5,499 research outputs found
Excitation energies from density functional perturbation theory
We consider two perturbative schemes to calculate excitation energies, each
employing the Kohn-Sham Hamiltonian as the unperturbed system. Using accurate
exchange-correlation potentials generated from essentially exact densities and
their exchange components determined by a recently proposed method, we evaluate
energy differences between the ground state and excited states in first-order
perturbation theory for the Helium, ionized Lithium and Beryllium atoms. It was
recently observed that the zeroth-order excitations energies, simply given by
the difference of the Kohn-Sham eigenvalues, almost always lie between the
singlet and triplet experimental excitations energies, corrected for
relativistic and finite nuclear mass effects. The first-order corrections
provide about a factor of two improvement in one of the perturbative schemes
but not in the other. The excitation energies within perturbation theory are
compared to the excitations obtained within SCF and time-dependent
density functional theory. We also calculate the excitation energies in
perturbation theory using approximate functionals such as the local density
approximation and the optimized effective potential method with and without the
Colle-Salvetti correlation contribution
On optimality of kernels for approximate Bayesian computation using sequential Monte Carlo
Approximate Bayesian computation (ABC) has gained popularity over the past few years for the analysis of complex models arising in population genetics, epidemiology and system biology. Sequential Monte Carlo (SMC) approaches have become work-horses in ABC. Here we discuss how to construct the perturbation kernels that are required in ABC SMC approaches, in order to construct a sequence of distributions that start out from a suitably defined prior and converge towards the unknown posterior. We derive optimality criteria for different kernels, which are based on the Kullback-Leibler divergence between a distribution and the distribution of the perturbed particles. We will show that for many complicated posterior distributions, locally adapted kernels tend to show the best performance. We find that the added moderate cost of adapting kernel functions is easily regained in terms of the higher acceptance rate. We demonstrate the computational efficiency gains in a range of toy examples which illustrate some of the challenges faced in real-world applications of ABC, before turning to two demanding parameter inference problems in molecular biology, which highlight the huge increases in efficiency that can be gained from choice of optimal kernels. We conclude with a general discussion of the rational choice of perturbation kernels in ABC SMC settings
Scalable Bayesian nonparametric measures for exploring pairwise dependence via Dirichlet Process Mixtures
In this article we propose novel Bayesian nonparametric methods using
Dirichlet Process Mixture (DPM) models for detecting pairwise dependence
between random variables while accounting for uncertainty in the form of the
underlying distributions. A key criteria is that the procedures should scale to
large data sets. In this regard we find that the formal calculation of the
Bayes factor for a dependent-vs.-independent DPM joint probability measure is
not feasible computationally. To address this we present Bayesian diagnostic
measures for characterising evidence against a "null model" of pairwise
independence. In simulation studies, as well as for a real data analysis, we
show that our approach provides a useful tool for the exploratory nonparametric
Bayesian analysis of large multivariate data sets
Energy and variance optimization of many body wave functions
We present a simple, robust and efficient method for varying the parameters
in a many-body wave function to optimize the expectation value of the energy.
The effectiveness of the method is demonstrated by optimizing the parameters in
flexible Jastrow factors, that include 3-body electron-electron-nucleus
correlation terms, for the NO and decapentaene (CH)
molecules. The basic idea is to add terms to the straightforward expression for
the Hessian that are zero when the integrals are performed exactly, but that
cancel much of the statistical fluctuations for a finite Monte Carlo sample.
The method is compared to what is currently the most popular method for
optimizing many-body wave functions, namely minimization of the variance of the
local energy. The most efficient wave function is obtained by optimizing a
linear combination of the energy and the variance.Comment: 4 pages, 4 figures, minor corrections of inexact statements, missing
Alleviation of the Fermion-sign problem by optimization of many-body wave functions
We present a simple, robust and highly efficient method for optimizing all
parameters of many-body wave functions in quantum Monte Carlo calculations,
applicable to continuum systems and lattice models. Based on a strong
zero-variance principle, diagonalization of the Hamiltonian matrix in the space
spanned by the wav e function and its derivatives determines the optimal
parameters. It systematically reduces the fixed-node error, as demonstrated by
the calculation of the binding energy of the small but challenging C
molecule to the experimental accuracy of 0.02 eV
Competing mechanisms of stress-assisted diffusivity and stretch-activated currents in cardiac electromechanics
We numerically investigate the role of mechanical stress in modifying the
conductivity properties of the cardiac tissue and its impact in computational
models for cardiac electromechanics. We follow a theoretical framework recently
proposed in [Cherubini, Filippi, Gizzi, Ruiz-Baier, JTB 2017], in the context
of general reaction-diffusion-mechanics systems using multiphysics continuum
mechanics and finite elasticity. In the present study, the adapted models are
compared against preliminary experimental data of pig right ventricle
fluorescence optical mapping. These data contribute to the characterization of
the observed inhomogeneity and anisotropy properties that result from
mechanical deformation. Our novel approach simultaneously incorporates two
mechanisms for mechano-electric feedback (MEF): stretch-activated currents
(SAC) and stress-assisted diffusion (SAD); and we also identify their influence
into the nonlinear spatiotemporal dynamics. It is found that i) only specific
combinations of the two MEF effects allow proper conduction velocity
measurement; ii) expected heterogeneities and anisotropies are obtained via the
novel stress-assisted diffusion mechanisms; iii) spiral wave meandering and
drifting is highly mediated by the applied mechanical loading. We provide an
analysis of the intrinsic structure of the nonlinear coupling using
computational tests, conducted using a finite element method. In particular, we
compare static and dynamic deformation regimes in the onset of cardiac
arrhythmias and address other potential biomedical applications
CO2 laser ranging systems study
The conceptual design and error performance of a CO2 laser ranging system are analyzed. Ranging signal and subsystem processing alternatives are identified, and their comprehensive evaluation yields preferred candidate solutions which are analyzed to derive range and range rate error contributions. The performance results are presented in the form of extensive tables and figures which identify the ranging accuracy compromises as a function of the key system design parameters and subsystem performance indexes. The ranging errors obtained are noted to be within the high accuracy requirements of existing NASA/GSFC missions with a proper system design
Early assessment of vestibular function after unilateral cochlear implant surgery
Introduction : Cochlear implantation (CI) has been reported to negatively effect on the vestibular function. The study of the vestibular function has variably been conducted by different types of diagnostic tools. The combined use of modern, rapidly performable diagnostic tools could reveal useful for standardizing the evaluation protocol.
Methods: In a group of 28 subjects undergoing CI, the video Head Impulse Test (vHIT), the cervical Vestibular Evoked Myogenic Potentials (cVEMPS) and the short-form of Dizziness Handicap Inventory (DHI) questionnaire were investigated pre-operatively and post-operatively (implant on and off) in both the implanted and the contralateral, non-implanted ear. All surgeries were performed with a round window approach (RWA), except for three otosclerosis cases were the extended RWA (eRWA) was used.
Results: The vHIT of the lateral semicircular canal showed a pre-operative vestibular involvement in nearly 50% of the cases, whilst the three canals were contemporarily affected in only 14% of them. In all the hypo-functional subjects, cVEMPs were absent. A low VOR gain in all the investigated SSCC was found in 4 subjects (14%). In those subjects, (21.7%) in whom cVEMPs were pre-operatively present and normal in the operated side, absence of response was post-operatives recorded.
Discussion/Conclusion: The vestibular protocol applied for the study showed to be appropriate for distinguishing between the CI operated and the non-operated ear. In this regard, cVEMPs showed to be more sensitive than vHIT for revealing a vestibular sufferance after CI, although without statistical significance. Finally, the use of the RWA surgery was apparently not avoiding signs of vestibular impairment to occur
Excitation energies of retinal chromophores: Critical role of the structural model
We employ a variety of highly-correlated approaches including quantum Monte Carlo (QMC) and the n-electron valence state perturbation theory (NEVPT2) to compute the vertical excitation energies of retinal protonated Schiff base (RPSB) models in the gas phase. We find that the NEVPT2 excitation energies are in good agreement with the QMC values and confirm our previous findings that the complete-active-space perturbation (CASPT2) approach yields accurate excitations for RPSB models only when the more recent zero-order IPEA Hamiltonian is employed. The excitations computed with the original zero-order formulation of CASPT2 are instead systematically red-shifted by more than 0.3 eV. We then focus on the full 11-cis retinal chromophore and show that the M06-2X and MP2 approaches provide reliable ground-state equilibrium structures for this system while the complete-active-space self-consistent field (CASSCF) geometry is characterized by significantly higher ground-state energies at the NEVPT2 and CASPT2 level. Our calibration of the structural model together with the general agreement of all highly-correlated excited-state methods allows us to reliably assign a value of about 2.3 eV to the vertical excitation of 11-cis RPSB in the gas-phase
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