Search results for "Modelling and simulation"
showing 10 items of 97 documents
Reconstruction and analysis of genome-scale metabolic model of a photosynthetic bacterium
2010
Abstract Background Synechocystis sp. PCC6803 is a cyanobacterium considered as a candidate photo-biological production platform - an attractive cell factory capable of using CO2 and light as carbon and energy source, respectively. In order to enable efficient use of metabolic potential of Synechocystis sp. PCC6803, it is of importance to develop tools for uncovering stoichiometric and regulatory principles in the Synechocystis metabolic network. Results We report the most comprehensive metabolic model of Synechocystis sp. PCC6803 available, iSyn669, which includes 882 reactions, associated with 669 genes, and 790 metabolites. The model includes a detailed biomass equation which encompasses…
On the complete interface development of Al/Cu magnetic pulse welding via experimental characterizations and multiphysics numerical simulations
2021
Abstract A complex Al/Cu magnetic pulse welding interface is systematically investigated using experimental characterizations and numerical simulations. A Coupled electromagnetic-mechanical simulation is proposed to compute the impact velocity and impact angle along the entire interface. This model allows to further understand the formation mechanism of various interface characteristics during MPW. The results revealed that the impact velocity gradually decreases in conjunction with the gradual increase of the impact angle. These simulations elucidate the experimentally observed successive interface morphologies, i.e., the unwelded zone, vortex zone, intermediate (IM) layers and wavy interf…
SNVSniffer: an integrated caller for germline and somatic single-nucleotide and indel mutations
2016
Various approaches to calling single-nucleotide variants (SNVs) or insertion-or-deletion (indel) mutations have been developed based on next-generation sequencing (NGS). However, most of them are dedicated to a particular type of mutation, e.g. germline SNVs in normal cells, somatic SNVs in cancer/tumor cells, or indels only. In the literature, efficient and integrated callers for both germline and somatic SNVs/indels have not yet been extensively investigated. We present SNVSniffer, an efficient and integrated caller identifying both germline and somatic SNVs/indels from NGS data. In this algorithm, we propose the use of Bayesian probabilistic models to identify SNVs and investigate a mult…
Protein-protein interactions can be predicted using coiled coil co-evolution patterns
2016
AbstractProtein-protein interactions are sometimes mediated by coiled coil structures. The evolutionary conservation of interacting orthologs in different species, along with the presence or absence of coiled coils in them, may help in the prediction of interacting pairs. Here, we illustrate how the presence of coiled coils in a protein can be exploited as a potential indicator for its interaction with another protein with coiled coils. The prediction capability of our strategy improves when restricting our dataset to highly reliable, known protein-protein interactions. Our study of the co-evolution of coiled coils demonstrates that pairs of interacting proteins can be distinguished from no…
Identification of control targets in Boolean molecular network models via computational algebra
2015
Motivation: Many problems in biomedicine and other areas of the life sciences can be characterized as control problems, with the goal of finding strategies to change a disease or otherwise undesirable state of a biological system into another, more desirable, state through an intervention, such as a drug or other therapeutic treatment. The identification of such strategies is typically based on a mathematical model of the process to be altered through targeted control inputs. This paper focuses on processes at the molecular level that determine the state of an individual cell, involving signaling or gene regulation. The mathematical model type considered is that of Boolean networks. The pot…
A second strain gradient elasticity theory with second velocity gradient inertia – Part II: Dynamic behavior
2013
Abstract This paper is the sequel of a companion Part I paper devoted to the constitutive equations and to the quasi-static behavior of a second strain gradient material model with second velocity gradient inertia. In the present Part II paper, a multi-cell homogenization procedure (developed in the Part I paper) is applied to a nonhomogeneous body modelled as a simple material cell system, in conjunction with the principle of virtual work (PVW) for inertial actions (i.e. momenta and inertia forces), which at the macro-scale level takes on the typical format as for a second velocity gradient inertia material model. The latter (macro-scale) PVW is used to determine the equilibrium equations …
A gradient elasticity theory for second-grade materials and higher order inertia
2012
Abstract Second-grade elastic materials featured by a free energy depending on the strain and the strain gradient, and a kinetic energy depending on the velocity and the velocity gradient, are addressed. An inertial energy balance principle and a virtual work principle for inertial actions are envisioned to enrich the set of traditional theoretical tools of thermodynamics and continuum mechanics. The state variables include the body momentum and the surface momentum, related to the velocity in a nonstandard way, as well as the concomitant mass-accelerations and inertial forces, which do intervene into the motion equations and into the force boundary conditions. The boundary traction is the …
On the instability of an axially moving elastic plate
2010
Problems of stability of an axially moving elastic band travelling at constant velocity between two supports and experiencing small transverse vibrations are considered in a 2D formulation. The model of a thin elastic plate subjected to bending and tension is used to describe the bending moment and the distribution of membrane forces. The stability of the plate is investigated with the help of an analytical approach. In the frame of a general dynamic analysis, it is shown that the onset of instability takes place in the form of divergence (buckling). Then the static forms of instability are investigated, and critical regimes are studied as functions of geometric and mechanical problem param…
Solving gap metabolites and blocked reactions in genome-scale models: application to the metabolic network of Blattabacterium cuenoti
2013
Abstract Background Metabolic reconstruction is the computational-based process that aims to elucidate the network of metabolites interconnected through reactions catalyzed by activities assigned to one or more genes. Reconstructed models may contain inconsistencies that appear as gap metabolites and blocked reactions. Although automatic methods for solving this problem have been previously developed, there are many situations where manual curation is still needed. Results We introduce a general definition of gap metabolite that allows its detection in a straightforward manner. Moreover, a method for the detection of Unconnected Modules, defined as isolated sets of blocked reactions connect…
A generalized model of elastic foundation based on long-range interactions: Integral and fractional model
2009
The common models of elastic foundations are provided by supposing that they are composed by elastic columns with some interactions between them, such as contact forces that yield a differential equation involving gradients of the displacement field. In this paper, a new model of elastic foundation is proposed introducing into the constitutive equation of the foundation body forces depending on the relative vertical displacements and on a distance-decaying function ruling the amount of interactions. Different choices of the distance-decaying function correspond to different kind of interactions and foundation behavior. The use of an exponential distance-decaying function yields an integro-d…