Search results for "Simulation"
showing 10 items of 5095 documents
Ultrafast myoglobin structural dynamics observed with an X-ray free-electron laser.
2014
Light absorption can trigger biologically relevant protein conformational changes. The light-induced structural rearrangement at the level of a photoexcited chromophore is known to occur in the femtosecond timescale and is expected to propagate through the protein as a quake-like intramolecular motion. Here we report direct experimental evidence of such ‘proteinquake’ observed in myoglobin through femtosecond X-ray solution scattering measurements performed at the Linac Coherent Light Source X-ray free-electron laser. An ultrafast increase of myoglobin radius of gyration occurs within 1 picosecond and is followed by a delayed protein expansion. As the system approaches equilibrium it underg…
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…
Individual repeatability in timing and spatial flexibility of migration routes of trans-Saharan migratory raptors
2015
Satellite-tracking technology has allowed scientists to make a quantum leap in the field of migration ecology. Nowadays, the basic description of migratory routes of many species of birds has been reported. However, the investigation of bird migration at individual level (i.e. repeatability in migratory routes and timing) still remains seldom explored. Here, we investigated repeated migratory trips of a trans-Saharan endangered migratory raptor, the Egyptian Vulture Neophron percnopterus, tracked by GPS satellite telemetry. We compared between- and within-individual variation in migratory routes and timing in order to assess the degree of repeatability (or conversely, the flexibility) in mi…
Enchytraeid population dynamics: Resource limitation and size-dependent mortality
2009
Abstract Enchytraeids are regarded as keystone soil organisms in forest ecosystems. Their abundance and biomass fluctuate widely. Predicting the consequences of anthropogenic disturbances requires an understanding of the mechanisms underlying enchytraeid population dynamics. Here I develop a simple model, which predicts that the type of dynamics is controlled by resource input rate. If fungal resource input is a discrete event once a year, an exponential growth phase is followed by starvation and sharp decline of enchytraeid abundance. Model simulations with three different forcing functions were compared to field data. Initial parameter values were obtained from various independent sources…
Assessment of Granger causality by nonlinear model identification: application to short-term cardiovascular variability.
2007
A method for assessing Granger causal relationships in bivariate time series, based on nonlinear autoregressive (NAR) and nonlinear autoregressive exogenous (NARX) models is presented. The method evaluates bilateral interactions between two time series by quantifying the predictability improvement (PI) of the output time series when the dynamics associated with the input time series are included, i.e., moving from NAR to NARX prediction. The NARX model identification was performed by the optimal parameter search (OPS) algorithm, and its results were compared to the least-squares method to determine the most appropriate method to be used for experimental data. The statistical significance of…
Mutual nonlinear prediction of cardiovascular variability series: Comparison between exogenous and autoregressive exogenous models
2007
A model-based approach to perform mutual nonlinear prediction of short cardiovascular variability series is presented. The approach is based on identifying exogenous (X) and autoregressive exogenous (ARX) models by K-nearest neighbors local linear approximation, and estimates the predictability of a series given the other as the squared correlation between original and predicted values of the series. The method was first tested on simulations reproducing different types of interaction between non-identical Henon maps, and then applied to heart rate (HR) and blood pressure (BP) variability series measured in healthy subjects at rest and after head-up tilt. Simulations showed that different c…
Spin qubits with electrically gated polyoxometalate molecules
2007
Spin qubits offer one of the most promising routes to the implementation of quantum computers. Very recent results in semiconductor quantum dots show that electrically-controlled gating schemes are particularly well-suited for the realization of a universal set of quantum logical gates. Scalability to a larger number of qubits, however, remains an issue for such semiconductor quantum dots. In contrast, a chemical bottom-up approach allows one to produce identical units in which localized spins represent the qubits. Molecular magnetism has produced a wide range of systems with tailored properties, but molecules permitting electrical gating have been lacking. Here we propose to use the polyox…
Design and computer simulations of 2D MeX2 solid-state nanopores for DNA and protein detection analysis
2020
Solid-state nanopores (SSN) have emerged as versatile devices for biomolecule analysis. One of the most promising applications of SSN is DNA and protein sequencing, at a low cost and faster than the current standard methods. SSN sequencing is based on the measurement of ionic current variations when a biomolecule embedded in electrolyte is driven through a nanopore under an applied electric potential. As a biomolecule translocates through the nanopore, it occupies the pore volume and blocks the passage of ions. Hence, ultrafast monitoring of ionic flow during the passage of a biomolecule yields information about its structure and chemical properties. The size of the sensing region in SSN is…
Hybrid Quantum Mechanics/Molecular Mechanics Simulations with Two-Dimensional Interpolated Corrections: Application to Enzymatic Processes
2006
Hybrid quantum mechanics/molecular mechanics (QM/MM) techniques are widely used to study chemical reactions in large systems. Because of the computational cost associated with the high dimensionality of these systems, the quantum description is usually restricted to low-level methods, such as semiempirical Hamiltonians. In some cases, the description obtained at this computational level is quite poor and corrections must be considered. We here propose a simple but efficient way to include higher-level corrections to be used in potential energy surface explorations and in the calculation of potentials of mean force. We evaluate a correction energy term as the difference between a high-level …
Bicausative matrices to measure structural change: Are they a good tool?
1999
The causative-matrix method to analyze temporal change assumes that a matrix transforms one Markovian transition matrix into another by a left multiplication of the first matrix; the method is demand-driven when applied to input-output economics. An extension is presented without assuming the demand-driven or supply-driven hypothesis. Starting from two flow matrices X and Y, two diagonal matrices are searched, one premultiplying and the second postmultiplying X, to obtain a result the closer as possible to Y by least squares. The paper proves that the method is deceptive because the diagonal matrices are unidentified and the interpretation of results is unclear. Keywords : Input-Output ; Ch…