Search results for "QM"
showing 10 items of 284 documents
Congenital anomalies from a physics perspective. The key role of "manufacturing" volatility
2020
Genetic and environmental factors are traditionally seen as the sole causes of congenital anomalies. In this paper we introduce a third possible cause, namely random "manufacturing" discrepancies with respect to ``design'' values. A clear way to demonstrate the existence of this component is to ``shut'' the two others and to see whether or not there is remaining variability. Perfect clones raised under well controlled laboratory conditions fulfill the conditions for such a test. Carried out for four different species, the test reveals a variability remainder of the order of 10%-20% in terms of coefficient of variation. As an example, the CV of the volume of E.coli bacteria immediately after…
CeLL, an agent based model for exploring the spatial influence influence of climate change on Lobesia botrana population dynamics
2016
International audience; The European Grapevine moth (Lobesia botrana) is one of the most noxious vineyard-pests in the European and Mediterranean area. Its larvae feed on grapevine flowers and berries, and usually cause considerable damage, also by facilitating saphrophytic infections to berries.The biology of L. botrana has been investigated since the 80s. A number of studies has tested its physiology and behaviour in experimental conditions (Hurtrel et Thiéry 1999), in field conditions (Stockel et al. 1994), and using mathematical modelling techniques. Whereas the modelling approaches that have been proposed in the literature are hetereogeneus they generally focus on the phenology and pop…
Decoding sweet taste from chemical structures
2019
International audience
L'annuaire des Centres de Ressources Biologiques français
2011
International audience
The I3-CRB project and the French biological ressources centers
2010
International audience
Sesquiterpene volatile organic compounds (VOCs) are markers of elicitation by sulfated laminarine in grapevine
2015
SPE IPM UB CT1; International audience; Inducing resistance in plants by the application of elicitors of defense reactions is an attractive plant protection strategy, particularly for grapevine (Vitis vinifera), which is susceptible to severe fungal diseases. Although induced resistance (IR) can be successful under controlled conditions, in most cases, IR is not sufficiently effective for practical disease control under outdoor conditions. Progress in the application of IR requires a better understanding of grapevine defense mechanisms and the ability to monitor defense markers to identify factors, such as physiological and environmental factors, that can impact IR in the vineyard. Volatile…
The catalytic mechanism of glyceraldehyde 3-phosphate dehydrogenase from Trypanosoma cruzi elucidated via the QM/MM approach
2013
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) has been identified as a key enzyme involved in glycolysis processes for energy production in the Trypanosoma cruzi parasite. This enzyme catalyses the oxidative phosphorylation of glyceraldehyde 3-phosphate (G3P) in the presence of inorganic phosphate (Pi) and nicotinamide adenosine dinucleotide (NAD+). The catalytic mechanism used by GAPDH has been intensively investigated. However, the individual roles of Pi and the C3 phosphate of G3P (Ps) sites, as well as some residues such as His194 in the catalytic mechanism, remain unclear. In this study, we have employed Molecular Dynamics (MD) simulations within hybrid quantum mechanical/molecular …
Dehydrochlorination of Hexachlorocyclohexanes Catalyzed by the LinA Dehydrohalogenase. A QM/MM Study
2015
The elucidation of the catalytic role of LinA dehydrohalogenase in the degradation processes of hexachlorocyclohexane (HCH) isomers is extremely important to further studies on the bioremediation of HCH polluted areas. Herein, QM/MM free energy simulations are employed to provide the details of the dehydrochlorination reaction of two HCH isomers (γ and β). In particular, the role of the protonation state of one of the catalytic residues-His73-is explored. Based on our calculations, two distinct minimum free energy pathways (concerted and stepwise) were found for γ-HCH and β-HCH. The choice of the reaction channel for the dehydrochlorination reactions of γ- and β-HCH was shown to depend on t…
DNA nucleobase properties and photoreactivity: Modeling environmental effects
2009
Abstract The accurate ab initio quantum chemical (QM) method multiconfigurational second-order perturbation (CASSPT2)/complete active space self-consistent field (CASSCF) has been used in conjunction with molecular mechanics (MM) procedures to compute molecular properties and photoinduced reactivity of DNA/RNA nucleobases (NABs) in isolation and within a realistic environment, in which the double helix strand, the aqueous media, and the external counterions are included. It is illustrated that the use of an MM model is helpful both to account for short- and long-range effects of the system surrounding the QM molecular core and to provide the proper structural constraints that allow more acc…
Protein Flexibility and Preorganization in the Design of Enzymes. The Kemp Elimination Catalyzed by HG3.17
2015
A recently designed enzyme, HG3.17, obtained by directed evolution, has shown a catalytic activity close to natural enzymes. Hybrid QM/MM molecular dynamics simulations for the Kemp elimination in this new enzyme have provided a deep insight into the origin of its catalytic efficiency. In this case, we have first demonstrated the presence of different conformations with significantly different reactivity. The larger reactivity is related with a better electrostatic preorganization of the environment that creates a more favorable electrostatic potential for the reaction to proceed. In HG3.17, efforts to improve the catalytic properties must be focused in possible mutations increasing the pre…