Browse
Submit Data
Databases
API
Help

Dataset Information

20 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A direct Primitive Variable Recovery Scheme for hyperbolic conservative equations: The case of relativistic hydrodynamics.

ABSTRACT: In this article we develop a Primitive Variable Recovery Scheme (PVRS) to solve any system of coupled differential conservative equations. This method obtains directly the primitive variables applying the chain rule to the time term of the conservative equations. With this, a traditional finite volume method for the flux is applied in order avoid violation of both, the entropy and "Rankine-Hugoniot" jump conditions. The time evolution is then computed using a forward finite difference scheme. This numerical technique evades the recovery of the primitive vector by solving an algebraic system of equations as it is often used and so, it generalises standard techniques to solve these kind of coupled systems. The article is presented bearing in mind special relativistic hydrodynamic numerical schemes with an added pedagogical view in the appendix section in order to easily comprehend the PVRS. We present the convergence of the method for standard shock-tube problems of special relativistic hydrodynamics and a graphical visualisation of the errors using the fluctuations of the numerical values with respect to exact analytic solutions. The PVRS circumvents the sometimes arduous computation that arises from standard numerical methods techniques, which obtain the desired primitive vector solution through an algebraic polynomial of the charges.

SUBMITTER: Aguayo-Ortiz A

PROVIDER: S-EPMC5901931 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Grid-based Methods in Relativistic Hydrodynamics and Magnetohydrodynamics.

Project description:An overview of grid-based numerical methods used in relativistic hydrodynamics (RHD) and magnetohydrodynamics (RMHD) is presented. Special emphasis is put on a comprehensive review of the application of high-resolution shock-capturing methods. Results of a set of demanding test bench simulations obtained with different numerical methods are compared in an attempt to assess the present capabilities and limits of the various numerical strategies. Applications to three astrophysical phenomena are briefly discussed to motivate the need for and to demonstrate the success of RHD and RMHD simulations in their understanding. The review further provides FORTRAN programs to compute the exact solution of the Riemann problem in RMHD, and to simulate 1D RMHD flows in Cartesian coordinates.Electronic supplementary materialSupplementary material is available for this article at 10.1007/lrca-2015-3.

| S-EPMC6319500 | biostudies-literature

A closure scheme for chemical master equations.

Project description:Probability reigns in biology, with random molecular events dictating the fate of individual organisms, and propelling populations of species through evolution. In principle, the master probability equation provides the most complete model of probabilistic behavior in biomolecular networks. In practice, master equations describing complex reaction networks have remained unsolved for over 70 years. This practical challenge is a reason why master equations, for all their potential, have not inspired biological discovery. Herein, we present a closure scheme that solves the master probability equation of networks of chemical or biochemical reactions. We cast the master equation in terms of ordinary differential equations that describe the time evolution of probability distribution moments. We postulate that a finite number of moments capture all of the necessary information, and compute the probability distribution and higher-order moments by maximizing the information entropy of the system. An accurate order closure is selected, and the dynamic evolution of molecular populations is simulated. Comparison with kinetic Monte Carlo simulations, which merely sample the probability distribution, demonstrates this closure scheme is accurate for several small reaction networks. The importance of this result notwithstanding, a most striking finding is that the steady state of stochastic reaction networks can now be readily computed in a single-step calculation, without the need to simulate the evolution of the probability distribution in time.

| S-EPMC3761596 | biostudies-literature

Discrete phase space-continuous time relativistic Klein-Gordon and Dirac equations, and a new non-singular Yukawa potential.

Project description:This paper deals with the second quantization of interacting relativistic Fermionic and Bosonic fields in the arena of discrete phase space and continuous time. The mathematical formulation involves partial difference equations. The corresponding Feynman diagrams and a new [Formula: see text]-matrix theory is developed. In the special case of proton-proton Møller scattering via an exchange of a neutral meson, the explicit second order element [Formula: see text] is deduced. In the approximation of very low external three-momenta, a new Yukawa potential is explicitly derived from [Formula: see text]. Moreover, it is rigorously proved that this new Yukawa potential is divergence-free. The mass parameter of the exchanged meson may be set to zero to obtain a type of scalar Boson exchange between hypothetical Fermions. This provides a limiting case of a new Coulomb type potential directly from the new singularity free Yukawa potential. A divergence-free Coulomb potential between two Fermions at two discrete points is shown to be proportional to the Euler beta function. Within this relativistic discrete phase space continuous time, a single quanta is shown to occupy the hyper-tori [Formula: see text] where [Formula: see text] is a circle of radius [Formula: see text].

| S-EPMC10663489 | biostudies-literature

Mixing between chemically variable primitive basalts creates and modifies crystal cargoes.

Project description:Basaltic crystal cargoes often preserve records of mantle-derived chemical variability that have been erased from their carrier liquids by magma mixing. However, the consequences of mixing between similarly primitive but otherwise chemically variable magmas remain poorly understood despite ubiquitous evidence of chemical variability in primary melt compositions and mixing-induced disequilibrium within erupted crystal cargoes. Here we report observations from magma-magma reaction experiments performed on analogues of primitive Icelandic lavas derived from distinct mantle sources to determine how their crystal cargoes respond to mixing-induced chemical disequilibrium. Chemical variability in our experimental products is controlled dominantly by major element diffusion in the melt that alters phase equilibria and triggers plagioclase resorption within regions that were initially plagioclase saturated. Isothermal mixing between chemically variable basaltic magmas may therefore play important but previously underappreciated roles in creating and modifying crystal cargoes by unlocking plagioclase-rich mushes and driving resorption, (re-)crystallisation and solid-state diffusion.

| S-EPMC8448736 | biostudies-literature

A novel iterative scheme and its application to differential equations.

Project description:The purpose of this paper is to employ an alternative approach to reconstruct the standard variational iteration algorithm II proposed by He, including Lagrange multiplier, and to give a simpler formulation of Adomian decomposition and modified Adomian decomposition method in terms of newly proposed variational iteration method-II (VIM). Through careful investigation of the earlier variational iteration algorithm and Adomian decomposition method, we find unnecessary calculations for Lagrange multiplier and also repeated calculations involved in each iteration, respectively. Several examples are given to verify the reliability and efficiency of the method.

| S-EPMC3976783 | biostudies-other

A finite difference scheme for integrating the Takagi-Taupin equations on an arbitrary orthogonal grid.

Project description:Calculating dynamical diffraction patterns for X-ray diffraction imaging techniques requires numerical integration of the Takagi-Taupin equations. This is usually performed with a simple, second-order finite difference scheme on a sheared computational grid in which two of the axes are aligned with the wavevectors of the incident and scattered beams. This dictates, especially at low scattering angles, an oblique grid of uneven step sizes. Here a finite difference scheme is presented that carries out this integration in slab-shaped samples on an arbitrary orthogonal grid by implicitly utilizing Fourier interpolation. The scheme achieves the expected second-order convergence and a similar error to the traditional approach for similarly dense grids.

| S-EPMC9434601 | biostudies-literature

Self-recovery scheme for audio restoration using auditory masking.

Project description:Self-recovery schemes identify and restore tampering, using as a reference a compressed representation of a signal embedded into itself. In addition, audio self-recovery must comply with a transparency threshold, adequate for applications such as on-line music distribution or speech transmission. In this manuscript, an audio self-recovery scheme is proposed. Auditory masking properties of the signals are used to determine the frequencies that better mask the embedding distortion. Frequencies in the Fourier domain are mapped to the intDCT domain for embedding and extraction of reference bits for signal restoration. The contribution of this work is the use of auditory masking properties for the frequency selection and the mapping to the intDCT domain. Experimental results demonstrate that the proposed scheme satisfies a threshold of -2 ODG, suitable for audio applications. The efficacy of the scheme, in terms of its restoration capabilities, is also shown.

| S-EPMC6161912 | biostudies-literature

Impact of different renal function equations on direct oral anticoagulant concentrations.

Project description:The purpose of this study is to investigate the correlation between glomerular filtration rate (GFR) estimated by different renal function equations and non-vitamin K antagonist oral anticoagulant concentration. Atrial fibrillation patients who aged ≥ 20 years and used dabigatran, rivaroxaban, or apixaban for thromboembolism prevention were enrolled to collect blood samples and measure drug concentrations using ultra-high-performance liquid chromatography with tandem mass spectrometry. The GFR was estimated using the Cockroft-Gault formula (abbreviated as creatinine clearance, CrCL), Chronic Kidney Disease Epidemiology Collaboration formula (CKD-EPI) featuring both creatinine and cystatin C, and the Modification of Diet in Renal Disease Study equation (MDRD). Multivariate regression was used to investigate the associations of different renal function estimates with drug concentrations. A total of 511 participants were enrolled, including 146 dabigatran users, 164 rivaroxaban users and 201 apixaban users. Compared to clinical trials, 35.4% of dabigatran, 4.9% of rivaroxaban, and 5.5% of apixaban concentrations were higher than the expected range (p < 0.001). CKD-EPI and MDRD estimates classified fewer patients as having GFR < 50 mL/min than CrCL in all 3 groups. Both CrCL and CKD-EPI were associated with higher-than-expected ranges of dabigatran or rivaroxaban concentrations. Nevertheless, none of the renal function equations was associated with higher-than-expected apixaban concentrations. For participants aged ≥ 75 years, CKD-EPI may be associated with higher-than-expected trough concentration of dabigatran. In conclusion, CrCL and CKD-EPI both can be used to identify patients with high trough concentrations of dabigatran or rivaroxaban. Among elderly patients who used dabigatran, CKD-EPI may be associated with increased drug concentration.

| S-EPMC8668925 | biostudies-literature

Advantages of a conservative velocity interpolation (CVI) scheme for particle-in-cell methods with application in geodynamic modeling.

Project description:The particle-in-cell method is generally considered a flexible and robust method to model the geodynamic problems with chemical heterogeneity. However, velocity interpolation from grid points to particle locations is often performed without considering the divergence of the velocity field, which can lead to significant particle dispersion or clustering if those particles move through regions of strong velocity gradients. This may ultimately result in cells void of particles, which, if left untreated, may, in turn, lead to numerical inaccuracies. Here we apply a two-dimensional conservative velocity interpolation (CVI) scheme to steady state and time-dependent flow fields with strong velocity gradients (e.g., due to large local viscosity variation) and derive and apply the three-dimensional equivalent. We show that the introduction of CVI significantly reduces the dispersion and clustering of particles in both steady state and time-dependent flow problems and maintains a locally steady number of particles, without the need for ad hoc remedies such as very high initial particle densities or reseeding during the calculation. We illustrate that this method provides a significant improvement to particle distributions in common geodynamic modeling problems such as subduction zones or lithosphere-asthenosphere boundary dynamics.

| S-EPMC5089062 | biostudies-literature

UM171 Enhances Lentiviral Gene Transfer and Recovery of Primitive Human Hematopoietic Cells.

Project description:Enhanced gene transfer efficiencies and higher yields of transplantable transduced human hematopoietic stem cells are continuing goals for improving clinical protocols that use stemcell-based gene therapies. Here, we examined the effect of the HSC agonist UM171 on these endpoints in both in vitro and in vivo systems. Using a 22-hr transduction protocol, we found that UM171 significantly enhances both the lentivirus-mediated transduction and yield of CD34+ and CD34+CD45RA- hematopoietic cells from human cord blood to give a 6-fold overall higher recovery of transduced hematopoietic stem cells, including cells with long-term lympho-myeloid repopulating activity in immunodeficient mice. The ability of UM171 to enhance gene transfer to primitive cord blood hematopoietic cells extended to multiple lentiviral pseudotypes, gamma retroviruses, and non-integrating lentiviruses and to adult bone marrow cells. UM171, thus, provides an interesting reagent for improving the ex vivo production of gene-modified cells and for reducing requirements of virus for a broad range of applications.

| S-EPMC6077133 | biostudies-other

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data