Search results for "Computational Mathematic"

A minimal Gō-model for rebuilding whole genome structures from haploid single-cell Hi-C data

2020

Abstract We present a minimal computational model, which allows very fast, on-the-fly construction of three dimensional haploid interphase genomes from single-cell Hi-C contact maps using the HOOMD-blue molecular dynamics package on graphics processing units. Chromosomes are represented by a string of connected beads, each of which corresponds to 100,000 base pairs, and contacts are mediated via a structure-based harmonic potential. We suggest and test two minimization protocols which consistently fold into conformationally similar low energy states. The latter are similar to previously published structures but are calculated in a fraction of the time. We find evidence that mere fulfillment…

Matrix solutions of diffusion equation

2002

Numerical viscosity in simulations of the two-dimensional Kelvin-Helmholtz instability

2020

The Kelvin-Helmholtz instability serves as a simple, well-defined setup for assessing the accuracy of different numerical methods for solving the equations of hydrodynamics. We use it to extend our previous analysis of the convergence and the numerical dissipation in models of the propagation of waves and in the tearing-mode instability in magnetohydrodynamic models. To this end, we perform two-dimensional simulations with and without explicit physical viscosity at different resolutions. A comparison of the growth of the modes excited by our initial perturbations allows us to estimate the effective numerical viscosity of two spatial reconstruction schemes (fifth-order monotonicity preservin…

A multiscale approach to liquid flows in pipes I: The single pipe

2012

Abstract In the present paper we study the propagation of pressure waves in a barotropic flow through a pipe, with a possibly varying cross-sectional area. The basic model is the Saint–Venant system. We derive two multiscale models for the cases of weak and strong damping, respectively, which describe the time evolution of the piezometric head and the velocity. If the damping is weak, then the corresponding first-order hyperbolic system is linear but contains an additional integro-differential equation that takes into account the damping. In the case of strong damping, the system is nonlinear. The full and multiscale models are compared numerically; we also discuss results obtained by a lar…

Consistent probabilistic description of the neutral Kaon system

2013

The neutral Kaon system has both CF violation in the mass matrix and a non-vanishing lifetime difference in the width matrix. This leads to an effective Hamiltonian which is not a normal operator, with incompatible (non-commuting) masses and widths. In the Weisskopf-Wigner Approach (WWA), by diagonalizing the entire Hamiltonian, the unphysical non-orthogonal "stationary" states K-L,K-S are obtained. These states have complex eigenvalues whose real (imaginary) part does not coincide with the eigenvalues of the mass (width). matrix. In this work we describe the system as an open Lindblad-type quantum mechanical system due to Kaon decays. This approach, in terms of density matrices for initial…

Spatially Dependent Decoherence and Anomalous Diffussion of Quantum Walks

2013

We analyze the long time behavior of a discrete time quantum walk subject to decoherence with a strong spatial dependence, acting on one half of the lattice. We show that, except for limiting cases on the decoherence parameter, the quantum walk at late times behaves sub-ballistically, meaning that the characteristic features of the quantum walk are not completely spoiled. Contrarily to expectations, the asymptotic behavior is non Markovian, and depends on the amount of decoherence. This feature can be clearly shown on the long time value of the Generalized Chiral Distribution (GCD).

SIMPRE1.2: Considering the hyperfine and quadrupolar couplings and the nuclear spin bath decoherence

2016

SIMPRE is a fortran77code which uses an effective electrostatic model of point charges to predict the magnetic behavior of rare-earth-based mononuclear complexes. In this manuscript, we present SIMPRE1.2, which now takes into account two further phenomena.Firstly, SIMPRE now considers the hyperfine and quadrupolar interactions within the rare-earth ion, resulting in a more complete and realistic set of energy levels and wave functions. Secondly,and in order to widen SIMPRE’s predictive capabilities regarding potential molecular spin qubits, it now includes a routine that calculates an upper-bound estimate of the decoherence time considering only the dipolar coupling between the electron spi…

Extreme increase in atomic transition probability of the Cs D_2 line in strong magnetic fields under selective reflection

2016

Selective reflection of 852-nm laser radiation from the interface between cesium vapor and the sapphire window of a 30-micrometer-thick microcell was used to record an extreme increase in the probability of the Fg=3→Fe=5 transitions associated with the Cs-atom D2 lines in magnetic fields with inductions ranging from 300 to 3200 Gauss. We showed that a group of seven transitions Fg=3, mF=−3, −2, −1, 0, +1, +2, +3→Fe=5, mF=−2, −1, 0, +1, +2, +3, +4 was formed in accordance with the selection rules ΔmF=+1 for σ+-circularly-polarized radiation. These seven transitions have much higher probabilities in 500–1000 Gauss magnetic fields, with three of the transitions having probabilities higher than…

A numerical study of postshock oscillations in slowly moving shock waves

2003

Abstract Godunov-type methods and other shock capturing schemes can display pathological behavior in certain flow situations. This paper discusses the numerical anomaly associated to slowly moving shocks. We present a series of numerical experiments that illustrate the formation and propagation of this pathology, and allows us to establish some conclusions and question some previous conjectures for the source of the numerical noise. A simple diagnosis on an explicit Steger-Warming scheme shows that some intermediate states in the first time steps deviate from the true direction and contaminate the flow structure. A remedy is presented in the form of a new flux split method with an entropy i…

Elastodynamic behavior of mechanical cloaks designed by direct lattice transformations

2020

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