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Nelander et al. made a model that derives network models from molecular profiles of perturbed cellular systems [ 12].
The models from molecular replacement were used as the starting points for several rounds of model building with COOT and refinement with PHENIX.
The BEAST software package is an ambitious attempt to provide a general framework for parameter estimation and hypothesis testing of evolutionary models from molecular sequence data.
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A multiscale modeling framework with a damage model developed from molecular dynamics simulation, is employed to study the physical mechanisms of damage initiation and propagation in CNT nanocomposites at the sub-microscale.
The discussion of recent results from animal models and from molecular studies emphasized the need for an earlier and better exchange between basic research and clinical challenges of pediatrics to promote the translation of experimental results to patient care (and back) which was also recently promoted, i.e., by the scientific journal of the European Respiratory Society [3].
The effective number of breeding eels NBGe* derived through the model from molecular-based measures of genetic differentiation (FSC) corresponds to virtually infinite combinations of male and female silver eels in varying sex ratios, according to eqn (4).
An accurate numerical model obtained from molecular dynamics simulation was used to explain the experimental results.
A second is a project which is building an in silico model of the human liver, tieing together models from the molecular level to the liver.
With this approach we have thus successfully combined a detailed microscopic model built from molecular biological data and a systems biological parameter optimization by comparing the completely assembled system to macroscopic experimental observations.
The structural model of AFAL obtained from molecular modeling was used to test the binding to different carbohydrate compounds and to estimate possible binding sites of the sugar and other ligands.
In the first example we show how an established model from the molecular systems biology literature is simulated in URDME.
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