Search results for "COMPUTATION"
showing 10 items of 7362 documents
A quantum mechanics/molecular mechanics study of the acylation reaction of TEM1 β-lactamase and penicillanate
2000
The acylation step in β-lactamase catalyzed hydrolysis of β-lactams has been explored by means of a quantum mechanics/molecular mechanics approach (AM1/CHARMM). The TEM1 enzyme, a class A β-lactamase, and the penicillanate constitute the system employed in our study. The entire molecular system is divided into a quantum and a classical region: the quantum part is composed by the substrate, the serine Ser70 and the essential moieties of key active site residues, Lys73, Ser130 and Glu166, as well as a water molecule present in the active site region, while the classical part is formed by the remaining residues and structural waters of the enzyme. In particular, the sequence of steps proposed …
Customised next-generation sequencing multigene panel to screen a large cohort of individuals with chromatin-related disorder
2020
BackgroundThe regulation of the chromatin state by epigenetic mechanisms plays a central role in gene expression, cell function, and maintenance of cell identity. Hereditary disorders of chromatin regulation are a group of conditions caused by abnormalities of the various components of the epigenetic machinery, namely writers, erasers, readers, and chromatin remodelers. Although neurological dysfunction is almost ubiquitous in these disorders, the constellation of additional features characterizing many of these genes and the emerging clinical overlap among them indicate the existence of a community of syndromes. The introduction of high-throughput next generation sequencing (NGS) methods f…
NOseq: amplicon sequencing evaluation method for RNA m6A sites after chemical deamination
2020
Abstract Methods for the detection of m6A by RNA-Seq technologies are increasingly sought after. We here present NOseq, a method to detect m6A residues in defined amplicons by virtue of their resistance to chemical deamination, effected by nitrous acid. Partial deamination in NOseq affects all exocyclic amino groups present in nucleobases and thus also changes sequence information. The method uses a mapping algorithm specifically adapted to the sequence degeneration caused by deamination events. Thus, m6A sites with partial modification levels of ∼50% were detected in defined amplicons, and this threshold can be lowered to ∼10% by combination with m6A immunoprecipitation. NOseq faithfully d…
Numerical simulations demonstrate that the double tapering of the spatualae of lizards and insects maximize both detachment resistance and stability
2011
Many biological attachment devices of insects, spiders and geckos consist of arrays of hairs (setae), which are terminated by contact elements of different shapes. However, the most frequently observed shape is a thin plate-like spatula. In spite of a rather wide range of sizes, most spatulae of different animals are not uniform, but rather possess a gradient in thickness and width. Here we show that the spatulae of insects and geckos become gradually thinner and wider approaching the end. This geometrical effect is explained in the present paper, by using a numerical approach for the modelling of the van der Waals adhesion and friction between the contact elements and the substrate. The ap…
Quantum logic gates by adiabatic passage
2006
International audience; We present adiabatic passage techniques for the realisation of one and two-qubit quantum Gates. These methods use evolution along dark-states of the system, avoiding decoherence effects such as spontaneous emission. The advantage of these methods is their robustness: they are insensitive to the fluctuations of the parameters and to partial knowledge of the system.
Geometric factors in the adiabatic evolution of classical systems
1992
Abstract The adiabatic evolution of the classical time-dependent generalized harmonic oscillator in one dimension is analyzed in detail. In particular, we define the adiabatic approximation, obtain a new derivation of Hannay's angle requiring no averaging principle and point out the existence of a geometric factor accompanying changes in the adiabatic invariant.
A computational model of postprandial adipose tissue lipid metabolism derived using human arteriovenous stable isotope tracer data
2019
Given the association of disturbances in non-esterified fatty acid (NEFA) metabolism with the development of Type 2 Diabetes and Non-Alcoholic Fatty Liver Disease, computational models of glucose-insulin dynamics have been extended to account for the interplay with NEFA. In this study, we use arteriovenous measurement across the subcutaneous adipose tissue during a mixed meal challenge test to evaluate the performance and underlying assumptions of three existing models of adipose tissue metabolism and construct a new, refined model of adipose tissue metabolism. Our model introduces new terms, explicitly accounting for the conversion of glucose to glyceraldehye-3-phosphate, the postprandial …
Confined But-2-ene catalytic isomerization inside H-ZSM-5 models: A DFT study
2015
The isomerization of cis-but-2-ene to trans-but-2-ene within a 22T H-ZSM-5 zeolite model, also in the presence of two adsorbed Pd atoms, has been studied by DFT calculations. The results obtained allow us to state that the cis/trans but-2-ene isomerization can easily proceed inside unsupported zeolite cavities. In this case, differently than in the gas phase reaction, the trans-but-2-ene is less stable than the cis-but-2-ene, when adsorbed on the zeolite inner surface. Excluding the adsorption-desorption steps, the isomerization process involves two intermediates and three transition states, whose energy content is always very low with respect to that of reagents and intermediate species. T…
iGEMS: an integrated model for identification of alternative exon usage events.
2016
Abstract DNA microarrays and RNAseq are complementary methods for studying RNA molecules. Current computational methods to determine alternative exon usage (AEU) using such data require impractical visual inspection and still yield high false-positive rates. Integrated Gene and Exon Model of Splicing (iGEMS) adapts a gene-level residuals model with a gene size adjusted false discovery rate and exon-level analysis to circumvent these limitations. iGEMS was applied to two new DNA microarray datasets, including the high coverage Human Transcriptome Arrays 2.0 and performance was validated using RT-qPCR. First, AEU was studied in adipocytes treated with (n = 9) or without (n = 8) the anti-diabe…
Flexible switching of feedback control mechanisms allows for learning of different task dynamics.
2013
To produce skilled movements, the brain flexibly adapts to different task requirements and movement contexts. Two core abilities underlie this flexibility. First, depending on the task, the motor system must rapidly switch the way it produces motor commands and how it corrects movements online, i.e. it switches between different (feedback) control policies. Second, it must also adapt to environmental changes for different tasks separately. Here we show these two abilities are related. In a bimanual movement task, we show that participants can switch on a movement-by-movement basis between two feedback control policies, depending only on a static visual cue. When this cue indicates that the …