Search results for "Computer simulation"
showing 10 items of 1054 documents
Molecular interaction of artemisinin with translationally controlled tumor protein (TCTP) of Plasmodium falciparum
2012
Malaria causes millions of death cases per year. Since Plasmodium falciparum rapidly develops drug resistance, it is of high importance to investigate potential drug targets which may lead to novel rational therapy approaches. Here we report on the interaction of translationally controlled tumor protein of P. falciparum (PfTCTP) with the anti-malarial drug artemisinin. Furthermore, we investigated the crystal structure of PfTCTP. Using mass spectrometry, bioinformatic approaches and surface plasmon resonance spectroscopy, we identified novel binding sites of artemisinin which are in direct neighborhood to amino acids 19-46, 108-134 and 140-163. The regions covered by these residues are know…
Inferring slowly-changing dynamic gene-regulatory networks
2015
Dynamic gene-regulatory networks are complex since the interaction patterns between their components mean that it is impossible to study parts of the network in separation. This holistic character of gene-regulatory networks poses a real challenge to any type of modelling. Graphical models are a class of models that connect the network with a conditional independence relationships between random variables. By interpreting these random variables as gene activities and the conditional independence relationships as functional non-relatedness, graphical models have been used to describe gene-regulatory networks. Whereas the literature has been focused on static networks, most time-course experi…
Hub-Centered Gene Network Reconstruction Using Automatic Relevance Determination
2012
Network inference deals with the reconstruction of biological networks from experimental data. A variety of different reverse engineering techniques are available; they differ in the underlying assumptions and mathematical models used. One common problem for all approaches stems from the complexity of the task, due to the combinatorial explosion of different network topologies for increasing network size. To handle this problem, constraints are frequently used, for example on the node degree, number of edges, or constraints on regulation functions between network components. We propose to exploit topological considerations in the inference of gene regulatory networks. Such systems are often…
Simulator for a Natural Gas Storage Realised in Depleted Deposit
2014
The present paper presents the implementation of a numerical model for a natural storage transformed into a deposit which takes into consideration the geometry of the storage, the properties of the rocks and in which the movements of the gases can be described. The model is two-dimensional nonstationary and allows the dynamic simulation of the processes of injection and extraction. The location of the wells and their flows can be thus studied and optimized to maximize the amount of the stored gases. The presented model allows the quick finding of solutions for a whole cycle of storage in a short time so that it could be used successfully in the operation process.
Analytical properties of horizontal visibility graphs in the Feigenbaum scenario
2012
Time series are proficiently converted into graphs via the horizontal visibility (HV) algorithm, which prompts interest in its capability for capturing the nature of different classes of series in a network context. We have recently shown [1] that dynamical systems can be studied from a novel perspective via the use of this method. Specifically, the period-doubling and band-splitting attractor cascades that characterize unimodal maps transform into families of graphs that turn out to be independent of map nonlinearity or other particulars. Here we provide an in depth description of the HV treatment of the Feigenbaum scenario, together with analytical derivations that relate to the degree di…
Conditions for the spread of conspicuous warning signals: A numerical model with novel insights
2007
The initial evolution of conspicuous warning signals presents an evolutionary problem because selection against rare conspicuous signals is presumed to be strong, and new signals are rare when they first arise. Several possible solutions have been offered to solve this apparent evolutionary paradox, but disagreement persists over the plausibility of some of the proposed mechanisms. In this paper, we construct a deterministic numerical simulation model that allows us to derive the strength of selection on novel warning signals in a wide range of biologically relevant situations. We study the effects of predator psychology (learning, rate of mistaken attacks, and neophobia) on selection. We a…
A numerical model of the cloud-topped planetary boundary-layer: influence of the physico-chemical properties of aerosol particles on the effective ra…
2000
The present investigation deals with the impact of different aeorosol types on the value of the effective radius of stratiform clouds. In several numerical sensitivity studies with the microphysical stratus model MISTRA, the aerosol composition was linearly changed from pure maritime to pure rural aerosol particles. Numerical results show that in environments with pure maritime aerosols, the effective radius is usually much larger than in continental regions. Values of the effective radius are also time-dependent with minima and maxima during day and night, respectively. In precipitating clouds, the effective radius might achieve values larger than 30 μm. In continental regions, the effecti…
New approach to characterisation of electric alloys under rotating magnetic flux density
1996
The computation of electrical machines using the characterisation of electric alloys proposed by several authors gives performances not verified by experiments on actual machines. By means of finite-element-method software, the authors show that the electromagnetic context where electrical alloys are built into rotating electrical machines is completely different from the actual characterisation system. A new testing device is proposed to take into account the phenomena highlighted.
Experimental investigation of low-frequency pulsed Lorentz force influence on the motion of Galinstan melt
2016
Abstract The paper presents the results of the numerical and physical experiments, aimed at assessing the influence of pulsed force of electromagnetic field on the melt motion and the fluid velocities. The experiment was performed on the eutectic alloy Galinstan in the cylindrical volume, where an ultrasonic Doppler velocimeter was employed for velocity measurements under conditions of pulsed and steady EM field application. A numerical simulation of the melt flow, forced by the steady EM force, involved a 2D axisymmetric model. The k-e turbulence model was used to obtain the information about the melt velocities. The verification of the numerical model was carried out for the steady case. …
Numerical model of turbulent CZ melt flow in the presence of AC and CUSP magnetic fields and its verification in a laboratory facility
2001
The paper describes a numerical simulation tool for heat and mass transfer processes in large diameter CZ crucibles under the influence of several non-rotating AC and CUSP magnetic fields. Such fields are expected to provide an additional means to influence the melt behaviour, particularly in the industrial growth of large diameter silicon crystals. The simulation tool is based on axisymmetric 2D models for the AC and CUSP magnetic fields in the whole CZ facility and turbulent hydrodynamics, temperature and mass transport in the melt under the influence of the electromagnetic fields. The simulation tool is verified by comparisons to experimental results from a laboratory CZ setup with eutec…