Search results for "Computer Simulation"
showing 10 items of 1054 documents
Measurement uncertainty estimation of a virtual instrument
2002
The law of uncertainty propagation is applied to a PC-based virtual instrument. According to the "guide to the expression of uncertainty in measurement", the measuring model and the various sources of uncertainty have been taken into account. The expressions of the combined output uncertainty in various basic digital signal processing blocks, are obtained starting from each input sample absolute accuracy, without taking into account the parameters which regard the overall behavior of an acquisition board, such as the effective number of bits. In order to verify this procedure, the results obtained by means of the theoretical analysis, are compared with the ones obtained from numerical simul…
Assessment of virtual instruments measurement uncertainty
2001
Abstract In this paper, two methods to evaluate the measurement uncertainty of a virtual instrument are presented: a numerical method simulating the physical process of the A/D conversion, and an approximated theoretical method applying the “uncertainty propagation law” of the “guide to the expression of uncertainty in measurement”. After a brief description of the features, the constitution and the working principle of the virtual instruments, the various uncertainty sources, are analyzed. With both methods, the combined standard uncertainty of the measurement result is obtained, starting from the standard uncertainty generated by each single source and without taking into account the para…
Efficient computation of root mean square deviations under rigid transformations
2013
The computation of root mean square deviations (RMSD) is an important step in many bioinformatics applications. If approached naively, each RMSD computation takes time linear in the number of atoms. In addition, a careful implementation is required to achieve numerical stability, which further increases runtimes. In practice, the structural variations under consideration are often induced by rigid transformations of the protein, or are at least dominated by a rigid component. In this work, we show how RMSD values resulting from rigid transformations can be computed in constant time from the protein's covariance matrix, which can be precomputed in linear time. As a typical application scenar…
Sequence Determines Degree of Knottedness in a Coarse-Grained Protein Model
2015
Knots are abundant in globular homopolymers but rare in globular proteins. To shed new light on this long-standing conundrum, we study the influence of sequence on the formation of knots in proteins under native conditions within the framework of the hydrophobic-polar (HP) lattice protein model. By employing large scale Wang-Landau simulations combined with suitable Monte Carlo trial moves we show that, even though knots are still abundant on average, sequence introduces large variability in the degree of self-entanglements. Moreover, we are able to design sequences which are either almost always or almost never knotted. Our findings serve as proof of concept that the introduction of just o…
Reconstructing the free-energy landscape of Met-enkephalin using dihedral principal component analysis and well-tempered metadynamics
2013
Well-Tempered Metadynamics (WTmetaD) is an efficient method to enhance the reconstruction of the free-energy surface of proteins. WTmetaD guarantees a faster convergence in the long time limit in comparison with the standard metadynamics. It still suffers however from the same limitation, i.e. the non trivial choice of pertinent collective variables (CVs). To circumvent this problem, we couple WTmetaD with a set of CVs generated from a dihedral Principal Component Analysis (dPCA) on the Ramachadran dihedral angles describing the backbone structure of the protein. The dPCA provides a generic method to extract relevant CVs built from internal coordinates. We illustrate the robustness of this …
Structures and folding pathways of topologically knotted proteins
2010
In the last decade, a new class of proteins has emerged that contain a topological knot in their backbone. Although these structures are rare, they nevertheless challenge our understanding of protein folding. In this review, we provide a short overview of topologically knotted proteins with an emphasis on newly discovered structures. We discuss the current knowledge in the field, including recent developments in both experimental and computational studies that have shed light on how these intricate structures fold.
Statistical properties of the site-frequency spectrum associated with lambda-coalescents.
2013
Abstract Statistical properties of the site-frequency spectrum associated with Λ-coalescents are our objects of study. In particular, we derive recursions for the expected value, variance, and covariance of the spectrum, extending earlier results of Fu (1995) for the classical Kingman coalescent. Estimating coalescent parameters introduced by certain Λ-coalescents for data sets too large for full-likelihood methods is our focus. The recursions for the expected values we obtain can be used to find the parameter values that give the best fit to the observed frequency spectrum. The expected values are also used to approximate the probability a (derived) mutation arises on a branch subtending a…
Computational fluid dynamics of the ascending aorta before the onset of type A aortic dissection.
2016
We performed a pre-dissection computational fluid analysis of an ascending aortic aneurysm associated with unicuspid aortic valve. The analysis showed an abnormal helical flow pattern inside the aneurysm and an increased wall stress on the right postero-lateral wall of the ascending aorta. These values were largely higher than the theoretical cut-off for aortic wall dissection, their topographic distribution followed the intimal tear site as subsequently diagnosed by computed tomography scan and confirmed during the operation for dissection repair.
Anatomic and flow dynamic considerations for safe right axillary artery cannulation.
2013
Objectives Neuroprotection is of paramount interest in cardiac surgery. Right axillary artery cannulation is well established in aortic surgery because it significantly improves survival and outcome, but malperfusion of the right brain after direct cannulation has been reported. Anatomically, 4 vessel segments are potentially amenable for cannulation of the subclavian and axillary arteries. Clinical studies vary widely in dissection sites and cannulation techniques. We investigated critical flow dynamics in the right brain caused by arterial inflow after direct cannulation and specified cannulation positions that provide optimal cerebral perfusion. Methods Distances from the lateral margin …
Prognostic scoring system predictive of survival after surgical resection of esophageal carcinoma.
2013
BACKGROUND The aim of our study was to develop a prognostic index score for patients undergoing surgical resection for esophageal cancer that accurately determines survival with specific clinicopathological characteristics. METHODS Clinical, histological, and demographical variables of 475 patients were entered in an univariate and multivariate regression model, followed by individual calculation of the Prognostic Indicator Score and model validation via simulation. RESULTS Significant variables included in the scoring system were number of positive lymph nodes, pT, pL, R, obesity, and American Society of Anesthesiologist classification. Survival probability and its associated hazard functi…