of the combustor and the HPT geometries, or a co-simulation between the combustor and the turbine with the exchange of boundary conditions between these two separate domains. The primary objective of this paper is to assess the effectiveness of the joint simulation versus the co-simulation and propose a more practical approach for modeling combustor and turbine interactions. First, a detailed grid independence study with hexahedral and polyhedral meshes is performed to select the required polyhedral mesh. Then, an optimal location of the interface between the combustor and the nozzle guide vane (NGV) is identified. Co-simulations are then performed by exchanging information between the combustor and the NGV at the interface, wherein the combustor is solved using LES while the NGV is solved using RANS. The joint combustor-NGV simulations are solved using LES. The effect of the combustor-NGV interaction on the flow field and hot streak migration is analyzed. The results suggest that the joint simulation is computationally efficient and more accurate since both components are modelled together.

Channeling in 4H-SiC from an Application Point of View

2019 ◽  
Vol 963 ◽  
pp. 386-389 ◽  
Author(s):  
Peter Pichler ◽  
Tomasz Sledziewski ◽  
Volker Häublein ◽  
Anton Bauer ◽  
Tobias Erlbacher
Keyword(s):  
Monte Carlo ◽  
Ion Implantation ◽  
Monte Carlo Simulations ◽  
Electronic Devices ◽  
Point Of View ◽  
Power Electronic ◽  
Application Point ◽  
Doping Profiles

During ion implantation into monocrystalline semiconductors, some of the implanted atoms will be deflected to crystal directions along which they may penetrate deeply into the crystal. We investigate such channeling effects for Al and N implantation into 4H-SiC by Monte Carlo simulations. The focus of the work is on the effects of channeling on doping profiles, the relevance for the net doping of typical power electronic devices, and the influence of scattering oxides.

scholarly journals Growth, Optical and Dielectric Studies on Pure and L-Lysine Doped KDP Crystals

2012 ◽  
Vol 2012 ◽  
pp. 1-6 ◽  
Author(s):  
N. Kanagathara ◽  
G. Anbalagan
Keyword(s):  
Dielectric Constant ◽  
Dielectric Loss ◽  
Single Crystals ◽  
Visible Region ◽  
Point Of View ◽  
Dielectric Study ◽  
Dielectric Studies ◽  
Slow Evaporation ◽  
Application Point ◽  
Kdp Crystals

Optically good quality single crystals of pure and L-lysine monohydrochloride-doped KDP crystals have been grown by a slow evaporation method. The grown crystals have been subjected to optical and dielectric studies. The UV-Vis spectrum shows the transmitting ability of the crystals in the entire visible region and transmittance percentage is increased for the doped KDP crystals. From the dielectric study, it is found that the dielectric constant and the dielectric loss of L-lysine-doped KDP crystals were lower than the pure KDP crystals. Hence L-lysine-doped KDP crystals are found to be more beneficial from an application point of view as compared to pure KDP crystals.

How Can Sol-Gel Contribute to Optical Devices?

2008 ◽  
Vol 391 ◽  
pp. 97-107 ◽  
Author(s):  
Marcos Zayat ◽  
David Levy
Keyword(s):  
Specific Activity ◽  
Sol Gel ◽  
Point Of View ◽  
Synthetic Methods ◽  
External Signal ◽  
Strong Argument ◽  
Scientific Instrumentation ◽  
Wide Range ◽  
Critical Components ◽  
High Flexibility

We emphasize in this chapter the Sol-Gel chemistry, which has gained a large number of researchers, developing interesting and sophisticated novel synthetic methods, offering a variety of approaches to new systems preparation, overcoming many of the synthetic difficulties of the past. A strong argument for using the Sol-Gel chemistry is found in the high flexibility of the method and the large choice of commercially available “dopants” that can be incorporated in the solid matrices, that might have a specific activity or reactivity to an external signal (i.e. light, magnetic, electrical, etc). From the point of view of nanotechnology applications, Sol-Gel materials are being required for critical components embedded in systems such as industrial equipment and scientific instrumentation, imaging and display, medical applications, aerospace and defense, etc. The rapidly developing sol-gel process has been used for the preparation of materials for a wide range of fields, adapting the chemistry and the novel synthetic routes to the specific systems, in order to achieve complicated developments oriented to nanotechnology applications. Clear examples can be found on Sol-Gel optics applications.

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